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Proteins. 2014 Oct;82(10):2574-84. doi: 10.1002/prot.24621. Epub 2014 Aug 11.

Predicting the side-chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models.

Author information

1
Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, Connecticut, 06520-8114; Integrated Graduate Program in Physical and Engineering Biology (IGPPEB), Yale University, New Haven, Connecticut, 06520-8114.

Abstract

The side-chain dihedral angle distributions of all amino acids have been measured from myriad high-resolution protein crystal structures. However, we do not yet know the dominant interactions that determine these distributions. Here, we explore to what extent the defining features of the side-chain dihedral angle distributions of different amino acids can be captured by a simple physical model. We find that a hard-sphere model for a dipeptide mimetic that includes only steric interactions plus stereochemical constraints is able to recapitulate the key features of the back-bone dependent observed amino acid side-chain dihedral angle distributions of Ser, Cys, Thr, Val, Ile, Leu, Phe, Tyr, and Trp. We find that for certain amino acids, performing the calculations with the amino acid of interest in the central position of a short α-helical segment improves the match between the predicted and observed distributions. We also identify the atomic interactions that give rise to the differences between the predicted distributions for the hard-sphere model of the dipeptide and that of the α-helical segment. Finally, we point out a case where the hard-sphere plus stereochemical constraint model is insufficient to recapitulate the observed side-chain dihedral angle distribution, namely the distribution P(χ₃) for Met.

KEYWORDS:

dipeptide; helical segment; protein crystal structure; protein structure prediction; side-chain dihedral angle distribution

PMID:
24912976
DOI:
10.1002/prot.24621
[Indexed for MEDLINE]

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