Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers

Journal Article · · Photosynthesis Research
Not provided.
Research Organization:
City Univ. of New York (CUNY), NY (United States)
Sponsoring Organization:
USDOE Office of Science (SC)
DOE Contract Number:
SC0001423
OSTI ID:
2419609
Journal Information:
Photosynthesis Research, Journal Name: Photosynthesis Research Journal Issue: 1 Vol. 156; ISSN 0166-8595
Publisher:
Springer
Country of Publication:
United States
Language:
English

References (68)

Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail journal September 2001
Comparison of proton transfer paths to the QA and QB sites of the Rb. sphaeroides photosynthetic reaction centers journal March 2022
PKAD: a database of experimentally measured pKa values of ionizable groups in proteins journal January 2019
Identification of the proton pathway in bacterial reaction centers: Inhibition of proton transfer by binding of Zn2+ or Cd2+ journal May 1999
Towards a quantitative description of excitonic couplings in photosynthetic pigment–protein complexes: quantum chemistry driven multiscale approaches journal January 2022
How Cytochromes with Different Folds Control Heme Redox Potentials journal July 2003
Long-range proton-coupled electron transfer in biological energy conversion: towards mechanistic understanding of respiratory complex I journal April 2018
Variation of Ser-L223 Hydrogen Bonding with the QB Redox State in Reaction Centers from Rhodobacter sphaeroides journal June 2004
Characterizing Protein Protonation Microstates Using Monte Carlo Sampling journal March 2022
Progress Toward a Molecular Mechanism of Water Oxidation in Photosystem II journal May 2017
Analysis of the electrochemistry of hemes with E m s spanning 800 mV journal May 2009
MCCE2: Improving protein p K a calculations with extensive side chain rotamer sampling journal January 2009
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics journal July 2017
Exploring Coupled Redox and pH Processes with a Force-Field-Based Approach: Applications to Five Different Systems journal February 2020
M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus journal February 2020
A chemically explicit model for the mechanism of proton pumping in heme–copper oxidases journal October 2008
Proton transfer in uncoupled variants of cytochrome c oxidase journal December 2019
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I journal April 2014
Proton-Coupled Electron Transfer in Cytochrome Oxidase journal December 2010
Exploring Graph Traversal Algorithms in Graph-Based Molecular Generation journal November 2021
Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields journal July 2020
Structural dynamics in the water and proton channels of photosystem II during the S2 to S3 transition journal November 2021
Identifying the proton loading site cluster in the ba cytochrome c oxidase that loads and traps protons journal October 2020
A giant molecular proton pump: structure and mechanism of respiratory complex I journal May 2015
Proton transfer reactions and hydrogen-bond networks in protein environments journal February 2014
Are Acidic and Basic Groups in Buried Proteins Predicted to be Ionized? journal May 2005
Electrostatic Potentials in Rhodopseudomonas viridis Reaction Centers:  Implications for the Driving Force and Directionality of Electron Transfer journal January 1996
Simulation of Electron-Proton Coupling with a Monte Carlo Method: Application to Cytochrome c3 Using Continuum Electrostatics journal June 1999
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation journal November 2012
Protonation reactions and their coupling in bacteriorhodopsin journal August 2000
Progress in the prediction of pKa values in proteins journal October 2011
Glassy Protein Dynamics and Gigantic Solvent Reorganization Energy of Plastocyanin journal April 2008
Hydrogen bond network analysis reveals the pathway for the proton transfer in the E-channel of T. thermophilus Complex I journal October 2020
Microscopic mechanisms that govern the titration response and p K a values of buried residues in staphylococcal nuclease mutants journal December 2016
Calculation of protonation patterns in proteins with structural relaxation and molecular ensembles - application to the photosynthetic reaction center journal September 1998
Density functional calculation of pK a values and redox potentials in the bovine Rieske iron-sulfur protein journal February 2002
Modification of quinone electrochemistry by the proteins in the biological electron transfer chains: examples from photosynthetic reaction centers journal October 2008
Light-Induced Structural Changes in Photosynthetic Reaction Center: Implications for Mechanism of Electron-Proton Transfer journal May 1997
Characterizing the proton loading site in cytochrome c oxidase journal August 2014
Molecular mechanisms for generating transmembrane proton gradients journal August 2013
Exploring the energetics of water permeation in photosystem II by multiple steered molecular dynamics simulations journal September 2012
Proton and electron transfer in bacterial reaction centers journal May 2000
Negatively Charged Residues and Hydrogen Bonds Tune the Ligand Histidine p K a Values of Rieske Iron−Sulfur Proteins journal October 2004
Measuring Electric Fields and Noncovalent Interactions Using the Vibrational Stark Effect journal March 2015
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks journal November 2003
Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient journal June 2021
Electrostatic Dominoes: Long Distance Propagation of Mutational Effects in Photosynthetic Reaction Centers of Rhodobacter capsulatus journal July 1995
Constant- p H molecular dynamics using stochastic titration journal September 2002
Tracing the Pathways of Waters and Protons in Photosystem II and Cytochrome c Oxidase journal January 2019
pH-Dependent Conformational Changes Due to Ionizable Residues in a Hydrophobic Protein Interior: The Study of L25K and L125K Variants of SNase journal June 2019
Electrostatic models for computing protonation and redox equilibria in proteins journal October 1999
Simulation and Modeling of the Rhodobacter sphaeroides Bacterial Reaction Center II:  Primary Charge Separation journal May 2003
Reservoir pH replica exchange journal August 2018
Proton exit pathways surrounding the oxygen evolving complex of photosystem II journal August 2021
The Light Reactions: A Guide to Recent Acquisitions for the Picture Gallery journal March 2005
Graphs of Hydrogen-Bond Networks to Dissect Protein Conformational Dynamics journal May 2022
Molecular Anatomy of Plant Photoprotective Switches: The Sensitivity of PsbS to the Environment, Residue by Residue journal March 2019
Proton and electron transfer in the acceptor quinone complex of photosynthetic reaction centers from Rhodobacter Sphaeroides journal January 2004
pH replica-exchange method based on discrete protonation states journal October 2011
Calculated Protein and Proton Motions Coupled to Electron Transfer:  Electron Transfer from Q A - to Q B in Bacterial Photosynthetic Reaction Centers journal June 1999
Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase journal October 2018
Mechanism of a proton pump analyzed with computer simulations journal April 2009
Proton-Transfer Pathways in Photosynthetic Reaction Centers Analyzed by Profile Hidden Markov Models and Network Calculations journal May 2009
Approach to Study pH-Dependent Protein Association Using Constant-pH Molecular Dynamics: Application to the Dimerization of β-Lactoglobulin journal February 2022
CHARMM-GUI: A web-based graphical user interface for CHARMM journal March 2008
Heme Protein Assemblies journal February 2004
A pH Replica Exchange Scheme in the Stochastic Titration Constant-pH MD Method journal March 2019
Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. journal July 1991