Preprints are available on bioRxiv.
1.
Pyles, Harley; Zhang, Shuai; Yoreo, James J. De; Baker, David
Controlling protein assembly on inorganic crystals through designed protein interfaces Journal Article
In: Nature, 2019.
@article{Pyles2019,
title = {Controlling protein assembly on inorganic crystals through designed protein interfaces},
author = {Harley Pyles and Shuai Zhang and James J. De Yoreo and David Baker },
url = {https://www.nature.com/articles/s41586-019-1361-6
https://www.bakerlab.org/wp-content/uploads/2019/07/2019_Pyles_MicaBinder.pdf},
doi = {10.1038/s41586-019-1361-6},
year = {2019},
date = {2019-07-10},
journal = {Nature},
abstract = {The ability of proteins and other macromolecules to interact with inorganic surfaces is essential to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains, but the structures of most protein–inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein–mineral interfaces, guided by the example of ice-binding proteins, which present arrays of threonine residues (matched to the ice lattice) that order clathrate waters into an ice-like structure6. Here we design proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the potassium ion (K+) sublattice on muscovite mica (001). At low K+ concentration, individual molecules bind independently to mica in the designed orientations, whereas at high K+ concentration, the designs form two-dimensional liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimetres. Incorporation of designed protein–protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micrometre-long single-protein-diameter wires and a designed trimeric interface yielded extensive honeycomb arrays. The nearest-neighbour distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nanometres with 2.1-nanometre selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein–inorganic lattice interactions can be systematically programmed and set the stage for designing protein–inorganic hybrid materials.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The ability of proteins and other macromolecules to interact with inorganic surfaces is essential to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains, but the structures of most protein–inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein–mineral interfaces, guided by the example of ice-binding proteins, which present arrays of threonine residues (matched to the ice lattice) that order clathrate waters into an ice-like structure6. Here we design proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the potassium ion (K+) sublattice on muscovite mica (001). At low K+ concentration, individual molecules bind independently to mica in the designed orientations, whereas at high K+ concentration, the designs form two-dimensional liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimetres. Incorporation of designed protein–protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micrometre-long single-protein-diameter wires and a designed trimeric interface yielded extensive honeycomb arrays. The nearest-neighbour distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nanometres with 2.1-nanometre selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein–inorganic lattice interactions can be systematically programmed and set the stage for designing protein–inorganic hybrid materials.
2.
Goobes, Gil; Goobes, Rivka; Shaw, Wendy J; Gibson, James M; Long, Joanna R; Raghunathan, Vinodhkumar; Schueler-Furman, Ora; Popham, Jennifer M; Baker, David; Campbell, Charles T; Stayton, Patrick S; Drobny, Gary P
The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite Journal Article
In: Magnetic resonance in chemistry, vol. 45, pp. S32-S47, 2008, ISSN: 1097-458X.
@article{223,
title = {The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite},
author = { Gil Goobes and Rivka Goobes and Wendy J Shaw and James M Gibson and Joanna R Long and Vinodhkumar Raghunathan and Ora Schueler-Furman and Jennifer M Popham and David Baker and Charles T Campbell and Patrick S Stayton and Gary P Drobny},
issn = {1097-458X},
year = {2008},
date = {2008-01-01},
journal = {Magnetic resonance in chemistry},
volume = {45},
pages = {S32-S47},
abstract = {Proteins are found to be involved in interaction with solid surfaces in numerous natural events. Acidic proteins that adsorb to crystal faces of a biomineral to control the growth and morphology of hard tissue are only one example. Deducing the mechanisms of surface recognition exercised by proteins has implications to osteogenesis, pathological calcification and other proteins functions at their adsorbed state. Statherin is an enamel pellicle protein that inhibits hydroxyapatite nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. Here, we highlight some of the insights we obtained recently using both thermodynamic and solid state NMR measurements to the adsorption process of statherin to hydroxyapatite. We combine macroscopic energy characterization with microscopic structural findings to present our views of protein adsorption mechanisms and the structural changes accompanying it and discuss the implications of these studies to understanding the functions of the protein adsorbed to the enamel surfaces. Copyright (c) 2007 John Wiley & Sons, Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Proteins are found to be involved in interaction with solid surfaces in numerous natural events. Acidic proteins that adsorb to crystal faces of a biomineral to control the growth and morphology of hard tissue are only one example. Deducing the mechanisms of surface recognition exercised by proteins has implications to osteogenesis, pathological calcification and other proteins functions at their adsorbed state. Statherin is an enamel pellicle protein that inhibits hydroxyapatite nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. Here, we highlight some of the insights we obtained recently using both thermodynamic and solid state NMR measurements to the adsorption process of statherin to hydroxyapatite. We combine macroscopic energy characterization with microscopic structural findings to present our views of protein adsorption mechanisms and the structural changes accompanying it and discuss the implications of these studies to understanding the functions of the protein adsorbed to the enamel surfaces. Copyright (c) 2007 John Wiley & Sons, Ltd.
3.
Goobes, Gil; Goobes, Rivka; Schueler-Furman, Ora; Baker, David; Stayton, Patrick S; Drobny, Gary P
Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals Journal Article
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 103, pp. 16083-8, 2006, ISSN: 0027-8424.
@article{292,
title = {Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals},
author = { Gil Goobes and Rivka Goobes and Ora Schueler-Furman and David Baker and Patrick S Stayton and Gary P Drobny},
issn = {0027-8424},
year = {2006},
date = {2006-10-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
pages = {16083-8},
abstract = {Statherin is an enamel pellicle protein that inhibits hydroxyapatite (HAP) nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. We report here from solid-state NMR measurements that the proteintextquoterights C-terminal region folds into an alpha-helix upon adsorption to HAP crystals. This region contains the binding sites for bacterial fimbriae that mediate bacterial cell adhesion to the surface of the tooth. The helical segment is shown through long-range distance measurements to fold back onto the intermediate region (residues Y16-P28) defining the global fold of the protein. Statherin, previously shown to be unstructured in solution, undergoes conformation selection on its substrate mineral surface. This surface-induced folding of statherin can be related to its functionality in inhibiting HAP crystal growth and can explain how oral pathogens selectively recognize HAP-bound statherin.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Statherin is an enamel pellicle protein that inhibits hydroxyapatite (HAP) nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. We report here from solid-state NMR measurements that the proteintextquoterights C-terminal region folds into an alpha-helix upon adsorption to HAP crystals. This region contains the binding sites for bacterial fimbriae that mediate bacterial cell adhesion to the surface of the tooth. The helical segment is shown through long-range distance measurements to fold back onto the intermediate region (residues Y16-P28) defining the global fold of the protein. Statherin, previously shown to be unstructured in solution, undergoes conformation selection on its substrate mineral surface. This surface-induced folding of statherin can be related to its functionality in inhibiting HAP crystal growth and can explain how oral pathogens selectively recognize HAP-bound statherin.
2022
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2021
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2020
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2019
FROM THE LAB
Harley Pyles, Shuai Zhang, James J. De Yoreo, David Baker
Controlling protein assembly on inorganic crystals through designed protein interfaces Journal Article
In: Nature, 2019.
@article{Pyles2019,
title = {Controlling protein assembly on inorganic crystals through designed protein interfaces},
author = {Harley Pyles and Shuai Zhang and James J. De Yoreo and David Baker },
url = {https://www.nature.com/articles/s41586-019-1361-6
https://www.bakerlab.org/wp-content/uploads/2019/07/2019_Pyles_MicaBinder.pdf},
doi = {10.1038/s41586-019-1361-6},
year = {2019},
date = {2019-07-10},
journal = {Nature},
abstract = {The ability of proteins and other macromolecules to interact with inorganic surfaces is essential to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains, but the structures of most protein–inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein–mineral interfaces, guided by the example of ice-binding proteins, which present arrays of threonine residues (matched to the ice lattice) that order clathrate waters into an ice-like structure6. Here we design proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the potassium ion (K+) sublattice on muscovite mica (001). At low K+ concentration, individual molecules bind independently to mica in the designed orientations, whereas at high K+ concentration, the designs form two-dimensional liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimetres. Incorporation of designed protein–protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micrometre-long single-protein-diameter wires and a designed trimeric interface yielded extensive honeycomb arrays. The nearest-neighbour distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nanometres with 2.1-nanometre selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein–inorganic lattice interactions can be systematically programmed and set the stage for designing protein–inorganic hybrid materials.
},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The ability of proteins and other macromolecules to interact with inorganic surfaces is essential to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains, but the structures of most protein–inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein–mineral interfaces, guided by the example of ice-binding proteins, which present arrays of threonine residues (matched to the ice lattice) that order clathrate waters into an ice-like structure6. Here we design proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the potassium ion (K+) sublattice on muscovite mica (001). At low K+ concentration, individual molecules bind independently to mica in the designed orientations, whereas at high K+ concentration, the designs form two-dimensional liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimetres. Incorporation of designed protein–protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micrometre-long single-protein-diameter wires and a designed trimeric interface yielded extensive honeycomb arrays. The nearest-neighbour distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nanometres with 2.1-nanometre selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein–inorganic lattice interactions can be systematically programmed and set the stage for designing protein–inorganic hybrid materials.
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2018
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2017–1998
ALL PAPERS
2008
Gil Goobes, Rivka Goobes, Wendy J Shaw, James M Gibson, Joanna R Long, Vinodhkumar Raghunathan, Ora Schueler-Furman, Jennifer M Popham, David Baker, Charles T Campbell, Patrick S Stayton, Gary P Drobny
The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite Journal Article
In: Magnetic resonance in chemistry, vol. 45, pp. S32-S47, 2008, ISSN: 1097-458X.
@article{223,
title = {The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite},
author = { Gil Goobes and Rivka Goobes and Wendy J Shaw and James M Gibson and Joanna R Long and Vinodhkumar Raghunathan and Ora Schueler-Furman and Jennifer M Popham and David Baker and Charles T Campbell and Patrick S Stayton and Gary P Drobny},
issn = {1097-458X},
year = {2008},
date = {2008-01-01},
journal = {Magnetic resonance in chemistry},
volume = {45},
pages = {S32-S47},
abstract = {Proteins are found to be involved in interaction with solid surfaces in numerous natural events. Acidic proteins that adsorb to crystal faces of a biomineral to control the growth and morphology of hard tissue are only one example. Deducing the mechanisms of surface recognition exercised by proteins has implications to osteogenesis, pathological calcification and other proteins functions at their adsorbed state. Statherin is an enamel pellicle protein that inhibits hydroxyapatite nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. Here, we highlight some of the insights we obtained recently using both thermodynamic and solid state NMR measurements to the adsorption process of statherin to hydroxyapatite. We combine macroscopic energy characterization with microscopic structural findings to present our views of protein adsorption mechanisms and the structural changes accompanying it and discuss the implications of these studies to understanding the functions of the protein adsorbed to the enamel surfaces. Copyright (c) 2007 John Wiley & Sons, Ltd.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Proteins are found to be involved in interaction with solid surfaces in numerous natural events. Acidic proteins that adsorb to crystal faces of a biomineral to control the growth and morphology of hard tissue are only one example. Deducing the mechanisms of surface recognition exercised by proteins has implications to osteogenesis, pathological calcification and other proteins functions at their adsorbed state. Statherin is an enamel pellicle protein that inhibits hydroxyapatite nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. Here, we highlight some of the insights we obtained recently using both thermodynamic and solid state NMR measurements to the adsorption process of statherin to hydroxyapatite. We combine macroscopic energy characterization with microscopic structural findings to present our views of protein adsorption mechanisms and the structural changes accompanying it and discuss the implications of these studies to understanding the functions of the protein adsorbed to the enamel surfaces. Copyright (c) 2007 John Wiley & Sons, Ltd.
2006
Gil Goobes, Rivka Goobes, Ora Schueler-Furman, David Baker, Patrick S Stayton, Gary P Drobny
Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals Journal Article
In: Proceedings of the National Academy of Sciences of the United States of America, vol. 103, pp. 16083-8, 2006, ISSN: 0027-8424.
@article{292,
title = {Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals},
author = { Gil Goobes and Rivka Goobes and Ora Schueler-Furman and David Baker and Patrick S Stayton and Gary P Drobny},
issn = {0027-8424},
year = {2006},
date = {2006-10-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {103},
pages = {16083-8},
abstract = {Statherin is an enamel pellicle protein that inhibits hydroxyapatite (HAP) nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. We report here from solid-state NMR measurements that the proteintextquoterights C-terminal region folds into an alpha-helix upon adsorption to HAP crystals. This region contains the binding sites for bacterial fimbriae that mediate bacterial cell adhesion to the surface of the tooth. The helical segment is shown through long-range distance measurements to fold back onto the intermediate region (residues Y16-P28) defining the global fold of the protein. Statherin, previously shown to be unstructured in solution, undergoes conformation selection on its substrate mineral surface. This surface-induced folding of statherin can be related to its functionality in inhibiting HAP crystal growth and can explain how oral pathogens selectively recognize HAP-bound statherin.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Statherin is an enamel pellicle protein that inhibits hydroxyapatite (HAP) nucleation and growth, lubricates the enamel surface, and is recognized by oral bacteria in periodontal diseases. We report here from solid-state NMR measurements that the proteintextquoterights C-terminal region folds into an alpha-helix upon adsorption to HAP crystals. This region contains the binding sites for bacterial fimbriae that mediate bacterial cell adhesion to the surface of the tooth. The helical segment is shown through long-range distance measurements to fold back onto the intermediate region (residues Y16-P28) defining the global fold of the protein. Statherin, previously shown to be unstructured in solution, undergoes conformation selection on its substrate mineral surface. This surface-induced folding of statherin can be related to its functionality in inhibiting HAP crystal growth and can explain how oral pathogens selectively recognize HAP-bound statherin.