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A general screened Coulomb potential based implicit solvent model: Calculation of secondary structure of small peptides
Author(s) -
Hassan Sergio A.,
Mehler Ernest L.
Publication year - 2001
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.1210
Subject(s) - chemistry , random coil , force field (fiction) , monte carlo method , solvent , coulomb , molecular dynamics , residue (chemistry) , computational chemistry , peptide , solvent effects , population , crystallography , thermodynamics , physics , organic chemistry , quantum mechanics , mathematics , circular dichroism , biochemistry , statistics , demography , sociology , electron
The screened Coulomb potential based implicit solvent model (SCP‐ISM) was recently proposed to describe bulk solvent effects in proteins. In this work it is combined with the Monte Carlo approach of conformational memories (CM) and the PAR22 force field of CHARMM to carry out sequence to structure calculations on peptides that have been shown to adopt α‐helix and β‐hairpin conformations. Simulations at 270 K and 300 K on the peptide, CH 3 CO‐(AAQAA) 3 ‐NHCH 3 , result in α‐helix containing populations of 60% and 53% at these two temperatures, respectively. The residue helicities were found to change dramatically between these two temperatures, and at the lower temperature are in good agreement with the experimental helicities estimated at 274 K. CM simulations on the second peptide, CH 3 CO‐V 5 D PGV 5 ‐NH 2 , were carried out to study the β‐hairpin forming propensity of D Pro. The calculations gave a population of about 40% β‐hairpin conformations at 300 K with the residues D Pro‐Gly forming all or part of the loop. Four main subfamilies of different β‐hairpin/β‐turn structures were found. It was observed that hydrophobic interactions between specific side chains play a fundamental role in the formation and stabilization of the different types of β‐turns. For both peptides, populations of about 40% random coil structures were found. Comparison with available theoretical and experimental results is presented and discussed. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 193–202, 2001