title: Microscopic mechanisms that govern the titration response and pKavalues of buried residues in staphylococcal nuclease mutants.
abstract: To probe the microscopic mechanisms that govern the titration behavior of buried ionizable groups, microsecond explicit solvent molecular dynamics simulations are carried out for several mutants of Staphylococcal nuclease using both fixed charge and polarizable force fields. While the ionization of Asp 66, Glu 66, and Lys 125 lead to enhanced structural fluctuations and partial unfolding of adjacent α-helical regions, the ionization of Lys 25 causes local unfolding of adjacent β sheets. Using the sampled conformational ensembles, good agreement with experimental pKavalues is obtained with Poisson-Boltzmann calculations using a protein dielectric constant of 2-4 for V66D/E; slightly larger dielectric constants are needed for Lys mutants especially L25K, suggesting that structural responses beyond microseconds are involved in ionization of Lys 25. Overall, the set of unbiased simulations provides insights into the spatial and temporal scales of protein and solvent motions that dictate the diverse titration behaviors of buried protein residues. Proteins 2017; 85:268-281. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Graduate Program in Biophysics, University of Wisconsin-Madison, 1525 Linden Drive, Madison, Wisconsin, 53706.
authors.forename: Yuqing
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cui
mesh_terms: D001224:Aspartic Acid / Q000737:chemistry*; D018698:Glutamic Acid / Q000737:chemistry*; D007526:Isoelectric Point; D007700:Kinetics; D008239:Lysine / Q000737:chemistry*; D008836:Micrococcal Nuclease / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D009154:Mutation; D000072417:Protein Domains; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013210:Staphylococcus / Q000737:chemistry* / Q000201:enzymology; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D001224:Aspartic Acid; D018698:Glutamic Acid; C104574:staphylococcal nuclease R; D008836:Micrococcal Nuclease; D008239:Lysine
keywords: Poisson-Boltzmann; molecular dynamics; pKa