A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2008-02, Vol.70 (3), p.626-638
• Main Authors: Yap, Eng-Hui, Fawzi, Nicolas Lux, Head-Gordon, Teresa
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; anisotropic hydrogen-bonding; Coarse-grained protein models; Computer Simulation; Hydrogen Bonding; Kinetics; Models, Chemical; Models, Molecular; Molecular Sequence Data; multi-scale models; Protein Folding; Protein Structure, Secondary; Proteins - chemistry; Proteins - metabolism; simulation; Thermodynamics
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.21515

We develop a sequence based α‐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 α‐helices and β‐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. Proteins 2008. © 2007 Wiley‐Liss, Inc.