Preprints are available on bioRxiv.
2022
FROM THE LAB
Sorry, no publications matched your criteria.
COLLABORATOR LED
Sorry, no publications matched your criteria.
2021
FROM THE LAB
Sorry, no publications matched your criteria.
COLLABORATOR LED
Sorry, no publications matched your criteria.
2020
FROM THE LAB
Sorry, no publications matched your criteria.
COLLABORATOR LED
Sorry, no publications matched your criteria.
2019
FROM THE LAB
Sorry, no publications matched your criteria.
COLLABORATOR LED
Sorry, no publications matched your criteria.
2018
FROM THE LAB
Sorry, no publications matched your criteria.
COLLABORATOR LED
Sorry, no publications matched your criteria.
2017–1998
ALL PAPERS
1999
Engineering and design Journal Article
David Baker, WF DeGrado
In: Current opinion in structural biology, vol. 9, pp. 485-6, 1999, ISSN: 1879-033X.
@article{47,
title = {Engineering and design},
author = { David Baker and WF DeGrado},
issn = {1879-033X},
year = {1999},
date = {1999-08-01},
journal = {Current opinion in structural biology},
volume = {9},
pages = {485-6},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Chain collapse can occur concomitantly with the rate-limiting step in protein folding Journal Article
K W Plaxco, I S Millett, D J Segel, S Doniach, David Baker
In: Nature structural biology, vol. 6, pp. 554-6, 1999, ISSN: 1072-8368.
@article{44,
title = {Chain collapse can occur concomitantly with the rate-limiting step in protein folding},
author = { K W Plaxco and I S Millett and D J Segel and S Doniach and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/plaxco99A.pdf},
issn = {1072-8368},
year = {1999},
date = {1999-06-01},
journal = {Nature structural biology},
volume = {6},
pages = {554-6},
abstract = {We have directly characterized the extent of chain collapse early in the folding of protein L using time-resolved small angle X-ray scattering. We find that, immediately after the initiation of refolding, the protein exhibits dimensions indistinguishable from those observed under highly denaturing, equilibrium conditions and that this expanded initial state collapses with the same rate as that of the overall folding reaction. The observation that chain compaction need not significantly precede the rate-limiting step of folding demonstrates that rapid chain collapse is not an obligatory feature of protein folding reactions.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We have directly characterized the extent of chain collapse early in the folding of protein L using time-resolved small angle X-ray scattering. We find that, immediately after the initiation of refolding, the protein exhibits dimensions indistinguishable from those observed under highly denaturing, equilibrium conditions and that this expanded initial state collapses with the same rate as that of the overall folding reaction. The observation that chain compaction need not significantly precede the rate-limiting step of folding demonstrates that rapid chain collapse is not an obligatory feature of protein folding reactions.
Matching theory and experiment in protein folding. Journal Article
E Alm, David Baker
In: Current opinion in structural biology, vol. 9, pp. 189-96, 1999, ISSN: 0959-440X.
@article{49,
title = {Matching theory and experiment in protein folding.},
author = { E Alm and David Baker},
issn = {0959-440X},
year = {1999},
date = {1999-04-01},
journal = {Current opinion in structural biology},
volume = {9},
pages = {189-96},
abstract = {There has been considerable progress made over the past year in linking experimental and theoretical approaches to protein folding. Recent results from several independent lines of investigation suggest that protein folding mechanisms and landscapes are largely determined by the topology of the native state and are relatively insensitive to details of the interatomic interactions. This dependence on low-resolution structural features, rather than high-resolution detail, suggests that it should be possible to describe the fundamental physics of the folding process using relatively low-resolution models. Recent experiments have set benchmarks for testing new models and progress has been made in developing theoretical models for interpreting and predicting experimental results.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There has been considerable progress made over the past year in linking experimental and theoretical approaches to protein folding. Recent results from several independent lines of investigation suggest that protein folding mechanisms and landscapes are largely determined by the topology of the native state and are relatively insensitive to details of the interatomic interactions. This dependence on low-resolution structural features, rather than high-resolution detail, suggests that it should be possible to describe the fundamental physics of the folding process using relatively low-resolution models. Recent experiments have set benchmarks for testing new models and progress has been made in developing theoretical models for interpreting and predicting experimental results.
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins Journal Article
K T Simons, I Ruczinski, C Kooperberg, B A Fox, C Bystroff, D Baker
In: Proteins, vol. 34, pp. 82-95, 1999, ISSN: 0887-3585.
@article{322,
title = {Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins},
author = { K T Simons and I Ruczinski and C Kooperberg and B A Fox and C Bystroff and D Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/simons98A.pdf},
issn = {0887-3585},
year = {1999},
date = {1999-01-01},
journal = {Proteins},
volume = {34},
pages = {82-95},
abstract = {We describe the development of a scoring function based on the decomposition P(structure/sequence) proportional to P(sequence/structure) *P(structure), which outperforms previous scoring functions in correctly identifying native-like protein structures in large ensembles of compact decoys. The first term captures sequence-dependent features of protein structures, such as the burial of hydrophobic residues in the core, the second term, universal sequence-independent features, such as the assembly of beta-strands into beta-sheets. The efficacies of a wide variety of sequence-dependent and sequence-independent features of protein structures for recognizing native-like structures were systematically evaluated using ensembles of approximately 30,000 compact conformations with fixed secondary structure for each of 17 small protein domains. The best results were obtained using a core scoring function with P(sequence/structure) parameterized similarly to our previous work (Simons et al., J Mol Biol 1997;268:209-225] and P(structure) focused on secondary structure packing preferences; while several additional features had some discriminatory power on their own, they did not provide any additional discriminatory power when combined with the core scoring function. Our results, on both the training set and the independent decoy set of Park and Levitt (J Mol Biol 1996;258:367-392), suggest that this scoring function should contribute to the prediction of tertiary structure from knowledge of sequence and secondary structure.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We describe the development of a scoring function based on the decomposition P(structure/sequence) proportional to P(sequence/structure) *P(structure), which outperforms previous scoring functions in correctly identifying native-like protein structures in large ensembles of compact decoys. The first term captures sequence-dependent features of protein structures, such as the burial of hydrophobic residues in the core, the second term, universal sequence-independent features, such as the assembly of beta-strands into beta-sheets. The efficacies of a wide variety of sequence-dependent and sequence-independent features of protein structures for recognizing native-like structures were systematically evaluated using ensembles of approximately 30,000 compact conformations with fixed secondary structure for each of 17 small protein domains. The best results were obtained using a core scoring function with P(sequence/structure) parameterized similarly to our previous work (Simons et al., J Mol Biol 1997;268:209-225] and P(structure) focused on secondary structure packing preferences; while several additional features had some discriminatory power on their own, they did not provide any additional discriminatory power when combined with the core scoring function. Our results, on both the training set and the independent decoy set of Park and Levitt (J Mol Biol 1996;258:367-392), suggest that this scoring function should contribute to the prediction of tertiary structure from knowledge of sequence and secondary structure.
Ab initio protein structure prediction of CASP III targets using ROSETTA Journal Article
K T Simons, R Bonneau, I Ruczinski, David Baker
In: Proteins, vol. Suppl 3, pp. 171-6, 1999, ISSN: 0887-3585.
@article{41,
title = {Ab initio protein structure prediction of CASP III targets using ROSETTA},
author = { K T Simons and R Bonneau and I Ruczinski and David Baker},
issn = {0887-3585},
year = {1999},
date = {1999-00-01},
journal = {Proteins},
volume = {Suppl 3},
pages = {171-6},
abstract = {To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons et al., J Mol Biol 1997; 268:209-225). The scoring function used in the simulated annealing procedure consists of sequence-dependent terms representing hydrophobic burial and specific pair interactions such as electrostatics and disulfide bonding and sequence-independent terms representing hard sphere packing, alpha-helix and beta-strand packing, and the collection of beta-strands in beta-sheets (Simons et al., Proteins 1999;34:82-95). For each of 21 small, ab initio targets, 1,200 final structures were constructed, each the result of 100,000 attempted fragment substitutions. The five structures submitted for the CASP III experiment were chosen from the approximately 25 structures with the lowest scores in the broadest minima (assessed through the number of structural neighbors; Shortle et al., Proc Natl Acad Sci USA 1998;95:1158-1162). The results were encouraging: highlights of the predictions include a 99-residue segment for MarA with an rmsd of 6.4 A to the native structure, a 95-residue (full length) prediction for the EH2 domain of EPS15 with an rmsd of 6.0 A, a 75-residue segment of DNAB helicase with an rmsd of 4.7 A, and a 67-residue segment of ribosomal protein L30 with an rmsd of 3.8 A. These results suggest that ab initio methods may soon become useful for low-resolution structure prediction for proteins that lack a close homologue of known structure.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons et al., J Mol Biol 1997; 268:209-225). The scoring function used in the simulated annealing procedure consists of sequence-dependent terms representing hydrophobic burial and specific pair interactions such as electrostatics and disulfide bonding and sequence-independent terms representing hard sphere packing, alpha-helix and beta-strand packing, and the collection of beta-strands in beta-sheets (Simons et al., Proteins 1999;34:82-95). For each of 21 small, ab initio targets, 1,200 final structures were constructed, each the result of 100,000 attempted fragment substitutions. The five structures submitted for the CASP III experiment were chosen from the approximately 25 structures with the lowest scores in the broadest minima (assessed through the number of structural neighbors; Shortle et al., Proc Natl Acad Sci USA 1998;95:1158-1162). The results were encouraging: highlights of the predictions include a 99-residue segment for MarA with an rmsd of 6.4 A to the native structure, a 95-residue (full length) prediction for the EH2 domain of EPS15 with an rmsd of 6.0 A, a 75-residue segment of DNAB helicase with an rmsd of 4.7 A, and a 67-residue segment of ribosomal protein L30 with an rmsd of 3.8 A. These results suggest that ab initio methods may soon become useful for low-resolution structure prediction for proteins that lack a close homologue of known structure.
1998
The single helix in protein L is largely disrupted at the rate-limiting step in folding Journal Article
David E Kim, Q Yi, S T Gladwin, J M Goldberg, David Baker
In: Journal of molecular biology, vol. 284, pp. 807-15, 1998, ISSN: 0022-2836.
@article{209,
title = {The single helix in protein L is largely disrupted at the rate-limiting step in folding},
author = { David E Kim and Q Yi and S T Gladwin and J M Goldberg and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/kim98A_0.pdf},
issn = {0022-2836},
year = {1998},
date = {1998-12-01},
journal = {Journal of molecular biology},
volume = {284},
pages = {807-15},
abstract = {To investigate the role of helix formation in the folding of protein L, a 62 residue alpha/beta protein, we studied the consequences of both single and multiple mutations in the helix on the kinetics of folding. A triple mutant with 11 additional carbon atoms in core residues in the amino-terminal portion of the helix folded substantially faster than wild type, suggesting that hydrophobic association with residues elsewhere in the protein occurs at the rate-limiting step in folding. However, helix-destabilizing mutations had little effect on the rate of folding; in particular, a triple glycine substitution on the solvent-exposed side of the helix increased the unfolding rate 56-fold while reducing the folding rate less than threefold. Thus, in contrast to the predictions of models of folding involving the coalescence of well-formed secondary structure elements, the single helix in protein L appears to be largely disrupted at the rate-limiting step in folding and unfolding.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
To investigate the role of helix formation in the folding of protein L, a 62 residue alpha/beta protein, we studied the consequences of both single and multiple mutations in the helix on the kinetics of folding. A triple mutant with 11 additional carbon atoms in core residues in the amino-terminal portion of the helix folded substantially faster than wild type, suggesting that hydrophobic association with residues elsewhere in the protein occurs at the rate-limiting step in folding. However, helix-destabilizing mutations had little effect on the rate of folding; in particular, a triple glycine substitution on the solvent-exposed side of the helix increased the unfolding rate 56-fold while reducing the folding rate less than threefold. Thus, in contrast to the predictions of models of folding involving the coalescence of well-formed secondary structure elements, the single helix in protein L appears to be largely disrupted at the rate-limiting step in folding and unfolding.
Metastable states and folding free energy barriers. Journal Article
David Baker
In: Nature structural biology, vol. 5, pp. 1021-4, 1998, ISSN: 1072-8368.
@article{203,
title = {Metastable states and folding free energy barriers.},
author = { David Baker},
issn = {1072-8368},
year = {1998},
date = {1998-12-01},
journal = {Nature structural biology},
volume = {5},
pages = {1021-4},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Limited internal friction in the rate-limiting step of a two-state protein folding reaction Journal Article
K W Plaxco, David Baker
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 95, pp. 13591-6, 1998, ISSN: 0027-8424.
@article{211,
title = {Limited internal friction in the rate-limiting step of a two-state protein folding reaction},
author = { K W Plaxco and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/plaxco98A.pdf},
issn = {0027-8424},
year = {1998},
date = {1998-11-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {95},
pages = {13591-6},
abstract = {Small, single-domain proteins typically fold via a compact transition-state ensemble in a process well fitted by a simple, two-state model. To characterize the rate-limiting conformational changes that underlie two-state folding, we have investigated experimentally the effects of changing solvent viscosity on the refolding of the IgG binding domain of protein L. In conjunction with numerical simulations, our results indicate that the rate-limiting conformational changes of the folding of this domain are strongly coupled to solvent viscosity and lack any significant "internal friction" arising from intrachain collisions. When compared with the previously determined solvent viscosity dependencies of other, more restricted conformational changes, our results suggest that the rate-limiting folding transition involves conformational fluctuations that displace considerable amounts of solvent. Reconciling evidence that the folding transition state ensemble is comprised of highly collapsed species with these and similar, previously reported results should provide a significant constraint for theoretical models of the folding process.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Small, single-domain proteins typically fold via a compact transition-state ensemble in a process well fitted by a simple, two-state model. To characterize the rate-limiting conformational changes that underlie two-state folding, we have investigated experimentally the effects of changing solvent viscosity on the refolding of the IgG binding domain of protein L. In conjunction with numerical simulations, our results indicate that the rate-limiting conformational changes of the folding of this domain are strongly coupled to solvent viscosity and lack any significant "internal friction" arising from intrachain collisions. When compared with the previously determined solvent viscosity dependencies of other, more restricted conformational changes, our results suggest that the rate-limiting folding transition involves conformational fluctuations that displace considerable amounts of solvent. Reconciling evidence that the folding transition state ensemble is comprised of highly collapsed species with these and similar, previously reported results should provide a significant constraint for theoretical models of the folding process.
Clustering of low-energy conformations near the native structures of small proteins Journal Article
D Shortle, K T Simons, David Baker
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 95, pp. 11158-62, 1998, ISSN: 0027-8424.
@article{213,
title = {Clustering of low-energy conformations near the native structures of small proteins},
author = { D Shortle and K T Simons and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/shortle98A.pdf},
issn = {0027-8424},
year = {1998},
date = {1998-09-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {95},
pages = {11158-62},
abstract = {Recent experimental studies of the denatured state and theoretical analyses of the folding landscape suggest that there are a large multiplicity of low-energy, partially folded conformations near the native state. In this report, we describe a strategy for predicting protein structure based on the working hypothesis that there are a greater number of low-energy conformations surrounding the correct fold than there are surrounding low-energy incorrect folds. To test this idea, 12 ensembles of 500 to 1,000 low-energy structures for 10 small proteins were analyzed by calculating the rms deviation of the Calpha coordinates between each conformation and every other conformation in the ensemble. In all 12 cases, the conformation with the greatest number of conformations within 4-A rms deviation was closer to the native structure than were the majority of conformations in the ensemble, and in most cases it was among the closest 1 to 5%. These results suggest that, to fold efficiently and retain robustness to changes in amino acid sequence, proteins may have evolved a native structure situated within a broad basin of low-energy conformations, a feature which could facilitate the prediction of protein structure at low resolution.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Recent experimental studies of the denatured state and theoretical analyses of the folding landscape suggest that there are a large multiplicity of low-energy, partially folded conformations near the native state. In this report, we describe a strategy for predicting protein structure based on the working hypothesis that there are a greater number of low-energy conformations surrounding the correct fold than there are surrounding low-energy incorrect folds. To test this idea, 12 ensembles of 500 to 1,000 low-energy structures for 10 small proteins were analyzed by calculating the rms deviation of the Calpha coordinates between each conformation and every other conformation in the ensemble. In all 12 cases, the conformation with the greatest number of conformations within 4-A rms deviation was closer to the native structure than were the majority of conformations in the ensemble, and in most cases it was among the closest 1 to 5%. These results suggest that, to fold efficiently and retain robustness to changes in amino acid sequence, proteins may have evolved a native structure situated within a broad basin of low-energy conformations, a feature which could facilitate the prediction of protein structure at low resolution.
Prediction of local structure in proteins using a library of sequence-structure motifs Journal Article
C Bystroff, D Baker
In: Journal of molecular biology, vol. 281, pp. 565-77, 1998, ISSN: 0022-2836.
@article{311,
title = {Prediction of local structure in proteins using a library of sequence-structure motifs},
author = { C Bystroff and D Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/bystroff98A.pdf},
issn = {0022-2836},
year = {1998},
date = {1998-08-01},
journal = {Journal of molecular biology},
volume = {281},
pages = {565-77},
abstract = {We describe a new method for local protein structure prediction based on a library of short sequence pattern that correlate strongly with protein three-dimensional structural elements. The library was generated using an automated method for finding correlations between protein sequence and local structure, and contains most previously described local sequence-structure correlations as well as new relationships, including a diverging type-II beta-turn, a frayed helix, and a proline-terminated helix. The query sequence is scanned for segments 7 to 19 residues in length that strongly match one of the 82 patterns in the library. Matching segments are assigned the three-dimensional structure characteristic of the corresponding sequence pattern, and backbone torsion angles for the entire query sequence are then predicted by piecing together mutually compatible segment predictions. In predictions of local structure in a test set of 55 proteins, about 50% of all residues, and 76% of residues covered by high-confidence predictions, were found in eight-residue segments within 1.4 A of their true structures. The predictions are complementary to traditional secondary structure predictions because they are considerably more specific in turn regions, and may contribute to ab initio tertiary structure prediction and fold recognition.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We describe a new method for local protein structure prediction based on a library of short sequence pattern that correlate strongly with protein three-dimensional structural elements. The library was generated using an automated method for finding correlations between protein sequence and local structure, and contains most previously described local sequence-structure correlations as well as new relationships, including a diverging type-II beta-turn, a frayed helix, and a proline-terminated helix. The query sequence is scanned for segments 7 to 19 residues in length that strongly match one of the 82 patterns in the library. Matching segments are assigned the three-dimensional structure characteristic of the corresponding sequence pattern, and backbone torsion angles for the entire query sequence are then predicted by piecing together mutually compatible segment predictions. In predictions of local structure in a test set of 55 proteins, about 50% of all residues, and 76% of residues covered by high-confidence predictions, were found in eight-residue segments within 1.4 A of their true structures. The predictions are complementary to traditional secondary structure predictions because they are considerably more specific in turn regions, and may contribute to ab initio tertiary structure prediction and fold recognition.
Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain Journal Article
V P Grantcharova, D S Riddle, J V Santiago, David Baker
In: Nature structural biology, vol. 5, pp. 714-20, 1998, ISSN: 1072-8368.
@article{204,
title = {Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain},
author = { V P Grantcharova and D S Riddle and J V Santiago and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/grantcharova98A.pdf},
issn = {1072-8368},
year = {1998},
date = {1998-08-01},
journal = {Nature structural biology},
volume = {5},
pages = {714-20},
abstract = {Experimental and theoretical studies on the folding of small proteins such as the chymotrypsin inhibitor 2 (CI-2) and the P22 Arc repressor suggest that the folding transition state is an expanded version of the native state with most interactions partially formed. Here we report that this picture does not hold generally: a hydrogen bond network involving two beta-turns and an adjacent hydrophobic cluster appear to be formed in the folding transition state of the src SH3 domain, while the remainder of the polypeptide chain is largely unstructured. Comparison with data on other small proteins suggests that this structural polarization is a consequence of the topology of the SH3 domain fold. The non-uniform distribution of structure in the folding transition state provides a challenging test for computational models of the folding process.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Experimental and theoretical studies on the folding of small proteins such as the chymotrypsin inhibitor 2 (CI-2) and the P22 Arc repressor suggest that the folding transition state is an expanded version of the native state with most interactions partially formed. Here we report that this picture does not hold generally: a hydrogen bond network involving two beta-turns and an adjacent hydrophobic cluster appear to be formed in the folding transition state of the src SH3 domain, while the remainder of the polypeptide chain is largely unstructured. Comparison with data on other small proteins suggests that this structural polarization is a consequence of the topology of the SH3 domain fold. The non-uniform distribution of structure in the folding transition state provides a challenging test for computational models of the folding process.
The sequences of small proteins are not extensively optimized for rapid folding by natural selection Journal Article
D E Kim, H Gu, D Baker
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 95, pp. 4982-6, 1998, ISSN: 0027-8424.
@article{312,
title = {The sequences of small proteins are not extensively optimized for rapid folding by natural selection},
author = { D E Kim and H Gu and D Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/kim98A.pdf},
issn = {0027-8424},
year = {1998},
date = {1998-04-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {95},
pages = {4982-6},
abstract = {The thermodynamic stabilities of small protein domains are clearly subject to natural selection, but it is less clear whether the rapid folding rates typically observed for such proteins are consequences of direct evolutionary optimization or reflect intrinsic physical properties of the polypeptide chain. This issue can be investigated by comparing the folding rates of laboratory-generated protein sequences to those of naturally occurring sequences provided that the method by which the sequences are generated has no kinetic bias. Herein we report the folding thermodynamics and kinetics of 12 heavily mutated variants of the small IgG binding domain of protein L retrieved from high-complexity combinatorial libraries by using a phage-display selection for proper folding that does not discriminate between rapidly and slowly folding proteins. Although the stabilities of all variants were decreased, many of the variants fold faster than wild type. Taken together with similar results for the src homology 3 domain, this observation suggests that the sequences of small proteins have not been extensively optimized for rapid folding; instead, rapid folding appears to be a consequence of selection for stability.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The thermodynamic stabilities of small protein domains are clearly subject to natural selection, but it is less clear whether the rapid folding rates typically observed for such proteins are consequences of direct evolutionary optimization or reflect intrinsic physical properties of the polypeptide chain. This issue can be investigated by comparing the folding rates of laboratory-generated protein sequences to those of naturally occurring sequences provided that the method by which the sequences are generated has no kinetic bias. Herein we report the folding thermodynamics and kinetics of 12 heavily mutated variants of the small IgG binding domain of protein L retrieved from high-complexity combinatorial libraries by using a phage-display selection for proper folding that does not discriminate between rapidly and slowly folding proteins. Although the stabilities of all variants were decreased, many of the variants fold faster than wild type. Taken together with similar results for the src homology 3 domain, this observation suggests that the sequences of small proteins have not been extensively optimized for rapid folding; instead, rapid folding appears to be a consequence of selection for stability.
Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water Journal Article
J A Rank, David Baker
In: Biophysical chemistry, vol. 71, pp. 199-204, 1998, ISSN: 0301-4622.
@article{210,
title = {Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water},
author = { J A Rank and David Baker},
issn = {0301-4622},
year = {1998},
date = {1998-04-01},
journal = {Biophysical chemistry},
volume = {71},
pages = {199-204},
abstract = {The contribution of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water was investigated by comparing the potential of mean force (PMF) between two methane molecules in TIP4P water to those in a series of related liquids in which the solvent-solvent interactions were progressively turned off while keeping the solvent-solute interactions unchanged. The magnitude of the attraction between methanes was not significantly changed when the hydrogen bonding interaction between solvent molecules was eliminated and the solvent was maintained in the liquid state by increasing either the pressure or the magnitude of the solvent-solvent van der Waals interaction. However, when solvent-solvent excluded volume interactions were eliminated, the methane molecules interacted no more strongly than in the gas phase. The results are consistent with the idea that the primary contribution of hydrogen bonding to the hydrophobic interaction is to keep water molecules in a liquid state; at constant density, packing interactions rather than hydrogen bonding appear to be critical as suggested by scaled particle theories of solvation. The overall shape of the PMF was, however, changed in the absence of hydrogen bonding, pointing to an influence of hydrogen bonding on the detailed form of the interactions between nonpolar solutes in water. The effects of correlations between the configurations sampled during the Monte Carlo procedure used in the free energy calculations on the estimation of errors was also characterized.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The contribution of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water was investigated by comparing the potential of mean force (PMF) between two methane molecules in TIP4P water to those in a series of related liquids in which the solvent-solvent interactions were progressively turned off while keeping the solvent-solute interactions unchanged. The magnitude of the attraction between methanes was not significantly changed when the hydrogen bonding interaction between solvent molecules was eliminated and the solvent was maintained in the liquid state by increasing either the pressure or the magnitude of the solvent-solvent van der Waals interaction. However, when solvent-solvent excluded volume interactions were eliminated, the methane molecules interacted no more strongly than in the gas phase. The results are consistent with the idea that the primary contribution of hydrogen bonding to the hydrophobic interaction is to keep water molecules in a liquid state; at constant density, packing interactions rather than hydrogen bonding appear to be critical as suggested by scaled particle theories of solvation. The overall shape of the PMF was, however, changed in the absence of hydrogen bonding, pointing to an influence of hydrogen bonding on the detailed form of the interactions between nonpolar solutes in water. The effects of correlations between the configurations sampled during the Monte Carlo procedure used in the free energy calculations on the estimation of errors was also characterized.
Contact order, transition state placement and the refolding rates of single domain proteins Journal Article
K W Plaxco, K T Simons, David Baker
In: Journal of molecular biology, vol. 277, pp. 985-94, 1998, ISSN: 0022-2836.
@article{207,
title = {Contact order, transition state placement and the refolding rates of single domain proteins},
author = { K W Plaxco and K T Simons and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/plaxco98B.pdf},
issn = {0022-2836},
year = {1998},
date = {1998-04-01},
journal = {Journal of molecular biology},
volume = {277},
pages = {985-94},
abstract = {Theoretical studies have suggested relationships between the size, stability and topology of a protein fold and the rate and mechanisms by which it is achieved. The recent characterization of the refolding of a number of simple, single domain proteins has provided a means of testing these assertions. Our investigations have revealed statistically significant correlations between the average sequence separation between contacting residues in the native state and the rate and transition state placement of folding for a non-homologous set of simple, single domain proteins. These indicate that proteins featuring primarily sequence-local contacts tend to fold more rapidly and exhibit less compact folding transition states than those characterized by more non-local interactions. No significant relationship is apparent between protein length and folding rates, but a weak correlation is observed between length and the fraction of solvent-exposed surface area buried in the transition state. Anticipated strong relationships between equilibrium folding free energy and folding kinetics, or between chemical denaturant and temperature dependence-derived measures of transition state placement, are not apparent. The observed correlations are consistent with a model of protein folding in which the size and stability of the polypeptide segments organized in the transition state are largely independent of protein length, but are related to the topological complexity of the native state. The correlation between topological complexity and folding rates may reflect chain entropy contributions to the folding barrier.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Theoretical studies have suggested relationships between the size, stability and topology of a protein fold and the rate and mechanisms by which it is achieved. The recent characterization of the refolding of a number of simple, single domain proteins has provided a means of testing these assertions. Our investigations have revealed statistically significant correlations between the average sequence separation between contacting residues in the native state and the rate and transition state placement of folding for a non-homologous set of simple, single domain proteins. These indicate that proteins featuring primarily sequence-local contacts tend to fold more rapidly and exhibit less compact folding transition states than those characterized by more non-local interactions. No significant relationship is apparent between protein length and folding rates, but a weak correlation is observed between length and the fraction of solvent-exposed surface area buried in the transition state. Anticipated strong relationships between equilibrium folding free energy and folding kinetics, or between chemical denaturant and temperature dependence-derived measures of transition state placement, are not apparent. The observed correlations are consistent with a model of protein folding in which the size and stability of the polypeptide segments organized in the transition state are largely independent of protein length, but are related to the topological complexity of the native state. The correlation between topological complexity and folding rates may reflect chain entropy contributions to the folding barrier.
Simplified proteins: minimalist solutions to the protein folding problem Journal Article
K W Plaxco, D S Riddle, V Grantcharova, David Baker
In: Current opinion in structural biology, vol. 8, pp. 80-5, 1998, ISSN: 0959-440X.
@article{208,
title = {Simplified proteins: minimalist solutions to the protein folding problem},
author = { K W Plaxco and D S Riddle and V Grantcharova and David Baker},
issn = {0959-440X},
year = {1998},
date = {1998-02-01},
journal = {Current opinion in structural biology},
volume = {8},
pages = {80-5},
abstract = {Recent research has suggested that stable, native proteins may be encoded by simple sequences of fewer than the full set of 20 proteogenic amino acids. Studies of the ability of simple amino acid sequences to encode stable, topologically complex, native conformations and to fold to these conformations in a biologically relevant time frame have provided insights into the sequence determinants of protein structure and folding kinetics. They may also have important implications for protein design and for theories of the origins of protein synthesis itself.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Recent research has suggested that stable, native proteins may be encoded by simple sequences of fewer than the full set of 20 proteogenic amino acids. Studies of the ability of simple amino acid sequences to encode stable, topologically complex, native conformations and to fold to these conformations in a biologically relevant time frame have provided insights into the sequence determinants of protein structure and folding kinetics. They may also have important implications for protein design and for theories of the origins of protein synthesis itself.
Prediction and structural characterization of an independently folding substructure in the src SH3 domain Journal Article
Q Yi, C Bystroff, P Rajagopal, R E Klevit, David Baker
In: Journal of molecular biology, vol. 283, pp. 293-300, 1998, ISSN: 0022-2836.
@article{212,
title = {Prediction and structural characterization of an independently folding substructure in the src SH3 domain},
author = { Q Yi and C Bystroff and P Rajagopal and R E Klevit and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/yi98A.pdf},
issn = {0022-2836},
year = {1998},
date = {1998-00-01},
journal = {Journal of molecular biology},
volume = {283},
pages = {293-300},
abstract = {Previous studies of the conformations of peptides spanning the length of the alpha-spectrin SH3 domain suggested that SH3 domains lack independently folding substructures. Using a local structure prediction method based on the I-sites library of sequence-structure motifs, we identified a seven residue peptide in the src SH3 domain predicted to adopt a native-like structure, a type II beta-turn bridging unpaired beta-strands, that was not contained intact in any of the SH3 domain peptides studied earlier. NMR characterization confirmed that the isolated peptide, FKKGERL, adopts a structure similar to that adopted in the native protein: the NOE and 3JNHalpha coupling constant patterns were indicative of a type II beta-turn, and NOEs between the Phe and the Leu side-chains suggest that they are juxtaposed as in the prediction and the native structure. These results support the idea that high-confidence I-sites predictions identify protein segments that are likely to form native-like structures early in folding.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Previous studies of the conformations of peptides spanning the length of the alpha-spectrin SH3 domain suggested that SH3 domains lack independently folding substructures. Using a local structure prediction method based on the I-sites library of sequence-structure motifs, we identified a seven residue peptide in the src SH3 domain predicted to adopt a native-like structure, a type II beta-turn bridging unpaired beta-strands, that was not contained intact in any of the SH3 domain peptides studied earlier. NMR characterization confirmed that the isolated peptide, FKKGERL, adopts a structure similar to that adopted in the native protein: the NOE and 3JNHalpha coupling constant patterns were indicative of a type II beta-turn, and NOEs between the Phe and the Leu side-chains suggest that they are juxtaposed as in the prediction and the native structure. These results support the idea that high-confidence I-sites predictions identify protein segments that are likely to form native-like structures early in folding.
1997
Folding dynamics of the src SH3 domain Journal Article
V P Grantcharova, David Baker
In: Biochemistry, vol. 36, pp. 15685-92, 1997, ISSN: 0006-2960.
@article{32,
title = {Folding dynamics of the src SH3 domain},
author = { V P Grantcharova and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/grantcharova97A.pdf},
issn = {0006-2960},
year = {1997},
date = {1997-12-01},
journal = {Biochemistry},
volume = {36},
pages = {15685-92},
abstract = {The thermodynamics and kinetics of folding of the chicken src SH3 domain were characterized using equilibrium and stopped-flow fluorescence, circular dichroism (CD), and nuclear magnetic resonance (NMR) hydrogen exchange experiments. As found for other SH3 domains, guanidinium chloride (GdmCl) denaturation melts followed by both fluorescence and circular dichroism were nearly superimposable, indicating the concerted formation of secondary and tertiary structure. Kinetic studies confirmed the two-state character of the folding reaction. Except for a very slow refolding phase due to proline isomerization, both folding and unfolding traces fit well to single exponentials over a wide range of GdmCl concentrations, and no burst phase in amplitude was observed during the dead time of the stopped-flow instrument. The entropy, enthalpy, and heat capacity changes upon unfolding were determined by global fitting of temperature melts at varying GdmCl concentrations (0.4-3.7 M). Estimates of the free energy of unfolding, DeltaGUH2O, from guanidine denaturation, thermal denaturation, and kinetic experiments were in good agreement. To complement these data on the global characteristics of src SH3 folding, individual hydrogen-deuterium (HD) exchange rates were measured for approximately half of the backbone amides in 0 and 0.7 M GdmCl. The calculated free energies of the opening reaction leading to exchange (DeltaGHD) indicated that unfolding is highly cooperative--slowly exchanging protons were distributed throughout the core of the protein. The slowly exchanging protons exhibited DeltaGHD values higher than the global DeltaGUH2O by approximately 1 kcal/mol, suggesting that the denatured state might be somewhat compact under native conditions. Comparison of the src SH3 with homologous SH3 domains as well as with other small well-characterized beta-sheet proteins provides insights into the determinants of folding kinetics and protein stability.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The thermodynamics and kinetics of folding of the chicken src SH3 domain were characterized using equilibrium and stopped-flow fluorescence, circular dichroism (CD), and nuclear magnetic resonance (NMR) hydrogen exchange experiments. As found for other SH3 domains, guanidinium chloride (GdmCl) denaturation melts followed by both fluorescence and circular dichroism were nearly superimposable, indicating the concerted formation of secondary and tertiary structure. Kinetic studies confirmed the two-state character of the folding reaction. Except for a very slow refolding phase due to proline isomerization, both folding and unfolding traces fit well to single exponentials over a wide range of GdmCl concentrations, and no burst phase in amplitude was observed during the dead time of the stopped-flow instrument. The entropy, enthalpy, and heat capacity changes upon unfolding were determined by global fitting of temperature melts at varying GdmCl concentrations (0.4-3.7 M). Estimates of the free energy of unfolding, DeltaGUH2O, from guanidine denaturation, thermal denaturation, and kinetic experiments were in good agreement. To complement these data on the global characteristics of src SH3 folding, individual hydrogen-deuterium (HD) exchange rates were measured for approximately half of the backbone amides in 0 and 0.7 M GdmCl. The calculated free energies of the opening reaction leading to exchange (DeltaGHD) indicated that unfolding is highly cooperative--slowly exchanging protons were distributed throughout the core of the protein. The slowly exchanging protons exhibited DeltaGHD values higher than the global DeltaGUH2O by approximately 1 kcal/mol, suggesting that the denatured state might be somewhat compact under native conditions. Comparison of the src SH3 with homologous SH3 domains as well as with other small well-characterized beta-sheet proteins provides insights into the determinants of folding kinetics and protein stability.
Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein Journal Article
H Gu, David E Kim, David Baker
In: Journal of molecular biology, vol. 274, pp. 588-96, 1997, ISSN: 0022-2836.
@article{33,
title = {Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein},
author = { H Gu and David E Kim and David Baker},
issn = {0022-2836},
year = {1997},
date = {1997-12-01},
journal = {Journal of molecular biology},
volume = {274},
pages = {588-96},
abstract = {To investigate the role of turns in protein folding, we have characterized the effects of combinatorial and site-directed mutations in the two beta-turns of peptostreptococcal protein L on folding thermodynamics and kinetics. Sequences of folded variants recovered from combinatorial libraries using a phase display selection method were considerably more variable in the second turn than in the first turn. These combinatorial mutants as well as strategically placed point mutants in the two turns had a similar range of thermodynamic stabilities, but strikingly different folding kinetics. A glycine to alanine substitution in the second beta-turn increased the rate of unfolding more than tenfold but had little effect on the rate of folding, while mutation of a symmetrically disposed glycine residue in the first turn had little effect on unfolding but slowed the rate of folding nearly tenfold. These results demonstrate that the role of beta-turns in protein folding is strongly context-dependent, and suggests that the first turn is formed and the second turn disrupted in the folding transition state.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
To investigate the role of turns in protein folding, we have characterized the effects of combinatorial and site-directed mutations in the two beta-turns of peptostreptococcal protein L on folding thermodynamics and kinetics. Sequences of folded variants recovered from combinatorial libraries using a phase display selection method were considerably more variable in the second turn than in the first turn. These combinatorial mutants as well as strategically placed point mutants in the two turns had a similar range of thermodynamic stabilities, but strikingly different folding kinetics. A glycine to alanine substitution in the second beta-turn increased the rate of unfolding more than tenfold but had little effect on the rate of folding, while mutation of a symmetrically disposed glycine residue in the first turn had little effect on unfolding but slowed the rate of folding nearly tenfold. These results demonstrate that the role of beta-turns in protein folding is strongly context-dependent, and suggests that the first turn is formed and the second turn disrupted in the folding transition state.
Local interactions and the optimization of protein folding Journal Article
R Doyle, K Simons, H Qian, David Baker
In: Proteins, vol. 29, pp. 282-91, 1997, ISSN: 0887-3585.
@article{31,
title = {Local interactions and the optimization of protein folding},
author = { R Doyle and K Simons and H Qian and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/doyle97A.pdf},
issn = {0887-3585},
year = {1997},
date = {1997-11-01},
journal = {Proteins},
volume = {29},
pages = {282-91},
abstract = {The role of local interactions in protein folding has recently been the subject of some controversy. Here we investigate an extension of Zwanzigtextquoterights simple and general model of folding in which local and nonlocal interactions are represented by functions of single and multiple conformational degrees of freedom, respectively. The kinetics and thermodynamics of folding are studied for a series of energy functions in which the energy of the native structure is fixed, but the relative contributions of local and nonlocal interactions to this energy are varied over a broad range. For funnel shaped energy landscapes, we find that 1) the rate of folding increases, but the stability of the folded state decreases, as the contribution of local interactions to the energy of the native structure increases, and 2) the amount of native structure in the unfolded state and the transition state vary considerably with the local interaction strength. Simple exponential kinetics and a well-defined free energy barrier separating folded and unfolded states are observed when nonlocal interactions make an appreciable contribution to the energy of the native structure; in such cases a transition state theory type approximation yields reasonably accurate estimates of the folding rate. Bumps in the folding funnel near the native state, which could result from desolvation effects, side chain freezing, or the breaking of nonnative contacts, significantly alter the dependence of the folding rate on the local interaction strength: the rate of folding decreases when the local interaction strength is increased beyond a certain point. A survey of the distribution of strong contacts in the protein structure database suggests that evolutionary optimization has involved both kinetics and thermodynamics: strong contacts are enriched at both very short and very long sequence separations.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The role of local interactions in protein folding has recently been the subject of some controversy. Here we investigate an extension of Zwanzigtextquoterights simple and general model of folding in which local and nonlocal interactions are represented by functions of single and multiple conformational degrees of freedom, respectively. The kinetics and thermodynamics of folding are studied for a series of energy functions in which the energy of the native structure is fixed, but the relative contributions of local and nonlocal interactions to this energy are varied over a broad range. For funnel shaped energy landscapes, we find that 1) the rate of folding increases, but the stability of the folded state decreases, as the contribution of local interactions to the energy of the native structure increases, and 2) the amount of native structure in the unfolded state and the transition state vary considerably with the local interaction strength. Simple exponential kinetics and a well-defined free energy barrier separating folded and unfolded states are observed when nonlocal interactions make an appreciable contribution to the energy of the native structure; in such cases a transition state theory type approximation yields reasonably accurate estimates of the folding rate. Bumps in the folding funnel near the native state, which could result from desolvation effects, side chain freezing, or the breaking of nonnative contacts, significantly alter the dependence of the folding rate on the local interaction strength: the rate of folding decreases when the local interaction strength is increased beyond a certain point. A survey of the distribution of strong contacts in the protein structure database suggests that evolutionary optimization has involved both kinetics and thermodynamics: strong contacts are enriched at both very short and very long sequence separations.
Functional rapidly folding proteins from simplified amino acid sequences Journal Article
D S Riddle, J V Santiago, S T Bray-Hall, N Doshi, V P Grantcharova, Q Yi, David Baker
In: Nature structural biology, vol. 4, pp. 805-9, 1997, ISSN: 1072-8368.
@article{26,
title = {Functional rapidly folding proteins from simplified amino acid sequences},
author = { D S Riddle and J V Santiago and S T Bray-Hall and N Doshi and V P Grantcharova and Q Yi and David Baker},
issn = {1072-8368},
year = {1997},
date = {1997-10-01},
journal = {Nature structural biology},
volume = {4},
pages = {805-9},
abstract = {Early protein synthesis is thought to have involved a reduced amino acid alphabet. What is the minimum number of amino acids that would have been needed to encode complex protein folds similar to those found in nature today? Here we show that a small beta-sheet protein, the SH3 domain, can be largely encoded by a five letter amino acid alphabet but not by a three letter alphabet. Furthermore, despite the dramatic changes in sequence, the folding rates of the reduced alphabet proteins are very close to that of the naturally occurring SH3 domain. This finding suggests that despite the vast size of the search space, the rapid folding of biological sequences to their native states is not the result of extensive evolutionary optimization. Instead, the results support the idea that the interactions which stabilize the native state induce a funnel shape to the free energy landscape sufficient to guide the folding polypeptide chain to the proper structure.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Early protein synthesis is thought to have involved a reduced amino acid alphabet. What is the minimum number of amino acids that would have been needed to encode complex protein folds similar to those found in nature today? Here we show that a small beta-sheet protein, the SH3 domain, can be largely encoded by a five letter amino acid alphabet but not by a three letter alphabet. Furthermore, despite the dramatic changes in sequence, the folding rates of the reduced alphabet proteins are very close to that of the naturally occurring SH3 domain. This finding suggests that despite the vast size of the search space, the rapid folding of biological sequences to their native states is not the result of extensive evolutionary optimization. Instead, the results support the idea that the interactions which stabilize the native state induce a funnel shape to the free energy landscape sufficient to guide the folding polypeptide chain to the proper structure.
Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability Journal Article
M L Scalley, David Baker
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 94, pp. 10636-40, 1997, ISSN: 0027-8424.
@article{29,
title = {Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability},
author = { M L Scalley and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/scalley97A.pdf},
issn = {0027-8424},
year = {1997},
date = {1997-09-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {94},
pages = {10636-40},
abstract = {The anomalous temperature dependence of protein folding has received considerable attention. Here we show that the temperature dependence of the folding of protein L becomes extremely simple when the effects of temperature on protein stability are corrected for; the logarithm of the folding rate is a linear function of 1/T on constant stability contours in the temperature-denaturant plane. This convincingly demonstrates that the anomalous temperature dependence of folding derives from the temperature dependence of the interactions that stabilize proteins, rather than from the super Arrhenius temperature dependence predicted for the configurational diffusion constant on a rough energy landscape. However, because of the limited temperature range accessible to experiment, the results do not rule out models with higher order temperature dependences. The significance of the slope of the stability-corrected Arrhenius plots is discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The anomalous temperature dependence of protein folding has received considerable attention. Here we show that the temperature dependence of the folding of protein L becomes extremely simple when the effects of temperature on protein stability are corrected for; the logarithm of the folding rate is a linear function of 1/T on constant stability contours in the temperature-denaturant plane. This convincingly demonstrates that the anomalous temperature dependence of folding derives from the temperature dependence of the interactions that stabilize proteins, rather than from the super Arrhenius temperature dependence predicted for the configurational diffusion constant on a rough energy landscape. However, because of the limited temperature range accessible to experiment, the results do not rule out models with higher order temperature dependences. The significance of the slope of the stability-corrected Arrhenius plots is discussed.
Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns Journal Article
K F Han, C Bystroff, David Baker
In: Protein science, vol. 6, pp. 1587-90, 1997, ISSN: 0961-8368.
@article{36,
title = {Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns},
author = { K F Han and C Bystroff and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/han97A.pdf},
issn = {0961-8368},
year = {1997},
date = {1997-07-01},
journal = {Protein science},
volume = {6},
pages = {1587-90},
abstract = {We have used cluster analysis to identify recurring sequence patterns that transcend protein family boundaries. A subset of these patterns occur predominantly in a single type of local structure in proteins. Here we characterize the three-dimensional structures and contexts in which these sequence patterns occur, with particular attention to the interactions responsible for their structural selectivity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We have used cluster analysis to identify recurring sequence patterns that transcend protein family boundaries. A subset of these patterns occur predominantly in a single type of local structure in proteins. Here we characterize the three-dimensional structures and contexts in which these sequence patterns occur, with particular attention to the interactions responsible for their structural selectivity.
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions Journal Article
K T Simons, C Kooperberg, E Huang, David Baker
In: Journal of molecular biology, vol. 268, pp. 209-25, 1997, ISSN: 0022-2836.
@article{28,
title = {Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions},
author = { K T Simons and C Kooperberg and E Huang and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/simons97A.pdf},
issn = {0022-2836},
year = {1997},
date = {1997-04-01},
journal = {Journal of molecular biology},
volume = {268},
pages = {209-25},
abstract = {We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. Environment and residue pair specific contributions to the scoring functions appear as the first two terms in a series expansion for the residue probability distributions in the protein database; the decoupling of the distance and environment dependencies of the distributions resolves the major problems with current database-derived scoring functions noted by Thomas and Dill. The simulated annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small beta sheet containing proteins. Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles of these structures provide a particularly challenging set of decoys for evaluating scoring functions. We investigate the effects of multiple sequence information and different types of conformational constraints on the overall performance of the method, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. Environment and residue pair specific contributions to the scoring functions appear as the first two terms in a series expansion for the residue probability distributions in the protein database; the decoupling of the distance and environment dependencies of the distributions resolves the major problems with current database-derived scoring functions noted by Thomas and Dill. The simulated annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small beta sheet containing proteins. Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles of these structures provide a particularly challenging set of decoys for evaluating scoring functions. We investigate the effects of multiple sequence information and different types of conformational constraints on the overall performance of the method, and the ability of a variety of recently developed scoring functions to recognize the native-like conformations in the ensembles of simulated structures.
Kinetics of folding of the IgG binding domain of peptostreptococcal protein L. Journal Article
M L Scalley, Q Yi, H Gu, A McCormack, J R Yates, David Baker
In: Biochemistry, vol. 36, pp. 3373-82, 1997, ISSN: 0006-2960.
@article{34,
title = {Kinetics of folding of the IgG binding domain of peptostreptococcal protein L.},
author = { M L Scalley and Q Yi and H Gu and A McCormack and J R Yates and David Baker},
issn = {0006-2960},
year = {1997},
date = {1997-03-01},
journal = {Biochemistry},
volume = {36},
pages = {3373-82},
abstract = {The kinetics of folding of a tryptophan containing mutant of the IgG binding domain of protein L were characterized using stopped-flow circular dichroism, stopped-flow fluorescence, and HD exchange coupled with high-resolution mass spectrometry. Both the thermodynamics and kinetics of folding fit well to a simple two-state model: (1) Guanidine induced equilibrium denaturation transitions measured by fluorescence and circular dichroism were virtually superimposable. (2) The kinetics of folding/unfolding were single exponential under all conditions examined, and the rate constants obtained using all probes were similar. (3) Mass spectra from pulsed HD exchange refolding experiments showed that a species with very little protection from exchange is converted to a fully protected species (the native state) at a rate very similar to that of the overall change in tryptophan fluorescence; no intervening partially protected species were observed. (4) Rate constants (in H2O) and m values for folding and unfolding determined by fitting observed relaxation rates obtained over a broad range of denaturant concentrations to a two-state model were consistent with the equilibrium parameters deltaG and m: -RT ln(k(u)/k(f))/deltaG(U)H2O = 1.02; (m(u) + m(f))/m = 1.08. In contrast to results with a number of other proteins, there was no deviation from linearity in plots of ln k(obs) versus guanidine at low guanidine concentrations, both in the presence and absence of 0.4 M Na2SO4, suggesting that significantly stabilized intermediates do not accumulate during folding. Although all of the change in fluorescence signal during folding in phosphate buffer was accounted for by the simple exponential describing the overall folding reaction, fluorescence-quenching experiments using sodium iodide revealed a small reduction in the extent of quenching of the protein within the first two milliseconds after initiation of refolding in low concentrations of guanidine, suggesting a partial collapse of the unfolded chain may occur under these conditions. Comparison with results on the structurally and functionally similar IgG binding domain of streptococcal protein G show intriguing differences in the folding of the two proteins.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The kinetics of folding of a tryptophan containing mutant of the IgG binding domain of protein L were characterized using stopped-flow circular dichroism, stopped-flow fluorescence, and HD exchange coupled with high-resolution mass spectrometry. Both the thermodynamics and kinetics of folding fit well to a simple two-state model: (1) Guanidine induced equilibrium denaturation transitions measured by fluorescence and circular dichroism were virtually superimposable. (2) The kinetics of folding/unfolding were single exponential under all conditions examined, and the rate constants obtained using all probes were similar. (3) Mass spectra from pulsed HD exchange refolding experiments showed that a species with very little protection from exchange is converted to a fully protected species (the native state) at a rate very similar to that of the overall change in tryptophan fluorescence; no intervening partially protected species were observed. (4) Rate constants (in H2O) and m values for folding and unfolding determined by fitting observed relaxation rates obtained over a broad range of denaturant concentrations to a two-state model were consistent with the equilibrium parameters deltaG and m: -RT ln(k(u)/k(f))/deltaG(U)H2O = 1.02; (m(u) + m(f))/m = 1.08. In contrast to results with a number of other proteins, there was no deviation from linearity in plots of ln k(obs) versus guanidine at low guanidine concentrations, both in the presence and absence of 0.4 M Na2SO4, suggesting that significantly stabilized intermediates do not accumulate during folding. Although all of the change in fluorescence signal during folding in phosphate buffer was accounted for by the simple exponential describing the overall folding reaction, fluorescence-quenching experiments using sodium iodide revealed a small reduction in the extent of quenching of the protein within the first two milliseconds after initiation of refolding in low concentrations of guanidine, suggesting a partial collapse of the unfolded chain may occur under these conditions. Comparison with results on the structurally and functionally similar IgG binding domain of streptococcal protein G show intriguing differences in the folding of the two proteins.
A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding Journal Article
J A Rank, David Baker
In: Protein science, vol. 6, pp. 347-54, 1997, ISSN: 0961-8368.
@article{35,
title = {A desolvation barrier to hydrophobic cluster formation may contribute to the rate-limiting step in protein folding},
author = { J A Rank and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/rank97A.pdf},
issn = {0961-8368},
year = {1997},
date = {1997-02-01},
journal = {Protein science},
volume = {6},
pages = {347-54},
abstract = {To gain insight into the free energy changes accompanying protein hydrophobic core formation, we have used computer simulations to study the formation of small clusters of nonpolar solutes in water. A barrier to association is observed at the largest solute separation that does not allow substantial solvent penetration. The barrier reflects an effective increase in the size of the cavity occupied by the expanded but water-excluding cluster relative to both the close-packed cluster and the fully solvated separated solutes; a similar effect may contribute to the barrier to protein folding/unfolding. Importantly for the simulation of protein folding without explicit solvent, we find that the interactions between nonpolar solutes of varying size and number can be approximated by a linear function of the molecular surface, but not the solvent-accessible surface of the solutes. Comparison of the free energy of cluster formation to that of dimer formation suggests that the assumption of pair additivity implicit in current protein database derived potentials may be in error.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
To gain insight into the free energy changes accompanying protein hydrophobic core formation, we have used computer simulations to study the formation of small clusters of nonpolar solutes in water. A barrier to association is observed at the largest solute separation that does not allow substantial solvent penetration. The barrier reflects an effective increase in the size of the cavity occupied by the expanded but water-excluding cluster relative to both the close-packed cluster and the fully solvated separated solutes; a similar effect may contribute to the barrier to protein folding/unfolding. Importantly for the simulation of protein folding without explicit solvent, we find that the interactions between nonpolar solutes of varying size and number can be approximated by a linear function of the molecular surface, but not the solvent-accessible surface of the solutes. Comparison of the free energy of cluster formation to that of dimer formation suggests that the assumption of pair additivity implicit in current protein database derived potentials may be in error.
Blind predictions of local protein structure in CASP2 targets using the I-sites library Journal Article
C Bystroff, David Baker
In: Proteins, vol. Suppl 1, pp. 167-71, 1997, ISSN: 0887-3585.
@article{30,
title = {Blind predictions of local protein structure in CASP2 targets using the I-sites library},
author = { C Bystroff and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/bystroff97A.pdf},
issn = {0887-3585},
year = {1997},
date = {1997-00-01},
journal = {Proteins},
volume = {Suppl 1},
pages = {167-71},
abstract = {Blind predictions of the local structure of nine CASP2 targets were made using the I-sites library of short sequence--structure motifs, revealing strengths and weaknesses in this new knowledge-based method. Many turns between secondary structural elements were accurately predicted. Estimates of the confidence of prediction correlated well with the accuracy over the whole set. Bias toward structures used to develop the library was minimal, probably because of the extensive use of cross-validation. However, helix positions were better predicted by the PHD program. The method is likely to be sensitive to the quality of the sequence alignment. A general measure for evaluating local structure predictions is suggested.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Blind predictions of the local structure of nine CASP2 targets were made using the I-sites library of short sequence--structure motifs, revealing strengths and weaknesses in this new knowledge-based method. Many turns between secondary structural elements were accurately predicted. Estimates of the confidence of prediction correlated well with the accuracy over the whole set. Bias toward structures used to develop the library was minimal, probably because of the extensive use of cross-validation. However, helix positions were better predicted by the PHD program. The method is likely to be sensitive to the quality of the sequence alignment. A general measure for evaluating local structure predictions is suggested.
Characterization of the free energy spectrum of peptostreptococcal protein L Journal Article
Q Yi, M L Scalley, K T Simons, S T Gladwin, David Baker
In: Folding & design, vol. 2, pp. 271-80, 1997, ISSN: 1359-0278.
@article{27,
title = {Characterization of the free energy spectrum of peptostreptococcal protein L},
author = { Q Yi and M L Scalley and K T Simons and S T Gladwin and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/yi97A.pdf},
issn = {1359-0278},
year = {1997},
date = {1997-00-01},
journal = {Folding & design},
volume = {2},
pages = {271-80},
abstract = {BACKGROUND: Native state hydrogen/deuterium exchange studies on cytochrome c and RNase H revealed the presence of excited states with partially formed native structure. We set out to determine whether such excited states are populated for a very small and simple protein, the IgG-binding domain of peptostreptococcal protein L. RESULTS: Hydrogen/deuterium exchange data on protein L in 0-1.2 M guanidine fit well to a simple model in which the only contributions to exchange are denaturant-independent local fluctuations and global unfolding. A substantial discrepancy emerged between unfolding free energy estimates from hydrogen/deuterium exchange and linear extrapolation of earlier guanidine denaturation experiments. A better determined estimate of the free energy of unfolding obtained by global analysis of a series of thermal denaturation experiments in the presence of 0-3 M guanidine was in good agreement with the estimate from hydrogen/deuterium exchange. CONCLUSIONS: For protein L under native conditions, there do not appear to be partially folded states with free energies intermediate between that of the folded and unfolded states. The linear extrapolation method significantly underestimates the free energy of folding of protein L due to deviations from linearity in the dependence of the free energy on the denaturant concentration.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: Native state hydrogen/deuterium exchange studies on cytochrome c and RNase H revealed the presence of excited states with partially formed native structure. We set out to determine whether such excited states are populated for a very small and simple protein, the IgG-binding domain of peptostreptococcal protein L. RESULTS: Hydrogen/deuterium exchange data on protein L in 0-1.2 M guanidine fit well to a simple model in which the only contributions to exchange are denaturant-independent local fluctuations and global unfolding. A substantial discrepancy emerged between unfolding free energy estimates from hydrogen/deuterium exchange and linear extrapolation of earlier guanidine denaturation experiments. A better determined estimate of the free energy of unfolding obtained by global analysis of a series of thermal denaturation experiments in the presence of 0-3 M guanidine was in good agreement with the estimate from hydrogen/deuterium exchange. CONCLUSIONS: For protein L under native conditions, there do not appear to be partially folded states with free energies intermediate between that of the folded and unfolded states. The linear extrapolation method significantly underestimates the free energy of folding of protein L due to deviations from linearity in the dependence of the free energy on the denaturant concentration.
1996
Local sequence-structure correlations in proteins Journal Article
C Bystroff, K T Simons, K F Han, David Baker
In: Current opinion in biotechnology, vol. 7, pp. 417-21, 1996, ISSN: 0958-1669.
@article{214,
title = {Local sequence-structure correlations in proteins},
author = { C Bystroff and K T Simons and K F Han and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/bystroff96A.pdf},
issn = {0958-1669},
year = {1996},
date = {1996-08-01},
journal = {Current opinion in biotechnology},
volume = {7},
pages = {417-21},
abstract = {Considerable progress has been made in understanding the relationship between local amino acid sequence and local protein structure. Recent highlights include numerous studies of the structures adopted by short peptides, new approaches to correlating sequence patterns with structure patterns, and folding simulations using simple potentials.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Considerable progress has been made in understanding the relationship between local amino acid sequence and local protein structure. Recent highlights include numerous studies of the structures adopted by short peptides, new approaches to correlating sequence patterns with structure patterns, and folding simulations using simple potentials.
Global properties of the mapping between local amino acid sequence and local structure in proteins Journal Article
K F Han, David Baker
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 93, pp. 5814-8, 1996, ISSN: 0027-8424.
@article{215,
title = {Global properties of the mapping between local amino acid sequence and local structure in proteins},
author = { K F Han and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/han96A.pdf},
issn = {0027-8424},
year = {1996},
date = {1996-06-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {93},
pages = {5814-8},
abstract = {Local protein structure prediction efforts have consistently failed to exceed approximately 70% accuracy. We characterize the degeneracy of the mapping from local sequence to local structure responsible for this failure by investigating the extent to which similar sequence segments found in different proteins adopt similar three-dimensional structures. Sequence segments 3-15 residues in length from 154 different protein families are partitioned into neighborhoods containing segments with similar sequences using cluster analysis. The consistency of the sequence-to-structure mapping is assessed by comparing the local structures adopted by sequence segments in the same neighborhood in proteins of known structure. In the 154 families, 45% and 28% of the positions occur in neighborhoods in which one and two local structures predominate, respectively. The sequence patterns that characterize the neighborhoods in the first class probably include virtually all of the short sequence motifs in proteins that consistently occur in a particular local structure. These patterns, many of which occur in transitions between secondary structural elements, are an interesting combination of previously studied and novel motifs. The identification of sequence patterns that consistently occur in one or a small number of local structures in proteins should contribute to the prediction of protein structure from sequence.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Local protein structure prediction efforts have consistently failed to exceed approximately 70% accuracy. We characterize the degeneracy of the mapping from local sequence to local structure responsible for this failure by investigating the extent to which similar sequence segments found in different proteins adopt similar three-dimensional structures. Sequence segments 3-15 residues in length from 154 different protein families are partitioned into neighborhoods containing segments with similar sequences using cluster analysis. The consistency of the sequence-to-structure mapping is assessed by comparing the local structures adopted by sequence segments in the same neighborhood in proteins of known structure. In the 154 families, 45% and 28% of the positions occur in neighborhoods in which one and two local structures predominate, respectively. The sequence patterns that characterize the neighborhoods in the first class probably include virtually all of the short sequence motifs in proteins that consistently occur in a particular local structure. These patterns, many of which occur in transitions between secondary structural elements, are an interesting combination of previously studied and novel motifs. The identification of sequence patterns that consistently occur in one or a small number of local structures in proteins should contribute to the prediction of protein structure from sequence.
Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR Journal Article
Q Yi, David Baker
In: Protein science, vol. 5, pp. 1060-6, 1996, ISSN: 0961-8368.
@article{24,
title = {Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR},
author = { Q Yi and David Baker},
url = {https://www.bakerlab.org/wp-content/uploads/2016/06/yi96A.pdf},
issn = {0961-8368},
year = {1996},
date = {1996-06-01},
journal = {Protein science},
volume = {5},
pages = {1060-6},
abstract = {We use mass spectrometry in conjunction with hydrogen-deuterium exchange and NMR to characterize the conformational dynamics of the 62-residue IgG binding domain of protein L under conditions in which the native state is marginally stable. Mass spectra of protein L after short incubations in D2O reveal the presence of two distinct populations containing different numbers of protected protons. NMR experiments indicate that protons in the hydrophobic core are protected in one population, whereas all protons are exchanged for deuterons in the other. As the exchange period is increased, molecules are transferred from the former population to the latter. The absence of molecules with a subset of the core protons protected suggests that exchange occurs in part via a highly concerted transition to an excited state in which all protons exchange rapidly with deuterons. A steady increase in the molecular weight of the population with protected protons, and variation in the exchange rates of the individual protected protons indicates the presence of an additional exchange mechanism. A simple model in which exchange results from rapid (> 10(5)/s) local fluctuations around the native state superimposed upon transitions to an unfolded excited state at approximately 0.06/s is supported by qualitative agreement between the observed mass spectra and the mass spectra simulated according to the model using NMR-derived estimates of the proton exchange rates.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
We use mass spectrometry in conjunction with hydrogen-deuterium exchange and NMR to characterize the conformational dynamics of the 62-residue IgG binding domain of protein L under conditions in which the native state is marginally stable. Mass spectra of protein L after short incubations in D2O reveal the presence of two distinct populations containing different numbers of protected protons. NMR experiments indicate that protons in the hydrophobic core are protected in one population, whereas all protons are exchanged for deuterons in the other. As the exchange period is increased, molecules are transferred from the former population to the latter. The absence of molecules with a subset of the core protons protected suggests that exchange occurs in part via a highly concerted transition to an excited state in which all protons exchange rapidly with deuterons. A steady increase in the molecular weight of the population with protected protons, and variation in the exchange rates of the individual protected protons indicates the presence of an additional exchange mechanism. A simple model in which exchange results from rapid (> 10(5)/s) local fluctuations around the native state superimposed upon transitions to an unfolded excited state at approximately 0.06/s is supported by qualitative agreement between the observed mass spectra and the mass spectra simulated according to the model using NMR-derived estimates of the proton exchange rates.