Substrate channel in nitrogenase revealed by a molecular dynamics approach.
暂无分享,去创建一个
[1] K. Mason. X-Ray Emission , 2021, Encyclopedic Dictionary of Archaeology.
[2] I. Dance. A molecular pathway for the egress of ammonia produced by nitrogenase , 2013, Scientific Reports.
[3] L. Seefeldt,et al. Nitrogenase reduction of carbon-containing compounds. , 2013, Biochimica et biophysica acta.
[4] Ye Mei,et al. A numerically stable restrained electrostatic potential charge fitting method , 2013, J. Comput. Chem..
[5] L. Seefeldt,et al. Nitrogenase: a draft mechanism. , 2013, Accounts of chemical research.
[6] L. Seefeldt,et al. Carbon dioxide reduction to methane and coupling with acetylene to form propylene catalyzed by remodeled nitrogenase , 2012, Proceedings of the National Academy of Sciences.
[7] I. Dance. The controlled relay of multiple protons required at the active site of nitrogenase. , 2012, Dalton transactions.
[8] T. Straatsma,et al. Force-Field Development and Molecular Dynamics of [NiFe] Hydrogenase. , 2012, Journal of chemical theory and computation.
[9] Po-hung Wang,et al. Mechanistic insight into the blocking of CO diffusion in [NiFe]-hydrogenase mutants through multiscale simulation , 2012, Proceedings of the National Academy of Sciences.
[10] D. Rees,et al. Evidence for Interstitial Carbon in Nitrogenase FeMo Cofactor , 2011, Science.
[11] Frank Neese,et al. X-ray Emission Spectroscopy Evidences a Central Carbon in the Nitrogenase Iron-Molybdenum Cofactor , 2011, Science.
[12] R. Best,et al. A microscopic model for gas diffusion dynamics in a [NiFe]-hydrogenase. , 2011, Physical chemistry chemical physics : PCCP.
[13] L. Seefeldt,et al. Molybdenum Nitrogenase Catalyzes the Reduction and Coupling of CO to Form Hydrocarbons*♦ , 2011, The Journal of Biological Chemistry.
[14] Bert L. de Groot,et al. g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates , 2010 .
[15] J. W. Peters,et al. Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70(Ile) MoFe protein variant. , 2010, Journal of inorganic biochemistry.
[16] Anne Volbeda,et al. Introduction of methionines in the gas channel makes [NiFe] hydrogenase aero-tolerant. , 2009, Journal of the American Chemical Society.
[17] L. Seefeldt,et al. Mechanism of Mo-dependent nitrogenase. , 2009, Annual review of biochemistry.
[18] Dennis R. Dean,et al. A substrate channel in the nitrogenase MoFe protein , 2009, JBIC Journal of Biological Inorganic Chemistry.
[19] Bosco K. Ho,et al. HOLLOW: Generating Accurate Representations of Channel and Interior Surfaces in Molecular Structures , 2008, BMC Structural Biology.
[20] A. Volbeda,et al. Experimental approaches to kinetics of gas diffusion in hydrogenase , 2008, Proceedings of the National Academy of Sciences.
[21] J Andrew McCammon,et al. Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method. , 2008, The Journal of chemical physics.
[22] Berk Hess,et al. P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation. , 2008, Journal of chemical theory and computation.
[23] Jan H. Jensen,et al. Very fast empirical prediction and rationalization of protein pKa values , 2005, Proteins.
[24] Debarshi Mustafi,et al. Nitrogenase Complexes: Multiple Docking Sites for a Nucleotide Switch Protein , 2005, Science.
[25] L. Seefeldt,et al. Substrate interactions with the nitrogenase active site. , 2005, Accounts of chemical research.
[26] K Schulten,et al. Molecular dynamics and experimental investigation of H(2) and O(2) diffusion in [Fe]-hydrogenase. , 2005, Biochemical Society transactions.
[27] D. J. Price,et al. A modified TIP3P water potential for simulation with Ewald summation. , 2004, The Journal of chemical physics.
[28] L. Seefeldt,et al. An organometallic intermediate during alkyne reduction by nitrogenase. , 2004, Journal of the American Chemical Society.
[29] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[30] L. Seefeldt,et al. Substrate interactions with nitrogenase: Fe versus Mo. , 2004, Biochemistry.
[31] Wei Zhang,et al. A point‐charge force field for molecular mechanics simulations of proteins based on condensed‐phase quantum mechanical calculations , 2003, J. Comput. Chem..
[32] S. McDowell. Blue-shifting hydrogen bonding in N2⋯HKrF , 2003 .
[33] M. Durrant. An atomic-level mechanism for molybdenum nitrogenase. Part 2. Proton reduction, inhibition of dinitrogen reduction by dihydrogen, and the HD formation reaction. , 2002, Biochemistry.
[34] M. Durrant. An atomic-level mechanism for molybdenum nitrogenase. Part 1. Reduction of dinitrogen. , 2002, Biochemistry.
[35] D. Rees,et al. Nitrogenase MoFe-Protein at 1.16 Å Resolution: A Central Ligand in the FeMo-Cofactor , 2002, Science.
[36] L. Soulard. Molecular Dynamics and Experimental Study of Shock Polarization of Nitromethane , 2002 .
[37] B. Hess. Convergence of sampling in protein simulations. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.
[38] D. Dean,et al. Reduction of short chain alkynes by a nitrogenase α-70Ala-substituted MoFe protein , 2002 .
[39] Berk Hess,et al. GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .
[40] M. Durrant. Controlled protonation of iron-molybdenum cofactor by nitrogenase: a structural and theoretical analysis. , 2001, The Biochemical journal.
[41] K. Fisher,et al. Effects on substrate reduction of substitution of histidine-195 by glutamine in the alpha-subunit of the MoFe protein of Azotobacter vinelandii nitrogenase. , 1998, Biochemistry.
[42] D. Rees,et al. Structure of ADP·AIF4 –-stabilized nitrogenase complex and its implications for signal transduction , 1997, Nature.
[43] B. Burgess,et al. Mechanism of Molybdenum Nitrogenase , 1997 .
[44] Kenneth M. Merz,et al. Application of the Nosé−Hoover Chain Algorithm to the Study of Protein Dynamics , 1996 .
[45] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[46] M. Webb,et al. ATP Hydrolysis and Energy Transduction by Nitrogenase , 1995 .
[47] D. Rees,et al. The nitrogenase FeMo-cofactor and P-cluster pair: 2.2 A resolution structures. , 1993, Science.
[48] S A Benner,et al. The nitrogenase MoFe protein , 1993, FEBS letters.
[49] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .
[50] D C Rees,et al. Structural models for the metal centers in the nitrogenase molybdenum-iron protein. , 1992, Science.
[51] D. Rees,et al. Crystallographic structure of the nitrogenase iron protein from Azotobacter vinelandii. , 1992, Science.
[52] Dennis R. Salahub,et al. Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation , 1992 .
[53] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[54] M. Parrinello,et al. Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .
[55] W. Orme-Johnson,et al. Role of magnesium adenosine 5'-triphosphate in the hydrogen evolution reaction catalyzed by nitrogenase from Azotobacter vinelandii. , 1980, Biochemistry.
[56] R. Miller,et al. The coupling of electron transfer in nitrogenase to the hydrolysis of magnesium adenosine triphosphate. , 1979, Biochemical Society transactions.
[57] R. Burris,et al. Interactions among substrates and inhibitors of nitrogenase , 1975, Journal of bacteriology.