Published in Protein Sci on February 01, 2011
Effects of organic solvents and substrate binding on trypsin in acetonitrile and hexane media. J Mol Model (2013) 0.76
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput (2008) 34.90
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem (2004) 8.13
Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J Mol Biol (1992) 3.92
Improving enzymes by using them in organic solvents. Nature (2001) 3.84
Enzyme-catalyzed processes in organic solvents. Proc Natl Acad Sci U S A (1985) 2.10
Enzymatic catalysis in organic media at 100 degrees C. Science (1984) 2.00
Enzymatic catalysis and dynamics in low-water environments. Proc Natl Acad Sci U S A (1992) 1.66
Why are enzymes less active in organic solvents than in water? Trends Biotechnol (1997) 1.50
Structure and function of lipases. Adv Protein Chem (1994) 1.24
Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics. Biophys J (1999) 1.07
Activity and mobility of subtilisin in low water organic media: hydration is more important than solvent dielectric. Biochim Biophys Acta (1998) 1.03
Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies. Biophys J (2003) 1.01
Inhibitor-induced enzyme activation in organic solvents. J Biol Chem (1988) 1.01
Reaction rate with suspended lipase catalyst shows similar dependence on water activity in different organic solvents. Biochim Biophys Acta (1992) 0.96
Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase. BMC Struct Biol (2009) 0.90
Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents. FEBS J (2007) 0.89
Measuring enzyme motility in organic media using novel H-D exchange methodology. Biotechnol Bioeng (2000) 0.86
Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes. Biochemistry (1998) 0.83
Protein structure and dynamics in ionic liquids. Insights from molecular dynamics simulation studies. J Phys Chem B (2008) 0.82
Reorganization and conformational changes in the reduction of tetraheme cytochromes. Biophys J (2005) 0.82
Water dependent properties of cutinase in nonaqueous solvents: a computational study of enantioselectivity. Biophys J (2005) 0.82
Revertant mutants G550E and 4RK rescue cystic fibrosis mutants in the first nucleotide-binding domain of CFTR by different mechanisms. Proc Natl Acad Sci U S A (2006) 1.56
Progress in the prediction of pKa values in proteins. Proteins (2011) 1.36
Sulphate respiration from hydrogen in Desulfovibrio bacteria: a structural biology overview. Prog Biophys Mol Biol (2004) 1.25
Acidic range titration of HEWL using a constant-pH molecular dynamics method. Proteins (2008) 1.08
Role of the anti-sigma factor SpoIIAB in regulation of sigmaG during Bacillus subtilis sporulation. J Bacteriol (2004) 1.03
Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies. Biophys J (2003) 1.01
Proton pathways in a [NiFe]-hydrogenase: A theoretical study. Proteins (2008) 1.01
Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine. J Phys Chem B (2006) 1.00
Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail. J Biol Inorg Chem (2001) 0.99
Functional role of N-glycosylation from ADAM10 in processing, localization and activity of the enzyme. Biochim Biophys Acta (2008) 0.98
Hydrogenases in Desulfovibrio vulgaris Hildenborough: structural and physiologic characterisation of the membrane-bound [NiFeSe] hydrogenase. J Biol Inorg Chem (2005) 0.98
Mind the gap: cytochrome interactions reveal electron pathways across the periplasm of Shewanella oneidensis MR-1. Biochem J (2013) 0.96
Conformational changes induced by ATP-hydrolysis in an ABC transporter: a molecular dynamics study of the Sav1866 exporter. Proteins (2011) 0.92
Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems? Proteins (2011) 0.92
Tailoring cutinase activity towards polyethylene terephthalate and polyamide 6,6 fibers. J Biotechnol (2007) 0.91
Constant-pH molecular dynamics simulations reveal a β-rich form of the human prion protein. J Phys Chem B (2010) 0.91
Characterization of the protein unfolding processes induced by urea and temperature. Biophys J (2007) 0.91
Mechanisms underlying dioxygen reduction in laccases. Structural and modelling studies focusing on proton transfer. BMC Struct Biol (2010) 0.91
The pH-dependent conformational states of kyotorphin: a constant-pH molecular dynamics study. Biophys J (2006) 0.90
The multicopper oxidase from the archaeon Pyrobaculum aerophilum shows nitrous oxide reductase activity. FEBS J (2010) 0.90
Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents. FEBS J (2007) 0.89
On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium. J Phys Chem B (2005) 0.89
Molecular dynamics at constant pH and reduction potential: application to cytochrome c(3). J Am Chem Soc (2009) 0.89
Reorganization in apo- and holo-beta-lactoglobulin upon protonation of Glu89: molecular dynamics and pKa calculations. Proteins (2004) 0.89
Coastal upwelling supplies oxygen-depleted water to the Columbia River estuary. PLoS One (2011) 0.88
Proximal mutations at the type 1 copper site of CotA laccase: spectroscopic, redox, kinetic and structural characterization of I494A and L386A mutants. Biochem J (2008) 0.87
Redox properties of Thermus thermophilus ba3: different electron-proton coupling in oxygen reductases? Biophys J (2007) 0.87
Conformational and orientational guidance of the analgesic dipeptide kyotorphin induced by lipidic membranes: putative correlation toward receptor docking. J Phys Chem B (2006) 0.86
A robust metallo-oxidase from the hyperthermophilic bacterium Aquifex aeolicus. FEBS J (2007) 0.85
Putative dioxygen-binding sites and recognition of tigecycline and minocycline in the tetracycline-degrading monooxygenase TetX. Acta Crystallogr D Biol Crystallogr (2013) 0.84
Superoxide reduction by Nanoarchaeum equitans neelaredoxin, an enzyme lacking the highly conserved glutamate iron ligand. J Biol Inorg Chem (2007) 0.84
Investigation of protonatable residues in Rhodothermus marinus caa3 haem-copper oxygen reductase: comparison with Paracoccus denitrificans aa3 haem-copper oxygen reductase. J Biol Inorg Chem (2003) 0.84
Insights into the molecular mechanism of an ABC transporter: conformational changes in the NBD dimer of MJ0796. J Phys Chem B (2010) 0.84
Pathways of H2 toward the active site of [NiFe]-hydrogenase. Biophys J (2006) 0.83
Conformational analysis in a multidimensional energy landscape: study of an arginylglutamate repeat. J Phys Chem B (2009) 0.82
Reorganization and conformational changes in the reduction of tetraheme cytochromes. Biophys J (2005) 0.82
The role of Asp116 in the reductive cleavage of dioxygen to water in CotA laccase: assistance during the proton-transfer mechanism. Acta Crystallogr D Biol Crystallogr (2012) 0.82
Water dependent properties of cutinase in nonaqueous solvents: a computational study of enantioselectivity. Biophys J (2005) 0.82
Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex. PLoS Comput Biol (2011) 0.81
Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: molecular dynamics studies of HlyB. Protein Sci (2011) 0.81
Theoretical identification of proton channels in the quinol oxidase aa3 from Acidianus ambivalens. Biophys J (2004) 0.81
Structural analysis of Thermus thermophilus HB27 mannosyl-3-phosphoglycerate synthase provides evidence for a second catalytic metal ion and new insight into the retaining mechanism of glycosyltransferases. J Biol Chem (2010) 0.81
Reversibility of prion misfolding: insights from constant-pH molecular dynamics simulations. J Phys Chem B (2012) 0.81
Redox-Bohr and other cooperativity effects in the nine-heme cytochrome C from Desulfovibrio desulfuricans ATCC 27774: crystallographic and modeling studies. J Biol Chem (2003) 0.80
Thermodynamic redox behavior of the heme centers of cbb3 heme-copper oxygen reductase from Bradyrhizobium japonicum. Biochemistry (2007) 0.80
Unfolding the conformational behavior of peptide dendrimers: insights from molecular dynamics simulations. J Am Chem Soc (2011) 0.79
Dioxygen and nitric oxide pathways and affinity to the catalytic site of rubredoxin:oxygen oxidoreductase from Desulfovibrio gigas. J Biol Inorg Chem (2009) 0.79
A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies. Phys Chem Chem Phys (2013) 0.79
Conformational and dynamics changes induced by bile acids binding to chicken liver bile acid binding protein. Proteins (2008) 0.79
Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations. J Chem Inf Model (2012) 0.79
Structural features of [NiFeSe] and [NiFe] hydrogenases determining their different properties: a computational approach. J Biol Inorg Chem (2012) 0.78
Structural effects of pH and deacylation on surfactant protein C in an organic solvent mixture: a constant-pH MD study. J Chem Inf Model (2013) 0.78
Membrane-induced conformational changes of kyotorphin revealed by molecular dynamics simulations. J Phys Chem B (2010) 0.78
The role of Lys147 in the interaction between MPSA-gold nanoparticles and the α-hemolysin nanopore. Langmuir (2012) 0.78
Docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase. J Biol Inorg Chem (2003) 0.78
Modeling electron transfer thermodynamics in protein complexes: interaction between two cytochromes c(3). Biophys J (2004) 0.78
Molecular modeling of hair keratin/peptide complex: Using MM-PBSA calculations to describe experimental binding results. Proteins (2012) 0.77
Specific amino acids of Olive mild mosaic virus coat protein are involved in transmission by Olpidium brassicae. J Gen Virol (2011) 0.77
Molecular determinants for FMN-binding in Desulfovibrio gigas flavoredoxin. FEBS Lett (2007) 0.77
Interaction of counterions with subtilisin in acetonitrile: insights from molecular dynamics simulations. J Phys Chem B (2012) 0.77
Natural domain design: enhanced thermal stability of a zinc-lacking ferredoxin isoform shows that a hydrophobic core efficiently replaces the structural metal site. Biochemistry (2006) 0.76
Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking. Biochemistry (2015) 0.76
Electric-field-induced redox potential shifts of tetraheme cytochromes c3 immobilized on self-assembled monolayers: surface-enhanced resonance Raman spectroscopy and simulation studies. Biophys J (2005) 0.76
Thermodynamic redox behavior of the heme centers in A-type heme-copper oxygen reductases: comparison between the two subfamilies. Biophys J (2008) 0.76
Structural determinants for the membrane insertion of the transmembrane peptide of hemagglutinin from influenza virus. J Chem Inf Model (2012) 0.76
Correction: Photonic Activation of Plasminogen Induced by Low Dose UVB. PLoS One (2015) 0.75
Design of a peptidic turn with high affinity for Hg(II). Inorg Chem (2012) 0.75
Water encapsulation in a polyoxapolyaza macrobicyclic compound. J Org Chem (2012) 0.75
The Bsmoc group as a novel scaffold for the design of irreversible inhibitors of cysteine proteases. Bioorg Med Chem Lett (2006) 0.75
Parametrization of 1-butyl-3-methylimidazolium hexafluorophosphate/nitrate ionic liquid for the GROMOS force field. J Phys Chem B (2006) 0.75
Protein thermal stabilization by charged compatible solutes: Computational studies in rubredoxin from Desulfovibrio gigas. Proteins (2008) 0.75
Correction to "Structural Effects of pH and Deacylation on Surfactant Protein C in an Organic Solvent Mixture: A Constant-pH MD Study". J Chem Inf Model (2014) 0.75
Simulation of multihaem cytochromes. FEBS Lett (2011) 0.75