-
2
-
-
0030723218
-
A low-barrier hydrogen bond in the catalytic triad of serine proteases? Theory versus experiment
-
Ash, E. L., J. L. Sudmeier, E. C. De Fabo, and W. W. Bachovchin. 1997. A low-barrier hydrogen bond in the catalytic triad of serine proteases? Theory versus experiment. Science. 278:1128-1132.
-
(1997)
Science
, vol.278
, pp. 1128-1132
-
-
Ash, E.L.1
Sudmeier, J.L.2
De Fabo, E.C.3
Bachovchin, W.W.4
-
4
-
-
33947094423
-
Nitrogen-15 nuclear magnetic resonance spectroscopy. The state of histidine in the catalytic triad of α-lytic protease. Implications for the charge-relay mechanism of peptide-bond cleavage by serine proteases
-
Bachovchin, W. W., and J. D. Roberts. 1978. Nitrogen-15 nuclear magnetic resonance spectroscopy. The state of histidine in the catalytic triad of α-lytic protease. Implications for the charge-relay mechanism of peptide-bond cleavage by serine proteases. J. Am. Chem. Soc. 100: 8041-8047.
-
(1978)
J. Am. Chem. Soc.
, vol.100
, pp. 8041-8047
-
-
Bachovchin, W.W.1
Roberts, J.D.2
-
5
-
-
0014689979
-
Role of a buried acid group in the mechanism of action of chymotrypsin
-
Blow, D. M., J. J. Birktoft, and B. S. Hartlet. 1969. Role of a buried acid group in the mechanism of action of chymotrypsin. Nature. 221: 337-340.
-
(1969)
Nature
, vol.221
, pp. 337-340
-
-
Blow, D.M.1
Birktoft, J.J.2
Hartlet, B.S.3
-
6
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
7
-
-
0003525155
-
-
John Wiley and Sons, New York
-
Brooks, C. L., III, M. Karplus, and B. M. Pettitt. 1987. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. John Wiley and Sons, New York.
-
(1987)
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
-
-
Brooks C.L. III1
Karplus, M.2
Pettitt, B.M.3
-
8
-
-
0016912106
-
Some pertinent aspects of mechanisms as determined with small molecules
-
Bruice, T. C. 1976. Some pertinent aspects of mechanisms as determined with small molecules. Annu. Rev. Biochem. 45:331-373.
-
(1976)
Annu. Rev. Biochem.
, vol.45
, pp. 331-373
-
-
Bruice, T.C.1
-
9
-
-
0026684043
-
A 500 ps molecular dynamics simulation study of interleukin-1β in water
-
Chandrasekhar, I., G. M. Clore, A. Szabo, A. M. Gronenborn, and B. R. Brooks. 1992. A 500 ps molecular dynamics simulation study of interleukin-1β in water. J. Mol. Biol. 226:239-250.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 239-250
-
-
Chandrasekhar, I.1
Clore, G.M.2
Szabo, A.3
Gronenborn, A.M.4
Brooks, B.R.5
-
10
-
-
0028030684
-
Low-barrier hydrogen bonds and enzymatic catalysis
-
Cleland, W. W., and M. M. Kreevoy. 1994. Low-barrier hydrogen bonds and enzymatic catalysis. Science. 264:1887-1890.
-
(1994)
Science
, vol.264
, pp. 1887-1890
-
-
Cleland, W.W.1
Kreevoy, M.M.2
-
11
-
-
11944273044
-
An alternative geometry for the catalytic triad of serine proteases
-
Corey, D. R., M. E. McGrath, J. R. Vasquez, R. J. Retterick, and C. S. Craik. 1992. An alternative geometry for the catalytic triad of serine proteases. J. Am. Chem. Soc. 114:4507-4509.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 4507-4509
-
-
Corey, D.R.1
McGrath, M.E.2
Vasquez, J.R.3
Retterick, R.J.4
Craik, C.S.5
-
12
-
-
0031686334
-
Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations
-
Creveld, L. D., A. Amadei, R. C. van Schaik, H. A. M. Pepermans, J. de Vlieg, and H. J. C. Berendsen. 1998. Identification of functional and unfolding motions of cutinase as obtained from molecular dynamics computer simulations. Proteins. 33:253-264.
-
(1998)
Proteins
, vol.33
, pp. 253-264
-
-
Creveld, L.D.1
Amadei, A.2
Van Schaik, R.C.3
Pepermans, H.A.M.4
De Vlieg, J.5
Berendsen, H.J.C.6
-
13
-
-
0030768420
-
Structure as basis for understanding interfacial properties of lipases
-
Cygler, M., and J. D. Schrag. 1997. Structure as basis for understanding interfacial properties of lipases. Methods Enzymol. 284:3-27.
-
(1997)
Methods Enzymol.
, vol.284
, pp. 3-27
-
-
Cygler, M.1
Schrag, J.D.2
-
14
-
-
0015935205
-
The charge relay system in chymotrypsin and chymotrypsinogen
-
Fersht, A. R., and J. Sperling. 1973. The charge relay system in chymotrypsin and chymotrypsinogen. J. Mol. Biol. 74:137-149.
-
(1973)
J. Mol. Biol.
, vol.74
, pp. 137-149
-
-
Fersht, A.R.1
Sperling, J.2
-
15
-
-
0028040716
-
A tow-barrier hydrogen bond in the catalytic triad of serine proteases
-
Frey, P. A., S. A. Whitt, and J. B. Tobin. 1994. A tow-barrier hydrogen bond in the catalytic triad of serine proteases. Science. 264:1927-1930.
-
(1994)
Science
, vol.264
, pp. 1927-1930
-
-
Frey, P.A.1
Whitt, S.A.2
Tobin, J.B.3
-
16
-
-
0031127432
-
Understanding enzymatic catalysis: The importance of short, strong, hydrogen bonds
-
Geralt, J. A., M. M. Kreevoy, W. W. Cleland, and P. A. Frey. 1997. Understanding enzymatic catalysis: the importance of short, strong, hydrogen bonds. Chem. Biol. 4:259-267.
-
(1997)
Chem. Biol.
, vol.4
, pp. 259-267
-
-
Geralt, J.A.1
Kreevoy, M.M.2
Cleland, W.W.3
Frey, P.A.4
-
17
-
-
0030090490
-
Short strong hydrogen bonds: Can they explain enzymatic catalysis?
-
Guthrie, J. P. 1996. Short strong hydrogen bonds: can they explain enzymatic catalysis? Chem. Biol. 3:163-170.
-
(1996)
Chem. Biol.
, vol.3
, pp. 163-170
-
-
Guthrie, J.P.1
-
18
-
-
0026520387
-
Converting trypsin to chymotrypsin: The role of surface loops
-
Hedstrom, L., L. Szilagyi, and W. J. Rutter. 1992. Converting trypsin to chymotrypsin: the role of surface loops. Science. 255:1249-1253.
-
(1992)
Science
, vol.255
, pp. 1249-1253
-
-
Hedstrom, L.1
Szilagyi, L.2
Rutter, W.J.3
-
19
-
-
0004014257
-
-
Department of Biochemistry and Molecular Biology, University College, London
-
Hubbard, S. J., and J. M. Thornton. 1993. NACCESS. Department of Biochemistry and Molecular Biology, University College, London.
-
(1993)
NACCESS
-
-
Hubbard, S.J.1
Thornton, J.M.2
-
20
-
-
0004016501
-
Comparison of simple potential functions for simulating water
-
Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impley, and M. L. Klein. 1983. Comparison of simple potential functions for simulating water. J. Chem. Phys. 79:926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impley, R.W.4
Klein, M.L.5
-
21
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein stuctures
-
Kraulis, P. J. 1991. MOLSCRIPT: a program to produce both detailed and schematic plots of protein stuctures. J. Appl. Crystallogr. 24:946-950.
-
(1991)
J. Appl. Crystallogr.
, vol.24
, pp. 946-950
-
-
Kraulis, P.J.1
-
22
-
-
0017324044
-
Serine proteases: Structure and mechanism of catalysis
-
Kraut, J. 1977. Serine proteases: structure and mechanism of catalysis. Annu. Rev. Biochem. 46:331-358.
-
(1977)
Annu. Rev. Biochem.
, vol.46
, pp. 331-358
-
-
Kraut, J.1
-
23
-
-
0032540681
-
- from 1,2-dichloroethane at the active site of Xanthobacter autotrophicus haloalkane dehalogenase
-
- from 1,2-dichloroethane at the active site of Xanthobacter autotrophicus haloalkane dehalogenase. J. Am. Chem. Soc. 120:5611-5621.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 5611-5621
-
-
Lightstone, F.C.1
Zheng, Y.-J.2
Bruice, T.C.3
-
24
-
-
0031574909
-
Atomic resolution (1.0 Å) crystal structure of Fusarium solani cutinase: Stereochemical analysis
-
Longhi, C. M., V. Lamzin, A. Nichols, and C. Cambillau. 1997. Atomic resolution (1.0 Å) crystal structure of Fusarium solani cutinase: stereochemical analysis. J. Mol. Biol. 268:779-799.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 779-799
-
-
Longhi, C.M.1
Lamzin, V.2
Nichols, A.3
Cambillau, C.4
-
25
-
-
0030470263
-
Dynamics of Fusarium solani cutinase investigated through structural comparisons among different crystal forms of its variants
-
Longhi, S., A. Nicolas, L. Creveld, M. Egmond, C. T. Verrips, J. de Vlieg, C. Martinez, and C. Cambillau. 1996. Dynamics of Fusarium solani cutinase investigated through structural comparisons among different crystal forms of its variants. Proteins. 26:442-458.
-
(1996)
Proteins
, vol.26
, pp. 442-458
-
-
Longhi, S.1
Nicolas, A.2
Creveld, L.3
Egmond, M.4
Verrips, C.T.5
De Vlieg, J.6
Martinez, C.7
Cambillau, C.8
-
26
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
-
(1998)
J. Phys. Chem. B.
, vol.102
, pp. 3586-3616
-
-
MacKerell A.D., Jr.1
Bashford, D.2
Bellott, M.3
Dunbrack R.L., Jr.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher W.E. III20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
27
-
-
0027957435
-
Cutinase, a lipolytic enzyme with a preformed oxyanion hole
-
Martinez, C., A. Nicholas, H. van Tilbeurgh, M. P. Egloff, C. Cudrey, R. Verger, and C. Cambillau. 1994. Cutinase, a lipolytic enzyme with a preformed oxyanion hole. Biochemistry. 33:83-89.
-
(1994)
Biochemistry
, vol.33
, pp. 83-89
-
-
Martinez, C.1
Nicholas, A.2
Van Tilbeurgh, H.3
Egloff, M.P.4
Cudrey, C.5
Verger, R.6
Cambillau, C.7
-
29
-
-
0030041250
-
Contribution of cutinase serine 42 side-chain to the stabilization of the oxyanion transition state
-
Nicolas, A., M. Egmond, C. T. Verips, J. de Vlieg, S. Longhi, C. Cambillau, and C. Martinez. 1996. Contribution of cutinase serine 42 side-chain to the stabilization of the oxyanion transition state. Biochemistry. 35:398-410.
-
(1996)
Biochemistry
, vol.35
, pp. 398-410
-
-
Nicolas, A.1
Egmond, M.2
Verips, C.T.3
De Vlieg, J.4
Longhi, S.5
Cambillau, C.6
Martinez, C.7
-
30
-
-
0029939820
-
Effects of point mutants at the flexible loop glycine-67 of Escherichia coli dihydrofolate reductase on its stability and function
-
Ohmae, E., K. Iriyama, S. Ichihara, and K. Gekko. 1996. Effects of point mutants at the flexible loop glycine-67 of Escherichia coli dihydrofolate reductase on its stability and function. J. Biochem. 119:703-710.
-
(1996)
J. Biochem.
, vol.119
, pp. 703-710
-
-
Ohmae, E.1
Iriyama, K.2
Ichihara, S.3
Gekko, K.4
-
31
-
-
0029562951
-
Molecular dynamics simulation of E. coli ribonuclease H1 in solution: Correlation with NMR and x-ray data and insights into biological function
-
Philippopoulos, M., and C. Lim. 1995. Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and x-ray data and insights into biological function. J. Mol. Biol. 254:771-792.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 771-792
-
-
Philippopoulos, M.1
Lim, C.2
-
33
-
-
0032558938
-
His-Asp catalytic dyad of ribonuclease A: Conformational stability of the wild-type, D121N, D121A, and H119A enzymes
-
Quirk, D. J., C. Park, J. E. Thompson, and R. T. Raines. 1998. His-Asp catalytic dyad of ribonuclease A: conformational stability of the wild-type, D121N, D121A, and H119A enzymes. Biochemistry. 37: 17958-17964.
-
(1998)
Biochemistry
, vol.37
, pp. 17958-17964
-
-
Quirk, D.J.1
Park, C.2
Thompson, J.E.3
Raines, R.T.4
-
34
-
-
0016395451
-
Synthesis and evaluation of a model for the so-called "charge-relay" system of the serine esterase
-
Rogers, G. A., and T. C. Bruice. 1974. Synthesis and evaluation of a model for the so-called "charge-relay" system of the serine esterase. J. Am. Chem. Soc. 96:2473-2481.
-
(1974)
J. Am. Chem. Soc.
, vol.96
, pp. 2473-2481
-
-
Rogers, G.A.1
Bruice, T.C.2
-
35
-
-
0032567157
-
Characterization of the short strong hydrogen bond in benzoylacetone by Ab initio calculations and accurate diffraction experiments. Implications for the electronic nature of low-barrier hydrogen bonds in enzymatic reactions
-
Schiott, B., B. B. Iversen, G. K. Hellerup Madsen, and T. C. Bruice. 1998. Characterization of the short strong hydrogen bond in benzoylacetone by Ab initio calculations and accurate diffraction experiments. Implications for the electronic nature of low-barrier hydrogen bonds in enzymatic reactions. J. Am. Chem. Soc. 120:12117-12124.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 12117-12124
-
-
Schiott, B.1
Iversen, B.B.2
Hellerup Madsen, G.K.3
Bruice, T.C.4
-
36
-
-
0030874881
-
Upases and α/β hydrolase fold
-
Schrag, J. D., and M. Cygler. 1997. Upases and α/β hydrolase fold. Methods Enzymol. 284:85-107.
-
(1997)
Methods Enzymol.
, vol.284
, pp. 85-107
-
-
Schrag, J.D.1
Cygler, M.2
-
37
-
-
0020020315
-
Crystallographic and NMR studies of the serine proteases
-
Steitz, T. A., and R. G. Shulman. 1982. Crystallographic and NMR studies of the serine proteases. Annu. Rev. Biophys. Bioeng. 11:419-444.
-
(1982)
Annu. Rev. Biophys. Bioeng.
, vol.11
, pp. 419-444
-
-
Steitz, T.A.1
Shulman, R.G.2
-
38
-
-
0000118827
-
Harmonic and quasiharmonic descriptions of crambin
-
Teeter, M. M., and D. A. Case. 1990. Harmonic and quasiharmonic descriptions of crambin. J. Phys. Chem. 94:8091-8097.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8091-8097
-
-
Teeter, M.M.1
Case, D.A.2
-
39
-
-
22944467757
-
Computer experiments on classical fluids
-
Verlet, L. 1967. Computer experiments on classical fluids. Phys. Rev. 159:98-113.
-
(1967)
Phys. Rev.
, vol.159
, pp. 98-113
-
-
Verlet, L.1
-
40
-
-
0031557394
-
Domain motions in dihydrofolate reductase: A molecular dynamics study
-
Verma, C. S., L. S. D. Caves, R. E. Hubbard, and G. C. K. Roberts. 1997. Domain motions in dihydrofolate reductase: a molecular dynamics study. J. Mol. Biol. 266:776-796.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 776-796
-
-
Verma, C.S.1
Caves, L.S.D.2
Hubbard, R.E.3
Roberts, G.C.K.4
-
42
-
-
0032538627
-
Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites
-
Warshel, A. 1998. Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites. J. Biol. Chem. 273: 27035-27038.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 27035-27038
-
-
Warshel, A.1
-
43
-
-
0032568612
-
Computer simulations of enzyme catalysis: Finding out what has been optimized by nature
-
Warshel, A., and J. Florian. 1998. Computer simulations of enzyme catalysis: finding out what has been optimized by nature. Proc. Natl. Acad. Sci. USA. 95:5950-5955.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 5950-5955
-
-
Warshel, A.1
Florian, J.2
-
44
-
-
0024538543
-
How do serine proteases really work?
-
Warshel, A., G. Naray-Szabo, F. Sussman, and J.-K. Hwang. 1989. How do serine proteases really work? Biochemistry. 28:3629-3637.
-
(1989)
Biochemistry
, vol.28
, pp. 3629-3637
-
-
Warshel, A.1
Naray-Szabo, G.2
Sussman, F.3
Hwang, J.-K.4
-
45
-
-
0030462453
-
Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds
-
Warshel, A., and A. Papazyan. 1996. Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds. Proc. Natl. Acad. Sci. USA. 93:13665-13670.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 13665-13670
-
-
Warshel, A.1
Papazyan, A.2
-
46
-
-
0029040169
-
On low-barrier hydrogen bonds and enzyme catalysis
-
Warshel, A., A. Papazyan, and P. A. Kollman. 1995. On low-barrier hydrogen bonds and enzyme catalysis. Science. 269:102-104.
-
(1995)
Science
, vol.269
, pp. 102-104
-
-
Warshel, A.1
Papazyan, A.2
Kollman, P.A.3
-
47
-
-
0024278562
-
Evaluation of catalytic free energies in genetically modified proteins
-
Warshel, A., F. Sussman, and J.-K. Hwang. 1988. Evaluation of catalytic free energies in genetically modified proteins. J. Mol. Biol. 201: 139-159.
-
(1988)
J. Mol. Biol.
, vol.201
, pp. 139-159
-
-
Warshel, A.1
Sussman, F.2
Hwang, J.-K.3
-
48
-
-
0000453071
-
Importance of hydrogen-bond formation in stabilizing the transition state of subtilisin
-
Wells, J. A., B. C. Cunningham, T. P. Graycar, and D. A. Estell. 1986. Importance of hydrogen-bond formation in stabilizing the transition state of subtilisin. Philos. Trans. R. Soc. Lond. A. 317:415-423.
-
(1986)
Philos. Trans. R. Soc. Lond. A.
, vol.317
, pp. 415-423
-
-
Wells, J.A.1
Cunningham, B.C.2
Graycar, T.P.3
Estell, D.A.4
|