Histone H2A isoforms: Potential implications in epigenome plasticity and diseases in eukaryotes

Epigenetic mechanisms including the post-translational modifications of histones, incorporation of histonevariants and DNA methylation have been suggested to play an important role in genome plasticity by allowingthe cellular environment to define gene expression and the phenotype of an organism. Studies over the pastdecade have elucidated how these epigenetic mechanisms are significant in orchestrating various biologicalprocesses and contribute to different pathophysiological states. However, the role of histone isoforms and theirimpact on different phenotypes and physiological processes associated with diseases are not fully clear. Thisreview is focussed on the recent advances in our understanding of the complexity of eukaryotic H2A isoformsand their roles in defining nucleosome organization. We elaborate on their potential roles in genomic complexity and regulation of gene expression, and thereby on their overall contribution towards cellular phenotypeand development of diseases

In silico analysis of peptide binding features of HLA-B*4006.

HLA-B*4006 is the most common allele amongst Indians. It belongs to the ‘HLA-B44 supertype’ family of alleles that constitute an important component of the peptide binding repertoire in populations world over. Its peptide binding characteristics remain poorly examined. The amino acid sequence and structural considerations suggest a small, poorly hydrophobic ‘F’ pocket for this allele that may adversely affect the interaction with the C terminal residue of the antigenic peptide. Contribution of auxiliary anchor residues (P3) of the peptide has also been indicated. To examine these aspects by in silico analysis, HLA-B*4001, 4002, and 4006 alleles were modeled using HLA-B*4402 as a template. Eleven peptides, known to bind alleles of this family, were used for docking and molecular dynamics studies. Interaction between the amino group (main-chain) of P3 residue and Tyr99 of the alleles was seen in majority of peptide-complexes. Hydrophobic interactions between Tyr7 and Tyr159 with N terminal residues of the peptide were also seen in all the complexes. Replacement of Trp95 by leucine in HLA-B*4006 resulted in reduction of binding free energy in 8 out of 9 complexes. In summary, the analysis of the modeled structures and HLA-peptide complexes strongly supports the adverse effect of Trp95 at pocket F and the possible role of the third residue of the antigenic peptide as an auxiliary anchor in HLA-B*4006 peptide complexes. In the light of suggested promiscuous peptide binding pattern and association with risk for tuberculosis/HIV for this allele, the ascertainment of the predicted effects of Trp95 and role of P3 residue as an auxiliary anchor by this preliminary in silico analysis thus helps define direction of the further studies.