Title: Flavitrack analysis of the structure and function of West Nile non-structural proteins

Authors: Petr Danecek, Catherine H. Schein

Addresses: Sealy Center for Structural Biology and Molecular Biophysics, Sealy Center for Vaccine Development, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0857, USA. ' Sealy Center for Structural Biology and Molecular Biophysics, Sealy Center for Vaccine Development, Departments of Biochemistry and Molecular Biology and Microbiology and Immunology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-0857, USA

Abstract: The Flavitrack database groups Flaviviruses (FV), evolutionarily related organisms with high subtype variability, according to their phenotypes. Here, PCPMer tools were used to calculate consensus sequences based on conservation of Physicochemical Properties (PCP) for 919 sequences of NS2a, a non-structural protein involved in preventing host interferon response to infection. Conserved PCP-motifs were detected, primarily in the N-terminal half of NS2a. One model structure, based on a nuclear receptor, groups residues essential for West Nile (WN) infectivity (I59, V61, and M103) in a pocket on the protein surface. These methods will aid in the design of vaccines and specific therapies against FV.

Keywords: consensus sequences; Flavitrack analysis; NS2a; PCPMer; West Nile virus; non-structural proteins; protein structure; protein function; bioinformatics; Flaviviruses; physicochemical properties; PCP motifs; vaccines; therapies.

DOI: 10.1504/IJBRA.2010.032117

International Journal of Bioinformatics Research and Applications, 2010 Vol.6 No.2, pp.134 - 146

Published online: 10 Mar 2010 *

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