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A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.

ABSTRACT: We develop a sequence based alpha-carbon model to incorporate a mean field estimate of the orientation dependence of the polypeptide chain that gives rise to specific hydrogen bond pairing to stabilize alpha-helices and beta-sheets. We illustrate the success of the new protein model in capturing thermodynamic measures and folding mechanism of proteins L and G. Compared to our previous coarse-grained model, the new model shows greater folding cooperativity and improvements in designability of protein sequences, as well as predicting correct trends for kinetic rates and mechanism for proteins L and G. We believe the model is broadly applicable to other protein folding and protein-protein co-assembly processes, and does not require experimental input beyond the topology description of the native state. Even without tertiary topology information, it can also serve as a mid-resolution protein model for more exhaustive conformational search strategies that can bridge back down to atomic descriptions of the polypeptide chain.

SUBMITTER: Yap EH

PROVIDER: S-EPMC3474853 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature

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A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.

Yap Eng-Hui EH Fawzi Nicolas Lux NL Head-Gordon Teresa T

Proteins 20080201 3

We develop a sequence based alpha-carbon model to incorporate a mean field estimate of the orientation dependence of the polypeptide chain that gives rise to specific hydrogen bond pairing to stabilize alpha-helices and beta-sheets. We illustrate the success of the new protein model in capturing thermodynamic measures and folding mechanism of proteins L and G. Compared to our previous coarse-grained model, the new model shows greater folding cooperativity and improvements in designability of pro ...[more]

PMID: 17879350

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A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.

Publications

A coarse-grained alpha-carbon protein model with anisotropic hydrogen-bonding.

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