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Updated: Jun 3, 2026

Formation of Ordered Biomolecular Structures by the Self-assembly of Short Peptides
Published on: November 21, 2013
Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations,
Víctor Cruz1, Javier Ramos, Javier Martínez-Salazar
1BIOPHYM, Instituto de Estructura de la Materia, CSIC, Madrid, Spain. victor.cruz@iem.cfmac.csic.es
Abstract:
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 Car-Parrinello MD calculations of the dipeptide in water.
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