Table of Contents
Journal of Biophysics
Volume 2011, Article ID 219515, 11 pages
http://dx.doi.org/10.1155/2011/219515
Research Article

Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

1School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Avenue, Atlanta, GA 30332-0230, USA
2School of Biology, Georgia Institute of Technology, 901 Atlantic Avenue, Atlanta, GA 30332-0230, USA

Received 27 September 2010; Revised 31 December 2010; Accepted 24 January 2011

Academic Editor: Eaton Edward Lattman

Copyright © 2011 Thomas R. Caulfield et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

The supplementary material contains additional material for methods and measurements conducted. The contents include: examples of the range of motion possible using the biasing entropic method (MdMD), matrix plots for anticodons over simulation time from different starting points that examine relatedness of the tRNAs, the overall extension-compactness of the tRNA from a Rg and RMSD calculations with and without the presence of counterions like Mg++, and graph of MdMD convergence compared to unbiased MD. Also included are a schematic of the tRNA angles and a flowchart of the MdMD algorithm.

  1. Supplementary Material