Discrete analyses of protein dynamics.

Journal of Biomolecular Structure & Dynamics
Tarun Jairaj NarwaniAlexandre G de Brevern

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. 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. AbbreviationsNeqnumber of equivalentPBProtein...Continue Reading

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Citations

Nov 9, 2019·Source Code for Biology and Medicine·Guilhem FaureAlexandre G de Brevern

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Methods Mentioned

BETA
X-ray

Software Mentioned

PolyProline
DSSP
ORION
house
R
GROMACS
Python
Dynasome
Snoopy
PBxplore

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