Published in Proc Natl Acad Sci U S A on February 07, 2007
Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Proc Natl Acad Sci U S A (2008) 1.31
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proc Natl Acad Sci U S A (2008) 1.27
Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: application of density functional theory to cytochrome ba3 of Thermus thermophilus. J Am Chem Soc (2008) 1.26
Bubbles, gating, and anesthetics in ion channels. Biophys J (2008) 1.02
Kinetic gating of the proton pump in cytochrome c oxidase. Proc Natl Acad Sci U S A (2009) 1.01
High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na⁺-coupled ATP synthase. Nat Commun (2014) 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
Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach. Biochim Biophys Acta (2011) 0.90
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
Mechanism and kinetics of a sodium-driven bacterial flagellar motor. Proc Natl Acad Sci U S A (2013) 0.88
Origin and evolution of the sodium -pumping NADH: ubiquinone oxidoreductase. PLoS One (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
Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis. Chem Sci (2015) 0.83
Molecular mechanisms for generating transmembrane proton gradients. Biochim Biophys Acta (2013) 0.81
Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations. Biochim Biophys Acta (2016) 0.79
Biological proton pumping in an oscillating electric field. Phys Rev Lett (2009) 0.79
The new unified theory of ATP synthesis/hydrolysis and muscle contraction, its manifold fundamental consequences and mechanistic implications and its applications in health and disease. Int J Mol Sci (2008) 0.78
Analyzing the electrogenicity of cytochrome c oxidase. Proc Natl Acad Sci U S A (2016) 0.75
pH signature for the responses of arbuscular mycorrhizal fungi to external stimuli. Plant Signal Behav (2008) 0.75
Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase. Proc Natl Acad Sci U S A (2016) 0.75
Optimization by simulated annealing. Science (1983) 71.02
Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism. Nature (1961) 17.36
Structure at 2.8 A resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature (1995) 8.22
Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 A. Science (1995) 5.43
Oxygen activation and the conservation of energy in cell respiration. Nature (1992) 4.09
Proton pump coupled to cytochrome c oxidase in mitochondria. Nature (1977) 3.27
Fluctuation driven ratchets: Molecular motors. Phys Rev Lett (1994) 2.85
A novel scenario for the evolution of haem-copper oxygen reductases. Biochim Biophys Acta (2001) 2.51
The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Proc Natl Acad Sci U S A (2003) 2.37
Water-gated mechanism of proton translocation by cytochrome c oxidase. Biochim Biophys Acta (2003) 2.26
Proton transport through water-filled carbon nanotubes. Phys Rev Lett (2003) 1.86
Oxygen and proton pathways in cytochrome c oxidase. Proteins (1998) 1.80
Cytochrome c oxidase: 25 years of the elusive proton pump. Biochim Biophys Acta (2004) 1.71
Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase. Nature (2006) 1.65
A mechanistic principle for proton pumping by cytochrome c oxidase. Nature (2005) 1.59
Cytochrome c oxidase: catalytic cycle and mechanisms of proton pumping--a discussion. Biochemistry (1999) 1.50
A simple kinetic model describes the processivity of myosin-v. Biophys J (2003) 1.43
Bound water in the proton translocation mechanism of the haem-copper oxidases. FEBS Lett (1997) 1.41
Tracing the D-pathway in reconstituted site-directed mutants of cytochrome c oxidase from Paracoccus denitrificans. Biochemistry (2000) 1.37
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
Redox-coupled proton translocation in biological systems: proton shuttling in cytochrome c oxidase. Proc Natl Acad Sci U S A (2003) 1.26
Kinesin crouches to sprint but resists pushing. Proc Natl Acad Sci U S A (2005) 1.25
Proton pumping by cytochrome oxidase: progress, problems and postulates. Biochim Biophys Acta (2000) 1.22
Intramolecular proton-transfer reactions in a membrane-bound proton pump: the effect of pH on the peroxy to ferryl transition in cytochrome c oxidase. Biochemistry (2003) 1.18
Involvement of intramitochondrial protons in redox reactions of cytochrome alpha. FEBS Lett (1978) 1.09
Proton transfer during the reaction between fully reduced cytochrome c oxidase and dioxygen: pH and deuterium isotope effects. Biochemistry (1992) 1.07
Titration behavior of residues at the entrance of the D-pathway of cytochrome c oxidase from paracoccus denitrificans investigated by continuum electrostatic calculations. Biophys J (2005) 1.02
A cooperative model for protonmotive heme-copper oxidases. The role of heme a in the proton pump of cytochrome c oxidase. FEBS Lett (1998) 0.92
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell (2008) 6.98
Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys Rev Lett (2006) 4.04
Theory, analysis, and interpretation of single-molecule force spectroscopy experiments. Proc Natl Acad Sci U S A (2008) 3.51
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B (2009) 3.17
Are current molecular dynamics force fields too helical? Biophys J (2008) 3.13
Reaction coordinates and rates from transition paths. Proc Natl Acad Sci U S A (2005) 3.12
Coarse master equations for peptide folding dynamics. J Phys Chem B (2008) 3.01
Water in nonpolar confinement: from nanotubes to proteins and beyond. Annu Rev Phys Chem (2008) 2.57
Osmotic water transport through carbon nanotube membranes. Proc Natl Acad Sci U S A (2003) 2.41
Water-gated mechanism of proton translocation by cytochrome c oxidase. Biochim Biophys Acta (2003) 2.26
SAXS ensemble refinement of ESCRT-III CHMP3 conformational transitions. Structure (2011) 2.24
Crystal structure and allosteric activation of protein kinase C βII. Cell (2011) 2.19
Proton-coupled electron transfer in cytochrome oxidase. Chem Rev (2010) 2.05
Binding-induced folding of a natively unstructured transcription factor. PLoS Comput Biol (2008) 2.04
Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments. J Mol Biol (2005) 1.99
Reactive flux and folding pathways in network models of coarse-grained protein dynamics. J Chem Phys (2009) 1.93
Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc Natl Acad Sci U S A (2005) 1.91
Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor. Structure (2005) 1.86
Proton transport through water-filled carbon nanotubes. Phys Rev Lett (2003) 1.86
Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. Biophys J (2007) 1.78
Electric field and temperature effects on water in the narrow nonpolar pores of carbon nanotubes. J Chem Phys (2004) 1.78
Coarse-grained models for simulations of multiprotein complexes: application to ubiquitin binding. J Mol Biol (2007) 1.74
Coordinate-dependent diffusion in protein folding. Proc Natl Acad Sci U S A (2009) 1.73
Pore opening and closing of a pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A (2010) 1.71
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. J Am Chem Soc (2002) 1.69
Single-file transport of water molecules through a carbon nanotube. Phys Rev Lett (2002) 1.67
Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase. Nature (2006) 1.65
Coarse master equation from Bayesian analysis of replica molecular dynamics simulations. J Phys Chem B (2005) 1.64
Exploring the proton pump mechanism of cytochrome c oxidase in real time. Proc Natl Acad Sci U S A (2007) 1.63
Water clusters in nonpolar cavities. Proc Natl Acad Sci U S A (2004) 1.59
Nucleic acid transport through carbon nanotube membranes. Proc Natl Acad Sci U S A (2004) 1.58
Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation. Proc Natl Acad Sci U S A (2004) 1.56
Diffusive model of protein folding dynamics with Kramers turnover in rate. Phys Rev Lett (2006) 1.53
Convergence and error estimation in free energy calculations using the weighted histogram analysis method. J Comput Chem (2011) 1.52
Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations. Biophys J (2004) 1.49
Watching a signaling protein function in real time via 100-ps time-resolved Laue crystallography. Proc Natl Acad Sci U S A (2012) 1.46
Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules. J Phys Chem B (2008) 1.46
Peptide folding kinetics from replica exchange molecular dynamics. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 1.45
Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations. Biophys J (2005) 1.43
Catalytic mechanism of RNA backbone cleavage by ribonuclease H from quantum mechanics/molecular mechanics simulations. J Am Chem Soc (2011) 1.42
The catalytic cycle of cytochrome c oxidase is not the sum of its two halves. Proc Natl Acad Sci U S A (2003) 1.41
Static and dynamic correlations in water at hydrophobic interfaces. Proc Natl Acad Sci U S A (2008) 1.41
Prediction of charge-induced molecular alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophys J (2004) 1.38
The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting. Dev Cell (2007) 1.36
Native contacts determine protein folding mechanisms in atomistic simulations. Proc Natl Acad Sci U S A (2013) 1.33
Real-time electron transfer in respiratory complex I. Proc Natl Acad Sci U S A (2008) 1.33
Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Proc Natl Acad Sci U S A (2008) 1.31
Time-resolved single-turnover of ba3 oxidase from Thermus thermophilus. Biochim Biophys Acta (2007) 1.29
Protein conformational transitions explored by mixed elastic network models. Proteins (2007) 1.26
Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils. Biophys J (2007) 1.26
Protein folding kinetics under force from molecular simulation. J Am Chem Soc (2008) 1.25
Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. J Comput Chem (2009) 1.24
Hybrid structural model of the complete human ESCRT-0 complex. Structure (2009) 1.23
Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy. Proc Natl Acad Sci U S A (2011) 1.22
Replica exchange simulations of transient encounter complexes in protein-protein association. Proc Natl Acad Sci U S A (2008) 1.21
The molecular mechanism of substrate engagement and immunosuppressant inhibition of calcineurin. PLoS Biol (2013) 1.21
Conserved lysine residues of the membrane subunit NuoM are involved in energy conversion by the proton-pumping NADH:ubiquinone oxidoreductase (Complex I). Biochim Biophys Acta (2008) 1.20
Phosphate release coupled to rotary motion of F1-ATPase. Proc Natl Acad Sci U S A (2013) 1.18
Kinetics and mechanism of proton transport across membrane nanopores. Phys Rev Lett (2006) 1.14
Molecular binding: Under water's influence. Nat Chem (2010) 1.13
The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase. Biochim Biophys Acta (2010) 1.12
Structural basis of p38α regulation by hematopoietic tyrosine phosphatase. Nat Chem Biol (2011) 1.11
Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography. J Mol Biol (2006) 1.10
Metastable water clusters in the nonpolar cavities of the thermostable protein tetrabrachion. J Am Chem Soc (2007) 1.10
Metal-bridging mechanism for O-O bond cleavage in cytochrome C oxidase. Inorg Chem (2003) 1.09
Slow conformational dynamics and unfolding of the calmodulin C-terminal domain. J Am Chem Soc (2007) 1.09
Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes. Phys Rev Lett (2005) 1.09
Time-resolved ATR-FTIR spectroscopy of the oxygen reaction in the D124N mutant of cytochrome c oxidase from Paracoccus denitrificans. Biochemistry (2007) 1.06
Nonspecific binding limits the number of proteins in a cell and shapes their interaction networks. Proc Natl Acad Sci U S A (2010) 1.06
Solution structure of the ESCRT-I and -II supercomplex: implications for membrane budding and scission. Structure (2012) 1.06
Water in the polar and nonpolar cavities of the protein interleukin-1β. J Phys Chem B (2010) 1.05
Effect of flexibility on hydrophobic behavior of nanotube water channels. J Chem Phys (2005) 1.04
Mechanistic stoichiometry of proton translocation by cytochrome cbb3. Proc Natl Acad Sci U S A (2012) 1.03
Macroscopically ordered water in nanopores. Proc Natl Acad Sci U S A (2008) 1.02
Kinetic gating of the proton pump in cytochrome c oxidase. Proc Natl Acad Sci U S A (2009) 1.01
Redox titration of all electron carriers of cytochrome c oxidase by Fourier transform infrared spectroscopy. Biochemistry (2006) 1.01
Atomistic insights into rhodopsin activation from a dynamic model. J Am Chem Soc (2008) 1.00
Comment on "Force-clamp spectroscopy monitors the folding trajectory of a single protein". Science (2005) 1.00
Protein side-chain motion and hydration in proton-transfer pathways. Results for cytochrome p450cam. J Am Chem Soc (2003) 1.00
Differential inhibition of HIV-1 and SIV envelope-mediated cell fusion by C34 peptides derived from the C-terminal heptad repeat of gp41 from diverse strains of HIV-1, HIV-2, and SIV. J Med Chem (2005) 0.99
Drying transition in the hydrophobic gate of the GLIC channel blocks ion conduction. Biophys J (2012) 0.99
Error and efficiency of replica exchange molecular dynamics simulations. J Chem Phys (2009) 0.99
New perspectives on proton pumping in cellular respiration. Chem Rev (2015) 0.99
Gating transition of pentameric ligand-gated ion channels. Biophys J (2009) 0.99
Identity of distributions of direct uphill and downhill translocation times for particles traversing membrane channels. Phys Rev Lett (2006) 0.98
Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications. Proc Natl Acad Sci U S A (2012) 0.98
Interfacial thermodynamics of confined water near molecularly rough surfaces. Faraday Discuss (2010) 0.97
Resting and active states of the ERK2:HePTP complex. J Am Chem Soc (2011) 0.97
Sequence analysis of the cbb3 oxidases and an atomic model for the Rhodobacter sphaeroides enzyme. Biochemistry (2006) 0.97
The proton donor for O-O bond scission by cytochrome c oxidase. Proc Natl Acad Sci U S A (2008) 0.97
Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase. Biochim Biophys Acta (2009) 0.96
Identification of a histidine-tyrosine cross-link in the active site of the cbb3-type cytochrome c oxidase from Rhodobacter sphaeroides. Proc Natl Acad Sci U S A (2006) 0.96
Nanosecond electron tunneling between the hemes in cytochrome bo3. Proc Natl Acad Sci U S A (2007) 0.96
An elementary reaction step of the proton pump is revealed by mutation of tryptophan-164 to phenylalanine in cytochrome c oxidase from Paracoccus denitrificans. Biochemistry (2005) 0.95