Published in J Am Chem Soc on July 07, 2017
The Protein Data Bank. Nucleic Acids Res (2000) 187.10
VMD: visual molecular dynamics. J Mol Graph (1996) 117.02
MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr (2009) 53.36
Announcing the worldwide Protein Data Bank. Nat Struct Biol (2003) 17.06
Binding energy, specificity, and enzymic catalysis: the circe effect. Adv Enzymol Relat Areas Mol Biol (1975) 6.87
Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins (1988) 4.37
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. J Chem Theory Comput (2011) 3.98
Energetics of enzyme catalysis. Proc Natl Acad Sci U S A (1978) 3.34
Evolution of enzyme function and the development of catalytic efficiency. Biochemistry (1976) 3.26
Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 angstrom resolution using amino acid sequence data. Nature (1975) 3.15
Modeling electrostatic effects in proteins. Biochim Biophys Acta (2006) 2.91
Enzyme catalysis: not different, just better. Nature (1991) 2.77
Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop. Science (1990) 2.60
Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites. J Biol Chem (1998) 2.58
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. J Chem Theory Comput (2011) 2.35
Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. Proc Natl Acad Sci U S A (2000) 2.18
Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Protein Eng (1992) 2.15
Triosephosphate isomerase catalysis is diffusion controlled. Appendix: Analysis of triose phosphate equilibria in aqueous solution by 31P NMR. Biochemistry (1988) 1.97
Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis. Biochemistry (1990) 1.94
The mechanism of the triosephosphate isomerase reaction. J Biol Chem (1959) 1.88
Stabilization of a reaction intermediate as a catalytic device: definition of the functional role of the flexible loop in triosephosphate isomerase. Biochemistry (1990) 1.81
Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J Mol Graph Model (1999) 1.77
Understanding the rates of certain enzyme-catalyzed reactions: proton abstraction from carbon acids, acyl-transfer reactions, and displacement reactions of phosphodiesters. Biochemistry (1993) 1.75
Enzymatic catalysis of proton transfer at carbon: activation of triosephosphate isomerase by phosphite dianion. Biochemistry (2007) 1.72
A role for flexible loops in enzyme catalysis. Curr Opin Struct Biol (2010) 1.62
On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase. Philos Trans R Soc Lond B Biol Sci (1981) 1.61
Optimal alignment for enzymatic proton transfer: structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution. Proc Natl Acad Sci U S A (2002) 1.53
Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization. Biochemistry (2000) 1.52
Specificity and kinetics of triose phosphate isomerase from chicken muscle. Biochem J (1972) 1.51
Contribution of phosphate intrinsic binding energy to the enzymatic rate acceleration for triosephosphate isomerase. J Am Chem Soc (2001) 1.40
Computational modeling of the catalytic reaction in triosephosphate isomerase. J Mol Biol (2004) 1.36
Proton transfer at carbon. Curr Opin Chem Biol (2001) 1.36
Hydron transfer catalyzed by triosephosphate isomerase. Products of the direct and phosphite-activated isomerization of [1-(13)C]-glycolaldehyde in D(2)O. Biochemistry (2009) 1.33
On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi. J Chem Theory Comput (2013) 1.32
Neutral imidazole is the electrophile in the reaction catalyzed by triosephosphate isomerase: structural origins and catalytic implications. Biochemistry (1991) 1.31
Hydron transfer catalyzed by triosephosphate isomerase. Products of isomerization of (R)-glyceraldehyde 3-phosphate in D2O. Biochemistry (2005) 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
Triosephosphate isomerase: a highly evolved biocatalyst. Cell Mol Life Sci (2010) 1.30
Electrophilic catalysis in triosephosphate isomerase: the role of histidine-95. Biochemistry (1991) 1.28
Triosephosphate isomerase: a theoretical comparison of alternative pathways. J Am Chem Soc (2001) 1.27
Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization. Biochemistry (2009) 1.27
Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution. J Biol Chem (2003) 1.25
Computer simulation and analysis of the reaction pathway of triosephosphate isomerase. Biochemistry (1991) 1.24
Energetics of 3-oxo-delta 5-steroid isomerase: source of the catalytic power of the enzyme. Biochemistry (1991) 1.24
Hydron transfer catalyzed by triosephosphate isomerase. Products of isomerization of dihydroxyacetone phosphate in D2O. Biochemistry (2005) 1.23
Reaction energetics of a mutant triosephosphate isomerase in which the active-site glutamate has been changed to aspartate. Biochemistry (1986) 1.21
Triosephosphate isomerase requires a positively charged active site: the role of lysine-12. Biochemistry (1994) 1.19
Specificity in transition state binding: the Pauling model revisited. Biochemistry (2013) 1.19
Role of Lys-12 in catalysis by triosephosphate isomerase: a two-part substrate approach. Biochemistry (2010) 1.18
A paradigm for enzyme-catalyzed proton transfer at carbon: triosephosphate isomerase. Biochemistry (2012) 1.15
To build an enzyme.... Philos Trans R Soc Lond B Biol Sci (1991) 1.14
An analysis of the substrate-induced rate effect in the phosphoglucomutase system. Biochemistry (1976) 1.13
The enhancement of enzymatic rate accelerations by Brønsted acid-base catalysis. Biochemistry (1998) 1.05
Crystal structure of the K12M/G15A triosephosphate isomerase double mutant and electrostatic analysis of the active site. Biochemistry (1994) 1.04
Structures of the "open" and "closed" state of trypanosomal triosephosphate isomerase, as observed in a new crystal form: implications for the reaction mechanism. Proteins (1993) 1.04
Rescue of K12G triosephosphate isomerase by ammonium cations: the reaction of an enzyme in pieces. J Am Chem Soc (2010) 1.02
A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding. Protein Eng (1997) 1.02
Evidence for founder effect of the Glu104Asp substitution and identification of new mutations in triosephosphate isomerase deficiency. Hum Mutat (1997) 1.02
Triosephosphate isomerase by consensus design: dramatic differences in physical properties and activity of related variants. J Mol Biol (2011) 1.01
Mechanism for activation of triosephosphate isomerase by phosphite dianion: the role of a ligand-driven conformational change. J Am Chem Soc (2011) 1.01
Formation and stability of the enolates of N-protonated proline methyl ester and proline zwitterion in aqueous solution: a nonenzymatic model for the first step in the racemization of proline catalyzed by proline racemase. Biochemistry (2003) 0.99
Mechanism for activation of triosephosphate isomerase by phosphite dianion: the role of a hydrophobic clamp. J Am Chem Soc (2012) 0.97
Wildtype and engineered monomeric triosephosphate isomerase from Trypanosoma brucei: partitioning of reaction intermediates in D2O and activation by phosphite dianion. Biochemistry (2011) 0.95
Enzyme architecture: on the importance of being in a protein cage. Curr Opin Chem Biol (2014) 0.95
Magnitude and origin of the enhanced basicity of the catalytic glutamate of triosephosphate isomerase. J Am Chem Soc (2013) 0.94
Structural determinants for ligand binding and catalysis of triosephosphate isomerase. Eur J Biochem (2001) 0.91
Computer simulation of the triosephosphate isomerase catalyzed reaction. J Biol Chem (1996) 0.90
Role of a guanidinium cation-phosphodianion pair in stabilizing the vinyl carbanion intermediate of orotidine 5'-phosphate decarboxylase-catalyzed reactions. Biochemistry (2013) 0.89
Enzyme architecture: deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase. J Am Chem Soc (2014) 0.87
Catalytic stimulation by restrained active-site floppiness--the case of high density lipoprotein-bound serum paraoxonase-1. J Mol Biol (2015) 0.86
The activating oxydianion binding domain for enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation: specificity and enzyme architecture. J Am Chem Soc (2015) 0.86
Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes. ACS Catal (2015) 0.84
Energetics of triosephosphate isomerase: the fate of the 1(R)-3H label of tritiated dihydroxyacetone phsophate in the isomerase reaction. Biochemistry (1976) 0.83
Cooperative Electrostatic Interactions Drive Functional Evolution in the Alkaline Phosphatase Superfamily. J Am Chem Soc (2015) 0.82
The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules. Biochemistry (1995) 0.82
Reflections on the catalytic power of a TIM-barrel. Bioorg Chem (2014) 0.82
Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase. J Am Chem Soc (2015) 0.82
Molecular dynamics simulations of "loop closing" in the enzyme triose phosphate isomerase. J Mol Biol (1987) 0.81
Triosephosphate isomerase I170V alters catalytic site, enhances stability and induces pathology in a Drosophila model of TPI deficiency. Biochim Biophys Acta (2014) 0.80
The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): a QM/FE approach. J Comput Chem (2003) 0.79
The role of phosphate in a multistep enzymatic reaction: reactions of the substrate and intermediate in pieces. J Am Chem Soc (2015) 0.78
Structure-Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase. Biochemistry (2016) 0.76
Enzyme activation through the utilization of intrinsic dianion binding energy. Protein Eng Des Sel (2016) 0.76
Simulation analysis of triose phosphate isomerase: conformational transition and catalysis. Faraday Discuss (1992) 0.76
Simple model for the effect of Glu165----Asp165 mutation on the rate of catalysis in triose phosphate isomerase. J Mol Biol (1986) 0.76
Structure-Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. J Am Chem Soc (2016) 0.75
CADEE: Computer-Aided Directed Evolution of Enzymes. IUCrJ (2017) 0.75
Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1. J Am Chem Soc (2016) 0.75
Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase. J Am Chem Soc (2015) 0.82
Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase. Philos Trans A Math Phys Eng Sci (2016) 0.79
Enzyme Architecture: Self-Assembly of Enzyme and Substrate Pieces of Glycerol-3-Phosphate Dehydrogenase into a Robust Catalyst of Hydride Transfer. J Am Chem Soc (2016) 0.75
Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1. J Am Chem Soc (2016) 0.75
Structure-Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. J Am Chem Soc (2016) 0.75
Simulating the reactions of substituted pyridinio-N-phosphonates with pyridine as a model for biological phosphoryl transfer. Org Biomol Chem (2017) 0.75
DNA Polymerase λ Active Site Favors a Mutagenic Mispair Between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template. A Free Energy Perturbation Study. J Phys Chem B (2017) 0.75