Assessment of the Intrinsic Conformational Preferences of Dipeptide Amino Acids in Aqueous Solution by Combined Umbrella Sampling/MBAR Statistics. A Comparison with Experimental Results

The propensities of 19 amino acid dipeptides have been calculated by a distributed umbrella sampling molecular dynamics simulation procedure using the OPLS-AA force field. The potential of mean force maps was estimated with the multiple Bennett acceptance ratio statistics. The resulting propensities...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2012-01, Vol.116 (1), p.469-475
Main Authors: Cruz, Victor L, Ramos, Javier, Martinez-Salazar, Javier
Format: Article
Language:English
Subjects:
Algorithms
Amides - chemistry
Amino acids
Assessments
B: Biophysical Chemistry
Dipeptides - chemistry
Dynamical systems
Equivalence
Molecular Dynamics Simulation
Sampling
Simulation
Statistics
Water - chemistry
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Summary:The propensities of 19 amino acid dipeptides have been calculated by a distributed umbrella sampling molecular dynamics simulation procedure using the OPLS-AA force field. The potential of mean force maps was estimated with the multiple Bennett acceptance ratio statistics. The resulting propensities compare satisfactorily well with very recently published experimental data on equivalent systems. In particular, α conformation-probabilities for all of the dipeptides remain much lower than either β or PII propensities. This result is in agreement with most experimental data for dipeptides. However, it is also in contrast with most simulation studies performed so far with other force fields, where α conformations result even more probable than PII or β ones. We discuss the behavior of the OPLS-AA force field, which can be useful for the improvement of this model in reproducing the recent experimental observations on amino acid dipeptides.
ISSN:1520-6106
1520-5207
DOI:10.1021/jp206757j