메뉴 건너뛰기




Volumn 34, Issue 1, 1999, Pages 29-48

New general approach for determining the solution structure of a ligand bound weakly to a receptor: Structure of a fibrinogen Aα-like peptide bound to thrombin(S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking program

Author keywords

Fibrinogen A ; Flexible docking; MR; Thrombin

Indexed keywords

FIBRINOGEN; LIGAND; MUTANT PROTEIN; PROLINE; RECEPTOR; THROMBIN;

EID: 0032910684     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990101)34:1<29::AID-PROT4>3.0.CO;2-U     Document Type: Article
Times cited : (28)

References (78)
  • 1
    • 0025252231 scopus 로고
    • 1H]-NMR spectroscopy: Combined use with isotope labelling for studies of macromolecular conformation and intermolecular interactions
    • 1H]-NMR spectroscopy: combined use with isotope labelling for studies of macromolecular conformation and intermolecular interactions. Q Rev Biophys 1990;23:39-96.
    • (1990) Q Rev Biophys , vol.23 , pp. 39-96
    • Otting, G.1    Wüthrich, K.2
  • 2
    • 0028673539 scopus 로고
    • Nuclear magnetic resonance methods for studying protein ligand complexes
    • Petros AM, Fesik SW. Nuclear magnetic resonance methods for studying protein ligand complexes. Methods Enzymol 1994;239: 717-739.
    • (1994) Methods Enzymol , vol.239 , pp. 717-739
    • Petros, A.M.1    Fesik, S.W.2
  • 3
    • 0028823713 scopus 로고
    • Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy
    • Gronenborn AM, Clore GM. Structures of protein complexes by multidimensional heteronuclear magnetic resonance spectroscopy. Crit Rev Biochem Mol Biol 1995;30:351-385.
    • (1995) Crit Rev Biochem Mol Biol , vol.30 , pp. 351-385
    • Gronenborn, A.M.1    Clore, G.M.2
  • 4
    • 0027215829 scopus 로고
    • The two-dimensional transferred nuclear overhauser effect: Theory and practice
    • Campbell AP, Sykes BD. The two-dimensional transferred nuclear Overhauser effect: theory and practice. Annu Rev Biophys Biomol Struct 1993;22:99-122.
    • (1993) Annu Rev Biophys Biomol Struct , vol.22 , pp. 99-122
    • Campbell, A.P.1    Sykes, B.D.2
  • 5
    • 0028728698 scopus 로고
    • Recent developments in transferred NOE methods
    • Ni F. Recent developments in transferred NOE methods. Prog NMR Spectrosc 1994;26:517-606.
    • (1994) Prog NMR Spectrosc , vol.26 , pp. 517-606
    • Ni, F.1
  • 6
    • 12044258461 scopus 로고
    • Use of the transferred nuclear overhauser effect to determine the conformations of ligands bound to proteins
    • Ni F, Scheraga HA. Use of the transferred nuclear Overhauser effect to determine the conformations of ligands bound to proteins. Acct Chem Res 1994;27:257-264.
    • (1994) Acct Chem Res , vol.27 , pp. 257-264
    • Ni, F.1    Scheraga, H.A.2
  • 7
    • 0029123503 scopus 로고
    • Solution structure of a brodimoprim analogue in its complex with Lactobacillus casei dihydrofolate reductase
    • Morgan WD, Birdsall B, Polshakov VI, Sali D, Komhis I, Feeney J. Solution structure of a brodimoprim analogue in its complex with Lactobacillus casei dihydrofolate reductase. Biochemistry 1995;34: 11690-11702.
    • (1995) Biochemistry , vol.34 , pp. 11690-11702
    • Morgan, W.D.1    Birdsall, B.2    Polshakov, V.I.3    Sali, D.4    Komhis, I.5    Feeney, J.6
  • 8
    • 0029619426 scopus 로고
    • Solution structure of a band 3 peptide inhibitor bound to aldolase: A proposed mechanism for regulating binding by tyrosine phosphorylation
    • Schneider ML, Post CB. Solution structure of a band 3 peptide inhibitor bound to aldolase: a proposed mechanism for regulating binding by tyrosine phosphorylation. Biochemistry 1995;34:16574-16584.
    • (1995) Biochemistry , vol.34 , pp. 16574-16584
    • Schneider, M.L.1    Post, C.B.2
  • 9
    • 0030064185 scopus 로고    scopus 로고
    • Structural resiliency of an EGF-like subdomain bound to its target protein, thrombin
    • Hrabal R, Komives EA, Ni F. Structural resiliency of an EGF-like subdomain bound to its target protein, thrombin. Protein Sci 1996;5:195-230.
    • (1996) Protein Sci , vol.5 , pp. 195-230
    • Hrabal, R.1    Komives, E.A.2    Ni, F.3
  • 11
    • 0032574755 scopus 로고    scopus 로고
    • Structural examination of the influence of phoshorylation on the binding of fibrinopeptide a to bovine thrombin
    • Maurer MC, Peng J-L, An SS, Trosset J-Y, Henschen-Edman A, Scheraga HA. Structural examination of the influence of phoshorylation on the binding of fibrinopeptide A to bovine thrombin. Biochemistry 1998;37:5888-5902.
    • (1998) Biochemistry , vol.37 , pp. 5888-5902
    • Maurer, M.C.1    Peng, J.-L.2    An, S.S.3    Trosset, J.-Y.4    Henschen-Edman, A.5    Scheraga, H.A.6
  • 12
    • 0002828995 scopus 로고    scopus 로고
    • B-spline method for energy minimization in grid-based molecular mechanics calculations
    • Oberlin D, Jr., Scheraga HA. B-spline method for energy minimization in grid-based molecular mechanics calculations. J Comput Chem 1998;19:71-85.
    • (1998) J Comput Chem , vol.19 , pp. 71-85
    • Oberlin D., Jr.1    Scheraga, H.A.2
  • 14
    • 0016694927 scopus 로고
    • Mechanism of action of thrombin on fibrinogen: On the role of the A-chain of bovine thrombin in specificity and in differentiating between thrombin and trypsin
    • Hageman TC, Endres GF, Scheraga HA. Mechanism of action of thrombin on fibrinogen: on the role of the A-chain of bovine thrombin in specificity and in differentiating between thrombin and trypsin. Arch Biochem Biophys 1975;171:327-336.
    • (1975) Arch Biochem Biophys , vol.171 , pp. 327-336
    • Hageman, T.C.1    Endres, G.F.2    Scheraga, H.A.3
  • 15
    • 0024431034 scopus 로고
    • The refined 1.9Å crystal structure of human α-thrombin: Interaction with D-Phe-Pro-Arg chloromethylketone and the significance of the Tyr-Pro-Pro-Trp insertion segment
    • Bode W, Mayr I, Baumann U, Huber R, Stone SR, Hofsteenge J. The refined 1.9Å crystal structure of human α-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and the significance of the Tyr-Pro-Pro-Trp insertion segment. EMBO J 1989;8:3467-3475.
    • (1989) EMBO J , vol.8 , pp. 3467-3475
    • Bode, W.1    Mayr, I.2    Baumann, U.3    Huber, R.4    Stone, S.R.5    Hofsteenge, J.6
  • 16
    • 0027409404 scopus 로고
    • A player of many parts: The spotlight falls on thrombin's structure
    • Stubbs MT, Bode W. A player of many parts: the spotlight falls on thrombin's structure. Thromb Res 1993;69:1-58.
    • (1993) Thromb Res , vol.69 , pp. 1-58
    • Stubbs, M.T.1    Bode, W.2
  • 17
    • 0025329390 scopus 로고
    • The structure of a complex of recombinant hirudin and human α-thrombin
    • Rydel TJ, Ravichandran KG, Tulinsky A, et al. The structure of a complex of recombinant hirudin and human α-thrombin. Science 1990;249:277-280.
    • (1990) Science , vol.249 , pp. 277-280
    • Rydel, T.J.1    Ravichandran, K.G.2    Tulinsky, A.3
  • 18
    • 0027050807 scopus 로고
    • The refined 1.9 Å X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human α-thrombin: Structural analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure function relationships
    • Bode W, Turk D, Karshikov A. The refined 1.9 Å X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human α-thrombin: structural analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure function relationships. Protein Sci 1992;1:426-471.
    • (1992) Protein Sci , vol.1 , pp. 426-471
    • Bode, W.1    Turk, D.2    Karshikov, A.3
  • 19
    • 0026657151 scopus 로고
    • The structure of residues 7-16 of the Aα chain of human fibrinogen bound to bovine thrombin at 2.3 Å resolution
    • Martin PD, Robertson W, Turk D, Huber R, Bode W, Edwards BFP. The structure of residues 7-16 of the Aα chain of human fibrinogen bound to bovine thrombin at 2.3 Å resolution. J Biol Chem 1992;267:7911-7920.
    • (1992) J Biol Chem , vol.267 , pp. 7911-7920
    • Martin, P.D.1    Robertson, W.2    Turk, D.3    Huber, R.4    Bode, W.5    Edwards, B.F.P.6
  • 20
    • 0027177515 scopus 로고
    • The role of thrombin's Tyr-Pro-Pro-Trp motif in the interaction with fibrinogen, thrombomodulin, protein C, antithrombin III, and the Kunitz inhibitors
    • Le Bonniec BF, Guinto ER, MacGillivray RTA, Stone SR, Esmon CT. The role of thrombin's Tyr-Pro-Pro-Trp motif in the interaction with fibrinogen, thrombomodulin, protein C, antithrombin III, and the Kunitz inhibitors. J Biol Chem 1993;268:19055-19061.
    • (1993) J Biol Chem , vol.268 , pp. 19055-19061
    • Le Bonniec, B.F.1    Guinto, E.R.2    MacGillivray, R.T.A.3    Stone, S.R.4    Esmon, C.T.5
  • 21
    • 0022369895 scopus 로고
    • Human α-thrombin binding to nonpolymerized fibrin-sepharose: Evidence for an anionic binding region
    • Berliner LJ, Sugawara Y, Fenton JW II. Human α-thrombin binding to nonpolymerized fibrin-Sepharose: evidence for an anionic binding region. Biochemistry 1985;24:7005-7009.
    • (1985) Biochemistry , vol.24 , pp. 7005-7009
    • Berliner, L.J.1    Sugawara, Y.2    Fenton J.W. II3
  • 22
    • 0024514373 scopus 로고
    • The hirudin-binding site of human α-thrombin: Identification of lysyl residues which participate in the combining site of hirudin-thrombin complex
    • Chang J-Y. The hirudin-binding site of human α-thrombin: identification of lysyl residues which participate in the combining site of hirudin-thrombin complex. J Biol Chem 1989;264:7141-7146.
    • (1989) J Biol Chem , vol.264 , pp. 7141-7146
    • Chang, J.-Y.1
  • 25
    • 0024584913 scopus 로고
    • Molecular modeling of protein-glycosaminoglycan interactions
    • Cardin AD, Weintraub HJR. Molecular modeling of protein-glycosaminoglycan interactions. Arteriosclerosis 1989;9:21-32.
    • (1989) Arteriosclerosis , vol.9 , pp. 21-32
    • Cardin, A.D.1    Weintraub, H.J.R.2
  • 26
    • 0020645340 scopus 로고
    • Interaction of thrombin and fibrinogen and the polymerization of fibrin monomer
    • Scheraga HA. Interaction of thrombin and fibrinogen and the polymerization of fibrin monomer. Ann NY Acad Sci 1983;408:330-343.
    • (1983) Ann NY Acad Sci , vol.408 , pp. 330-343
    • Scheraga, H.A.1
  • 27
    • 0022924075 scopus 로고
    • Chemical basis of thrombin interactions with fibrinogen
    • Scheraga HA. Chemical basis of thrombin interactions with fibrinogen. Ann NY Acad Sci 1986;485:124-133.
    • (1986) Ann NY Acad Sci , vol.485 , pp. 124-133
    • Scheraga, H.A.1
  • 28
    • 0024544276 scopus 로고
    • High-resolution NMR studies of fibrinogen-like peptides in solution: Structure of a thrombin-bound peptide corresponding to residues 7-16 of the Aα chain of human fibrinogen
    • Ni F, Meinwald YC, Vásquez M, Scheraga HA. High-resolution NMR studies of fibrinogen-like peptides in solution: structure of a thrombin-bound peptide corresponding to residues 7-16 of the Aα chain of human fibrinogen. Biochemistry 1989;28:3094-3105.
    • (1989) Biochemistry , vol.28 , pp. 3094-3105
    • Ni, F.1    Meinwald, Y.C.2    Vásquez, M.3    Scheraga, H.A.4
  • 29
    • 0029151607 scopus 로고
    • Thrombin-bound structures of designed analogs of human fibrinopeptide a determined by quantitative transferred NOE spectroscopy: A new structural basis for thrombin specificity
    • Ni F, Zhu Y, Scheraga HA. Thrombin-bound structures of designed analogs of human fibrinopeptide A determined by quantitative transferred NOE spectroscopy: a new structural basis for thrombin specificity. J Mol Biol 1995;252:656-671.
    • (1995) J Mol Biol , vol.252 , pp. 656-671
    • Ni, F.1    Zhu, Y.2    Scheraga, H.A.3
  • 30
    • 0025969580 scopus 로고
    • A synthetic analog of fibrinogen α 27-50 is an inhibitor of thrombin
    • Binnie CG, Lord ST. A synthetic analog of fibrinogen α 27-50 is an inhibitor of thrombin. Thromb Haemost 1991;65:165-168.
    • (1991) Thromb Haemost , vol.65 , pp. 165-168
    • Binnie, C.G.1    Lord, S.T.2
  • 31
    • 0008264410 scopus 로고    scopus 로고
    • Regulation of thrombin activity by ligand-induced conformational changes: A review
    • Gershkovich AA. Regulation of thrombin activity by ligand-induced conformational changes: a review. Biochemistry (Moscow) 1996;61:817-824.
    • (1996) Biochemistry (Moscow) , vol.61 , pp. 817-824
    • Gershkovich, A.A.1
  • 32
    • 0029819059 scopus 로고    scopus 로고
    • Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen Aα: Geometry of the catalytic triad and interactions of the P1′, P2′, and P3′ substrate residues
    • Martin PD, Malkowski MG, DiMaio J, Konishi Y, Ni F, Edwards BFP. Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen Aα: geometry of the catalytic triad and interactions of the P1′, P2′, and P3′ substrate residues. Biochemistry 1996;35:13030-13039.
    • (1996) Biochemistry , vol.35 , pp. 13030-13039
    • Martin, P.D.1    Malkowski, M.G.2    DiMaio, J.3    Konishi, Y.4    Ni, F.5    Edwards, B.F.P.6
  • 33
    • 0028897211 scopus 로고
    • Expression and folding of recombinant bovine prethrombin-2 and its activation to thrombin
    • DiBella EE, Maurer MC, Scheraga HA. Expression and folding of recombinant bovine prethrombin-2 and its activation to thrombin. J Biol Chem 1995;270:163-169.
    • (1995) J Biol Chem , vol.270 , pp. 163-169
    • DiBella, E.E.1    Maurer, M.C.2    Scheraga, H.A.3
  • 34
    • 0021364597 scopus 로고
    • Sensitive quantitative analysis of disulfide bonds in polypeptides and proteins
    • Thannhauser TW, Konishi Y, Scheraga HA. Sensitive quantitative analysis of disulfide bonds in polypeptides and proteins. Anal Biochem 1984;138:181-188.
    • (1984) Anal Biochem , vol.138 , pp. 181-188
    • Thannhauser, T.W.1    Konishi, Y.2    Scheraga, H.A.3
  • 35
    • 0024278405 scopus 로고
    • Structural studies of a folding intermediate of bovine pancreatic ribonuclease a by continuous recycled flow
    • Adler M, Scheraga HA. Structural studies of a folding intermediate of bovine pancreatic ribonuclease A by continuous recycled flow. Biochemistry 1988;27:2471-2480.
    • (1988) Biochemistry , vol.27 , pp. 2471-2480
    • Adler, M.1    Scheraga, H.A.2
  • 37
    • 79960698472 scopus 로고
    • Water suppression that works. Excitation sculpting using arbitrary waveforms and pulsed field gradients
    • Hwang T-L, Shaka AJ. Water suppression that works. Excitation sculpting using arbitrary waveforms and pulsed field gradients. J Magn Reson Ser A 1995;112:275-279.
    • (1995) J Magn Reson Ser A , vol.112 , pp. 275-279
    • Hwang, T.-L.1    Shaka, A.J.2
  • 38
    • 0023919814 scopus 로고
    • High resolution NMR studies of fibrinogen-like peptides in solution: Resonance assignments and conformational analysis of residues 1-23 of the Aα chain of human fibrinogen
    • Ni F, Scheraga HA, Lord ST. High resolution NMR studies of fibrinogen-like peptides in solution: resonance assignments and conformational analysis of residues 1-23 of the Aα chain of human fibrinogen. Biochemistry 1988;27:4481-4491.
    • (1988) Biochemistry , vol.27 , pp. 4481-4491
    • Ni, F.1    Scheraga, H.A.2    Lord, S.T.3
  • 40
    • 0017877274 scopus 로고
    • Nuclear magnetic resonance study of fibrinogen-like peptides and their structure in dimethyl sulfoxide and water
    • Von Dreele PH, Rae ID, Scheraga HA. Nuclear magnetic resonance study of fibrinogen-like peptides and their structure in dimethyl sulfoxide and water. Biochemistry 1978;17:956-962.
    • (1978) Biochemistry , vol.17 , pp. 956-962
    • Von Dreele, P.H.1    Rae, I.D.2    Scheraga, H.A.3
  • 41
    • 0342887354 scopus 로고
    • Clean selective excitation of heteronuclear spin systems
    • Bernassau J-M, Nuzillard J-M. Clean selective excitation of heteronuclear spin systems. J Magn Reson Ser A 1993;104:212-221.
    • (1993) J Magn Reson Ser A , vol.104 , pp. 212-221
    • Bernassau, J.-M.1    Nuzillard, J.-M.2
  • 42
    • 58149364806 scopus 로고
    • Improved HMQC-type and HSQC-type 1D spectra using pulsed field gradients
    • Parella T, Sánchez-Ferrando F, Virgili A. Improved HMQC-type and HSQC-type 1D spectra using pulsed field gradients. J Magn Reson Ser A 1995;114:32-38.
    • (1995) J Magn Reson Ser A , vol.114 , pp. 32-38
    • Parella, T.1    Sánchez-Ferrando, F.2    Virgili, A.3
  • 43
    • 0000393431 scopus 로고
    • Theory and applications of the transferred nuclear overhauser effect to the study of the conformations of small ligands bound to proteins
    • Clore GM, Gronenborn AM. Theory and applications of the transferred nuclear Overhauser effect to the study of the conformations of small ligands bound to proteins. J Magn Reson 1982;48: 402-417.
    • (1982) J Magn Reson , vol.48 , pp. 402-417
    • Clore, G.M.1    Gronenborn, A.M.2
  • 44
    • 0001342923 scopus 로고
    • Theory of the time dependent transferred nuclear overhauser effect: Applications to structural analysis of ligand-protein complexes in solution
    • Clore GM, Gronenborn AM. Theory of the time dependent transferred nuclear overhauser effect: applications to structural analysis of ligand-protein complexes in solution. J Magn Reson 1983;53: 423-442.
    • (1983) J Magn Reson , vol.53 , pp. 423-442
    • Clore, G.M.1    Gronenborn, A.M.2
  • 45
    • 0026089657 scopus 로고
    • Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS, and GLOMSA
    • Güntert P, Braun W, Wüthrich K. Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS, and GLOMSA. J Mol Biol 1991;217: 517-530.
    • (1991) J Mol Biol , vol.217 , pp. 517-530
    • Güntert, P.1    Braun, W.2    Wüthrich, K.3
  • 46
    • 0026011496 scopus 로고
    • Structure determination of the Antp(C39→s) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS, and GLOMSA
    • Güntert P, Qian YQ, Otting G, Müller M, Gehring W, Wüthrich K. Structure determination of the Antp(C39→S) homeodomain from nuclear magnetic resonance data in solution using a novel strategy for the structure calculation with the programs DIANA, CALIBA, HABAS, and GLOMSA. J Mol Biol 1991;217:531-540.
    • (1991) J Mol Biol , vol.217 , pp. 531-540
    • Güntert, P.1    Qian, Y.Q.2    Otting, G.3    Müller, M.4    Gehring, W.5    Wüthrich, K.6
  • 47
    • 0026259488 scopus 로고
    • Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints
    • Güntert P, Wüthrich K. Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J Biomol NMR 1991;1:447-456.
    • (1991) J Biomol NMR , vol.1 , pp. 447-456
    • Güntert, P.1    Wüthrich, K.2
  • 48
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Némethy G, Gibson KD, Palmer KA, et al. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 1992;96: 6472-6484.
    • (1992) J Phys Chem , vol.96 , pp. 6472-6484
    • Némethy, G.1    Gibson, K.D.2    Palmer, K.A.3
  • 49
    • 0345483185 scopus 로고    scopus 로고
    • PRODOCK: A software package for protein modeling and docking
    • in press
    • Trosset J-Y, Scheraga HA. PRODOCK: A software package for protein modeling and docking. J Comp Chem 1999, in press.
    • (1999) J Comp Chem
    • Trosset, J.-Y.1    Scheraga, H.A.2
  • 50
    • 0032493375 scopus 로고    scopus 로고
    • Reaching the global minimum in docking simulations: A Monte Carlo energy minimization approach using bezier splines
    • Trosset J-Y, Scheraga HA. Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines. Proc Natl Acad Sci USA 1998;95:8011-8015.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 8011-8015
    • Trosset, J.-Y.1    Scheraga, H.A.2
  • 51
    • 0023998438 scopus 로고
    • Determination of three dimensional structures of protein by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2
    • Nilges M, Gronenborn AM, Brünger AT, Clore GM. Determination of three dimensional structures of protein by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng 1988;2:27-38.
    • (1988) Protein Eng , vol.2 , pp. 27-38
    • Nilges, M.1    Gronenborn, A.M.2    Brünger, A.T.3    Clore, G.M.4
  • 52
    • 0022036264 scopus 로고
    • Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins
    • Noguti T, Gō N. Efficient Monte Carlo method for simulation of fluctuating conformations of native proteins. Biopolymers 1985;24: 527-546.
    • (1985) Biopolymers , vol.24 , pp. 527-546
    • Noguti, T.1    Go, N.2
  • 53
    • 0023430366 scopus 로고
    • Monte Carlo minimization approach to the multiple-minima problem in protein folding
    • Li Z, Scheraga HA. Monte Carlo minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 1987;84:6611-6615.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 54
    • 0001643360 scopus 로고
    • Structure and free energy of complex thermodynamic systems
    • Li Z, Scheraga HA. Structure and free energy of complex thermodynamic systems. J Mol Struct (Theochem) 1988;179:333-352.
    • (1988) J Mol Struct (Theochem) , vol.179 , pp. 333-352
    • Li, Z.1    Scheraga, H.A.2
  • 55
    • 0020949717 scopus 로고
    • Algorithm 611. Subroutines for unconstrained minimization using a model/trust-region approach
    • Gay DM. Algorithm 611. Subroutines for unconstrained minimization using a model/trust-region approach. Assoc Comput Math Trans Math Software 1983;9:503-524.
    • (1983) Assoc Comput Math Trans Math Software , vol.9 , pp. 503-524
    • Gay, D.M.1
  • 56
    • 0024550340 scopus 로고
    • High resolution NMR studies of fibrinogen-like peptides in solution: Interaction of thrombin with residues 1-23 of the Aα chain of human fibrinogen
    • Ni F, Konishi Y, Frazier RB, Lord ST, Scheraga HA. High resolution NMR studies of fibrinogen-like peptides in solution: interaction of thrombin with residues 1-23 of the Aα chain of human fibrinogen. Biochemistry 1989;28:3082-3094.
    • (1989) Biochemistry , vol.28 , pp. 3082-3094
    • Ni, F.1    Konishi, Y.2    Frazier, R.B.3    Lord, S.T.4    Scheraga, H.A.5
  • 57
    • 0004167344 scopus 로고
    • Nuclear magnetic resonance studies of thrombin fibrinopeptide and thrombin-hirudin complexes
    • Berliner LJ, editor New York: Plenum Press
    • Ni F, Gibson KD, Scheraga HA. Nuclear magnetic resonance studies of thrombin fibrinopeptide and thrombin-hirudin complexes. In: Berliner LJ, editor. Thrombin: structure and function. New York: Plenum Press; 1992. p 63-85.
    • (1992) Thrombin: Structure and Function , pp. 63-85
    • Ni, F.1    Gibson, K.D.2    Scheraga, H.A.3
  • 58
    • 0026635368 scopus 로고
    • Thrombin hydrolysis of an N-terminal peptide from fibrinogen lille: Kinetic and NMR studies
    • Zheng Z, Ashton RW, Ni F, Scheraga HA. Thrombin hydrolysis of an N-terminal peptide from fibrinogen Lille: kinetic and NMR studies. Biochemistry 1992;31:4426-4431.
    • (1992) Biochemistry , vol.31 , pp. 4426-4431
    • Zheng, Z.1    Ashton, R.W.2    Ni, F.3    Scheraga, H.A.4
  • 60
    • 0026459469 scopus 로고
    • Solution structure of a platelet receptor peptide bound to bovine α-thrombin
    • Ni F, Ripoll DR, Martin PD, Edwards BFP. solution structure of a platelet receptor peptide bound to bovine α-thrombin. Biochemistry 1992;31:11551-11557.
    • (1992) Biochemistry , vol.31 , pp. 11551-11557
    • Ni, F.1    Ripoll, D.R.2    Martin, P.D.3    Edwards, B.F.P.4
  • 61
    • 0028381004 scopus 로고
    • Accounting for ligand-protein interactions in the relaxation-matrix analysis of transferred nuclear overhauser effects
    • Ni F, Zhu Y. Accounting for ligand-protein interactions in the relaxation-matrix analysis of transferred nuclear Overhauser effects. J Magn Reson Ser B 1994;103:180-184.
    • (1994) J Magn Reson Ser B , vol.103 , pp. 180-184
    • Ni, F.1    Zhu, Y.2
  • 62
    • 0011491177 scopus 로고
    • Structure determination of tetrasaccharide: Transient nuclear overhauser effects in the rotating frame
    • Bothner-By AA, Stephens RL, Lee J. Structure determination of tetrasaccharide: transient nuclear Overhauser effects in the rotating frame. J Am Chem Soc 1984;106:811-813.
    • (1984) J Am Chem Soc , vol.106 , pp. 811-813
    • Bothner-By, A.A.1    Stephens, R.L.2    Lee, J.3
  • 63
    • 0029243119 scopus 로고
    • Identification of protein-mediated indirect NOE effects in a disaccharide-Fab' complex by transferred ROESY
    • Arepalli SR, Glaudemans CPJ, Daves GD Jr, Kovac P, Bax A. Identification of protein-mediated indirect NOE effects in a disaccharide-Fab' complex by transferred ROESY. J Magn Res Ser B 1995;106:195-198.
    • (1995) J Magn Res Ser B , vol.106 , pp. 195-198
    • Arepalli, S.R.1    Glaudemans, C.P.J.2    Daves G.D., Jr.3    Kovac, P.4    Bax, A.5
  • 64
    • 0345483182 scopus 로고
    • Two-dimensional transferred nuclear-overhauser effects with incomplete averaging of free- and bound-ligand resonances
    • Ni F. Two-dimensional transferred nuclear-Overhauser effects with incomplete averaging of free-and bound-ligand resonances. J Magn Reson Ser B 1995;106:147-155.
    • (1995) J Magn Reson Ser B , vol.106 , pp. 147-155
    • Ni, F.1
  • 65
    • 0001151042 scopus 로고    scopus 로고
    • An efficient, differentiable, hydration potential for peptides and proteins
    • Augspurger JD, Scheraga HA. An efficient, differentiable, hydration potential for peptides and proteins. J Comp Chem 1996;17: 1549-1558.
    • (1996) J Comp Chem , vol.17 , pp. 1549-1558
    • Augspurger, J.D.1    Scheraga, H.A.2
  • 66
    • 0026548768 scopus 로고
    • The interaction of thrombin with fibrinogen. A structural basis for its specificity
    • Stubbs MT, Oschkinat H, Mayr I, et al. The interaction of thrombin with fibrinogen. A structural basis for its specificity. Eur J Biochem 1992;206:187-195.
    • (1992) Eur J Biochem , vol.206 , pp. 187-195
    • Stubbs, M.T.1    Oschkinat, H.2    Mayr, I.3
  • 67
    • 0027487088 scopus 로고
    • Crystal structure of the complex of human α-thrombin and nonhydrolyzable bifunctional inhibitors, hirutonin-2 and hirutonin-6
    • Zdanov A, Wu S, DiMaio J, et al. Crystal structure of the complex of human α-thrombin and nonhydrolyzable bifunctional inhibitors, hirutonin-2 and hirutonin-6. Proteins 1993;17:252-265.
    • (1993) Proteins , vol.17 , pp. 252-265
    • Zdanov, A.1    Wu, S.2    DiMaio, J.3
  • 68
    • 0025338124 scopus 로고
    • Thrombin-bound conformation of the C-terminal fragments of hirudin determined by transferred nuclear overhauser effects
    • Ni F, Konishi Y, Scheraga HA. Thrombin-bound conformation of the C-terminal fragments of hirudin determined by transferred nuclear Overhauser effects. Biochemistry 1990;29:4479-4489.
    • (1990) Biochemistry , vol.29 , pp. 4479-4489
    • Ni, F.1    Konishi, Y.2    Scheraga, H.A.3
  • 69
    • 0026493575 scopus 로고
    • Structure of the hirulog 3-thrombin complex and nature of the S′ subsites of substrates and inhibitors
    • Qiu X, Padmanabhan KP, Carperos VE, et al. Structure of the hirulog 3-thrombin complex and nature of the S′ subsites of substrates and inhibitors. Biochemistry 1992;31:11689-11697.
    • (1992) Biochemistry , vol.31 , pp. 11689-11697
    • Qiu, X.1    Padmanabhan, K.P.2    Carperos, V.E.3
  • 70
    • 16144365754 scopus 로고    scopus 로고
    • Enzyme flexibility, solvent and "weak" interactions characterize thrombin-ligand interactions: Implications for drug design
    • Engh RA, Brandstetter H, Sucher G, et al. Enzyme flexibility, solvent and "weak" interactions characterize thrombin-ligand interactions: implications for drug design. Structure 1996;4:1353-1362.
    • (1996) Structure , vol.4 , pp. 1353-1362
    • Engh, R.A.1    Brandstetter, H.2    Sucher, G.3
  • 71
    • 0030802519 scopus 로고    scopus 로고
    • The co-crystal structure of unliganded bovine α-thrombin and prethrombin-2: Movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding
    • Malkowski MG, Martin PD, Guzik JC, Edwards BFP. The co-crystal structure of unliganded bovine α-thrombin and prethrombin-2: movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding. Protein Sci 1997;6:1438-1448.
    • (1997) Protein Sci , vol.6 , pp. 1438-1448
    • Malkowski, M.G.1    Martin, P.D.2    Guzik, J.C.3    Edwards, B.F.P.4
  • 72
    • 54749102266 scopus 로고    scopus 로고
    • Thrombin specificity: Further evidence for the importance of the β-insertion loop and Trp 96. Implications of the hydrophobic interaction between Trp 96 and Pro 60B Pro60C for the activity of thrombin
    • DiBella EE, Scheraga HA. Thrombin specificity: further evidence for the importance of the β-insertion loop and Trp 96. Implications of the hydrophobic interaction between Trp 96 and Pro 60B Pro60C for the activity of thrombin. J Protein Chem 1998;17:197-208.
    • (1998) J Protein Chem , vol.17 , pp. 197-208
    • DiBella, E.E.1    Scheraga, H.A.2
  • 74
    • 0029014036 scopus 로고
    • An allosteric switch controls the procoagulant and anticoagulant activities of thrombin
    • Dang QD, Vindigni A, Di Cera E. An allosteric switch controls the procoagulant and anticoagulant activities of thrombin. Proc Natl Acad Sci USA 1995;92:5977-5981.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 5977-5981
    • Dang, Q.D.1    Vindigni, A.2    Di Cera, E.3
  • 78
    • 0030933791 scopus 로고    scopus 로고
    • Critical role of W60d in thrombin allostery
    • Guinto ER, Di Cera E. Critical role of W60d in thrombin allostery. Biophys Chem 1997;64:103-109.
    • (1997) Biophys Chem , vol.64 , pp. 103-109
    • Guinto, E.R.1    Di Cera, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.