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

PubWeight™: 0.83‹?›

🔗 View Article (PMID 25678950)

Published in Chem Sci on January 01, 2015

Authors

Puja Goyal1, Shuo Yang1, Qiang Cui1

Author Affiliations

1: Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706.

Articles cited by this

All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B (1998) 54.00

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem (2004) 17.97

A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine. Annu Rev Genet (2005) 16.79

Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature (1995) 8.22

Calculations of electrostatic interactions in biological systems and in solutions. Q Rev Biophys (1984) 5.18

Redox-coupled crystal structural changes in bovine heart cytochrome c oxidase. Science (1998) 5.01

Prediction of pH-dependent properties of proteins. J Mol Biol (1994) 4.99

The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides. J Mol Biol (2002) 3.19

Quantum mechanical methods for enzyme kinetics. Annu Rev Phys Chem (2001) 2.50

Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase. Proc Natl Acad Sci U S A (2006) 2.48

Water-gated mechanism of proton translocation by cytochrome c oxidase. Biochim Biophys Acta (2003) 2.26

Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem (2008) 2.09

Cytochrome c oxidase: exciting progress and remaining mysteries. J Bioenerg Biomembr (2008) 2.07

The artificial leaf. Acc Chem Res (2012) 2.06

Proton-coupled electron transfer in cytochrome oxidase. Chem Rev (2010) 2.05

Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B (2006) 1.83

Mutations in mitochondrial cytochrome c oxidase genes segregate with late-onset Alzheimer disease. Proc Natl Acad Sci U S A (1997) 1.80

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies. J Phys Chem B (2009) 1.66

Possible proton relay pathways in cytochrome c oxidase. Proc Natl Acad Sci U S A (1995) 1.62

Mechanism and energetics of proton translocation by the respiratory heme-copper oxidases. Biochim Biophys Acta (2007) 1.60

Proton solvation and transport in aqueous and biomolecular systems: insights from computer simulations. J Phys Chem B (2007) 1.59

Energetics in the pathogenesis of neurodegenerative diseases. Trends Neurosci (2000) 1.56

MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling. J Comput Chem (2009) 1.55

Cytochrome c oxidase: catalytic cycle and mechanisms of proton pumping--a discussion. Biochemistry (1999) 1.50

The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations. Proteins (2006) 1.49

Proton transfer in carbonic anhydrase is controlled by electrostatics rather than the orientation of the acceptor. Biochemistry (2008) 1.45

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. J Phys Chem A (2007) 1.44

The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping. Proc Natl Acad Sci U S A (2009) 1.42

DFTB3: Extension of the self-consistent-charge density-functional tight-binding method (SCC-DFTB). J Chem Theory Comput (2012) 1.40

Electrostatic study of the proton pumping mechanism in bovine heart cytochrome C oxidase. J Am Chem Soc (2004) 1.37

Grand canonical Monte Carlo simulations of water in protein environments. J Chem Phys (2004) 1.36

Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway. Proc Natl Acad Sci U S A (2005) 1.34

Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys (2005) 1.33

Monte Carlo simulations of proton pumps: on the working principles of the biological valve that controls proton pumping in cytochrome c oxidase. Proc Natl Acad Sci U S A (2006) 1.32

Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Proc Natl Acad Sci U S A (2008) 1.31

Structures and proton-pumping strategies of mitochondrial respiratory enzymes. Annu Rev Biophys Biomol Struct (2001) 1.30

Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants. J Am Chem Soc (2002) 1.30

Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proc Natl Acad Sci U S A (2008) 1.27

Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake. Biochemistry (2009) 1.26

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols. J Phys Chem B (2005) 1.23

A mitochondrial DNA mutation linked to colon cancer results in proton leaks in cytochrome c oxidase. Proc Natl Acad Sci U S A (2009) 1.19

Simulating redox coupled proton transfer in cytochrome c oxidase: looking for the proton bottleneck. FEBS Lett (2005) 1.18

Parametrization and Benchmark of DFTB3 for Organic Molecules. J Chem Theory Comput (2012) 1.17

A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. J Phys Chem B (2005) 1.15

Electronic continuum model for molecular dynamics simulations of biological molecules. J Chem Theory Comput (2010) 1.15

Storage of an excess proton in the hydrogen-bonded network of the d-pathway of cytochrome C oxidase: identification of a protonated water cluster. J Am Chem Soc (2007) 1.14

Functional hydration and conformational gating of proton uptake in cytochrome c oxidase. J Mol Biol (2009) 1.13

Energy diagrams and mechanism for proton pumping in cytochrome c oxidase. Biochim Biophys Acta (2007) 1.13

Direct observation of protonation reactions during the catalytic cycle of cytochrome c oxidase. Proc Natl Acad Sci U S A (2003) 1.12

Accounting for electronic polarization in non-polarizable force fields. Phys Chem Chem Phys (2011) 1.12

Controlled uncoupling and recoupling of proton pumping in cytochrome c oxidase. Proc Natl Acad Sci U S A (2006) 1.11

Calculated proton uptake on anaerobic reduction of cytochrome C oxidase: is the reaction electroneutral? Biochemistry (2006) 1.08

Microscopic pKa analysis of Glu286 in cytochrome c oxidase (Rhodobacter sphaeroides): toward a calibrated molecular model. Biochemistry (2009) 1.07

Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol (2013) 1.05

A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate. J Mol Biol (2008) 1.05

Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase. Biochim Biophys Acta (2006) 1.05

Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps. J Phys Chem A (2006) 1.04

Variable proton-pumping stoichiometry in structural variants of cytochrome c oxidase. Biochim Biophys Acta (2010) 1.03

Insights into the mechanism of proton transport in cytochrome c oxidase. J Am Chem Soc (2012) 1.02

Proton translocation by cytochrome c oxidase can take place without the conserved glutamic acid in subunit I. Biochemistry (2000) 1.02

Proton binding to proteins: a free-energy component analysis using a dielectric continuum model. Biophys J (2005) 1.02

Kinetic models of redox-coupled proton pumping. Proc Natl Acad Sci U S A (2007) 1.02

Impaired proton pumping in cytochrome c oxidase upon structural alteration of the D pathway. Biochim Biophys Acta (2008) 1.01

Intricate role of water in proton transport through cytochrome c oxidase. J Am Chem Soc (2010) 0.99

Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects. Biochim Biophys Acta (2011) 0.98

Optimization of bacteriorhodopsin for bioelectronic devices. Trends Biotechnol (2002) 0.98

Exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from Thermus thermophilus. Proc Natl Acad Sci U S A (2012) 0.98

Replacing Asn207 by aspartate at the neck of the D channel in the aa3-type cytochrome c oxidase from Rhodobacter sphaeroides results in decoupling the proton pump. Biochemistry (2006) 0.97

Proton transfer function of carbonic anhydrase: Insights from QM/MM simulations. Biochim Biophys Acta (2009) 0.97

Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase. Biochim Biophys Acta (2009) 0.96

G204D, a mutation that blocks the proton-conducting D-channel of the aa3-type cytochrome c oxidase from Rhodobacter sphaeroides. Biochemistry (2005) 0.96

Gating and regulation of the cytochrome c oxidase proton pump. Biochim Biophys Acta (2011) 0.95

Electrostatic control of proton pumping in cytochrome c oxidase. Biochim Biophys Acta (2007) 0.95

Mutations which decouple the proton pump of the cytochrome c oxidase from Rhodobacter sphaeroides perturb the environment of glutamate 286. FEBS Lett (2006) 0.95

Properties of Arg481 mutants of the aa3-type cytochrome c oxidase from Rhodobacter sphaeroides suggest that neither R481 nor the nearby D-propionate of heme a3 is likely to be the proton loading site of the proton pump. Biochemistry (2009) 0.94

Decoupling mutations in the D-channel of the aa(3)-type cytochrome c oxidase from Rhodobacter sphaeroides suggest that a continuous hydrogen-bonded chain of waters is essential for proton pumping. Biochemistry (2010) 0.93

Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach. Biochim Biophys Acta (2011) 0.90

Charge parameterization of the metal centers in cytochrome c oxidase. J Comput Chem (2008) 0.90

Application of the SCC-DFTB method to neutral and protonated water clusters and bulk water. J Phys Chem B (2011) 0.90

The mechanism for proton pumping in cytochrome c oxidase from an electrostatic and quantum chemical perspective. Biochim Biophys Acta (2011) 0.90

Density functional tight binding: values of semi-empirical methods in an ab initio era. Phys Chem Chem Phys (2014) 0.89

Changing hydration level in an internal cavity modulates the proton affinity of a key glutamate in cytochrome c oxidase. Proc Natl Acad Sci U S A (2013) 0.89

Capturing the energetics of water insertion in biological systems: the water flooding approach. Proteins (2012) 0.89

The self-consistent charge density functional tight binding method applied to liquid water and the hydrated excess proton: benchmark simulations. J Phys Chem B (2010) 0.88

Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel. J Chem Theory Comput (2014) 0.87

Glu-286 rotation and water wire reorientation are unlikely the gating elements for proton pumping in cytochrome C oxidase. Biophys J (2011) 0.86

Exploring the possible role of Glu286 in CcO by electrostatic energy computations combined with molecular dynamics. J Phys Chem B (2013) 0.82

Role of aspartate 132 at the orifice of a proton pathway in cytochrome c oxidase. Proc Natl Acad Sci U S A (2013) 0.82

Molecular mechanisms for generating transmembrane proton gradients. Biochim Biophys Acta (2013) 0.81

Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B (2014) 0.80

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. J Phys Chem B (2013) 0.80

An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces. J Chem Theory Comput (2013) 0.79

Functional effects of mutations in cytochrome c oxidase related to prostate cancer. Biochim Biophys Acta (2011) 0.79

Application of the SCC-DFTB method to hydroxide water clusters and aqueous hydroxide solutions. J Phys Chem B (2013) 0.79