@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}

}

@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}

}

@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}

}

@article{570,

title = {The role of pro regions in protein folding.},

author = { D Baker and A K Shiau and D A Agard},

url = {https://www.bakerlab.org/wp-content/uploads/2016/06/theroleofproregions_Baker1993.pdf},

issn = {0955-0674},

year  = {1993},

date = {1993-12-01},

journal = {Current Opinion in Cell Biology},

volume = {5},

pages = {966-70},

abstract = {In vivo, many proteases are synthesized as larger precursors. During the maturation process, the catalytically active protease domain is released from the larger polypeptide or pro-enzyme by one or more proteolytic processing steps. In several well studied cases, amino-terminal pro regions have been shown to play a fundamental role in the folding of the associated protease domains. The mechanism by which pro regions facilitate folding appears to be significantly different from that used by the molecular chaperones. Recent results suggest that the pro region assisted folding mechanism may be used by a wide variety of proteases, and perhaps even by non-proteases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{329,

title = {A protein-folding reaction under kinetic control},

author = { D Baker and J L Sohl and D A Agard},

issn = {0028-0836},

year  = {1992},

date = {1992-03-01},

journal = {Nature},

volume = {356},

pages = {263-5},

abstract = {Synthesis of alpha-lytic protease is as a precursor containing a 166 amino-acid pro region transiently required for the correct folding of the protease domain. By omitting the pro region in an in vitro refolding reaction we trapped an inactive, but folding competent state (I) having an expanded radius yet native-like secondary structure. The I state is stable for weeks at physiological pH in the absence of denaturant, but rapidly folds to the active, native state on addition of the pro region as a separate polypeptide chain. The mechanism of action of the pro region is distinct from that of the chaperonins: rather than reducing the rate of off-pathway reactions, the pro region accelerates the rate-limiting step on the folding pathway by more than 10(7). Because both the I and native states are stable under identical conditions with no detectable interconversion, the folding of alpha-lytic protease must be under kinetic and not thermodynamic control.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}