Microscopic basis for kinetic gating in cytochrome c oxidase: insights from QM/MM analysis

Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models

(2014) Puja Goyal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Density functional tight binding: values of semi-empirical methods in an ab initio era

(2014) Qiang Cui et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Molecular mechanisms for generating transmembrane proton gradients

(2013) M.R. Gunner et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces

(2013) Toshifumi Mori et al.   Journal of Chemical Theory and Computation

Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel

(2013) Ruibin Liang et al.   Journal of Chemical Theory and Computation

Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site

(2013) Gabriel J. Rocklin et al.   JOURNAL OF MOLECULAR BIOLOGY

Charging Free Energy Calculations Using the Generalized Solvent Boundary Potential (GSBP) and Periodic Boundary Condition: A Comparative Analysis Using Ion Solvation and Oxidation Free Energy in Proteins

(2013) Xiya Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Application of the SCC-DFTB Method to Hydroxide Water Clusters and Aqueous Hydroxide Solutions

(2013) Tae Hoon Choi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Exploring the Possible Role of Glu286 in CcO by Electrostatic Energy Computations Combined with Molecular Dynamics

(2013) Anna Lena Woelke et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Role of aspartate 132 at the orifice of a proton pathway in cytochrome c oxidase

(2013) A.-L. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase

(2013) P. Goyal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capturing the energetics of water insertion in biological systems: The water flooding approach

(2013) Suman Chakrabarty et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Artificial Leaf

(2012) Daniel G. Nocera   ACCOUNTS OF CHEMICAL RESEARCH

Parametrization and Benchmark of DFTB3 for Organic Molecules

(2012) Michael Gaus et al.   Journal of Chemical Theory and Computation

Exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from Thermus thermophilus

(2012) H.-Y. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional effects of mutations in cytochrome c oxidase related to prostate cancer

(2011) Ida Namslauer et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects

(2011) Suman Chakrabarty et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Gating and regulation of the cytochrome c oxidase proton pump

(2011) Shelagh Ferguson-Miller et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Proton-pumping mechanism of cytochrome c oxidase: A kinetic master-equation approach

(2011) Young C. Kim et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

The mechanism for proton pumping in cytochrome c oxidase from an electrostatic and quantum chemical perspective

(2011) Margareta R.A. Blomberg et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase

(2011) Shuo Yang et al.   BIOPHYSICAL JOURNAL

DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)

(2011) Michael Gaus et al.   Journal of Chemical Theory and Computation

Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water

(2011) Puja Goyal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Insights into the Mechanism of Proton Transport in Cytochrome c Oxidase

(2011) Takefumi Yamashita et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Accounting for electronic polarization in non-polarizable force fields

(2011) Igor Leontyev et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Decoupling Mutations in the D-Channel of theaa3-Type CytochromecOxidase fromRhodobacter sphaeroidesSuggest That a Continuous Hydrogen-Bonded Chain of Waters Is Essential for Proton Pumping

(2010) Jiapeng Zhu et al.   BIOCHEMISTRY

Variable proton-pumping stoichiometry in structural variants of cytochrome c oxidase

(2010) Peter Brzezinski et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Proton-Coupled Electron Transfer in Cytochrome Oxidase

(2010) Ville R. I. Kaila et al.   CHEMICAL REVIEWS

Electronic Continuum Model for Molecular Dynamics Simulations of Biological Molecules

(2010) I. V. Leontyev et al.   Journal of Chemical Theory and Computation

The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations

(2010) C. Mark Maupin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Intricate Role of Water in Proton Transport through CytochromecOxidase

(2010) Hyun Ju Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Properties of Arg481 Mutants of theaa3-Type CytochromecOxidase fromRhodobacter sphaeroidesSuggest That neither R481 nor the Nearby D-Propionate of Hemea3Is Likely To Be the Proton Loading Site of the Proton Pump

(2009) Hyun Ju Lee et al.   BIOCHEMISTRY

Microscopic pKaAnalysis of Glu286 in CytochromecOxidase (Rhodobacter sphaeroides): Toward a Calibrated Molecular Model†

(2009) Nilanjan Ghosh et al.   BIOCHEMISTRY

Redox-Dependent Conformational Changes in CytochromecOxidase Suggest a Gating Mechanism for Proton Uptake

(2009) Ling Qin et al.   BIOCHEMISTRY

Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase

(2009) Ville R.I. Kaila et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations

(2009) Demian Riccardi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Functional Hydration and Conformational Gating of Proton Uptake in Cytochrome c Oxidase

(2009) Rowan M. Henry et al.   JOURNAL OF MOLECULAR BIOLOGY

A mitochondrial DNA mutation linked to colon cancer results in proton leaks in cytochrome c oxidase

(2009) I. Namslauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping

(2009) H.-Y. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods

(2008) Hao Hu et al.   Annual Review of Physical Chemistry

Proton Transfer in Carbonic Anhydrase Is Controlled by Electrostatics Rather than the Orientation of the Acceptor†

(2008) Demian Riccardi et al.   BIOCHEMISTRY

Electrostatic control of proton pumping in cytochrome c oxidase

(2008) Elisa Fadda et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Impaired proton pumping in cytochrome c oxidase upon structural alteration of the D pathway

(2008) Håkan Lepp et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Cytochrome c oxidase: exciting progress and remaining mysteries

(2008) Peter Brzezinski et al.   JOURNAL OF BIOENERGETICS AND BIOMEMBRANES

A D-Pathway Mutation Decouples the Paracoccus denitrificans Cytochrome c Oxidase by Altering the Side-Chain Orientation of a Distant Conserved Glutamate

(2008) Katharina L. Dürr et al.   JOURNAL OF MOLECULAR BIOLOGY

Progress inAb InitioQM/MM Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies†

(2008) Shina C. L. Kamerlin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase

(2008) V. R. I. Kaila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase

(2008) A. V. Pisliakov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Charge parameterization of the metal centers in cytochromecoxidase

(2007) Mikael P. Johansson et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY