Paper Citing NAMD - Abstract
Zeng, Yingying; Larson, Steven B.; Heitsch, Christine E.; McPherson, Alexander; Harvey, Stephen C.
A model for the structure of satellite tobacco mosaic virus
JOURNAL OF STRUCTURAL BIOLOGY, 180:110-116, OCT 2012
Satellite tobacco mosaic virus (STMV) is an icosahedral T = 1 single-stranded RNA virus with a genome containing 1058 nucleotides. X-ray crystallography revealed a structure containing 30 double-helical RNA segments, with each helix having nine base pairs and an unpaired nucleotide at the 3' end of each strand. Based on this structure, Larson and McPherson proposed a model of 30 hairpin-loop elements occupying the edges of the icosahedron and connected by single-stranded regions. More recently, Schroeder et al. have combined the results of chemical probing with a novel helix searching algorithm to propose a specific secondary structure for the STMV genome, compatible with the Larson-McPherson model. Here we report an all-atom model of STMV, using the complete protein and RNA sequences and the Schroeder RNA secondary structure. As far as we know, this is the first all-atom model for the complete structure of any virus (100% of the atoms) using the natural genomic sequence. (C) 2012 Elsevier Inc. All rights reserved.
