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Volumn 32, Issue 14, 2006, Pages 1155-1163

Comparison of NMR and MD N-H bond order parameters: Example of HIV-1 protease

Author keywords

Effective correlation time; HIV 1 protease; Model free approach; Molecular dynamics simulation; N H bond order parameter

Indexed keywords

AMINO ACIDS; COMPUTER SIMULATION; CONFORMATIONS; CORRELATION METHODS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; PARAMETER ESTIMATION; SOLUTIONS;

EID: 34548416551     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927020601078489     Document Type: Article
Times cited : (2)

References (67)
  • 1
    • 0034846397 scopus 로고    scopus 로고
    • Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations
    • C. Peter, X. Daura, W.F. van Gunsteren. Calculation of NMR-relaxation parameters for flexible molecules from molecular dynamics simulations. J. Biomol. NMR, 20, 297 (2001).
    • (2001) J. Biomol. NMR , vol.20 , pp. 297
    • Peter, C.1    Daura, X.2    van Gunsteren, W.F.3
  • 2
    • 0034806777 scopus 로고    scopus 로고
    • The β-peptide hairpin in solution: Conformational study of a β-hexapeptide in methanol by NMR spectroscopy and MD simulation
    • X. Daura, K. Gademann, H. Schafer, B. Jaun, D. Seebach, W.F. van Gunsteren. The β-peptide hairpin in solution: conformational study of a β-hexapeptide in methanol by NMR spectroscopy and MD simulation. J. Am. Chem. Soc, 123, 2393 (2001).
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 2393
    • Daura, X.1    Gademann, K.2    Schafer, H.3    Jaun, B.4    Seebach, D.5    van Gunsteren, W.F.6
  • 3
    • 0029162947 scopus 로고
    • Comparision of MD simulation and NMR experiments for Hen lysozyme. Analysis of local fluctuation, cooperative motions, and global change
    • L.J. Smith, A.E. Mark, CM. Dobson, W.F. van Gunsteren. Comparision of MD simulation and NMR experiments for Hen lysozyme. Analysis of local fluctuation, cooperative motions, and global change. Biochemistry, 34, 10918 (1995).
    • (1995) Biochemistry , vol.34 , pp. 10918
    • Smith, L.J.1    Mark, A.E.2    Dobson, C.M.3    van Gunsteren, W.F.4
  • 4
    • 0033979148 scopus 로고    scopus 로고
    • Dynamics of the Hck-SH3 domain: Comparison of experiments with multiple molecular dynamics simulations
    • D.A. Horita, W. Zhang, T.E. Smithgall, W.H. Gmeiner, R.A. Byrd. Dynamics of the Hck-SH3 domain: comparison of experiments with multiple molecular dynamics simulations. Protein Sci., 9, 95 (2000).
    • (2000) Protein Sci , vol.9 , pp. 95
    • Horita, D.A.1    Zhang, W.2    Smithgall, T.E.3    Gmeiner, W.H.4    Byrd, R.A.5
  • 5
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules 1. Theory and range of validity
    • G. Lipari, A. Szabo. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules 1. Theory and range of validity. J. Am. Chem. Soc., 104, 4546 (1982).
    • (1982) J. Am. Chem. Soc , vol.104 , pp. 4546
    • Lipari, G.1    Szabo, A.2
  • 7
    • 0025046144 scopus 로고
    • Deviations from the simple two-parameter model free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins
    • G.M. Clore, A. Szabo, A. Bax, L. Kay, P.C. Driscoll, A.M. Gronenborn. Deviations from the simple two-parameter model free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. Chem. Soc., 112, 4989 (1990).
    • (1990) J. Am. Chem. Soc , vol.112 , pp. 4989
    • Clore, G.M.1    Szabo, A.2    Bax, A.3    Kay, L.4    Driscoll, P.C.5    Gronenborn, A.M.6
  • 8
    • 0031173942 scopus 로고    scopus 로고
    • Solution conformation and dynamics of a tetrasaccharide related to the Lewis X antigen deduced by NMR relaxation measurements
    • A. Povida, J.L. Asensio, M. Martín-Pastor, J. Jiménez- Barbero. Solution conformation and dynamics of a tetrasaccharide related to the Lewis X antigen deduced by NMR relaxation measurements. J. Biomol. NMR, 10, 29 (1997).
    • (1997) J. Biomol. NMR , vol.10 , pp. 29
    • Povida, A.1    Asensio, J.L.2    Martín-Pastor, M.3    Jiménez- Barbero, J.4
  • 9
    • 0032695224 scopus 로고    scopus 로고
    • Backbone dynamics of the human CC-chemokine eotaxin
    • J. Ye, K.L. Mayer, M.J. Stone. Backbone dynamics of the human CC-chemokine eotaxin. J. Biomol. NMR, 15, 115 (1999).
    • (1999) J. Biomol. NMR , vol.15 , pp. 115
    • Ye, J.1    Mayer, K.L.2    Stone, M.J.3
  • 10
    • 0032884804 scopus 로고    scopus 로고
    • 15N NMR dynamic study of an isolated alpha-helical peptide (1-36)-bacteriorhodopsm reveals the equilibrium helixcoil transitions
    • 15N NMR dynamic study of an isolated alpha-helical peptide (1-36)-bacteriorhodopsm reveals the equilibrium helixcoil transitions. J. Biomol. NMR, 14, 345 (1999).
    • (1999) J. Biomol. NMR , vol.14 , pp. 345
    • Orekhov, V.V.1    Korzhneva, D.M.2    Diercks, T.3    Kessler, H.4    Arsenie, A.S.5
  • 12
    • 0034885557 scopus 로고    scopus 로고
    • Backbone dynamics of the natively unfolded pro-peptide of subtilisin by heteronuclear NMR relaxation studies
    • A.V. Buevich, U.P. Shinde, M. Inouye, J. Baum. Backbone dynamics of the natively unfolded pro-peptide of subtilisin by heteronuclear NMR relaxation studies. J. Biomol. NMR, 20, 233 (2001).
    • (2001) J. Biomol. NMR , vol.20 , pp. 233
    • Buevich, A.V.1    Shinde, U.P.2    Inouye, M.3    Baum, J.4
  • 13
    • 0035072684 scopus 로고    scopus 로고
    • Anisotropic rotational diffusion in model-free analysis for a ternary DHFR complex
    • M.J. Osborne, P.E. Wright. Anisotropic rotational diffusion in model-free analysis for a ternary DHFR complex. J. Biomol. NMR, 19, 209 (2001).
    • (2001) J. Biomol. NMR , vol.19 , pp. 209
    • Osborne, M.J.1    Wright, P.E.2
  • 14
    • 3042846786 scopus 로고    scopus 로고
    • Model-free analysis of protein dynamics: Assessment of accuracy and model selection protocols based on molecular dynamics simulation
    • J. Chen, CL. Brooks III, P.E. Wright. Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. J. Biomol. NMR, 29, 243 (2004).
    • (2004) J. Biomol. NMR , vol.29 , pp. 243
    • Chen, J.1    Brooks III, C.L.2    Wright, P.E.3
  • 15
    • 33745623124 scopus 로고    scopus 로고
    • Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data
    • E.J. d'Auvergne, P.R. Gooley. Model-free model elimination: a new step in the model-free dynamic analysis of NMR relaxation data. J. Biomol. NMR, 35, 117 (2006).
    • (2006) J. Biomol. NMR , vol.35 , pp. 117
    • d'Auvergne, E.J.1    Gooley, P.R.2
  • 16
    • 0026684043 scopus 로고
    • A 500 ps molecular dynamics simulation study of interleukin-1β in water: Correlation with nuclear magnetic resonance spectroscopy and crystallography
    • I. Chandrasekhar, G.M. Core, A. Szabo, A.M. Gronenborn, B.R. Brooks. A 500 ps molecular dynamics simulation study of interleukin-1β in water: correlation with nuclear magnetic resonance spectroscopy and crystallography. J. Mol. Biol., 226, 239 (1992).
    • (1992) J. Mol. Biol , vol.226 , pp. 239
    • Chandrasekhar, I.1    Core, G.M.2    Szabo, A.3    Gronenborn, A.M.4    Brooks, B.R.5
  • 17
    • 0032199623 scopus 로고    scopus 로고
    • Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics
    • D. Jin, M. Andrec, G.T. Montelione, R.M. Levy. Propagation of experimental uncertainties using the Lipari-Szabo model-free analysis of protein dynamics. J. Biomol. NMR, 12, 471 (1998).
    • (1998) J. Biomol. NMR , vol.12 , pp. 471
    • Jin, D.1    Andrec, M.2    Montelione, G.T.3    Levy, R.M.4
  • 18
    • 0027333332 scopus 로고
    • 15N NMR relaxation measurements with a molecular dynamics simulation: Backbone dynamics of the glucocorticoid receptor DNA-binding domain
    • 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticoid receptor DNA-binding domain. Proteins Struct. Funct. Genet., 17, 375 (1993).
    • (1993) Proteins Struct. Funct. Genet , vol.17 , pp. 375
    • Eriksson, M.A.L.1    Berglund, H.2    Hard, T.3    Nilsson, L.4
  • 19
    • 0029031765 scopus 로고
    • 15N-NMR relaxation analysis and molecular dynamic simulation: Examination of dynamic models
    • 15N-NMR relaxation analysis and molecular dynamic simulation: examination of dynamic models. Biochemistry, 34, 6587 (1995).
    • (1995) Biochemistry , vol.34 , pp. 6587
    • Yamasaki, K.1    Saito, M.2    Oobatke, M.3    Kanaya, S.4
  • 20
    • 0030877076 scopus 로고    scopus 로고
    • Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics
    • M. Philippopoulos, A.M. Mandel, A.G. Palmer III, C. Lim. Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics. Proteins Struct. Fold. Gen., 28, 481 (1997).
    • (1997) Proteins Struct. Fold. Gen , vol.28 , pp. 481
    • Philippopoulos, M.1    Mandel, A.M.2    Palmer III, A.G.3    Lim, C.4
  • 21
    • 0032501383 scopus 로고    scopus 로고
    • X. Luo, R. Kato, J.R. Collins. Dynamic flexibility of proteininhibitor complexes: a study of the HIV-I protease/KNI-272 complex. J. Am. Chem. Soc., 120, 12410 (1998).
    • X. Luo, R. Kato, J.R. Collins. Dynamic flexibility of proteininhibitor complexes: a study of the HIV-I protease/KNI-272 complex. J. Am. Chem. Soc., 120, 12410 (1998).
  • 23
    • 11244289541 scopus 로고    scopus 로고
    • Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme
    • T.A. Soares, X. Daura, C Oostenbrink, L.J. Smith, W.F. van Gunsteren. Validation of the GROMOS force-field parameter set 45A3 against nuclear magnetic resonance data of hen egg lysozyme. J. Biomol. NMR, 30, 407 (2004).
    • (2004) J. Biomol. NMR , vol.30 , pp. 407
    • Soares, T.A.1    Daura, X.2    Oostenbrink, C.3    Smith, L.J.4    van Gunsteren, W.F.5
  • 25
    • 23344451429 scopus 로고    scopus 로고
    • Relating side-chain mobility in proteins to rotameric transitions: Insights from molecular dynamics simulations and NMR
    • H. Hu, J. Hermans, A.L. Lee. Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR. J. Biomol. NMR, 32, 151 (2005).
    • (2005) J. Biomol. NMR , vol.32 , pp. 151
    • Hu, H.1    Hermans, J.2    Lee, A.L.3
  • 26
    • 0036147844 scopus 로고    scopus 로고
    • Rapid structural, fluctuations of the free HIV protease flaps in solution: Relationship to crystal structures and comparison with predictions of dynamics calculations
    • D.I. Freedberg, R. Ishima, J. Jacob, Y.X. Wang, I. Kustanovich, J.M. Louis, D.A. Torchia. 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, 221 (2002).
    • (2002) Protein Sci , vol.11 , pp. 221
    • 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
  • 27
    • 0032511368 scopus 로고    scopus 로고
    • Flexibility and function in HIV protease: Dynamics of the HIV-I protease bound to the asymmetric inhibitor Kynostatin 272 (KNI-272)
    • D.I. Freedberg, Y. Wang, S.J. Stahl, J.D. Kaufman, P.T. Wingfleld, Y. Kiso, D.A. Torchia. Flexibility and function in HIV protease: dynamics of the HIV-I protease bound to the asymmetric inhibitor Kynostatin 272 (KNI-272). J. Am. Chem. Soc., 120, 7916 (1998).
    • (1998) J. Am. Chem. Soc , vol.120 , pp. 7916
    • Freedberg, D.I.1    Wang, Y.2    Stahl, S.J.3    Kaufman, J.D.4    Wingfleld, P.T.5    Kiso, Y.6    Torchia, D.A.7
  • 28
    • 0033200247 scopus 로고    scopus 로고
    • Flap opening and dimmer-interface flexibility in the free and inhibitor bound HIV-protease, and their implementation for function
    • R. Ishima, D.I. Freedberg, Y.X. Wang, J.M. Louis, D.A. Torchia. Flap opening and dimmer-interface flexibility in the free and inhibitor bound HIV-protease, and their implementation for function. Struct. Fold. Des., 7, 1047 (1999).
    • (1999) Struct. Fold. Des , vol.7 , pp. 1047
    • Ishima, R.1    Freedberg, D.I.2    Wang, Y.X.3    Louis, J.M.4    Torchia, D.A.5
  • 32
    • 0024555898 scopus 로고
    • Three dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1
    • M.A. Navia, P.M. Frizgerald, B.M. McKeever, C.T. Lue, J.C. Heimbach, W.K. Herber. Three dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature, 337, 615 (1989).
    • (1989) Nature , vol.337 , pp. 615
    • Navia, M.A.1    Frizgerald, P.M.2    McKeever, B.M.3    Lue, C.T.4    Heimbach, J.C.5    Herber, W.K.6
  • 33
  • 34
    • 20244373125 scopus 로고
    • X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes
    • R. Lopatto, T.L. Blundell, A. Hemmings, J. Overington, A. Wilderspin, S.P. Wood. X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes. Nature, 342, 299 (1989).
    • (1989) Nature , vol.342 , pp. 299
    • Lopatto, R.1    Blundell, T.L.2    Hemmings, A.3    Overington, J.4    Wilderspin, A.5    Wood, S.P.6
  • 35
    • 0026344399 scopus 로고
    • The three-dimensional, structure of aspartyl protease from, the HIV-1 isolate BRU
    • S. Spinelli, Q.Z. Liu, P.M. Alzari, P.H. Hirel, R.J. Poljak. The three-dimensional, structure of aspartyl protease from, the HIV-1 isolate BRU. Biochemie, 73, 1391 (1991).
    • (1991) Biochemie , vol.73 , pp. 1391
    • Spinelli, S.1    Liu, Q.Z.2    Alzari, P.M.3    Hirel, P.H.4    Poljak, R.J.5
  • 36
    • 0035314020 scopus 로고    scopus 로고
    • 1.9 Å X-ray study shows close-flap conformation in crystals of tethered HIV-1. PR
    • B. Pillai, K.K. Kannan, M.V. Hosur. 1.9 Å X-ray study shows close-flap conformation in crystals of tethered HIV-1. PR. Proteins Struct. Funct. Genet., 43, 57 (2001).
    • (2001) Proteins Struct. Funct. Genet , vol.43 , pp. 57
    • Pillai, B.1    Kannan, K.K.2    Hosur, M.V.3
  • 39
    • 0027468137 scopus 로고
    • Molecular dynamic simulation of HIV-1 protease in a crystalline environment and in solution
    • D.M. York, TA. Darden, L.G. Pedersen, M.W. Anderson. Molecular dynamic simulation of HIV-1 protease in a crystalline environment and in solution. Biochemistry, 32, 1443 (1993).
    • (1993) Biochemistry , vol.32 , pp. 1443
    • York, D.M.1    Darden, T.A.2    Pedersen, L.G.3    Anderson, M.W.4
  • 40
    • 0033525464 scopus 로고    scopus 로고
    • X-ray structure and conformational. Dynamics of the HIV-1 protease in complex with the inhibitor SDZ283-910: Agreement of time-resolved spectroscopy and molecular dynamic simulation
    • S. Ringhofer, J. Kallen, R. Dutzler, A. Billich, A.J.W.G. Visser, D. Scholz. X-ray structure and conformational. Dynamics of the HIV-1 protease in complex with the inhibitor SDZ283-910: agreement of time-resolved spectroscopy and molecular dynamic simulation. J. Mol. Biol., 286, 1147 (1999).
    • (1999) J. Mol. Biol , vol.286 , pp. 1147
    • Ringhofer, S.1    Kallen, J.2    Dutzler, R.3    Billich, A.4    Visser, A.J.W.G.5    Scholz, D.6
  • 41
    • 0028173594 scopus 로고
    • Molecular dynamics simulation of HIV-1 protease with peptide substrate
    • R.W. Harrison, I.T. Weber. Molecular dynamics simulation of HIV-1 protease with peptide substrate. Protein Eng., 7, 1353 (1994).
    • (1994) Protein Eng , vol.7 , pp. 1353
    • Harrison, R.W.1    Weber, I.T.2
  • 42
    • 0034647235 scopus 로고    scopus 로고
    • Molecular dynamics study of HIV-1 protease-substrate complex: Roles of the water molecules at the loop structures of the active site
    • N. Okimoto, T Tsukui, K. Kitayama, M. Hata, T. Hoshino, M. Tsuda. Molecular dynamics study of HIV-1 protease-substrate complex: roles of the water molecules at the loop structures of the active site. J. Am. Chem. Soc., 122, 5613 (2000).
    • (2000) J. Am. Chem. Soc , vol.122 , pp. 5613
    • Okimoto, N.1    Tsukui, T.2    Kitayama, K.3    Hata, M.4    Hoshino, T.5    Tsuda, M.6
  • 43
    • 0034602373 scopus 로고    scopus 로고
    • Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model
    • W. Wang, P.A. Kollman. Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. J. Mol. Biol., 303, 567 (2000).
    • (2000) J. Mol. Biol , vol.303 , pp. 567
    • Wang, W.1    Kollman, P.A.2
  • 44
    • 0034483901 scopus 로고    scopus 로고
    • Curling of flaps tips in HIV-1 protease as a mechanism for substrate entry band tolerance of drug resistance
    • W.R. Scott, C.A. Schiffer. Curling of flaps tips in HIV-1 protease as a mechanism for substrate entry band tolerance of drug resistance. Struct. Fold. Des., 8, 1259 (2000).
    • (2000) Struct. Fold. Des , vol.8 , pp. 1259
    • Scott, W.R.1    Schiffer, C.A.2
  • 45
    • 0036306459 scopus 로고    scopus 로고
    • Role of conformational fluctuation in the enzymatic reaction of HIV-1 protease
    • S. Piana, P. Carloni, M. Parrinello. Role of conformational fluctuation in the enzymatic reaction of HIV-1 protease. J. Mol. Biol., 319, 567 (2002).
    • (2002) J. Mol. Biol , vol.319 , pp. 567
    • Piana, S.1    Carloni, P.2    Parrinello, M.3
  • 46
    • 0036786493 scopus 로고    scopus 로고
    • Flexibility-assisted catalysis: Molecular mechanisms of compensatory mutations in HIV-I PR
    • S. Piana, P. Carloni, U. Rothlisberger. Flexibility-assisted catalysis: molecular mechanisms of compensatory mutations in HIV-I PR. Protein Sci., 11, 2393 (2002).
    • (2002) Protein Sci , vol.11 , pp. 2393
    • Piana, S.1    Carloni, P.2    Rothlisberger, U.3
  • 47
    • 0037963159 scopus 로고    scopus 로고
    • Cooperative fluctuation of unliganded and substrate bounded HIV-1 protease: A structure based analysis on a variety of conformation from. crystallography and molecular dynamic simulations
    • N. Kurt, W.R. Scott, C.A. Schiffer, T. Haliloglu. Cooperative fluctuation of unliganded and substrate bounded HIV-1 protease: a structure based analysis on a variety of conformation from. crystallography and molecular dynamic simulations. Proteins Struct. Funct. Genet., 51, 409 (2003).
    • (2003) Proteins Struct. Funct. Genet , vol.51 , pp. 409
    • Kurt, N.1    Scott, W.R.2    Schiffer, C.A.3    Haliloglu, T.4
  • 48
    • 0032562224 scopus 로고    scopus 로고
    • Domain flexibility in retroviral proteases: Structural implications for drug resistant
    • R.B. Rose, CS. Craik, R.M. Stroud. Domain flexibility in retroviral proteases: structural implications for drug resistant. Biochemistry, 37, 2607 (1998).
    • (1998) Biochemistry , vol.37 , pp. 2607
    • Rose, R.B.1    Craik, C.S.2    Stroud, R.M.3
  • 49
    • 0036001242 scopus 로고    scopus 로고
    • High-performance liquid chromatographic method for the simultaneous determination of the six HIV-protease inhibitors and two non-nucleoside reverse transcriptase inhibitors in human plasma
    • K. Titier, F. Lagrange, F. Pehourcq, L. Edno-Mcheik, N. Moore, M. Mblimard. High-performance liquid chromatographic method for the simultaneous determination of the six HIV-protease inhibitors and two non-nucleoside reverse transcriptase inhibitors in human plasma. Ther. Drug Monit., 24, 417 (2002).
    • (2002) Ther. Drug Monit , vol.24 , pp. 417
    • Titier, K.1    Lagrange, F.2    Pehourcq, F.3    Edno-Mcheik, L.4    Moore, N.5    Mblimard, M.6
  • 50
    • 0037329153 scopus 로고    scopus 로고
    • HIV protease inhibitors: Antiretroviral agents with anti-inflammatory, anti-angiogenic and anti-tumour activity
    • P. Monini, C. Sgadari, G. Barillari, B. Ensoli. HIV protease inhibitors: antiretroviral agents with anti-inflammatory, anti-angiogenic and anti-tumour activity J. Antimicrob. Chemother., 51, 207 (2003).
    • (2003) J. Antimicrob. Chemother , vol.51 , pp. 207
    • Monini, P.1    Sgadari, C.2    Barillari, G.3    Ensoli, B.4
  • 51
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • E. Lindahl, B. Hess, D. van der Spoel. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Mod., 7, 306 (2001).
    • (2001) J. Mol. Mod , vol.7 , pp. 306
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 52
    • 0035425883 scopus 로고    scopus 로고
    • An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
    • L.D. Schuler, X. Daura, W.F. van Gunsteren. An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J. Comput. Chem., 22, 1205 (2001).
    • (2001) J. Comput. Chem , vol.22 , pp. 1205
    • Schuler, L.D.1    Daura, X.2    van Gunsteren, W.F.3
  • 53
    • 0033998647 scopus 로고    scopus 로고
    • Conformation flexibility of the catalytic Asp dyad in HIV-1 protease: An ab initio study of the free enzyme
    • S. Piana, P. Carloni. Conformation flexibility of the catalytic Asp dyad in HIV-1 protease: an ab initio study of the free enzyme. Proteins Struct. Funct. Genet., 39, 26 (2000).
    • (2000) Proteins Struct. Funct. Genet , vol.39 , pp. 26
    • Piana, S.1    Carloni, P.2
  • 54
    • 0037627173 scopus 로고    scopus 로고
    • Effect of artificial periodicity in simulation of biomolecules under Ewald boundary conditions: A continuum electrostatic study
    • PH. Hunenberger, J.A. McCammon. Effect of artificial periodicity in simulation of biomolecules under Ewald boundary conditions: a continuum electrostatic study. Biophys. Chem., 78, 69 (1999).
    • (1999) Biophys. Chem , vol.78 , pp. 69
    • Hunenberger, P.H.1    McCammon, J.A.2
  • 55
    • 0343005873 scopus 로고    scopus 로고
    • Molecular dynamics simulations of a polyalanine octapeptide under ewald boundary conditions: Influence of artificial periodicity on peptide conformation
    • W. Weber, P.H. Hunenberger, J.A. McCammon. Molecular dynamics simulations of a polyalanine octapeptide under ewald boundary conditions: influence of artificial periodicity on peptide conformation. J. Phys. Chem. B, 104, 3668 (2000).
    • (2000) J. Phys. Chem. B , vol.104 , pp. 3668
    • Weber, W.1    Hunenberger, P.H.2    McCammon, J.A.3
  • 56
    • 33646940952 scopus 로고
    • Numerical, integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • J.P. Ryckaert, G. Ciccotti, H.J.C. Berendsen. Numerical, integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comp. Phys., 23, 327 (1977).
    • (1977) J. Comp. Phys , vol.23 , pp. 327
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 57
    • 0034823221 scopus 로고    scopus 로고
    • Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: A comparison of spectral densities for the ßARKl PH domain
    • S. Pfeiffer, D. Fushman, D. Cowburn. Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the ßARKl PH domain. J. Am. Chem. Soc., 123, 3021 (2001).
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 3021
    • Pfeiffer, S.1    Fushman, D.2    Cowburn, D.3
  • 61
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • N. Guex, M.C. Peitsch. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Eledrophoresis, 18, 2714 (1997).
    • (1997) Eledrophoresis , vol.18 , pp. 2714
    • Guex, N.1    Peitsch, M.C.2
  • 63
    • 0034056585 scopus 로고    scopus 로고
    • An alternate binding site for the P1 ± P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease
    • S. Munshi, Z. Chen, Y. Yan, Y. Li, D.B. Olsen, H.B. Schock, B.B. Galvin, B. Dorsey, L.C. Kuo. An alternate binding site for the P1 ± P3 group of a class of potent HIV-1 protease inhibitors as a result of concerted structural change in the 80s loop of the protease. Acta Cryst. Sect. D, 56, 381 (2000).
    • (2000) Acta Cryst. Sect. D , vol.56 , pp. 381
    • Munshi, S.1    Chen, Z.2    Yan, Y.3    Li, Y.4    Olsen, D.B.5    Schock, H.B.6    Galvin, B.B.7    Dorsey, B.8    Kuo, L.C.9
  • 64
    • 0029913459 scopus 로고    scopus 로고
    • Conformation stability and catalytic activity of HIV-1 protease are both enhanced at high salt concentration
    • Z. Szeltner, L. Polgar. Conformation stability and catalytic activity of HIV-1 protease are both enhanced at high salt concentration. J. Biol. Chem., 271, 5458 (1996).
    • (1996) J. Biol. Chem , vol.271 , pp. 5458
    • Szeltner, Z.1    Polgar, L.2
  • 65
    • 0027957967 scopus 로고
    • Dissociation and association of the HIV-1 Protease dimmer subunits: Equilibria and rates
    • P.L. Darke, S.P. Jordan, D.L. Hall, J.A. Zugay, J.A. Shafer, L.C. Kuo. Dissociation and association of the HIV-1 Protease dimmer subunits: equilibria and rates. Biochemistry, 33, 98 (1994).
    • (1994) Biochemistry , vol.33 , pp. 98
    • Darke, P.L.1    Jordan, S.P.2    Hall, D.L.3    Zugay, J.A.4    Shafer, J.A.5    Kuo, L.C.6
  • 66
    • 0026325601 scopus 로고
    • Kinetic studies of human immunodeficiency virus type 1 protease and its active-site hydrogen bond mutant A28S*
    • E. Ido, H.P Han, F.J. Kezdy, J. Tang. Kinetic studies of human immunodeficiency virus type 1 protease and its active-site hydrogen bond mutant A28S*. J. Biol. Chem., 266, 24359 (1991).
    • (1991) J. Biol. Chem , vol.266 , pp. 24359
    • Ido, E.1    Han, H.P.2    Kezdy, F.J.3    Tang, J.4
  • 67
    • 0028070285 scopus 로고
    • Substrate-dependent mechanisms in the catalysis of human immunodeficiency virus protease
    • L. Polgar, Z. Szeltner, I. Boros. Substrate-dependent mechanisms in the catalysis of human immunodeficiency virus protease. Biochemistry, 33, 9351 (1994).
    • (1994) Biochemistry , vol.33 , pp. 9351
    • Polgar, L.1    Szeltner, Z.2    Boros, I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.