CO-dynamics in the active site of cytochrome c oxidase

Multisurface Adiabatic Reactive Molecular Dynamics

(2014) Tibor Nagy et al.   Journal of Chemical Theory and Computation

Reaction-Pathway Selection in the Structural Dynamics of a Heme Protein

(2013) Karin Nienhaus et al.   CHEMISTRY-A EUROPEAN JOURNAL

“Strange Kinetics” in the Temperature Dependence of Methionine Ligand Rebinding Dynamics in Cytochrome c

(2013) Ping Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mobility of Xe Atoms within the Oxygen Diffusion Channel of Cytochrome ba3 Oxidase

(2012) V. Mitch Luna et al.   BIOCHEMISTRY

From Static Structure to Living Protein: Computational Analysis of Cytochrome c Oxidase Main-chain Flexibility

(2012) Leann Buhrow et al.   BIOPHYSICAL JOURNAL

Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin

(2012) Nuria Plattner et al.   BIOPHYSICAL JOURNAL

Molecular Dynamics Simulation of Nitric Oxide in Myoglobin

(2012) Myung Won Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural changes that occur upon photolysis of the Fe(II)a3–CO complex in the cytochrome ba3-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to CuB

(2011) Bin Liu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Temporal quantum mechanics/molecular mechanics: Extending the time scales accessible in molecular dynamics simulations of reactions

(2011) Prakash Dayal et al.   CHEMICAL PHYSICS LETTERS

Photodissociation Dynamics of ClCN at Different Wavelengths

(2011) Stephan Lutz et al.   CHEMPHYSCHEM

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKaValues

(2011) Chresten R. Søndergaard et al.   Journal of Chemical Theory and Computation

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

High Resolution Structure of the ba3 Cytochrome c Oxidase from Thermus thermophilus in a Lipidic Environment

(2011) Theresa Tiefenbrunn et al.   PLoS One

Force Field Optimization using Dynamics and Ensemble Averaged Data: Vibrational Spectra and Relaxation in Bound MbCO

(2010) Michael Devereux et al.   Journal of Chemical Information and Modeling

Explicit Hydrogen-Bond Potentials and Their Application to NMR Scalar Couplings in Proteins

(2010) Jing Huang et al.   Journal of Chemical Theory and Computation

Bovine cytochromecoxidase structures enable O2reduction with minimization of reactive oxygens and provide a proton-pumping gate

(2010) Kazumasa Muramoto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His–Tyr bond

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

Structural Assignment of Spectra by Characterization of Conformational Substates in Bound MbCO

(2009) Michael Devereux et al.   BIOPHYSICAL JOURNAL

Structural Identification of Spectroscopic Substates in Neuroglobin

(2009) Karin Nienhaus et al.   CHEMPHYSCHEM

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Ligand Migration between Internal Docking Sites in Photodissociated Carbonmonoxy Neuroglobin

(2009) Stephan Lutz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Heme Cavity Dynamics of Photodissociated CO fromba3-CytochromecOxidase: The Role of Ring-D Propionate

(2009) Massimiliano Porrini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Role of Higher CO-Multipole Moments in Understanding the Dynamics of Photodissociated Carbonmonoxide in Myoglobin

(2008) Nuria Plattner et al.   BIOPHYSICAL JOURNAL

Atomistic Simulation of Adiabatic Reactive Processes Based on Multi-State Potential Energy Surfaces

(2008) Jonas Danielsson et al.   Journal of Chemical Theory and Computation

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Reactive force fields for proton transfer dynamics

(2007) Sven Lammers et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY