Assessment of the intrinsic conformational preferences of dipeptide amino acids in aqueous solution by combined umbrella sampling/MBAR statistics. A comparison with experimental results.

Info útil

Autor(es):

Cruz, V. L., Ramos, J. y Martinez-Salazar, J.

Año:

2012

Publicación

The Journal of Physical Chemistry B, 116(1), 469-475.

Proyecto
/Iniciativa

Neurosim

DOI

10.1021/jp206757j

Cómo citar
/How to cite

Cruz, V. L., Ramos, J. and Martinez-Salazar, J. (2012). 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 Journal of Physical Chemistry B, 116(1), 469-475. doi: 10.1021/jp206757j

Abstract/Resumen

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.