Molecular dynamics of phenylalanine transfer RNA

Journal of Biomolecular Structure & Dynamics
M PrabhakaranJ A McCammon

Abstract

The atomic motions of yeast phenylalanine transfer RNA have been simulated using the molecular dynamics algorithm. Two simulations were carried out for a period of 12 picoseconds, one with a normal Van der Waals potential and the other with a modified Van der Waals potential intended to mimic the effect of solvent. An analysis of large scale motions, surface exposure, root mean square displacements, helical oscillations and relaxation mechanisms reveals the maintenance of stability in the simulated structures and the general similarity of the various dynamic features of the two simulations. The regions of conformational flexibility and rigidity for tRNA(Phe) have been shown in a quantitative measure through this approach.

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Citations

Feb 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·U C SinghP Kollman
Oct 1, 1984·Journal of Biomolecular Structure & Dynamics·D L BeveridgeM Mezei
Feb 1, 1985·Journal of Biomolecular Structure & Dynamics·M VojtískováE Palecek
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Jul 1, 2011·Journal of Biophysics·Thomas R CaulfieldGeoffrey C Rollins
Nov 26, 2009·FEBS Letters·Rebecca W AlexanderZaida Luthey-Schulten
May 6, 2015·International Journal of Molecular Sciences·Xabier Agirrezabala, Mikel Valle
Nov 1, 1984·Biopolymers·C S TungJ A McCammon
Feb 11, 2010·Physical Chemistry Chemical Physics : PCCP·Milo M LinAhmed H Zewail
Aug 1, 1989·Journal of Biomolecular Structure & Dynamics·M Prabahakaran, S C Harvey
Jun 19, 2002·Accounts of Chemical Research·Jan Norberg, Lennart Nilsson
Mar 16, 1984·Science·S C HarveyJ A McCammon

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