Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues. (February 2015)

• Record Type: Journal Article
• Authors: Topham, Christopher M.; Smith, Jeremy C.
• Is Part Of: Computational biology and chemistry. Volume 54(2015)
• Page Start: 33
• Page End: 43
• Publication Date: 2015-02
• Subjects: Peptide reference structure -- Relative amino acid solvent-accessible surface area -- Peptide geometry -- Protein conformation -- Quantum chemical modelling; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2014.11.007
• Languages: English
• ISSNs: 1476-9271

Abstract

Graphical abstract: Highlights: Geometry-optimised extended conformation tri-peptides obtained for 43 amino acids. Peptide models suitable for relative residue accessible area calculations in proteins. Systematic effects of internal energy strain on solvent accessibility are observed. Results accord with conformational dependence of protein backbone covalent geometry. Use of standard covalent peptide geometry in conformational searching is discussed. Abstract: Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, C α and C β atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of 'hard' degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available.