-
1
-
-
0027957967
-
Dissociation and association of the HIV-1 protease dimer subunits: Equilibria and rates
-
Darke PL, et al. (1994) Dissociation and association of the HIV-1 protease dimer subunits: Equilibria and rates. Biochemistry 33(1):98-105. (Pubitemid 24046501)
-
(1994)
Biochemistry
, vol.33
, Issue.1
, pp. 98-105
-
-
Darke, P.L.1
Jordan, S.P.2
Hall, D.L.3
Zugay, J.A.4
Shafer, J.A.5
Kuo, L.C.6
-
2
-
-
0029002115
-
Stability of dimeric retroviral proteases
-
Darke PL (1994) Stability of dimeric retroviral proteases. Methods Enzymol 241:104-127.
-
(1994)
Methods Enzymol
, vol.241
, pp. 104-127
-
-
Darke, P.L.1
-
3
-
-
0242353303
-
Solution Structure of the Mature HIV-1 Protease Monomer: Insight into the tertiary fold and stability of a precursor
-
DOI 10.1074/jbc.M307549200
-
Ishima R, Torchia DA, Lynch SM, Gronenborn AM, Louis JM (2003) Solution structure of the mature HIV-1 protease monomer: Insight into the tertiary fold and stability of a precursor. J Biol Chem 278(44):43311-43319. (Pubitemid 37345952)
-
(2003)
Journal of Biological Chemistry
, vol.278
, Issue.44
, pp. 43311-43319
-
-
Ishima, R.1
Torchia, D.A.2
Lynch, S.M.3
Gronenborn, A.M.4
Louis, J.M.5
-
4
-
-
3543142335
-
Initial cleavage of the human immunodeficiency virus type 1 GagPol precursor by its activated protease occurs by an intramolecular mechanism
-
DOI 10.1128/JVI.78.16.8477-8485.2004
-
Pettit SC, Everitt LE, Choudhury S, Dunn BM, Kaplan AH (2004) Initial cleavage of the human immunodeficiency virus type 1 GagPol precursor by its activated protease occurs by an intramolecular mechanism. J Virol 78(16):8477-8485. (Pubitemid 39025113)
-
(2004)
Journal of Virology
, vol.78
, Issue.16
, pp. 8477-8485
-
-
Pettit, S.C.1
Everitt, L.E.2
Choudhury, S.3
Dunn, B.M.4
Kaplan, A.H.5
-
5
-
-
0027936212
-
Kinetics and mechanism of autoprocessing of human immunodeficiency virus type 1 protease from an analog of the Gag-Pol polyprotein
-
DOI 10.1073/pnas.91.17.7970
-
Louis JM, Nashed NT, Parris KD, Kimmel AR, Jerina DM (1994) Kinetics and mechanism of autoprocessing of human immunodeficiency virus type 1 protease from an analog of the Gag-Pol polyprotein. Proc Natl Acad Sci USA 91(17):7970-7974. (Pubitemid 24253867)
-
(1994)
Proceedings of the National Academy of Sciences of the United States of America
, vol.91
, Issue.17
, pp. 7970-7974
-
-
Louis, J.M.1
Hashed, N.T.2
Parris, K.D.3
Kimmel, A.R.4
Jerina, D.M.5
-
6
-
-
0029833678
-
Influence of flanking sequences on the dimer stability of human immunodeficiency virus type 1 protease
-
DOI 10.1021/bi960984y
-
Wondrak EM, Louis JM (1996) Influence of flanking sequences on the dimer stability of human immunodeficiency virus type 1 protease. Biochemistry 35(39):12957-12962. (Pubitemid 26337353)
-
(1996)
Biochemistry
, vol.35
, Issue.39
, pp. 12957-12962
-
-
Wondrak, E.M.1
Louis, J.M.2
-
7
-
-
17444392445
-
Autoprocessing of HIV-1 protease is tightly coupled to protein folding
-
DOI 10.1038/12327
-
Louis JM, Clore GM, Gronenborn AM (1999) Autoprocessing of HIV-1 protease is tightly coupled to protein folding. Nat Struct Biol 6(9):868-875. (Pubitemid 29415180)
-
(1999)
Nature Structural Biology
, vol.6
, Issue.9
, pp. 868-875
-
-
Louis, J.M.1
Marius, C.G.2
Gronenborn, A.M.3
-
8
-
-
0033551697
-
Proteolytic processing of HIV-1 protease precursor, kinetics and mechanism
-
Louis JM, Wondrak EM, Kimmel AR, Wingfield PT, Nashed NT (1999) Proteolytic processing of HIV-1 protease precursor, kinetics and mechanism. J Biol Chem 274(33):23437-23442.
-
(1999)
J Biol Chem
, vol.274
, Issue.33
, pp. 23437-23442
-
-
Louis, J.M.1
Wondrak, E.M.2
Kimmel, A.R.3
Wingfield, P.T.4
Nashed, N.T.5
-
9
-
-
0030066643
-
A transient precursor of the HIV-1 protease. Isolation, characterization, and kinetics of maturation
-
Wondrak EM, Nashed NT, Haber MT, Jerina DM, Louis JM (1996) A transient precursor of the HIV-1 protease. Isolation, characterization, and kinetics of maturation. J Biol Chem 271(8):4477-4481.
-
(1996)
J Biol Chem
, vol.271
, Issue.8
, pp. 4477-4481
-
-
Wondrak, E.M.1
Nashed, N.T.2
Haber, M.T.3
Jerina, D.M.4
Louis, J.M.5
-
10
-
-
0036147844
-
Rapid structural fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations
-
DOI 10.1110/ps.33202
-
Freedberg DI, et al. (2002) Rapid structural fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations. Protein Sci 11(2):221-232. (Pubitemid 34075785)
-
(2002)
Protein Science
, vol.11
, Issue.2
, pp. 221-232
-
-
Freedberg, D.I.1
Ishima, R.2
Jacob, J.3
Wang, Y.-X.4
Kustanovich, I.5
Louis, J.M.6
Torchia, D.A.7
-
11
-
-
0034483901
-
Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance
-
DOI 10.1016/S0969-2126(00)00537-2, PII S0969212600005372
-
Scott WRP, Schiffer CA (2000) Curling of flap tips in HIV-1 protease as a mechanism for substrate entry and tolerance of drug resistance. Structure 8(12):1259-1265. (Pubitemid 32149752)
-
(2000)
Structure
, vol.8
, Issue.12
, pp. 1259-1265
-
-
Scott, W.R.P.1
Schiffer, C.A.2
-
12
-
-
33744940504
-
Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model
-
DOI 10.1529/biophysj.105.074575
-
Chang CE, Shen T, Trylska J, Tozzini V, McCammon JA (2006) Gated binding of ligands to HIV-1 protease: Brownian dynamics simulations in a coarse-grained model. Biophys J 90(11):3880-3885. (Pubitemid 43846106)
-
(2006)
Biophysical Journal
, vol.90
, Issue.11
, pp. 3880-3885
-
-
Chang, C.-E.1
Shen, T.2
Trylska, J.3
Tozzini, V.4
McCammon, J.A.5
-
13
-
-
33645909557
-
Flap opening mechanism of HIV-1 protease
-
Tóth G, Borics A (2006) Flap opening mechanism of HIV-1 protease. J Mol Graph Model 24(6):465-474.
-
(2006)
J Mol Graph Model
, vol.24
, Issue.6
, pp. 465-474
-
-
Tóth, G.1
Borics, A.2
-
14
-
-
32244437816
-
HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations
-
DOI 10.1073/pnas.0508452103
-
Hornak V, Okur A, Rizzo RC, Simmerling C (2006) HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci USA 103(4):915-920. (Pubitemid 43212196)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.4
, pp. 915-920
-
-
Hornak, V.1
Okur, A.2
Rizzo, R.C.3
Simmerling, C.4
-
15
-
-
77957948558
-
Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing
-
Sadiq SK, De Fabritiis G (2010) Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing. Proteins 78(14):2873-2885.
-
(2010)
Proteins
, vol.78
, Issue.14
, pp. 2873-2885
-
-
Sadiq, S.K.1
De Fabritiis, G.2
-
16
-
-
33645227102
-
Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate
-
Prabu-Jeyabalan M, Nalivaika EA, Romano K, Schiffer CA (2006) Mechanism of substrate recognition by drug-resistant human immunodeficiency virus type 1 protease variants revealed by a novel structural intermediate. J Virol 80(7):3607-3616.
-
(2006)
J Virol
, vol.80
, Issue.7
, pp. 3607-3616
-
-
Prabu-Jeyabalan, M.1
Nalivaika, E.A.2
Romano, K.3
Schiffer, C.A.4
-
17
-
-
0036121219
-
Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes
-
DOI 10.1016/S0969-2126(02)00720-7, PII S0969212602007207
-
Prabu-Jeyabalan M, Nalivaika E, Schiffer CA (2002) Substrate shape determines specificity of recognition for HIV-1 protease: Analysis of crystal structures of six substrate complexes. Structure 10(3):369-381. (Pubitemid 34230624)
-
(2002)
Structure
, vol.10
, Issue.3
, pp. 369-381
-
-
Prabu-Jeyabalan, M.1
Nalivaika, E.2
Schiffer, C.A.3
-
18
-
-
0034283345
-
How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease
-
Prabu-Jeyabalan M, Nalivaika E, Schiffer CA (2000) How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J Mol Biol 301(5):1207-1220.
-
(2000)
J Mol Biol
, vol.301
, Issue.5
, pp. 1207-1220
-
-
Prabu-Jeyabalan, M.1
Nalivaika, E.2
Schiffer, C.A.3
-
19
-
-
33645767675
-
Substrate envelope and drug resistance: Crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease
-
Prabu-Jeyabalan M, et al. (2006) Substrate envelope and drug resistance: Crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease. Antimicrob Agents Chemother 50(4):1518-1521.
-
(2006)
Antimicrob Agents Chemother
, vol.50
, Issue.4
, pp. 1518-1521
-
-
Prabu-Jeyabalan, M.1
-
20
-
-
53349152834
-
Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease
-
Tang C, Louis JM, Aniana A, Suh JY, Clore GM (2008) Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease. Nature 455(7213):693-696.
-
(2008)
Nature
, vol.455
, Issue.7213
, pp. 693-696
-
-
Tang, C.1
Louis, J.M.2
Aniana, A.3
Suh, J.Y.4
Clore, G.M.5
-
21
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
DOI 10.1038/nsb0902-646
-
Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9(9):646-652. (Pubitemid 34977295)
-
(2002)
Nature Structural Biology
, vol.9
, Issue.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
22
-
-
67650099787
-
Acemd: Accelerating biomolecular dynamics in the microsecond time scale
-
Harvey MJ, Giupponi G, Fabritiis GD (2009) Acemd: Accelerating biomolecular dynamics in the microsecond time scale. J Chem Theory Comput 5(6):1632-1639.
-
(2009)
J Chem Theory Comput
, vol.5
, Issue.6
, pp. 1632-1639
-
-
Harvey, M.J.1
Giupponi, G.2
Fabritiis, G.D.3
-
23
-
-
77949978021
-
High-throughput all-atom molecular dynamics simulations using distributed computing
-
Buch I, Harvey MJ, Giorgino T, Anderson DP, De Fabritiis G (2010) High-throughput all-atom molecular dynamics simulations using distributed computing. J Chem Inf Model 50(3):397-403.
-
(2010)
J Chem Inf Model
, vol.50
, Issue.3
, pp. 397-403
-
-
Buch, I.1
Harvey, M.J.2
Giorgino, T.3
Anderson, D.P.4
De Fabritiis, G.5
-
24
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
Boehr DD, Nussinov R, Wright PE (2009) The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 5(11):789-796.
-
(2009)
Nat Chem Biol
, vol.5
, Issue.11
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
25
-
-
36849039429
-
A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
-
DOI 10.1038/nature06407, PII NATURE06407
-
Henzler-Wildman KA, et al. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450(7171):913-916. (Pubitemid 350231333)
-
(2007)
Nature
, vol.450
, Issue.7171
, pp. 913-916
-
-
Henzler-Wildman, K.A.1
Lei, M.2
Thai, V.3
Kerns, S.J.4
Karplus, M.5
Kern, D.6
-
27
-
-
34247338100
-
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
-
Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC (2007) Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys 126(15):155101.
-
(2007)
J Chem Phys
, vol.126
, Issue.15
, pp. 155101
-
-
Chodera, J.D.1
Singhal, N.2
Pande, V.S.3
Dill, K.A.4
Swope, W.C.5
-
28
-
-
79957488000
-
Markov models of molecular kinetics: Generation and validation
-
Prinz JH, et al. (2011) Markov models of molecular kinetics: Generation and validation. J Chem Phys 134(17):174105.
-
(2011)
J Chem Phys
, vol.134
, Issue.17
, pp. 174105
-
-
Prinz, J.H.1
-
29
-
-
44949178407
-
Coarse master equations for peptide folding dynamics
-
Buchete NV, Hummer G (2008) Coarse master equations for peptide folding dynamics. J Phys Chem B 112(19):6057-6069.
-
(2008)
J Phys Chem B
, vol.112
, Issue.19
, pp. 6057-6069
-
-
Buchete, N.V.1
Hummer, G.2
-
30
-
-
70450255797
-
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
-
Noé F, Schütte C, Vanden-Eijnden E, Reich L, Weikl TR (2009) Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci USA 106(45):19011-19016.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.45
, pp. 19011-19016
-
-
Noé, F.1
Schütte, C.2
Vanden-Eijnden, E.3
Reich, L.4
Weikl, T.R.5
-
31
-
-
76149136021
-
Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)
-
Voelz VA, Bowman GR, Beauchamp K, Pande VS (2010) Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc 132(5):1526-1528.
-
(2010)
J Am Chem Soc
, vol.132
, Issue.5
, pp. 1526-1528
-
-
Voelz, V.A.1
Bowman, G.R.2
Beauchamp, K.3
Pande, V.S.4
-
32
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
Buch I, Giorgino T, De Fabritiis G (2011) Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci USA 108(25):10184-10189.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, Issue.25
, pp. 10184-10189
-
-
Buch, I.1
Giorgino, T.2
De Fabritiis, G.3
-
33
-
-
0033200247
-
Flap opening and dimer-interface flexibility in the free and inhibitor- bound HIV protease, and their implications for function
-
DOI 10.1016/S0969-2126(99)80172-5
-
Ishima R, Freedberg DI, Wang YX, Louis JM, Torchia DA (1999) Flap opening and dimer-interface flexibility in the free and inhibitor-bound HIV protease, and their implications for function. Structure 7(9):1047-1055. (Pubitemid 29436502)
-
(1999)
Structure
, vol.7
, Issue.9
, pp. 1047-1055
-
-
Ishima, R.1
Freedberg, D.I.2
Wang, Y.-X.3
Louis, J.M.4
Torchia, D.A.5
-
34
-
-
0037634016
-
A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex
-
DOI 10.1110/ps.0300703
-
Katoh E, et al. (2003) A solution NMR study of the binding kinetics and the internal dynamics of an HIV-1 protease-substrate complex. Protein Sci 12(7):1376-1385. (Pubitemid 36759342)
-
(2003)
Protein Science
, vol.12
, Issue.7
, pp. 1376-1385
-
-
Katoh, E.1
Louis, J.M.2
Yamazaki, T.3
Gronenborn, A.M.4
Torchia, D.A.5
Ishima, R.6
-
35
-
-
69049084558
-
Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations
-
Pietrucci F, Marinelli F, Carloni P, Laio A (2009) Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. J Am Chem Soc 131(33):11811-11818.
-
(2009)
J Am Chem Soc
, vol.131
, Issue.33
, pp. 11811-11818
-
-
Pietrucci, F.1
Marinelli, F.2
Carloni, P.3
Laio, A.4
-
36
-
-
33744730369
-
Closing of the flaps of HIV-1 protease induced by substrate binding: A model of a flap closing mechanism in retroviral aspartic proteases
-
DOI 10.1021/bi060188k
-
Tóth G, Borics A (2006) Closing of the flaps of HIV-1 protease induced by substrate binding: A model of a flap closing mechanism in retroviral aspartic proteases. Biochemistry 45(21):6606-6614. (Pubitemid 43825361)
-
(2006)
Biochemistry
, vol.45
, Issue.21
, pp. 6606-6614
-
-
Toth, G.1
Borics, A.2
-
37
-
-
33644948688
-
HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state
-
Hornak V, Okur A, Rizzo RC, Simmerling C (2006) HIV-1 protease flaps spontaneously close to the correct structure in simulations following manual placement of an inhibitor into the open state. J Am Chem Soc 128(9):2812-2813.
-
(2006)
J Am Chem Soc
, vol.128
, Issue.9
, pp. 2812-2813
-
-
Hornak, V.1
Okur, A.2
Rizzo, R.C.3
Simmerling, C.4
-
38
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, et al. (2000) The protein data bank. Nucleic Acids Res 28(1):235-242. (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
39
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan Y, et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24(16):1999-2012.
-
(2003)
J Comput Chem
, vol.24
, Issue.16
, pp. 1999-2012
-
-
Duan, Y.1
-
40
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (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
Impey, R.W.4
Klein, M.L.5
-
42
-
-
73349117827
-
An implementation of the smooth particle mesh Ewald method on GPU hardware
-
Harvey M, De Fabritiis G (2009) An implementation of the smooth particle mesh Ewald method on GPU hardware. J Chem Theory Comput 5(9):2371-2377.
-
(2009)
J Chem Theory Comput
, vol.5
, Issue.9
, pp. 2371-2377
-
-
Harvey, M.1
De Fabritiis, G.2
-
43
-
-
84863672816
-
Emma - A software package for Markov model building and analysis
-
Senne M, Trendelkamp-Schroer B, Mey ASJS, Schütte C, Noé F (2012) Emma - a software package for Markov model building and analysis. J Chem Theory Comput 8(7):2223-2238.
-
(2012)
J Chem Theory Comput
, vol.8
, Issue.7
, pp. 2223-2238
-
-
Senne, M.1
Trendelkamp-Schroer, B.2
Mey, A.S.J.S.3
Schütte, C.4
Noé, F.5
-
44
-
-
34247339716
-
Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states
-
Noé F, Horenko I, Schütte C, Smith JC (2007) Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states. J Chem Phys 126(15):155102.
-
(2007)
J Chem Phys
, vol.126
, Issue.15
, pp. 155102
-
-
Noé, F.1
Horenko, I.2
Schütte, C.3
Smith, J.C.4
|