Literature DB >> 33322722

Impact of Sucrose as Osmolyte on Molecular Dynamics of Mouse Acetylcholinesterase.

Sofya V Lushchekina1, Gaetan Inidjel2,3, Nicolas Martinez2,3, Patrick Masson4, Marie Trovaslet-Leroy5, Florian Nachon5, Michael Marek Koza2, Tilo Seydel2, Judith Peters2,3.   

Abstract

The enzyme model, mouse acetylcholinesterase, which exhibits its active site at the bottom of a narrow gorge, was investigated in the presence of different concentrations of sucrose to shed light on the protein and water dynamics in cholinesterases. The study was conducted by incoherent neutron scattering, giving access to molecular dynamics within the time scale of sub-nano to nanoseconds, in comparison with molecular dynamics simulations. With increasing sucrose concentration, we found non-linear effects, e.g., first a decrease in the dynamics at 5 wt% followed by a gain at 10 wt% sucrose. Direct comparisons with simulations permitted us to understand the following findings: at 5 wt%, sugar molecules interact with the protein surface through water molecules and damp the motions to reduce the overall protein mobility, although the motions inside the gorge are enhanced due to water depletion. When going to 10 wt% of sucrose, some water molecules at the protein surface are replaced by sugar molecules. By penetrating the protein surface, they disrupt some of the intra-protein contacts, and induce new ones, creating new pathways for correlated motions, and therefore, increasing the dynamics. This exhaustive study allowed for an explanation of the detail interactions leading to the observed non-linear behavior.

Entities:  

Keywords:  MD simulations; cholinesterase; molecular dynamics; neutron scattering; osmotic stress

Year:  2020        PMID: 33322722      PMCID: PMC7763276          DOI: 10.3390/biom10121664

Source DB:  PubMed          Journal:  Biomolecules        ISSN: 2218-273X


  37 in total

1.  Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase.

Authors:  K Tai; T Shen; U Börjesson; M Philippopoulos; J A McCammon
Journal:  Biophys J       Date:  2001-08       Impact factor: 4.033

Review 2.  Thermodynamic binding and site occupancy in the light of the Schellman exchange concept.

Authors:  Serge N Timasheff
Journal:  Biophys Chem       Date:  2002-12-10       Impact factor: 2.352

3.  Structural insights into ligand interactions at the acetylcholinesterase peripheral anionic site.

Authors:  Yves Bourne; Palmer Taylor; Zoran Radić; Pascale Marchot
Journal:  EMBO J       Date:  2003-01-02       Impact factor: 11.598

4.  Fast dynamics and stabilization of proteins: binary glasses of trehalose and glycerol.

Authors:  Marcus T Cicerone; Christopher L Soles
Journal:  Biophys J       Date:  2004-06       Impact factor: 4.033

5.  Conditioning action of the environment on the protein dynamics studied through elastic neutron scattering.

Authors:  A Paciaroni; E Cornicchi; A De Francesco; M Marconi; G Onori
Journal:  Eur Biophys J       Date:  2006-06-08       Impact factor: 1.733

6.  Experimental determination of the nature of diffusive motions of water molecules at low temperatures.

Authors: 
Journal:  Phys Rev A Gen Phys       Date:  1985-03

7.  Crystal structure of snake venom acetylcholinesterase in complex with inhibitory antibody fragment Fab410 bound at the peripheral site: evidence for open and closed states of a back door channel.

Authors:  Yves Bourne; Ludovic Renault; Pascale Marchot
Journal:  J Biol Chem       Date:  2014-11-19       Impact factor: 5.157

8.  How does huperzine A enter and leave the binding gorge of acetylcholinesterase? Steered molecular dynamics simulations.

Authors:  Yechun Xu; Jianhua Shen; Xiaomin Luo; Israel Silman; Joel L Sussman; Kaixian Chen; Hualiang Jiang
Journal:  J Am Chem Soc       Date:  2003-09-17       Impact factor: 15.419

9.  CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses.

Authors:  Olgun Guvench; Elizabeth R Hatcher; Richard M Venable; Richard W Pastor; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2009-08-20       Impact factor: 6.006

10.  ProDy: protein dynamics inferred from theory and experiments.

Authors:  Ahmet Bakan; Lidio M Meireles; Ivet Bahar
Journal:  Bioinformatics       Date:  2011-04-05       Impact factor: 6.937

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