Our work on basic mechanisms and practical implications of allostery, have continuously propelled us to be among the world leaders in the cutting-edge research on allostery. As an indicator of the group’s achievements, the Special Issue “Allostery: From Mechanisms to Therapies” of the Journal of Molecular Biology published this year was edited by Igor Berezovsky and Ruth Nussinov [1]. The Issue contains a collection of works, covering different aspects of allostery on multiple scales, from intramolecular regulation of protein function to intercellular signalling.
Continuing our broad studies on fundamental and practical aspects on allostery [2-6] we contributed to this Issue two original works: (i) one considers the role of evolutionary conservatism and diversity in establishing of allosteric communication in different types of folds/domains and their multidomain/chain assemblies [7]; (ii) another project explores features of allosteric ligands, sites, and interactions with the aim to develop computational models for allosteric drug design [8]. More specifically, in the first work we learn directly from nature how various major folds provide structural platforms for allosteric regulation of many enzymatic and signalling functions. We obtained a picture of conserved allosteric communication characteristic in different fold types, including α/ß and ß-barrels, ß-propellers, Ig-like fold, ankyrin and α/ß leucine-rich repeat proteins, modifications of the structuredriven signalling patterns via sequence-determined divergence to specific functions, as well as the emergence and potential diversification of allosteric regulation in multi-domain proteins and oligomeric assemblies. Our observations facilitate the engineering and de novo design of proteins [9] with allosterically regulated functions, including development of therapeutic biologics.
We continue to develop a computational framework for reconstructing whole-genome chromatin ensemble from Hi-C data [12], and for exploring how structures and dynamics of chromatin drive genome expression. The current twostage protocol includes Markov state modelling (MSM) for reconstructing the structural hierarchy of chromatin organization with partitioning and effective interactions, and the stochastic embedding procedure (SEP) for obtaining the 3D ensemble reconstruction.
Figure 4. The flowchart of the computational framework for the analysis of chromatin hierarchy and the 3D whole-genome chromatin reconstruction.
Igor Berezovsky studied physics at the Moscow Engineering Physics Institute (MSc, 1993) and obtained PhD in physics and mathematics from the Moscow Institute of Physics and Technology (1997). He started his scientific career at the Engelhardt Institute of Molecular Biology (Moscow) where he conducted his MSc and PhD research, then worked as a research fellow (until 1998). After postdoctoral researcher at the Weizmann Institute of Science (1999-2002) and the Harvard University (2003-2006), Igor was a senior scientist/group leader at the Bergen Center for Computational Science, University of Bergen (Norway) before joining the Bioinformatics Institute in January 2014.
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