Computational protocol: Analysis of SAT Type Foot-And-Mouth Disease Virus Capsid Proteins and the Identification of Putative Amino Acid Residues Affecting Virus Stability

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Protocol publication

[…] Three-dimensional models of protomers comprising the four capsid proteins (1A, 1B, 1C and 1D) of the SAT2 viruses were constructed based on the crystallographic coordinates of O1BFS (1FOD) , while pentameric models were built using the capsid coordinates, A1061 (1ZBE). The models were based on an optimal amino acid alignment of the capsid proteins. Sequence alignments were performed with ClustalX software using the default parameter setting. The modelling scripts were generated using the structural module in the FunGIMS software pakage and models were built using the Modeller 9v1 programme . The homology structure was calculated by the satisfaction of spatial restraints as described by empirical databases. Structures were visualised with PyMol v0.98 (DeLano Scientific LLC). A PROPKA analysis of each protomer was carried out to identify major protonation states affected by a pH of 6.0. Yasara was used to analyse any hydrogen bond networks that were present.pH-dependent differences between pentamers were investigated using a molecular dynamics simulation for ∼2.5 ns . The simulation was performed at a pH of 6.0, water density of 0.997 g/ml and a NaCl concentration of 0.9% using the Amber99 force-field with periodic boundary conditions at a temperature of 298 K. A molecule consisting of two protomers (henceforth called the dimer) was also generated to analyse the interface between two pentamers. […]

Pipeline specifications

Software tools Clustal W, MODELLER, PyMOL, PROPKA, YASARA
Applications Drug design, Protein structure analysis
Diseases Foot-and-Mouth Disease, Infection