Application of the primary hydration shell approach to locally enhanced sampling simulated annealing: Computer simulation of thyrotropin-releasing hormone in water

Avia Rosenhouse-Dantsker, Roman Osman

Research output: Contribution to journalArticlepeer-review

9 Scopus citations

Abstract

A unified model of simulated annealing with locally enhanced sampling (LES) in a primary hydration shell (PHS) aqueous environment is developed and tested by predicting the structure of the tripeptide thyrotropin-releasing hormone (TRH) in solution. The model extends the formulation of the restraining force in the PHS method as a function of temperature, number of copies in the LES method, and shell thickness. The dependence of the restraining force on temperature can be shown to follow the relationship √c1T - c2, which can be derived from the expression for kinetic energy in molecular dynamics simulations. The calibration of the restraining force for different simulation conditions reveals the dependence of c1 and c2 on the number of copies in the LES method and the thickness of the PHS. The predicted structure of TRH is in very good agreement with results from NMR experiments and from a 10-ns PHS simulation at 300 K. The method promises to be useful in predicting structure of peptides and proteins in an aqueous environment.

Original languageEnglish
Pages (from-to)66-79
Number of pages14
JournalBiophysical Journal
Volume79
Issue number1
DOIs
StatePublished - Jul 2000

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