dc.contributor.author | Archontis, Georgios Z. | en |
dc.contributor.author | Simonson, T. | en |
dc.creator | Archontis, Georgios Z. | en |
dc.creator | Simonson, T. | en |
dc.date.accessioned | 2019-12-02T15:28:35Z | |
dc.date.available | 2019-12-02T15:28:35Z | |
dc.date.issued | 2005 | |
dc.identifier.uri | http://gnosis.library.ucy.ac.cy/handle/7/58492 | |
dc.description.abstract | Proton binding plays a critical role in protein structure and function. We report pKa calculations for three aspartates in two proteins, using a linear response approach, as well as a "standard" Poisson-Boltzmann approach. Averaging over conformations from the two endpoints of the proton-binding reaction, the protein's atomic degrees of freedom are explicitly modeled. Treating macroscopically the protein's electronic polarizability and the solvent, a meaningful model is obtained, without adjustable parameters. It reproduces qualitatively the electrostatic potentials, proton-binding free energies, Marcus reorganization free energies, and pKa shifts from explicit solvent molecular dynamics simulations, and the pKa shifts from experiment. For thioredoxin Asp-26, which has a large pKa upshift, we correctly capture the balance between unfavorable carboxylate desolvation and favorable interactions with a nearby lysine | en |
dc.description.abstract | similarly for RNase A Asp-14, which has a large pKa downshift. For the unshifted thioredoxin Asp-20, desolvation by the protein cavity is overestimated by 2.9 pKa units | en |
dc.description.abstract | several effects could explain this. "Standard" Poisson-Boltzmann methods sidestep this problem by using a large, ad hoc protein dielectric | en |
dc.description.abstract | but protein charge-charge interactions are then incorrectly downscaled, giving an unbalanced description of the reaction and a large error for the shifted pKa values of Asp-26 and Asp-14. © 2005 by the Biophysical Society. | en |
dc.source | Biophysical journal | en |
dc.source.uri | https://www.scopus.com/inward/record.uri?eid=2-s2.0-22244488061&doi=10.1529%2fbiophysj.104.055996&partnerID=40&md5=bfa9c28ca59d2f8b707765a29979c3a8 | |
dc.subject | model | en |
dc.subject | article | en |
dc.subject | protein | en |
dc.subject | error | en |
dc.subject | protein function | en |
dc.subject | protein binding | en |
dc.subject | simulation | en |
dc.subject | Thermodynamics | en |
dc.subject | Electrostatics | en |
dc.subject | energy | en |
dc.subject | molecular interaction | en |
dc.subject | mathematical analysis | en |
dc.subject | analytic method | en |
dc.subject | carboxylic acid | en |
dc.subject | electricity | en |
dc.subject | precipitation | en |
dc.subject | Hydrogen-Ion Concentration | en |
dc.subject | Biophysics | en |
dc.subject | molecular dynamics | en |
dc.subject | Proteins | en |
dc.subject | aspartic acid | en |
dc.subject | protein structure | en |
dc.subject | lysine | en |
dc.subject | proton | en |
dc.subject | Ribonucleases | en |
dc.subject | Models, Chemical | en |
dc.subject | solvent | en |
dc.subject | Protons | en |
dc.subject | polarization | en |
dc.subject | principal component analysis | en |
dc.subject | electric potential | en |
dc.subject | pKa | en |
dc.subject | averaging | en |
dc.subject | desolvation | en |
dc.subject | dielectric continuum model | en |
dc.subject | electrostatic potential | en |
dc.subject | free energy component analysis | en |
dc.subject | linear response method | en |
dc.subject | Marcus reorganization | en |
dc.subject | physical phenomena | en |
dc.subject | Poisson Boltzmann method | en |
dc.subject | ribonuclease A | en |
dc.subject | thioredoxin | en |
dc.title | Proton binding to proteins: A free-energy component analysis using a dielectric continuum model | en |
dc.type | info:eu-repo/semantics/article | |
dc.identifier.doi | 10.1529/biophysj.104.055996 | |
dc.description.volume | 88 | |
dc.description.issue | 6 | |
dc.description.startingpage | 3888 | |
dc.description.endingpage | 3904 | |
dc.author.faculty | Σχολή Θετικών και Εφαρμοσμένων Επιστημών / Faculty of Pure and Applied Sciences | |
dc.author.department | Τμήμα Φυσικής / Department of Physics | |
dc.type.uhtype | Article | en |
dc.description.notes | <p>Cited By :56</p> | en |
dc.source.abbreviation | Biophys.J. | en |
dc.contributor.orcid | Archontis, Georgios Z. [0000-0002-7750-8641] | |
dc.gnosis.orcid | 0000-0002-7750-8641 | |