title: Elucidating the Conformational Dependence of Calculated pKa Values.
abstract: The variability within calculated protein residue pKa values calculated using Poisson-Boltzmann continuum theory with respect to small conformational fluctuations is investigated. As a general rule, sites buried in the protein core have the largest pKa fluctuations but the least amount of conformational variability; conversely, sites on the protein surface generally have large conformational fluctuations but very small pKa fluctuations. These results occur because of the heterogeneous or uniform nature of the electrostatic microenvironments at the protein core or surface, respectively. Atypical surface sites with large pKa fluctuations occur at the interfaces between significant anionic and cationic potentials.
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: Dennis R
authors.initials: DR
authors.lastname: Livesay
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: Donald J
authors.initials: DJ
authors.lastname: Jacobs
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: Julie
authors.initials: J
authors.lastname: Kanjanapangka
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: Eric
authors.initials: E
authors.lastname: Chea
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: Hector
authors.initials: H
authors.lastname: Cortez
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: Jorge
authors.initials: J
authors.lastname: Garcia
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: Patrick
authors.initials: P
authors.lastname: Kidd
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: Mario Pulido
authors.initials: MP
authors.lastname: Marquez
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: Swati
authors.initials: S
authors.lastname: Pande
authors.affiliation: Department of Chemistry, Center for Macromolecular Modeling & Materials Design, and Department of Biological Sciences, California State Polytechnic University, Pomona, California, and Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina.
authors.forename: David
authors.initials: D
authors.lastname: Yang