Prediction and Analysis of Three-Dimensional Structure of the p7- Transactivated Protein1 of Hepatitis C Virus.

BACKGROUND: The p7-transactivated protein1 of Hepatitis C virus is a small integral membrane protein of 127 amino acids, which is crucial for assembly and release of infectious virions. Ab initio or comparative modelling, is an essential tool to solve the problem of protein structure prediction and to comprehend the physicochemical fundamental of how proteins fold in nature. RESULTS: Only one domain (1-127) of p7-transactivated protein1 has been predicted using the systematic in silico approach, ThreaDom. I-TASSER was ranked as the best server for full-length 3-D protein structural predictions of p7-transactivated protein1 where the benchmarked scoring system such as C-score, TM-score, RMSD and Z-score are used to obtain quantitative assessments of the I-TASSER models. Scanning protein motif databases, along with secondary and surface accessibility predictions integrated with post translational modification sites (PTMs) prediction revealed functional and protein binding motifs. Three protein binding motifs (two Asp/Glutamnse, CTNNB1- bd_N) with high sequence conservation and two PTMs prediction: Camp_phospho_site and Myristyl site were predicted using BLOCKS and PROSITE scan. These motifs and PTMs were related to the function of p7-transactivated protein1 protein in inducing ion channel/pore and release of infectious virions. Using SCOP, only one hit matched protein sequence at 71-120 was classified as small proteins and FYVE/PHD zinc finger superfamily. CONCLUSION: Integrating this information about the p7-transactivated protein1 with SCOP and CATH annotations of the templates facilitates the assignment of structure-function/ evolution relationships to the known and the newly determined protein structures.

Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

BACKGROUND: Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968-1999 to predict viral motifs involved in significant biological functions. RESULTS: 14 MEME blocks were generated and comparative analysis of the MEME blocks identified blocks 1, 2, 3 and 7 to correlate with several biological functions. Analysis of the different Hemagglutinin sequences elucidated that the single block 7 has the highest frequency of amino acid substitution and the highest number of co-mutating pairs. MEME 2 showed intermediate variability and MEME 1 was the most conserved. Interestingly, MEME blocks 2 and 7 had the highest incidence of potential post-translational modifications sites including phosphorylation sites, ASN glycosylation motifs and N-myristylation sites. Similarly, these 2 blocks overlap with previously identified antigenic sites and receptor binding sites. CONCLUSION: Our study identifies motifs in the Hemagglutinin protein with different amino acid substitution frequencies over a 31 years period, and derives relevant functional characteristics by correlation of these motifs with potential post-translational modifications sites, antigenic and receptor binding sites.

Natural genetic engineering of hepatitis C virus NS5A for immune system counterattack.

The Hepatitis C virus nonstructural 5A (NS5A) protein is a hydrophilic phosphoprotein with diverse functions. The domain assignment of NS5A had been refined using a systematic in silico bioinformatics approach using DOMAC, the protein is divided into three domains and domain III is subdivided into two subdomains using ProDom and SSEP servers. The fold structure for domains II and III were predicted using the meta-server 3D-Jury. Scanning motif databases (SMART, BLOCKS, and PROSITE) gave new motifs. Two important motifs, the interleukins 1 and 8 interaction motifs, relating to NS5A function in inducing the interleukin 8 promoter, were discovered from the BLOCKS scan. Protein-protein interaction motifs were predicted as hot loops and disordered regions, corresponding to binding regions with the ds-protein kinase R, viral polymerase, and Src homology 3 signaling proteins binding motif. Other hot loops were predicted in the V3 region and in the single-stranded DNA-binding protein motif. The different mechanisms by which the NS5A protein leads to immune system signaling dysfunction points to the natural genetic engineering of this protein.

Phylogenetic analysis and comparison between cow and buffalo (including Egyptian buffaloes) mitochondrial displacement-loop regions.

Mitochondrial DNA (mtDNA) analysis has been used extensively for phylogenetic analysis studies and systematics. The displacement loop (D-loop) region inside the mtDNA is a non-coding part whose analysis can indicate variations between closely related populations. This paper reports for the first time the characterization and analysis of the complete sequence of the D-loop region from Egyptian buffaloes and analysis in conjunction with previously published Indian and European Bubalus bubalis and Bos sub-tribe sequences. In the entire D-loop of the Egyptian buffaloes, we identified four haplotypes and nine polymorphic sites from the nine sequenced D-loop regions--while in the studied set of buffaloes we identified 28 polymorphic sites in the entire D-loop, and 49 polymorphic sites in the case of cows. Alignment between buffaloes and cows to evaluate the characteristics of the D-loop region showed that the second region of the conserved sequence block (CSB2) is apparently the most variable region in the D-loop between cows and buffaloes, with four insertions in all buffaloes and two substitutions, followed by the second region of the extended termination associated sequence (ETAS2) with a substitution rate of 1/10. The Egyptian buffaloes were shown to be closest to the Italian counterparts, exemplifying the closeness of ethnicity and the history of civilization of that region.