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Discrete analyses of protein dynamics

Abstract : Protein structures are highly dynamic macromolecules. This dynamics is often analysed through experimental and/or computational methods only for an isolated or a limited number of proteins. Here, we explore large-scale protein dynamics simulation to observe dynamics of local protein conformations using different perspectives. We analysed molecular dynamics to investigate protein flexibility locally, using classical approaches such as RMSf, solvent accessibility, but also innovative approaches such as local entropy. Firstly, we focussed on classical secondary structures and analysed specifically how β-strand, β−turns, and bends evolve during molecular simulations. We underlined interesting specific bias between β−turns and bends, which are considered as same category, while their dynamics show differences. Secondly, we used a structural alphabet that is able to approximate every part of the protein structures conformations, namely Protein Blocks (PBs) to analyse (i) how each initial local protein conformations evolve during dynamics and (ii) if some exchange can exist among these PBs. Interestingly, the results are largely complex than simple regular/rigid and coil/flexible exchange.
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Contributor : Alexandre G. de Brevern Connect in order to contact the contributor
Submitted on : Tuesday, August 11, 2020 - 2:16:52 PM
Last modification on : Thursday, April 7, 2022 - 1:58:30 PM
Long-term archiving on: : Friday, November 27, 2020 - 10:18:53 AM



Akhila Melarkode Vattekatte, Tarun Jairaj Narwani, Pierrick Craveur, Nicolas K Shinada, Aline Floch, et al.. Discrete analyses of protein dynamics. Journal of Biomolecular Structure and Dynamics, Taylor & Francis: STM, Behavioural Science and Public Health Titles, 2019, pp.1-15. ⟨10.1080/07391102.2019.1650112⟩. ⟨inserm-02266159⟩



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