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Histone dimer stability prediction

Nucleosome consists of an octamer of histone proteins (two copies of H2A/H2B dimers and H3/H4 tetramer), along with DNA. The binding affinities between histone proteins helps in in-silico prediction of nucleosome stability. Recent literature defines the non-redundant role of different histone isoforms. H2A and H2B have maximum number of isoforms. Hence, their multiple combinations may be playing an important role in changing nucleosomal organization in different biological functions. Therefore, the binding affinity between the histone H2A and H2B dimers among different combination of H2A and H2B isoforms are shown by calculating the potential energies. The co-crystallized structure of one of the isoform of H2A and H2B is taken as template to model other isoforms. The potential energy between all the dimers are calculated using Gromacs software. The heatmap plotted shows the potential energy values between dimers of histone H2A and H2B isoforms in human, mouse and rat. For details of molecular dynamics simulation of nucleosome please refer to Bhattacharya et al. 2017 (PMID:29047414)

H2A/H2B isoform dimer in Human

H2A/H2B isoform dimer in Rat

H2A/H2B isoform dimer in Mouse