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Role of hydrophilic and hydrophobic contacts in folding of the second β-hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model by Yaoqi Zhou; Apichart Linhananta is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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## Abstract Predicting the folding mechanism of the second β‐hairpin fragment of the Ig‐binding domain B of streptococcal protein G is unexpectedly challenging for simplified reduced models because the models developed so far indicated a different folding mechanism from what was suggested from high‐temperature unfolding and equilibrium free‐energy surface analysis based on established all‐atom empirical force fields in explicit or implicit solvent. This happened despite the use of empirical residue‐based interactions, multibody hydrophobic interactions, and inclusions of hydrogen bonding effects in the simplified models. This article employs a recently developed all‐atom (except nonpolar hydrogens) model interacting with simple square‐well potentials to fold the peptide fragment by molecular dynamics simulation methods. In this study, 193 out of 200 trajectories are folded at two reduced temperatures (3.5 and 3.7) close to the transition temperature __T__\* ∼ 4.0. Each simulation takes <7 h of CPU time on a Pentium 800‐MHz PC. Folding of the new all‐atom model is found to be initiated by collapse before the formation of main‐chain hydrogen bonds. This verifies the mechanism propose

Who reads Role of hydrophilic and hydrophobic contacts in folding of the second β-hairpin fragment of protein G: Molecular dynamics simulation studies of an all-atom model?

Author

Yaoqi Zhou; Apichart Linhananta

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2002

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)