Polarization effect within a protein crystal: A molecular dynamics simulation study

Zhu, T; Wu, C; Song, J; Reimers, JR; Li, Y

Polarization effect within a protein crystal: A molecular dynamics simulation study

Zhu, T Wu, C Song, J Reimers, JR Li, Y

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Publisher:: ELSEVIER
Publication Type:: Journal Article
Citation:: Chemical Physics Letters, 2018, 706, pp. 303-307
Issue Date:: 2018-08-16

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Field	Value	Language
dc.contributor.author	Zhu, T
dc.contributor.author	Wu, C
dc.contributor.author	Song, J
dc.contributor.author	Reimers, JR
dc.contributor.author	Li, Y
dc.date.accessioned	2022-01-18T01:41:45Z
dc.date.available	2022-01-18T01:41:45Z
dc.date.issued	2018-08-16
dc.identifier.citation	Chemical Physics Letters, 2018, 706, pp. 303-307
dc.identifier.issn	0009-2614
dc.identifier.issn	1873-4448
dc.identifier.uri	http://hdl.handle.net/10453/153254
dc.description.abstract	Systematical molecular dynamics with different force fields are performed to simulate the structure and dynamics of crystal of hen egg-white lysozyme, including AMBER and three versions of protein-specific charge, PPC. The electrostatic polarization within the crystal is studied with the comparison among four 250 ns trajectories under them. Results show that under appropriate parameterized PPC, the protein can be stable during simulations, indicated by both smaller root-mean-square deviation and closer crystallographic B-factors to the experimental values. This work also shows how the selection of dielectric constant affects the results of utilizing PPC.
dc.language	English
dc.publisher	ELSEVIER
dc.relation.ispartof	Chemical Physics Letters
dc.relation.isbasedon	10.1016/j.cplett.2018.06.018
dc.rights	info:eu-repo/semantics/openAccess
dc.subject	02 Physical Sciences, 03 Chemical Sciences, 10 Technology
dc.subject.classification	Chemical Physics
dc.title	Polarization effect within a protein crystal: A molecular dynamics simulation study
dc.type	Journal Article
utslib.citation.volume	706
utslib.for	0307 Theoretical and Computational Chemistry
utslib.for	02 Physical Sciences
utslib.for	03 Chemical Sciences
utslib.for	10 Technology
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Mathematical and Physical Sciences
utslib.copyright.status	open_access	*
dc.date.updated	2022-01-18T01:41:43Z
pubs.publication-status	Published
pubs.volume	706

Abstract:

Systematical molecular dynamics with different force fields are performed to simulate the structure and dynamics of crystal of hen egg-white lysozyme, including AMBER and three versions of protein-specific charge, PPC. The electrostatic polarization within the crystal is studied with the comparison among four 250 ns trajectories under them. Results show that under appropriate parameterized PPC, the protein can be stable during simulations, indicated by both smaller root-mean-square deviation and closer crystallographic B-factors to the experimental values. This work also shows how the selection of dielectric constant affects the results of utilizing PPC.

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http://hdl.handle.net/10453/153254