Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, quantum mechanics based calculations, and experimental data.
Info útil
Autor(es):
Cruz, V. L., Ramos, J. y Martinez-Salazar, J.
Año:
2011
Publicación
The Journal of Physical Chemistry B, 115(16), 4880-4886.
Proyecto
/Iniciativa
Neurosim
DOI
10.1021/jp2022727
Cómo citar
/How to cite
Cruz, V. L., Ramos, J. and Martinez-Salazar, J. (2011). Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, quantum mechanics based calculations, and experimental data. The Journal of Physical Chemistry B, 115(16), 4880-4886. doi: 10.1021/jp2022727
An exhaustive umbrella sampling simulation of the alanine dipeptide in solution is reported. The presence of stable Y conformations in solution is assessed by both quantum calculations and experimental data from X-ray and NMR protein-solved structures available in the protein coil library. The agreement between experimental and simulation Ramachandran plots of the dipeptide in solution is excellent. A suitable explanation of the stabilization of the Y conformation mediated by water for the alanine dipeptide is discussed on the basis of CarParrinello MD calculations of the dipeptide in water.