Discrete analyses of protein dynamics |
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Authors: | Tarun Jairaj Narwani Pierrick Craveur Nicolas K Shinada Aline Floch Hubert Santuz Akhila Melarkode Vattekatte |
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Institution: | 1. Biologie Intégrée du Globule Rouge UMR_S1134, Inserm, Univ. Paris, Univ. de la Réunion, Univ. des Antilles, Paris, France;2. Laboratoire D’Excellence GR-Ex, Paris, France;3. Institut National de la Transfusion Sanguine (INTS), Paris, France;4. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA;5. Discngine, SAS, Paris, France;6. Laboratoire D’Excellence GR-Ex, Paris, France;7. Etablissement Fran?ais du Sang Ile de France, Créteil, France;8. IMRB – INSERM U955 Team 2 ? Transfusion et Maladies du Globule Rouge ?, Paris Est- Créteil Univ, Créteil, France;9. UPEC, Université Paris Est-Créteil, Créteil, France;10. Faculté Des Sciences et Technologies, Saint Denis Messag, La Réunion, France |
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Abstract: | AbstractProtein 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. First, 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 the same category, while their dynamics show differences. Second, 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. Abbreviations Neq number of equivalent PB Protein Blocks PDB Protein DataBank RMSf root mean square fluctuations Communicated by Ramaswamy H. Sarma |
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Keywords: | Local protein conformations structural alphabet molecular dynamics disorder flexibility secondary structure Protein DataBank solvent accessibility |
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