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Volumn 37, Issue 4, 1999, Pages 512-529

MCSS functionality maps for a flexible protein

Author keywords

HIV 1 protease; LES; Ligand design; MCSS; Protein flexibility

Indexed keywords

FUNCTIONAL GROUP; LIGAND; METHANOL; PROTEINASE; VIRUS PROTEIN;

EID: 0032749096     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991201)37:4<512::AID-PROT3>3.0.CO;2-O     Document Type: Article
Times cited : (40)

References (43)
  • 1
    • 0344432969 scopus 로고
    • Advances in automated docking applied to human immunodeficiency virus type 1
    • Kuo LC, Shafer JA, editors. San Diego: Academic Press
    • Miller MD, Sheridan RP, Kearsley SK, Underwood DJ. Advances in automated docking applied to human immunodeficiency virus type 1. In: Kuo LC, Shafer JA, editors. Retroviral proteases, Methods in enzymology, Vol. 41. San Diego: Academic Press; 1994:38-54.
    • (1994) Retroviral Proteases, Methods in Enzymology , vol.41 , pp. 38-54
    • Miller, M.D.1    Sheridan, R.P.2    Kearsley, S.K.3    Underwood, D.J.4
  • 2
    • 0028943992 scopus 로고
    • In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors
    • Condra J, Schlef WA, Blahy OM et al. In vivo emergence of HIV-1 variants resistant to multiple protease inhibitors. Nature 1995;374: 569-571.
    • (1995) Nature , vol.374 , pp. 569-571
    • Condra, J.1    Schlef, W.A.2    Blahy, O.M.3
  • 3
    • 0028785287 scopus 로고
    • Ligand-induced distortion of an active site in thymidylate synthase upon binding anticancer drug 1843U89
    • Weichsel A, Montfrot W. Ligand-induced distortion of an active site in thymidylate synthase upon binding anticancer drug 1843U89. Nat Struct Biol 1995; 2:1095-1101.
    • (1995) Nat Struct Biol , vol.2 , pp. 1095-1101
    • Weichsel, A.1    Montfrot, W.2
  • 6
    • 0031892160 scopus 로고    scopus 로고
    • Protein conformer selection by ligand binding observed with crystallography
    • Cao Y, Musah R, Wilcox S, Goodin D, McRee D. Protein conformer selection by ligand binding observed with crystallography. Protein Sci 1998;7:72-78.
    • (1998) Protein Sci , vol.7 , pp. 72-78
    • Cao, Y.1    Musah, R.2    Wilcox, S.3    Goodin, D.4    McRee, D.5
  • 7
    • 16044375105 scopus 로고
    • Crystal structures of HIV-1 protease-inhibitor complexes
    • Appelt K. Crystal structures of HIV-1 protease-inhibitor complexes. Perspect Drug Discovery Design 1993;1:23-48.
    • (1993) Perspect Drug Discovery Design , vol.1 , pp. 23-48
    • Appelt, K.1
  • 8
    • 0029054198 scopus 로고
    • Slow ligand-induced transitions in the allosteric phosphofructokinase from Escherichia coli
    • Auzat I, Gawlita E, Garel J. Slow ligand-induced transitions in the allosteric phosphofructokinase from Escherichia coli. J Mol Biol 1995;249:478-492.
    • (1995) J Mol Biol , vol.249 , pp. 478-492
    • Auzat, I.1    Gawlita, E.2    Garel, J.3
  • 9
    • 0026065644 scopus 로고
    • Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding
    • Bystroff C, Kraut J. Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding. Biochemistry 1991;30:2227-2239.
    • (1991) Biochemistry , vol.30 , pp. 2227-2239
    • Bystroff, C.1    Kraut, J.2
  • 10
    • 0029643790 scopus 로고
    • Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere
    • Tong L, Pav S, Suet M, Lamarre D, Yoakim C, Beaulieu P, Anderson P. Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere. Structure 1995;3:33-40.
    • (1995) Structure , vol.3 , pp. 33-40
    • Tong, L.1    Pav, S.2    Suet, M.3    Lamarre, D.4    Yoakim, C.5    Beaulieu, P.6    Anderson, P.7
  • 11
    • 0028113299 scopus 로고
    • Residues in chaperonin GroEL required for polypeptide binding and release
    • Fenton WA, Furtak K, Horwich AL. Residues in chaperonin GroEL required for polypeptide binding and release. Nature 1994;371:614-619.
    • (1994) Nature , vol.371 , pp. 614-619
    • Fenton, W.A.1    Furtak, K.2    Horwich, A.L.3
  • 12
    • 0027943510 scopus 로고
    • The crystal structure of bacterial chaperonin GroEL at 2.8 Å
    • Braig K, Otwinowski Z, Hedge R, et al. The crystal structure of bacterial chaperonin GroEL at 2.8 Å. Nature 1994;371:578-586.
    • (1994) Nature , vol.371 , pp. 578-586
    • Braig, K.1    Otwinowski, Z.2    Hedge, R.3
  • 13
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: A multiple copy simultaneous search method
    • Miranker A, Karplus M. Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 1991;11: 29-34.
    • (1991) Proteins , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 14
    • 0005241362 scopus 로고
    • Active immunodeficiency virus protease is required for virus infectivity
    • Kohl NE, Emini EA, Scheif WA, et al. Active immunodeficiency virus protease is required for virus infectivity. Proc Natl Acad Sci USA 1988;85:4686-4690.
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 4686-4690
    • Kohl, N.E.1    Emini, E.A.2    Scheif, W.A.3
  • 15
    • 0027185772 scopus 로고
    • Structure of a nonpeptide inhibitor complexed with HIV-1 protease
    • Rutenber E, Fauman E, Keenan R, et al. Structure of a nonpeptide inhibitor complexed with HIV-1 protease J Biol Chem 1993;268:15343-15346.
    • (1993) J Biol Chem , vol.268 , pp. 15343-15346
    • Rutenber, E.1    Fauman, E.2    Keenan, R.3
  • 16
    • 0032562224 scopus 로고    scopus 로고
    • Domain flexibility in retroviral proteases: Structural implications for drug resistant mutations
    • Rose RB, Craik CS, Stroud RM. Domain flexibility in retroviral proteases: structural implications for drug resistant mutations. Biochemistry 1998;37:2607-2621.
    • (1998) Biochemistry , vol.37 , pp. 2607-2621
    • Rose, R.B.1    Craik, C.S.2    Stroud, R.M.3
  • 17
    • 0025600834 scopus 로고
    • Enhanced sampling in molecular dynamics: Use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
    • Elber R, Karplus M. Enhanced sampling in molecular dynamics: use of the time-dependent hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J Am Chem Soc 1990;112:9161-9175.
    • (1990) J Am Chem Soc , vol.112 , pp. 9161-9175
    • Elber, R.1    Karplus, M.2
  • 18
    • 0001031179 scopus 로고
    • Proteins, a theoretical perspective of dynamics, structure, and thermodynamics
    • Brooks CL, Karplus M, Pettitt BM. Proteins, a theoretical perspective of dynamics, structure, and thermodynamics. Advances in Chemical Physics, Vol. LXXI; 1988.
    • (1988) Advances in Chemical Physics , vol.71
    • Brooks, C.L.1    Karplus, M.2    Pettitt, B.M.3
  • 19
    • 0027407525 scopus 로고
    • Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamics
    • Venable RM, Brooks B, Carson FW. Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamics. Proteins 1993;15:374-384.
    • (1993) Proteins , vol.15 , pp. 374-384
    • Venable, R.M.1    Brooks, B.2    Carson, F.W.3
  • 20
    • 0028282687 scopus 로고
    • HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site
    • Eisen MB, Wiley DC, Karplus M, Hubbard RE. HOOK: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. Proteins 1994;19:199-221.
    • (1994) Proteins , vol.19 , pp. 199-221
    • Eisen, M.B.1    Wiley, D.C.2    Karplus, M.3    Hubbard, R.E.4
  • 21
    • 0029586802 scopus 로고
    • An automated method for dynamic ligand design
    • Miranker A, Karplus M. An automated method for dynamic ligand design. Proteins 1995;23:472-490.
    • (1995) Proteins , vol.23 , pp. 472-490
    • Miranker, A.1    Karplus, M.2
  • 22
    • 0345727597 scopus 로고    scopus 로고
    • Dynamic ligand design and combinatorial optimization: Application to endothiapepsin
    • in press
    • Stultz CM, Karplus M. Dynamic ligand design and combinatorial optimization: application to endothiapepsin. Proteins 2000: in press.
    • (2000) Proteins
    • Stultz, C.M.1    Karplus, M.2
  • 24
    • 0017411710 scopus 로고
    • The protein data bank: A computer-based archival file for macromolecular structures
    • Bernstein FC, Koetzle TF, Williams GJB, et al. The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
    • (1977) J Mol Biol , vol.112 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3
  • 25
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies and conformational analysis
    • Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies and conformational analysis. Proteins 1988;4:7-18.
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 26
    • 0032054517 scopus 로고    scopus 로고
    • Electrostatic effects in macromolecules: Fundamental concepts and practical modeling
    • Warshel A, Papazyan A. Electrostatic effects in macromolecules: fundamental concepts and practical modeling Curr Opin Struct Biol 1998;8:211-217.
    • (1998) Curr Opin Struct Biol , vol.8 , pp. 211-217
    • Warshel, A.1    Papazyan, A.2
  • 27
    • 0012227656 scopus 로고    scopus 로고
    • A comprehensive analytical treatment of continuum electrostatics
    • Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics. J Physical Chem 1996;100:1578-1599.
    • (1996) J Physical Chem , vol.100 , pp. 1578-1599
    • Schaefer, M.1    Karplus, M.2
  • 28
    • 0025225682 scopus 로고
    • X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor
    • Swain AL, Miller MM, Green J, et al. X-ray crystallographic structure of a complex between a synthetic protease of human immunodeficiency virus 1 and a substrate-based hydroxyethylamine inhibitor. Proc Nat Acad Sci USA 1990;87:8805-8809.
    • (1990) Proc Nat Acad Sci USA , vol.87 , pp. 8805-8809
    • Swain, A.L.1    Miller, M.M.2    Green, J.3
  • 30
    • 0029859529 scopus 로고    scopus 로고
    • Ionization states of the catalytic residues in HIV-1 protease
    • Smith R, Brereton IM, Chai RY, Kent SB. Ionization states of the catalytic residues in HIV-1 protease. Nat Struct Biol 1996;11:946-950.
    • (1996) Nat Struct Biol , vol.11 , pp. 946-950
    • Smith, R.1    Brereton, I.M.2    Chai, R.Y.3    Kent, S.B.4
  • 31
    • 0028114966 scopus 로고
    • NMR and X-ray evidence that the HIV protease catalytic aspartyl groups are protonated in the complex formed by the protease and a nonpeptide cyclic urea based inhibitor
    • Yamazaki T, Linda LK, Torchia DA, et al. NMR and X-ray evidence that the HIV protease catalytic aspartyl groups are protonated in the complex formed by the protease and a nonpeptide cyclic urea based inhibitor. J Am Chem Soc 1994;116: 10791-10792.
    • (1994) J Am Chem Soc , vol.116 , pp. 10791-10792
    • Yamazaki, T.1    Linda, L.K.2    Torchia, D.A.3
  • 33
    • 0024250301 scopus 로고
    • Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
    • Brunger AT, Karplus M. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins 1988;4:148-156.
    • (1988) Proteins , vol.4 , pp. 148-156
    • Brunger, A.T.1    Karplus, M.2
  • 34
    • 0024354001 scopus 로고
    • Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site of lysozyme
    • Brooks C, Karplus M. Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site of lysozyme. J Mol Biol 1989;208:159-181.
    • (1989) J Mol Biol , vol.208 , pp. 159-181
    • Brooks, C.1    Karplus, M.2
  • 35
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • Van Gunsteren WF, Berendsen HJC. Algorithms for macromolecular dynamics and constraint dynamics. Mol Phys 1977;34:1311-1327.
    • (1977) Mol Phys , vol.34 , pp. 1311-1327
    • Van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 36
    • 0000089213 scopus 로고
    • Energy equipartitioning in the classical time-dependent hartree approximation
    • Straub JE, Karplus M. Energy equipartitioning in the classical time-dependent hartree approximation. J Chem Phys 1991;94: 6737-6739.
    • (1991) J Chem Phys , vol.94 , pp. 6737-6739
    • Straub, J.E.1    Karplus, M.2
  • 37
    • 0001483109 scopus 로고
    • The thermal equilibrium aspects of the time-dependent-Hartree and the locally enhanced sampling approximations: Formal properties, a correction, and computational examples for rare gas clusters
    • Ulitsky A, Elber R. The thermal equilibrium aspects of the time-dependent-Hartree and the locally enhanced sampling approximations: formal properties, a correction, and computational examples for rare gas clusters J Chem Phys 1993;98:3380-3388.
    • (1993) J Chem Phys , vol.98 , pp. 3380-3388
    • Ulitsky, A.1    Elber, R.2
  • 40
    • 36449006131 scopus 로고
    • Modeling side chains in peptides and proteins: Applications of the locally enhanced sampling and the simulated annealing methods to finding minimum energy conformations
    • Roitberg A, Elber R. Modeling side chains in peptides and proteins: applications of the locally enhanced sampling and the simulated annealing methods to finding minimum energy conformations. J Chem Phys 1992;95:9277-9287.
    • (1992) J Chem Phys , vol.95 , pp. 9277-9287
    • Roitberg, A.1    Elber, R.2
  • 41
    • 0003995673 scopus 로고    scopus 로고
    • On the potential surface of the locally enhanced sampling approximation
    • Stultz CM, Karplus M. On the potential surface of the locally enhanced sampling approximation. J Chem Phys 1998;109:8809-8815.
    • (1998) J Chem Phys , vol.109 , pp. 8809-8815
    • Stultz, C.M.1    Karplus, M.2
  • 42
    • 0027219536 scopus 로고
    • Multiple copy simultaneous search and construction of ligands in binding sites: Application to inhibitors of HIV-1 aspartic proteinase
    • Caflisch A, Miranker A, Karplus M. Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. J Med Chem 1993;36:2142-2167.
    • (1993) J Med Chem , vol.36 , pp. 2142-2167
    • Caflisch, A.1    Miranker, A.2    Karplus, M.3
  • 43
    • 0030963674 scopus 로고    scopus 로고
    • Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs
    • McCarthy DJ, Hogle JM, Karplus M. Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs. Proteins 1997;29:32-58.
    • (1997) Proteins , vol.29 , pp. 32-58
    • McCarthy, D.J.1    Hogle, J.M.2    Karplus, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.