Skip to Main content Skip to Navigation
Journal articles

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.
Complete list of metadatas

https://www.hal.inserm.fr/inserm-02266159
Contributor : Alexandre G. de Brevern <>
Submitted on : Tuesday, August 11, 2020 - 2:16:52 PM
Last modification on : Tuesday, September 1, 2020 - 3:07:23 AM

Identifiers

Citation

Akhila Melarkode Vattekatte, Tarun Narwani, Pierrick Craveur, Nicolas 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⟩

Share

Metrics

Record views

26

Files downloads

85