-
1
-
-
0025290527
-
The structure and function of the aspartic proteinases
-
Davies, D. R. (1990) The structure and function of the aspartic proteinases, Annu. Rev. Biophys. Biophys. Chem. 19, 189-215.
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 189-215
-
-
Davies, D.R.1
-
3
-
-
0036882390
-
Structure and mechanism of the pepsin-like family of aspartic peptidases
-
Dunn, B. M. (2002) Structure and mechanism of the pepsin-like family of aspartic peptidases, Chem. Rev. 102, 4431-4458.
-
(2002)
Chem. Rev.
, vol.102
, pp. 4431-4458
-
-
Dunn, B.M.1
-
4
-
-
0021767550
-
The active site of aspartic proteinases
-
Pearl, L., and Blundell, T. (1984) The active site of aspartic proteinases, FEBS Lett. 174, 96-101.
-
(1984)
FEBS Lett.
, vol.174
, pp. 96-101
-
-
Pearl, L.1
Blundell, T.2
-
5
-
-
0023434194
-
Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: Implications for a mechanism of action
-
Suguna, K., Padlan, E. A., Smith, C. W., Carlson, W. D., and Davies, D. R. (1987) Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: Implications for a mechanism of action, Proc. Natl. Acad. Sci. U.S.A. 84, 7009-7013.
-
(1987)
Proc. Natl. Acad. Sci. U.S.A.
, vol.84
, pp. 7009-7013
-
-
Suguna, K.1
Padlan, E.A.2
Smith, C.W.3
Carlson, W.D.4
Davies, D.R.5
-
6
-
-
0027525478
-
Use of nitrogen-15 kinetic isotope efects to elucidate details of the chemical mechanism of human imunodeficiency virus-1 potease
-
Rodriguez, E. J., Angeles, T. S., and Meek, T. D. (1993) Use of nitrogen-15 kinetic isotope efects to elucidate details of the chemical mechanism of human imunodeficiency virus-1 potease, Biochemistry 32, 12380-12385.
-
(1993)
Biochemistry
, vol.32
, pp. 12380-12385
-
-
Rodriguez, E.J.1
Angeles, T.S.2
Meek, T.D.3
-
7
-
-
0028717766
-
Use of steady-state kinetic methods to elucidate the kinetic and chemical mechanisms of retroviral proteases
-
Meek, T. D., Rodriguez, E. J., and Angeles, T. S. (1994) Use of Steady-State Kinetic Methods to Elucidate the Kinetic and Chemical Mechanisms of Retroviral Proteases, Methods Enzymol. 241, 127-156.
-
(1994)
Methods Enzymol.
, vol.241
, pp. 127-156
-
-
Meek, T.D.1
Rodriguez, E.J.2
Angeles, T.S.3
-
9
-
-
0001739103
-
Hydration of carboxamides. Evaluation of the free energy change for addition of water to acetamide and formamide derivatives
-
Guthrie, J. P. (1974) Hydration of carboxamides. Evaluation of the free energy change for addition of water to acetamide and formamide derivatives, J. Am. Chem. Soc. 96, 3608-3615.
-
(1974)
J. Am. Chem. Soc.
, vol.96
, pp. 3608-3615
-
-
Guthrie, J.P.1
-
10
-
-
37049068464
-
Thermodynamics of protonation and hydration of aliphatic amides
-
Bagno, A., Lovato, G., and Scorrano, G. (1993) Thermodynamics of protonation and hydration of aliphatic amides, J. Chem. Soc., Perkin Trans. 2, 1091-1098.
-
(1993)
J. Chem. Soc., Perkin Trans.
, vol.2
, pp. 1091-1098
-
-
Bagno, A.1
Lovato, G.2
Scorrano, G.3
-
11
-
-
0027050188
-
Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases
-
Veerapandian, B., Cooper, J. B., Sali, A., Blundell, T. L., Rosati, R. L., Dominy, B. W., Damon, D. B., and Hoover, D. J. (1992) Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases, Protein Sci. 1, 322-328.
-
(1992)
Protein Sci.
, vol.1
, pp. 322-328
-
-
Veerapandian, B.1
Cooper, J.B.2
Sali, A.3
Blundell, T.L.4
Rosati, R.L.5
Dominy, B.W.6
Damon, D.B.7
Hoover, D.J.8
-
12
-
-
0026720426
-
Crystallographic analysis of transition-state mimics bound to penicillopepsin: Difluorostatine- and difluorostatone-containing peptides
-
James, M. N. G., Sielecki, A. R., Hayakawa, K., and Gelb, M. H. (1992) Crystallographic analysis of transition-state mimics bound to penicillopepsin: Difluorostatine- and difluorostatone-containing peptides, Biochemistry 31, 3872-3886.
-
(1992)
Biochemistry
, vol.31
, pp. 3872-3886
-
-
James, M.N.G.1
Sielecki, A.R.2
Hayakawa, K.3
Gelb, M.H.4
-
13
-
-
0034778987
-
Follow the protons: A low-barrier hydrogen bond unifies the mechanisms of the aspartic proteases
-
Northrop, D. B. (2001) Follow the protons: A low-barrier hydrogen bond unifies the mechanisms of the aspartic proteases, Acc. Chem. Res. 34, 790-797.
-
(2001)
Acc. Chem. Res.
, vol.34
, pp. 790-797
-
-
Northrop, D.B.1
-
15
-
-
4243810035
-
Simulation of enzyme-reactions using valence-bond force-fields and other hybrid quantum-classical approaches
-
Åqvist, J., and Warshel, A. (1993) Simulation of enzyme-reactions using valence-bond force-fields and other hybrid quantum-classical approaches, Chem. Rev. 93, 2523-2544.
-
(1993)
Chem. Rev.
, vol.93
, pp. 2523-2544
-
-
Åqvist, J.1
Warshel, A.2
-
16
-
-
0024406911
-
Complete mutagenesis of the HIV-1 protease
-
Loeb, D. D., Swanstrom, R., Everitt, L., Manchester, M., Stamper, S. E., and Hutchison, C. A., III (1989) Complete mutagenesis of the HIV-1 protease, Nature 340, 397-400.
-
(1989)
Nature
, vol.340
, pp. 397-400
-
-
Loeb, D.D.1
Swanstrom, R.2
Everitt, L.3
Manchester, M.4
Stamper, S.E.5
Hutchison III, C.A.6
-
17
-
-
0037154180
-
Four plasmepsins are active in the Plasmodium falciparum food vacuole, including a protease with an active-site histidine
-
Banerjee, R., Liu, J., Beatty, W., Pelosof, L., Klemba, M., and Goldberg, D. E. (2002) Four plasmepsins are active in the Plasmodium falciparum food vacuole, including a protease with an active-site histidine, Proc. Natl. Acad. Sci. U.S.A. 99, 990-995.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 990-995
-
-
Banerjee, R.1
Liu, J.2
Beatty, W.3
Pelosof, L.4
Klemba, M.5
Goldberg, D.E.6
-
18
-
-
9144243695
-
Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity
-
Ersmark, K., Feierberg, I., Bjelic, S., Hamelink, E., Hackett, F., Blackman, M. J., Hulten, J., Samuelsson, B., Åqvist, J., and Hallberg, A. (2004) Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity, J. Med. Chem. 47, 110-122.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 110-122
-
-
Ersmark, K.1
Feierberg, I.2
Bjelic, S.3
Hamelink, E.4
Hackett, F.5
Blackman, M.J.6
Hulten, J.7
Samuelsson, B.8
Åqvist, J.9
Hallberg, A.10
-
19
-
-
24944590349
-
Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulations
-
Ersmark, K., Nervall, M., Hamelink, E., Janka, L. K., Clemente, J. C., Dunn, B. M., Blackman, M. J., Samuelsson, B., Aqvist, J., and Hallberg, A. (2005) Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulations, J. Med. Chem. 48, 6090-6106.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 6090-6106
-
-
Ersmark, K.1
Nervall, M.2
Hamelink, E.3
Janka, L.K.4
Clemente, J.C.5
Dunn, B.M.6
Blackman, M.J.7
Samuelsson, B.8
Aqvist, J.9
Hallberg, A.10
-
20
-
-
0005241362
-
Active human immunodeficiency virus protease is required for viral infectivity
-
Kohl, N. E., Emini, E. A., Schleif, W. A., Davis, L. J., Heimbach, J. C., Dixon, R. A. F., Scolnick, E. M., and Sigal, I. S. (1988) Active human immunodeficiency virus protease is required for viral infectivity, Proc. Natl. Acad. Sci. U.S.A. 85, 4686-4690.
-
(1988)
Proc. Natl. Acad. Sci. U.S.A.
, vol.85
, pp. 4686-4690
-
-
Kohl, N.E.1
Emini, E.A.2
Schleif, W.A.3
Davis, L.J.4
Heimbach, J.C.5
Dixon, R.A.F.6
Scolnick, E.M.7
Sigal, I.S.8
-
21
-
-
0038184354
-
HIV-1 protease: Mechanism and drug discovery
-
Brik, A., and Wong, C. H. (2003) HIV-1 protease: Mechanism and drug discovery, Org. Biomol. Chem. 1, 5-14.
-
(2003)
Org. Biomol. Chem.
, vol.1
, pp. 5-14
-
-
Brik, A.1
Wong, C.H.2
-
22
-
-
0034616816
-
Ab initio evaluation of the potential surface for general base-catalyzed methanolysis of formamide: A reference solution reaction for studies of serine proteases
-
Strajbl, M., Florian, J., and Warshel, A. (2000) Ab initio evaluation of the potential surface for general base-catalyzed methanolysis of formamide: A reference solution reaction for studies of serine proteases, J. Am. Chem. Soc. 122, 5354-5366.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 5354-5366
-
-
Strajbl, M.1
Florian, J.2
Warshel, A.3
-
23
-
-
8744303696
-
Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site
-
Bjelic, S., and Aqvist, J. (2004) Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site, Biochemistry 43, 14521-14528.
-
(2004)
Biochemistry
, vol.43
, pp. 14521-14528
-
-
Bjelic, S.1
Aqvist, J.2
-
24
-
-
0141732211
-
Theoretical perspectives on the reaction mechanism of serine proteases: The reaction free energy profiles of the acylation process
-
Ishida, T., and Kato, S. (2003) Theoretical perspectives on the reaction mechanism of serine proteases: The reaction free energy profiles of the acylation process, J. Am. Chem. Soc. 125, 12035-12048.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 12035-12048
-
-
Ishida, T.1
Kato, S.2
-
25
-
-
0001333594
-
Nitrogen kinetic isotope effects on the acylation of aniline
-
Kaminski, Z. J., Paneth, P., and Oleary, M. H. (1991) Nitrogen kinetic isotope effects on the acylation of aniline, J. Org. Chem. 56, 5716-5718.
-
(1991)
J. Org. Chem.
, vol.56
, pp. 5716-5718
-
-
Kaminski, Z.J.1
Paneth, P.2
Oleary, M.H.3
-
27
-
-
33845280024
-
The aminolysis of methyl formate with aniline: Evidence for catalysis by a trapping mechanism
-
Yang, C. C., and Jencks, W. P. (1988) The aminolysis of methyl formate with aniline: Evidence for catalysis by a trapping mechanism, J. Am. Chem. Soc. 110, 2972-2973.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 2972-2973
-
-
Yang, C.C.1
Jencks, W.P.2
-
28
-
-
0026005186
-
Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism
-
Hyland, L. J., Tomaszek, T. A., and Meek, T. D. (1991) Human immunodeficiency virus-1 protease. 2. Use of pH rate studies and solvent kinetic isotope effects to elucidate details of chemical mechanism, Biochemistry 30, 8454-8463.
-
(1991)
Biochemistry
, vol.30
, pp. 8454-8463
-
-
Hyland, L.J.1
Tomaszek, T.A.2
Meek, T.D.3
-
29
-
-
0025991290
-
18O isotope exchange
-
18O isotope exchange, Biochemistry 30, 8441-8453.
-
(1991)
Biochemistry
, vol.30
, pp. 8441-8453
-
-
Hyland, L.J.1
Tomaszek, T.A.2
Roberts, G.D.3
Carr, S.A.4
Magaard, V.W.5
Bryan, H.L.6
Fakhoury, S.A.7
Moore, M.L.8
Minnich, M.D.9
Culp, J.S.10
Desjarlais, R.L.11
Meek, T.D.12
-
30
-
-
15744387343
-
Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases
-
Cascella, M., Micheletti, C., Rothlisberger, U., and Carloni, P. (2005) Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases, J. Am. Chem. Soc. 127, 3734-3742.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 3734-3742
-
-
Cascella, M.1
Micheletti, C.2
Rothlisberger, U.3
Carloni, P.4
-
31
-
-
0346225118
-
HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential
-
Chatfield, D. C., Eurenius, K. P., and Brooks, B. R. (1998) HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential, THEOCHEM 423, 79-92.
-
(1998)
Theochem
, vol.423
, pp. 79-92
-
-
Chatfield, D.C.1
Eurenius, K.P.2
Brooks, B.R.3
-
32
-
-
4043082181
-
Reaction mechanism of HIV-1 protease by hybrid Car-Parrinello/classical MD simulations
-
Piana, S., Bucher, D., Carloni, P., and Rothlisberger, U. (2004) Reaction mechanism of HIV-1 protease by hybrid Car-Parrinello/classical MD simulations, J. Phys. Chem. B 108, 11139-11149.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 11139-11149
-
-
Piana, S.1
Bucher, D.2
Carloni, P.3
Rothlisberger, U.4
-
33
-
-
1642452881
-
The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease
-
Trylska, J., Grochowski, P., and McCammon, J. A. (2004) The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease, Protein Sci. 13, 513-528.
-
(2004)
Protein Sci.
, vol.13
, pp. 513-528
-
-
Trylska, J.1
Grochowski, P.2
McCammon, J.A.3
-
34
-
-
0031799176
-
Computer simulation of phenyl ester cleavage by β-cyclodextrin in solution
-
Luzhkov, V., and Åqvist, J. (1998) Computer simulation of phenyl ester cleavage by β-cyclodextrin in solution, J. Am. Chem. Soc. 120, 6131-6137.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 6131-6137
-
-
Luzhkov, V.1
Åqvist, J.2
-
35
-
-
36849122972
-
High-temperature equation of state by a perturbation method. I. Nonpolar gases
-
Zwanzig, R. W. (1954) High-temperature equation of state by a perturbation method. I. Nonpolar gases, J. Chem. Phys. 22, 1420-1426.
-
(1954)
J. Chem. Phys.
, vol.22
, pp. 1420-1426
-
-
Zwanzig, R.W.1
-
36
-
-
0001957353
-
Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Part I: Elementary processes
-
Eigen, M. (1964) Proton transfer, acid-base catalysis, and enzymatic hydrolysis. Part I: Elementary processes, Angew. Chem., Int. Ed. 3, 1-72.
-
(1964)
Angew. Chem., Int. Ed.
, vol.3
, pp. 1-72
-
-
Eigen, M.1
-
37
-
-
0028903042
-
β-secondary and solvent deuterium kinetic isotope effects and the mechanisms of base-catalyzed and acid-catalyzed hydrolysis of penicillanic acid
-
Deraniyagala, S. A., Adediran, S. A., and Pratt, R. F. (1995) β-Secondary and solvent deuterium kinetic isotope effects and the mechanisms of base-catalyzed and acid-catalyzed hydrolysis of penicillanic acid, J. Org. Chem. 60, 1619-1625.
-
(1995)
J. Org. Chem.
, vol.60
, pp. 1619-1625
-
-
Deraniyagala, S.A.1
Adediran, S.A.2
Pratt, R.F.3
-
38
-
-
0001104686
-
Modelling of proton-transfer reactions in enzymes
-
(Náray-Szabó, G., and Warshel, A., Eds.), Kluwer Academic Publishers, Dordrecht, The Netherlands
-
Åqvist, J. (1997) Modelling of proton-transfer reactions in enzymes, in Computational approaches to biochemical reactivity (Náray-Szabó, G., and Warshel, A., Eds.) pp 341-362, Kluwer Academic Publishers, Dordrecht, The Netherlands.
-
(1997)
Computational Approaches to Biochemical Reactivity
, pp. 341-362
-
-
Åqvist, J.1
-
39
-
-
0037442916
-
Proton inventory study of the base-catalyzed hydrolysis of formamide. Consideration of the nucleophilic and general base mechanisms
-
Slebocka-Tilk, H., Neverov, A. A., and Brown, R. S. (2003) Proton inventory study of the base-catalyzed hydrolysis of formamide. Consideration of the nucleophilic and general base mechanisms, J. Am. Chem. Soc. 125, 1851-1858.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 1851-1858
-
-
Slebocka-Tilk, H.1
Neverov, A.A.2
Brown, R.S.3
-
40
-
-
0036900890
-
Structures of Ser205 mutant plasmepsin II from Plasmodium falciparum at 1.8 angstrom in complex with the inhibitors rs367 and rs370
-
Asojo, O. A., Afonina, E., Gulnik, S. V., Yu, B., Erickson, J. W., Randad, R., Medjahed, D., and Silva, A. M. (2002) Structures of Ser205 mutant plasmepsin II from Plasmodium falciparum at 1.8 angstrom in complex with the inhibitors rs367 and rs370, Acta Crystallogr. D58, 2001-2008.
-
(2002)
Acta Crystallogr.
, vol.D58
, pp. 2001-2008
-
-
Asojo, O.A.1
Afonina, E.2
Gulnik, S.V.3
Yu, B.4
Erickson, J.W.5
Randad, R.6
Medjahed, D.7
Silva, A.M.8
-
41
-
-
0027165319
-
Crystal structures of native and inhibited forms of human cathepsin D: Implications for lysosomal targeting and drug design
-
Baldwin, E. T., Bhat, T. N., Gulnik, S., Hosur, M. V., Sowder, R. C., Cachau, R. E., Collins, J., Silva, A. M., and Erickson, J. W. (1993) Crystal structures of native and inhibited forms of human cathepsin D: Implications for lysosomal targeting and drug design, Proc. Natl. Acad. Sci. U.S.A. 90, 6796-6800.
-
(1993)
Proc. Natl. Acad. Sci. U.S.A.
, vol.90
, pp. 6796-6800
-
-
Baldwin, E.T.1
Bhat, T.N.2
Gulnik, S.3
Hosur, M.V.4
Sowder, R.C.5
Cachau, R.E.6
Collins, J.7
Silva, A.M.8
Erickson, J.W.9
-
42
-
-
0024344021
-
Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 Å resolution
-
Miller, M., Schneider, J., Sathyanarayana, B. K., Toth, M. V., Marshall, G. R., Clawson, L., Selk, L., Kent, S. B. H., and Wlodawer, A. (1989) Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 Å resolution, Science 246, 1149-1152.
-
(1989)
Science
, vol.246
, pp. 1149-1152
-
-
Miller, M.1
Schneider, J.2
Sathyanarayana, B.K.3
Toth, M.V.4
Marshall, G.R.5
Clawson, L.6
Selk, L.7
Kent, S.B.H.8
Wlodawer, A.9
-
43
-
-
0027309442
-
Inhibitor binding to the Phe53Trp mutant of HIV-1 protease promotes conformational changes detectable by spectrofluorometry
-
Rodriguez, E. J., Debouck, C., Deckman, I. C., Abusoud, H., Raushel, F. M., and Meek, T. D. (1993) Inhibitor binding to the Phe53Trp mutant of HIV-1 protease promotes conformational changes detectable by spectrofluorometry, Biochemistry 32, 3557-3563.
-
(1993)
Biochemistry
, vol.32
, pp. 3557-3563
-
-
Rodriguez, E.J.1
Debouck, C.2
Deckman, I.C.3
Abusoud, H.4
Raushel, F.M.5
Meek, T.D.6
-
44
-
-
0001351236
-
Effect of substrate residues on the P2′ preference of retroviral proteinases
-
Boross, P., Bagossi, P., Copeland, T. D., Oroszlan, S., Louis, J. M., and Tozser, J. (1999) Effect of substrate residues on the P2′ preference of retroviral proteinases, Eur. J. Biochem. 264, 921-929.
-
(1999)
Eur. J. Biochem.
, vol.264
, pp. 921-929
-
-
Boross, P.1
Bagossi, P.2
Copeland, T.D.3
Oroszlan, S.4
Louis, J.M.5
Tozser, J.6
-
45
-
-
0035846971
-
Substrate specificity of human cathepsin D using internally quenched fluorescent peptides derived from reactive site loop of kallistatin
-
Pimenta, D. C., Oliveira, A., Juliano, M. A., and Juliano, L. (2001) Substrate specificity of human cathepsin D using internally quenched fluorescent peptides derived from reactive site loop of kallistatin, Biochim. Biophys. Acta 1544, 113-122.
-
(2001)
Biochim. Biophys. Acta
, vol.1544
, pp. 113-122
-
-
Pimenta, D.C.1
Oliveira, A.2
Juliano, M.A.3
Juliano, L.4
-
46
-
-
14844302643
-
Distal substrate interactions enhance plasmepsin activity
-
Istvan, E. S., and Goldberg, D. E. (2005) Distal substrate interactions enhance plasmepsin activity, J. Biol. Chem. 280, 6890-6896.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 6890-6896
-
-
Istvan, E.S.1
Goldberg, D.E.2
-
47
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L., Chandrasekhar, J., and Madura, J. D. (1983) Comparison of simple potential functions for simulating liquid 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
-
48
-
-
0032232405
-
Q: A molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems
-
Marelius, J., Kolmodin, K., Feierberg, I., and Åqvist, J. (1998) Q: A molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems, J. Mol. Graphics 16, 213-225.
-
(1998)
J. Mol. Graphics
, vol.16
, pp. 213-225
-
-
Marelius, J.1
Kolmodin, K.2
Feierberg, I.3
Åqvist, J.4
-
49
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen, W. L., Maxwell, D. S., and TiradoRives, J. (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids, J. Am. Chem. Soc. 118, 11225-11236.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tiradorives, J.3
-
50
-
-
0000115003
-
A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
-
Lee, F. S., and Warshel, A. (1992) A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations, J. Chem. Phys. 97, 3100-3107.
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 3100-3107
-
-
Lee, F.S.1
Warshel, A.2
-
51
-
-
36549094414
-
A surface constrained all-atom solvent model for effective simulations of polar solutions
-
King, G., and Warshel, A. (1989) A surface constrained all-atom solvent model for effective simulations of polar solutions, J. Chem. Phys. 91, 3647-3661.
-
(1989)
J. Chem. Phys.
, vol.91
, pp. 3647-3661
-
-
King, G.1
Warshel, A.2
-
52
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes, J. Comput. Phys. 23, 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
53
-
-
0037175033
-
Active site contribution to specificity of the aspartic proteases plasmepsins I and II
-
Siripurkpong, P., Yuvaniyama, J., Wilairat, P., and Goldberg, D. E. (2002) Active site contribution to specificity of the aspartic proteases plasmepsins I and II, J. Biol. Chem. 277, 41009-41013.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 41009-41013
-
-
Siripurkpong, P.1
Yuvaniyama, J.2
Wilairat, P.3
Goldberg, D.E.4
-
54
-
-
0036025574
-
Computational modeling of enzymatic keto-enol isomerization reactions
-
Feierberg, I., and Åqvist, J. (2002) Computational modeling of enzymatic keto-enol isomerization reactions, Theor. Chem. Acc. 108, 71-84.
-
(2002)
Theor. Chem. Acc.
, vol.108
, pp. 71-84
-
-
Feierberg, I.1
Åqvist, J.2
-
55
-
-
0023191215
-
On the rational design of renin inhibitors: X-ray studies of aspartic proteinases complexed with transition-state analogues
-
Blundell, T. L., Cooper, J., Foundling, S. I., Jones, D. M., Atrash, B., and Szelke, M. (1987) On the rational design of renin inhibitors: X-ray studies of aspartic proteinases complexed with transition-state analogues, Biochemistry 26, 5585-5590.
-
(1987)
Biochemistry
, vol.26
, pp. 5585-5590
-
-
Blundell, T.L.1
Cooper, J.2
Foundling, S.I.3
Jones, D.M.4
Atrash, B.5
Szelke, M.6
-
56
-
-
0026770573
-
Crystallographic analysis of transitionstate mimics bound to penicillopepsin: Phosphorus-containing peptide analogs
-
Fraser, M. E., Strynadka, N. C. J., Bartlett, P. A., Hanson, J. E., and James, M. N. G. (1992) Crystallographic analysis of transitionstate mimics bound to penicillopepsin: Phosphorus-containing peptide analogs, Biochemistry 31, 5201-5214.
-
(1992)
Biochemistry
, vol.31
, pp. 5201-5214
-
-
Fraser, M.E.1
Strynadka, N.C.J.2
Bartlett, P.A.3
Hanson, J.E.4
James, M.N.G.5
-
57
-
-
0036311072
-
Five atomic resolution structures of endothiapepsin inhibitor complexes: Implications for the aspartic proteinase mechanism
-
Coates, L., Erskine, P. T., Crump, M. P., Wood, S. P., and Cooper, J. B. (2002) Five atomic resolution structures of endothiapepsin inhibitor complexes: Implications for the aspartic proteinase mechanism, J. Mol. Biol. 318, 1405-1415.
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 1405-1415
-
-
Coates, L.1
Erskine, P.T.2
Crump, M.P.3
Wood, S.P.4
Cooper, J.B.5
-
58
-
-
0029859529
-
Ionization states of the catalytic residues in HIV-1 protease
-
Smith, R., Brereton, I. M., Chai, R. Y., and Kent, S. B. H. (1996) Ionization states of the catalytic residues in HIV-1 protease, Nat. Struct. Biol. 3, 946-950.
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 946-950
-
-
Smith, R.1
Brereton, I.M.2
Chai, R.Y.3
Kent, S.B.H.4
-
59
-
-
0037192144
-
HIV-1 protease: Characterization of a catalytically competent enzyme-substrate intermediate
-
Porter, D. J. T., Hanlon, M. H., and Furfine, E. S. (2002) HIV-1 protease: Characterization of a catalytically competent enzyme-substrate intermediate, Biochemistry 41, 1302-1307.
-
(2002)
Biochemistry
, vol.41
, pp. 1302-1307
-
-
Porter, D.J.T.1
Hanlon, M.H.2
Furfine, E.S.3
-
60
-
-
36849137629
-
Calculation of equilibrium constants for isotopic exchange reactions
-
Bigeleisen, J., and Mayer, M. G. (1947) Calculation of equilibrium constants for isotopic exchange reactions, J. Chem. Phys. 15, 261-267.
-
(1947)
J. Chem. Phys.
, vol.15
, pp. 261-267
-
-
Bigeleisen, J.1
Mayer, M.G.2
-
61
-
-
0034731015
-
H-Bonding in alcohols is reflected in the Cα-H bond strength: Variation of C-D vibrational frequency and fractionation factor
-
Gawlita, E., Lantz, M., Paneth, P., Bell, A. P., Tonge, P. J., and Anderson, V. E. (2000) H-Bonding in alcohols is reflected in the Cα-H bond strength: Variation of C-D vibrational frequency and fractionation factor, J. Am. Chem. Soc. 122, 11660-11669.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 11660-11669
-
-
Gawlita, E.1
Lantz, M.2
Paneth, P.3
Bell, A.P.4
Tonge, P.J.5
Anderson, V.E.6
-
62
-
-
0037189906
-
Computational study of the influence of solvent on O-16/O-18 equilibrium isotope effects in phosphate deprotonation reactions
-
Kolmodin, K., Luzhkov, V. B., and Åqvist, J. (2002) Computational study of the influence of solvent on O-16/O-18 equilibrium isotope effects in phosphate deprotonation reactions, J. Am. Chem. Soc. 124, 10130-10135.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 10130-10135
-
-
Kolmodin, K.1
Luzhkov, V.B.2
Åqvist, J.3
-
63
-
-
0032972250
-
The role of the flap residue, threonine 77, in the activation and catalytic activity of pepsin A
-
Okoniewska, M., Tanaka, T., and Yada, R. Y. (1999) The role of the flap residue, threonine 77, in the activation and catalytic activity of pepsin A, Protein Eng. 12, 55-61.
-
(1999)
Protein Eng.
, vol.12
, pp. 55-61
-
-
Okoniewska, M.1
Tanaka, T.2
Yada, R.Y.3
-
64
-
-
0028807052
-
Crystallographic studies on the binding modes of P-2-P-3 butanediamide renin inhibitors
-
Tong, L. A., Pav, S., Lamarre, D., Simoneau, B., Lavallee, P., and Jung, G. (1995) Crystallographic studies on the binding modes of P-2-P-3 butanediamide renin inhibitors, J. Biol. Chem. 270, 29520-29524.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 29520-29524
-
-
Tong, L.A.1
Pav, S.2
Lamarre, D.3
Simoneau, B.4
Lavallee, P.5
Jung, G.6
-
65
-
-
0035188306
-
Analysis of crystal structures of aspartic proteinases: On the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes
-
Andreeva, N. S., and Rumsh, L. D. (2001) Analysis of crystal structures of aspartic proteinases: On the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes, Protein Sci. 10, 2439-2450.
-
(2001)
Protein Sci.
, vol.10
, pp. 2439-2450
-
-
Andreeva, N.S.1
Rumsh, L.D.2
-
66
-
-
0030879653
-
Hemoglobin metabolism in the malaria parasite Plasmodium falciparum
-
Francis, S. E., Sullivan, D. J., and Goldberg, D. E. (1997) Hemoglobin metabolism in the malaria parasite Plasmodium falciparum, Annu. Rev. Microbiol. 51, 97-123.
-
(1997)
Annu. Rev. Microbiol.
, vol.51
, pp. 97-123
-
-
Francis, S.E.1
Sullivan, D.J.2
Goldberg, D.E.3
-
67
-
-
0015975955
-
Purification and properties of cathepsin D from human erythrocytes
-
Reichelt, D., Jacobsohn, E., and Haschen, R. J. (1974) Purification and properties of cathepsin D from human erythrocytes, Biochim. Biophys. Acta 341, 15-26.
-
(1974)
Biochim. Biophys. Acta
, vol.341
, pp. 15-26
-
-
Reichelt, D.1
Jacobsohn, E.2
Haschen, R.J.3
-
68
-
-
0035370444
-
Structural implications of drug-resistant mutants of HIV-1 protease: High-resolution crystal structures of the mutant protease/substrate analogue complexes
-
Mahalingam, B., Louis, J. M., Hung, J., Harrison, R. W., and Weber, I. T. (2001) Structural implications of drug-resistant mutants of HIV-1 protease: High-resolution crystal structures of the mutant protease/substrate analogue complexes, Proteins 43, 455-464.
-
(2001)
Proteins
, vol.43
, pp. 455-464
-
-
Mahalingam, B.1
Louis, J.M.2
Hung, J.3
Harrison, R.W.4
Weber, I.T.5
-
69
-
-
0033597637
-
Theoretical study of base-catalyzed amide hydrolysis: Gas- and aqueous-phase hydrolysis of formamide
-
Bakowies, D., and Kollman, P. A. (1999) Theoretical study of base-catalyzed amide hydrolysis: Gas- and aqueous-phase hydrolysis of formamide, J. Am. Chem. Soc. 121, 5712-5726.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 5712-5726
-
-
Bakowies, D.1
Kollman, P.A.2
-
70
-
-
0020173901
-
Electronic distributions within protein phenylalanine aromatic rings are reflected by three-dimensional oxygen atom environments
-
Thomas, K. A., Smith, G. M., Thomas, T. B., and Feldmann, R. J. (1982) Electronic distributions within protein phenylalanine aromatic rings are reflected by three-dimensional oxygen atom environments, Proc. Natl. Acad. Sci. U.S.A. 79, 4843-4847.
-
(1982)
Proc. Natl. Acad. Sci. U.S.A.
, vol.79
, pp. 4843-4847
-
-
Thomas, K.A.1
Smith, G.M.2
Thomas, T.B.3
Feldmann, R.J.4
-
71
-
-
0029862567
-
Involvement of a residue at position 75 in the catalytic mechanism of a fungal aspartic proteinase, Rhizomucor pusillus pepsin. Replacement of tyrosine 75 on the flap by asparagine enhances catalytic efficiency
-
Park, Y. N., Aikawa, J., Nishiyama, M., Horinouchi, S., and Beppu, T. (1996) Involvement of a residue at position 75 in the catalytic mechanism of a fungal aspartic proteinase, Rhizomucor pusillus pepsin. Replacement of tyrosine 75 on the flap by asparagine enhances catalytic efficiency, Protein Eng. 9, 869-875.
-
(1996)
Protein Eng.
, vol.9
, pp. 869-875
-
-
Park, Y.N.1
Aikawa, J.2
Nishiyama, M.3
Horinouchi, S.4
Beppu, T.5
-
72
-
-
0029989997
-
Computer simulation of the triosephosphate isomerase catalyzed reaction
-
Åqvist, J., and Fothergill, M. (1996) Computer simulation of the triosephosphate isomerase catalyzed reaction, J. Biol. Chem. 271, 10010-10016.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 10010-10016
-
-
Åqvist, J.1
Fothergill, M.2
-
73
-
-
0000230329
-
Energetics of enzyme catalysis
-
Warshel, A. (1978) Energetics of enzyme catalysis, Proc. Natl. Acad. Sci. U.S.A. 75, 5250-5254.
-
(1978)
Proc. Natl. Acad. Sci. U.S.A.
, vol.75
, pp. 5250-5254
-
-
Warshel, A.1
-
74
-
-
0000561390
-
Role of solvent reorganization energies in the catalytic activity of enzymes
-
Yadav, A., Jackson, R. M., Holbrook, J. J., and Warshel, A. (1991) Role of solvent reorganization energies in the catalytic activity of enzymes, J. Am. Chem. Soc. 113, 4800-4805.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 4800-4805
-
-
Yadav, A.1
Jackson, R.M.2
Holbrook, J.J.3
Warshel, A.4
-
75
-
-
24644461086
-
Mechanism of peptide bond synthesis on the ribosome
-
Trobro, S., and Åqvist, J. (2005) Mechanism of peptide bond synthesis on the ribosome, Proc. Natl. Acad. Sci. U.S.A. 102, 12395-12400.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 12395-12400
-
-
Trobro, S.1
Åqvist, J.2
-
76
-
-
0001672288
-
Chemical and electrochemical electrontransfer theory
-
Marcus, R. A. (1964) Chemical and electrochemical electrontransfer theory, Annu. Rev. Phys. Chem. 15, 155-196.
-
(1964)
Annu. Rev. Phys. Chem.
, vol.15
, pp. 155-196
-
-
Marcus, R.A.1
-
77
-
-
0000341206
-
The application of the Marcus relation to reactions in solution
-
Albery, W. J. (1980) The application of the Marcus relation to reactions in solution, Annu. Rev. Phys. Chem. 31, 227-263.
-
(1980)
Annu. Rev. Phys. Chem.
, vol.31
, pp. 227-263
-
-
Albery, W.J.1
-
78
-
-
0032500555
-
Solvation, reorganization energy, and biological catalysis
-
Cannon, W. R., and Benkovic, S. J. (1998) Solvation, reorganization energy, and biological catalysis, J. Biol. Chem. 273, 26257-26260.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 26257-26260
-
-
Cannon, W.R.1
Benkovic, S.J.2
-
79
-
-
0027438252
-
Rate-equilibria relationships in intramolecular proton transfer in human carbonic anhydrase III
-
Silverman, D. N., Tu, C. K., Chen, X., Tanhauser, S. M., Kresge, A. J., and Laipis, P. J. (1993) Rate-equilibria relationships in intramolecular proton transfer in human carbonic anhydrase III, Biochemistry 32, 10757-10762.
-
(1993)
Biochemistry
, vol.32
, pp. 10757-10762
-
-
Silverman, D.N.1
Tu, C.K.2
Chen, X.3
Tanhauser, S.M.4
Kresge, A.J.5
Laipis, P.J.6
-
80
-
-
0027012925
-
Computer simulations of enzymatic reactions: Examination of linear free-energy relationships and quantum-mechanical corrections in the initial proton-transfer step of carbonic-anhydrase
-
Warshel, A., Hwang, J. K., and Åqvist, J. (1992) Computer simulations of enzymatic reactions: Examination of linear free-energy relationships and quantum-mechanical corrections In the initial proton-transfer step of carbonic-anhydrase, Faraday Discuss., 225-238.
-
(1992)
Faraday Discuss
, pp. 225-238
-
-
Warshel, A.1
Hwang, J.K.2
Åqvist, J.3
-
82
-
-
0024995147
-
The interpretation of site-directed mutagenesis experiments by linear free energy relations
-
Straub, J. E., and Karplus, M. (1990) The interpretation of site-directed mutagenesis experiments by linear free energy relations, Protein Eng. 3, 673-675.
-
(1990)
Protein Eng.
, vol.3
, pp. 673-675
-
-
Straub, J.E.1
Karplus, M.2
-
83
-
-
0023662562
-
Structure-activity relationships in engineered proteins: Analysis of use of binding energy by linear free energy relationships
-
Fersht, A. R., Leatherbarrow, R. J., and Wells, T. N. C. (1987) Structure-activity relationships in engineered proteins: Analysis of use of binding energy by linear free energy relationships, Biochemistry 26, 6030-6038.
-
(1987)
Biochemistry
, vol.26
, pp. 6030-6038
-
-
Fersht, A.R.1
Leatherbarrow, R.J.2
Wells, T.N.C.3
-
84
-
-
0024478059
-
Direct Brönsted analysis of the restoration of activity to a mutant enzyme by exogenous amines
-
Toney, M. D., and Kirsch, J. F. (1989) Direct Brönsted analysis of the restoration of activity to a mutant enzyme by exogenous amines, Science 243, 1485-1488.
-
(1989)
Science
, vol.243
, pp. 1485-1488
-
-
Toney, M.D.1
Kirsch, J.F.2
-
85
-
-
0028076447
-
Linear free energy relationships in enzymes. Theoretical analysis of the reaction of tyrosyl-tRNA synthetase
-
Warshel, A., Schweins, T., and Fothergill, M. (1994) Linear free energy relationships in enzymes. Theoretical analysis of the reaction of tyrosyl-tRNA synthetase, J. Am. Chem. Soc. 116, 8437-8442,
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 8437-8442
-
-
Warshel, A.1
Schweins, T.2
Fothergill, M.3
-
86
-
-
1342281185
-
Analyzing free energy relationships for proton translocations in enzymes: Carbonic anhydrase revisited
-
Schutz, C. N., and Warshel, A. (2004) Analyzing free energy relationships for proton translocations in enzymes: Carbonic anhydrase revisited, J. Phys. Chem. B 108, 2066-2075.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 2066-2075
-
-
Schutz, C.N.1
Warshel, A.2
-
87
-
-
0037436389
-
Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum
-
Asojo, O. A., Gulnik, S. V., Afonina, E., Yu, B., Ellman, J. A., Haque, T. S., and Silva, A. M. (2003) Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum, J. Mol. Biol. 327, 173-181.
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 173-181
-
-
Asojo, O.A.1
Gulnik, S.V.2
Afonina, E.3
Yu, B.4
Ellman, J.A.5
Haque, T.S.6
Silva, A.M.7
-
88
-
-
0024281298
-
Theoretical calculations on the acidity of the active-site in aspartic proteinases
-
Goldblum, A. (1988) Theoretical calculations on the acidity of the active-site in aspartic proteinases, Biochemistry 27, 1653-1658.
-
(1988)
Biochemistry
, vol.27
, pp. 1653-1658
-
-
Goldblum, A.1
-
89
-
-
0029863567
-
Inhibition and catalytic mechanism of HIV-1 aspartic protease
-
Silva, A. M., Cachau, R. E., Sham, H. L., and Erickson, J. W. (1996) Inhibition and catalytic mechanism of HIV-1 aspartic protease, J. Mol. Biol. 255, 321-340.
-
(1996)
J. Mol. Biol.
, vol.255
, pp. 321-340
-
-
Silva, A.M.1
Cachau, R.E.2
Sham, H.L.3
Erickson, J.W.4
-
90
-
-
0034716728
-
Ab initio studies on the catalytic mechanism of aspartic proteinases: Nucleophilic versus general acid/general base mechanism
-
Park, H., Suh, J., and Lee, S. (2000) Ab initio studies on the catalytic mechanism of aspartic proteinases: Nucleophilic versus general acid/general base mechanism, J. Am. Chem. Soc. 122, 3901-3908.
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 3901-3908
-
-
Park, H.1
Suh, J.2
Lee, S.3
|