help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Rosenhouse-Dantsker, A.
Right arrow Articles by Osman, R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Rosenhouse-Dantsker, A.
Right arrow Articles by Osman, R.

Biophys J, July 2000, p. 66-79, Vol. 79, No. 1

Application of the Primary Hydration Shell Approach to Locally Enhanced Sampling Simulated Annealing: Computer Simulation of Thyrotropin-Releasing Hormone in Water

Avia Rosenhouse-Dantsker and Roman Osman

Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029 USA

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 <RAD><RCD><IT>c<SUB>1</SUB>T</IT></RCD></RAD> - 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.

Biophys J, July 2000, p. 66-79, Vol. 79, No. 1
© 2000 by the Biophysical Society   0006-3495/00/07/66/14  $2.00


This article has been cited by other articles:


Home page
 Biophys. JHome page
M. B. Hamaneh and M. Buck
Acceptable Protein and Solvent Behavior in Primary Hydration Shell Simulations of Hen Lysozyme
Biophys. J., April 1, 2007; 92(7): L49 - L51.
[Abstract] [Full Text] [PDF]

Home page
 Chem SensesHome page
P. Jiang, M. Cui, Q. Ji, L. Snyder, Z. Liu, L. Benard, R.F. Margolskee, R. Osman, and M. Max
Molecular Mechanisms of Sweet Receptor Function
Chem Senses, January 1, 2005; 30(suppl_1): i17 - i18.
[Full Text] [PDF]

Home page
 Biophys. JHome page
A. Kentsis, M. Mezei, and R. Osman
MC-PHS: A Monte Carlo Implementation of the Primary Hydration Shell for Protein Folding and Design
Biophys. J., February 1, 2003; 84(2): 805 - 815.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2000 by the Biophysical Society.