Computational protocol: Analysis and Phylogeny of Small Heat Shock Proteins from Marine Viruses and Their Cyanobacteria Host

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[…] We searched the presence of sHSPs in the complete sequenced genomes of viruses from the biological databases (GenBank, protein database, and genomes database) using BLASTp, tBLASTn and HMM profile. We have also searched sHSPs in complete sequenced genomes of their host cyanobacteria, Synechococcus and Prochlorococcus. We aligned sequences of small heat shock proteins (sHSPs) from several species with ClustalW. Secondary structures indicated in the alignment are assigned according to the determined crystal structure of wheat HSP16.9 []. GeneBank accession numbers of sequences of cyanophages and cyanobacteria used in this alignment are listed in the and , respectively. Phylogenetic tree was constructed using PhyML [] and BioNJ []. Only the ACD and C-terminal extension were used for the phylogenetic analysis. For PhyML, WAG Substitution model and the statistical confidence of the nodes was calculated by aLRT test. [...] 3D models of Synechococcus phage sHSP S-MbCM6 (HspSP-MbCM6) and Synechococcus sp. PCC 7335.1 sHSP (HspS-PCC7335.1) were constructed using I-TASSER which combines the methods of threading, ab initio modeling and structural refinement []. Structures of Hsp16.0 from Schizosaccharomyces pombe (PDB: 3w1z), Hsp16.9 from Triticum aestivum (PDB: 1gme) and αB-crystallin from human (2ygd) were used as templates for HspSP-MbCM6. 3w1z, 1gme and Hsp16.5 from Methanocaldococcus jannaschii (PDB: 4eld) served as template for HspS-PCC7335.1. Search of structure similiraty of obtained 3D models was conducted by PDBeFold [] against PDB database. The electrostatic potential surface of sHSP 3D models was realized with PyMOL software (http://pymol.org/). Pairwise 3D models alignment was performed using Matras software []. Docking of the C-terminal extension of cyanophage (HspSP-MbCM6) and cyanobacteria (HspS-PCC7335.1) into hydrophobic pockets of ß4/ß8 strands region revealed by electrostatic potential surface analysis, was conducted by structure alignment to tetramer of wheat Hsp16.9 (PDB: 1gme). […]

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