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

Eng H. Yap, Nicolas Lux Fawzi, Teresa Head-Gordon

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)626-638
Number of pages13
JournalProteins: Structure, Function and Genetics
Volume70
Issue number3
DOIs
StatePublished - Feb 15 2008
Externally publishedYes

Fingerprint

Hydrogen Bonding
Hydrogen bonds
Carbon
Proteins
Protein Folding
Topology
Peptides
Protein folding
Thermodynamics
Hydrogen
Kinetics

Keywords

  • Anisotropic hydrogen-bonding
  • Coarse-grained protein models
  • Kinetics
  • Multiscale models
  • Protein folding
  • Simulation

ASJC Scopus subject areas

  • Biochemistry
  • Genetics
  • Structural Biology

Cite this

A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding. / Yap, Eng H.; Fawzi, Nicolas Lux; Head-Gordon, Teresa.

In: Proteins: Structure, Function and Genetics, Vol. 70, No. 3, 15.02.2008, p. 626-638.

Research output: Contribution to journalArticle

Yap, Eng H. ; Fawzi, Nicolas Lux ; Head-Gordon, Teresa. / A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding. In: Proteins: Structure, Function and Genetics. 2008 ; Vol. 70, No. 3. pp. 626-638.
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