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dc.contributor.authorDahanayake, Jayangika Niroshani
dc.contributor.authorGautam, Devaki N.
dc.contributor.authorVerma, Rajni
dc.contributor.authorMitchell-Koch, Katie R.
dc.identifier.citationDahanayake, Jayangika Niroshani; Gautam, Devaki N.; Verma, Rajni; Mitchell-Koch, Katie R. 2016. To keep or not to keep? the question of crystallographic waters for enzyme simulations in organic solvent. Molecular Simulation, vol. 42:no. 12:pp 1001-1013en_US
dc.descriptionClick on the DOI link to access the article (may not be free).en_US
dc.description.abstractThe use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results.en_US
dc.description.sponsorshipThis work was supported by Wichita State University, Fairmount College of Liberal Arts and Sciences and K-INBRE startup funds under NIH National Institute of General Medical Sciences [grant number P20 GM103418]. Computing resources were funded by the National Science Foundation [grant number EIA-0216178], [grant number EPS-0236913], with matching support from the State of Kansas and the Wichita State University High Performance Computing Center.en_US
dc.publisherTaylor & Francis Groupen_US
dc.relation.ispartofseriesMolecular Simulation;v.42:no.12
dc.subjectCrystallographic wateren_US
dc.subjectMolecular dynamicsen_US
dc.subjectNon-aqueous enzymologyen_US
dc.subjectKWW modelen_US
dc.titleTo keep or not to keep? the question of crystallographic waters for enzyme simulations in organic solventen_US
dc.rights.holder© 2016 Informa UK Limited, an Informa Group company.en_US

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