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Volumn 1794, Issue 6, 2009, Pages 873-881

Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases

Author keywords

Crystallography; Molecular dynamic simulation; Small angle X ray scattering; Suramin; Thrombin

Indexed keywords

FIBRINOGEN; NANOPARTICLE; SURAMIN; THROMBIN;

EID: 67349239065     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2009.03.011     Document Type: Article
Times cited : (24)

References (62)
  • 1
    • 0027409404 scopus 로고
    • A player of many parts: the spotlight falls on thrombin's structure
    • Stubbs M.T., and Bode W. A player of many parts: the spotlight falls on thrombin's structure. Thromb. Res. 69 (1993) 1-58
    • (1993) Thromb. Res. , vol.69 , pp. 1-58
    • Stubbs, M.T.1    Bode, W.2
  • 2
    • 19744372264 scopus 로고    scopus 로고
    • Synthetic heparin derivatives as new anticoagulant drugs
    • de Kort M., Buijsman R.C., and van Boeckel C.A. Synthetic heparin derivatives as new anticoagulant drugs. Drug Discov. Today 10 (2005) 769-779
    • (2005) Drug Discov. Today , vol.10 , pp. 769-779
    • de Kort, M.1    Buijsman, R.C.2    van Boeckel, C.A.3
  • 3
    • 10344241475 scopus 로고    scopus 로고
    • Progress in the design of low molecular weight thrombin inhibitors
    • Srivastava S., Goswami L.N., and Dikshit D.K. Progress in the design of low molecular weight thrombin inhibitors. Med. Res. Rev. 25 (2005) 66-92
    • (2005) Med. Res. Rev. , vol.25 , pp. 66-92
    • Srivastava, S.1    Goswami, L.N.2    Dikshit, D.K.3
  • 5
    • 0034079646 scopus 로고    scopus 로고
    • Antitumour activity of suramin analogues in human tumour cell lines and primary cultures of tumour cells from patients
    • Dhar S., Gullbo J., Csoka K., Eriksson E., Nilsson K., Nickel P., Larsson R., and Nygren P. Antitumour activity of suramin analogues in human tumour cell lines and primary cultures of tumour cells from patients. Eur. J. Cancer 36 (2000) 803-809
    • (2000) Eur. J. Cancer , vol.36 , pp. 803-809
    • Dhar, S.1    Gullbo, J.2    Csoka, K.3    Eriksson, E.4    Nilsson, K.5    Nickel, P.6    Larsson, R.7    Nygren, P.8
  • 8
    • 34247874611 scopus 로고    scopus 로고
    • Suramin counteracts the haemostatic disturbances produced by Bothrops jararaca snake venom
    • Fernandes R.S., Assafim M., Arruda E.Z., Melo P.A., Zingali R.B., and Q Monteiro R. Suramin counteracts the haemostatic disturbances produced by Bothrops jararaca snake venom. Toxicon 49 (2007) 931-938
    • (2007) Toxicon , vol.49 , pp. 931-938
    • Fernandes, R.S.1    Assafim, M.2    Arruda, E.Z.3    Melo, P.A.4    Zingali, R.B.5    Q Monteiro, R.6
  • 9
    • 2942627710 scopus 로고    scopus 로고
    • Suramin interaction with human alpha-thrombin: inhibitory effects and binding studies
    • Monteiro R.Q., Campana P.T., Melo P.A., and Bianconi M.L. Suramin interaction with human alpha-thrombin: inhibitory effects and binding studies. Int. J. Biochem. Cell Biol. 36 (2004) 2077-2085
    • (2004) Int. J. Biochem. Cell Biol. , vol.36 , pp. 2077-2085
    • Monteiro, R.Q.1    Campana, P.T.2    Melo, P.A.3    Bianconi, M.L.4
  • 10
    • 0026317507 scopus 로고
    • A novel one-step purification of human α-thrombin after direct activation of crude prothrombin enriched from plasma
    • Ngai P.K., and Chang J.Y. A novel one-step purification of human α-thrombin after direct activation of crude prothrombin enriched from plasma. Biochem. J. 280 (1991) 805-808
    • (1991) Biochem. J. , vol.280 , pp. 805-808
    • Ngai, P.K.1    Chang, J.Y.2
  • 11
    • 0017725427 scopus 로고    scopus 로고
    • J.W. Fenton II, M.J. Fasco, A.B. Stackrow, D.L. Aronson, A.M. Young, J.S. Finlayson, Human thrombins. Production, evaluation, and properties of alpha-thrombin, J. Biol. Chem. 252, 3587-3598.
    • J.W. Fenton II, M.J. Fasco, A.B. Stackrow, D.L. Aronson, A.M. Young, J.S. Finlayson, Human thrombins. Production, evaluation, and properties of alpha-thrombin, J. Biol. Chem. 252, 3587-3598.
  • 12
    • 0028871804 scopus 로고
    • How to measure and predict the molar absorption coefficient of a protein
    • 1995
    • Pace C.N., Vajdos F., Fee L., Grimsley G., and Gray T. How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4 (1977) 2411-2423 1995
    • (1977) Protein Sci. , vol.4 , pp. 2411-2423
    • Pace, C.N.1    Vajdos, F.2    Fee, L.3    Grimsley, G.4    Gray, T.5
  • 18
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: an automated program for molecular replacement
    • Vagin A., and Teplyakov A. MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 30 (1997) 1022-1025
    • (1997) J. Appl. Cryst. , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 20
    • 0027050807 scopus 로고
    • The refined 1.9 Å crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment
    • Bode W., Turk D., and Karshikov A. The refined 1.9 Å crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment. Protein Sci. 1 (1992) 426-471
    • (1992) Protein Sci. , vol.1 , pp. 426-471
    • Bode, W.1    Turk, D.2    Karshikov, A.3
  • 21
  • 22
    • 13244281317 scopus 로고    scopus 로고
    • Coot: model-building tools for molecular graphics
    • Emsley P., and Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D60 (2004) 2126-2132
    • (2004) Acta Crystallogr. , vol.D60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 23
    • 0001099937 scopus 로고
    • Traitement statistique des erreurs dans la determination des structures cristallines
    • Luzzati V. Traitement statistique des erreurs dans la determination des structures cristallines. Acta Crystallogr. 5 (1952) 802-810
    • (1952) Acta Crystallogr. , vol.5 , pp. 802-810
    • Luzzati, V.1
  • 24
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R., MacArthur M., Moss D., and Thornton J. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26 (1993) 283-291
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.1    MacArthur, M.2    Moss, D.3    Thornton, J.4
  • 25
    • 0000268861 scopus 로고
    • Calculation of an omit map
    • Bhat B.W. Calculation of an omit map. J. Appl. Crystallogr. 21 (1988) 279-281
    • (1988) J. Appl. Crystallogr. , vol.21 , pp. 279-281
    • Bhat, B.W.1
  • 26
    • 0001408294 scopus 로고    scopus 로고
    • Computation of Bhat's OMIT maps with different coefficients
    • Vellieux F.M.D., and Dijkstra B.W. Computation of Bhat's OMIT maps with different coefficients. J. Appl. Crystallogr. 30 (1997) 396-399
    • (1997) J. Appl. Crystallogr. , vol.30 , pp. 396-399
    • Vellieux, F.M.D.1    Dijkstra, B.W.2
  • 27
    • 0028103275 scopus 로고
    • The CCP4 suite: programs for protein crystallography
    • Collaborative Computational Project, Number 4
    • Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50 (1994) 760-763
    • (1994) Acta Crystallogr. , vol.D50 , pp. 760-763
  • 28
    • 67349244205 scopus 로고    scopus 로고
    • DeLano Scientific LLC, San Carlos, CA, USA
    • W. L. DeLano, The PyMOL Molecular Graphics System. DeLano Scientific LLC, San Carlos, CA, USA (http://www.pymol.org), 2002.
    • (2002)
    • DeLano, W.L.1
  • 31
    • 0026910457 scopus 로고
    • Determination of the regularization parameter in indirect-transform methods using perceptual criteria
    • Svergun D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 25 (1992) 495-503
    • (1992) J. Appl. Crystallogr. , vol.25 , pp. 495-503
    • Svergun, D.I.1
  • 32
    • 0036932412 scopus 로고    scopus 로고
    • Solution studies and structural model of the extracellular domain of the human amyloid precursor protein
    • Gralle M., Botelho M.M., de Oliveira C.L., Torriani I., and Ferreira S.T. Solution studies and structural model of the extracellular domain of the human amyloid precursor protein. Biophys. J. 83 (2002) 3513-3524
    • (2002) Biophys. J. , vol.83 , pp. 3513-3524
    • Gralle, M.1    Botelho, M.M.2    de Oliveira, C.L.3    Torriani, I.4    Ferreira, S.T.5
  • 33
    • 34248397195 scopus 로고    scopus 로고
    • Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering
    • Mylonas E., and Svergun D.I. Accuracy of molecular mass determination of proteins in solution by small-angle X-ray scattering. J. Appl. Crystallogr. 40 (Supplement) (2007) s245-s249
    • (2007) J. Appl. Crystallogr. , vol.40 SUPPL.
    • Mylonas, E.1    Svergun, D.I.2
  • 35
    • 0035861454 scopus 로고    scopus 로고
    • Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF
    • de Groot B.L., and Grubmüller H. Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF. Science 294 (2001) 2353-2357
    • (2001) Science , vol.294 , pp. 2353-2357
    • de Groot, B.L.1    Grubmüller, H.2
  • 37
    • 33846823909 scopus 로고
    • Particle mesh Ewald - an N log(N) method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald - an N log(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 39
    • 0030158429 scopus 로고    scopus 로고
    • PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
    • van Aalten D.M.F., Bywater B., Findlay J.B.C., Hendlich M., Hooft R.W.W., and Vriend G. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aided Mol. Des. 10 (1996) 255-262
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 255-262
    • van Aalten, D.M.F.1    Bywater, B.2    Findlay, J.B.C.3    Hendlich, M.4    Hooft, R.W.W.5    Vriend, G.6
  • 40
    • 0346786323 scopus 로고    scopus 로고
    • Molecular dynamics simulation of a decasaccharide fragment of heparin in aqueous solution
    • Verli H., and Guimarães J.A. Molecular dynamics simulation of a decasaccharide fragment of heparin in aqueous solution. Carbohydr. Res. 339 (2004) 281-290
    • (2004) Carbohydr. Res. , vol.339 , pp. 281-290
    • Verli, H.1    Guimarães, J.A.2
  • 41
    • 27144559598 scopus 로고    scopus 로고
    • Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulation
    • Verli H., and Guimaraes J.A. Insights into the induced fit mechanism in antithrombin-heparin interaction using molecular dynamics simulation. J Mol. Graph. Model. 24 (2005) 203-212
    • (2005) J Mol. Graph. Model. , vol.24 , pp. 203-212
    • Verli, H.1    Guimaraes, J.A.2
  • 42
    • 13244270050 scopus 로고    scopus 로고
    • Crystal structure of thrombin bound to heparin
    • Carter W.J., Cama E., and Huntington J.A. Crystal structure of thrombin bound to heparin. J. Biol. Chem. 280 (2005) 2745-2749
    • (2005) J. Biol. Chem. , vol.280 , pp. 2745-2749
    • Carter, W.J.1    Cama, E.2    Huntington, J.A.3
  • 43
    • 22444436454 scopus 로고    scopus 로고
    • The limit of accuracy of protein modeling: influence of crystal packing on protein structure
    • Eyal E., Gerzon S., Potapov V., Edelman M., and Sobolev V. The limit of accuracy of protein modeling: influence of crystal packing on protein structure. J. Mol. Biol. 351 (2005) 431-442
    • (2005) J. Mol. Biol. , vol.351 , pp. 431-442
    • Eyal, E.1    Gerzon, S.2    Potapov, V.3    Edelman, M.4    Sobolev, V.5
  • 44
    • 34347227780 scopus 로고    scopus 로고
    • Molecular dynamics analysis of HIV-1 matrix protein: clarifying differences between crystallographic and solution structures
    • Verli H., Calazans A., Brindeiro R., Tanuri A., and Guimarães J.A. Molecular dynamics analysis of HIV-1 matrix protein: clarifying differences between crystallographic and solution structures. J. Mol. Graph. Model. 26 (2007) 62-68
    • (2007) J. Mol. Graph. Model. , vol.26 , pp. 62-68
    • Verli, H.1    Calazans, A.2    Brindeiro, R.3    Tanuri, A.4    Guimarães, J.A.5
  • 45
    • 33846813813 scopus 로고    scopus 로고
    • Structural and functional behavior of biologically active monomeric melittin
    • Terra R.M.S., Guimaraes J.A., and Verli H. Structural and functional behavior of biologically active monomeric melittin. J. Mol. Graph. Model. 25 (2007) 767-772
    • (2007) J. Mol. Graph. Model. , vol.25 , pp. 767-772
    • Terra, R.M.S.1    Guimaraes, J.A.2    Verli, H.3
  • 46
    • 0014669944 scopus 로고
    • The modification of yeast hexokinases by proteases and its relationship to the dissociation of hexokinase into subunits
    • Schulze I.T., and Colowick S.P. The modification of yeast hexokinases by proteases and its relationship to the dissociation of hexokinase into subunits. J. Biol. Chem. 244 (1969) 2306-2316
    • (1969) J. Biol. Chem. , vol.244 , pp. 2306-2316
    • Schulze, I.T.1    Colowick, S.P.2
  • 47
    • 0026743039 scopus 로고
    • Kinetics of the monomer-dimer reaction of yeast hexokinase PI
    • Hoggett J.G., and Kellett G.L. Kinetics of the monomer-dimer reaction of yeast hexokinase PI. Biochem. J. 287 (1992) 567-572
    • (1992) Biochem. J. , vol.287 , pp. 567-572
    • Hoggett, J.G.1    Kellett, G.L.2
  • 48
    • 4243120936 scopus 로고    scopus 로고
    • Invited review: beta-lactoglobulin: binding properties, structure, and function
    • Kontopidis G., Holt C., and Sawyer L. Invited review: beta-lactoglobulin: binding properties, structure, and function. J. Dairy Sci. 87 (2004) 785-796
    • (2004) J. Dairy Sci. , vol.87 , pp. 785-796
    • Kontopidis, G.1    Holt, C.2    Sawyer, L.3
  • 49
    • 0019133627 scopus 로고
    • Structure of a complex between yeast hexokinase A and glucose. I. Structure determination and refinement at 3.5 A resolution
    • Bennett Jr. W.S., and Steitz T.A. Structure of a complex between yeast hexokinase A and glucose. I. Structure determination and refinement at 3.5 A resolution. J. Mol. Biol. 140 (1980) 183
    • (1980) J. Mol. Biol. , vol.140 , pp. 183
    • Bennett Jr., W.S.1    Steitz, T.A.2
  • 50
    • 0034617194 scopus 로고    scopus 로고
    • The high resolution crystal structure of yeast hexokinase PII with the correct primary sequence provides new insights into its mechanism of action
    • Kuser P.R., Krauchenco S., Antunes O.A., and Polikarpov I. The high resolution crystal structure of yeast hexokinase PII with the correct primary sequence provides new insights into its mechanism of action. J. Biol. Chem. 275 (2000) 20814-20821
    • (2000) J. Biol. Chem. , vol.275 , pp. 20814-20821
    • Kuser, P.R.1    Krauchenco, S.2    Antunes, O.A.3    Polikarpov, I.4
  • 51
    • 0034825616 scopus 로고    scopus 로고
    • Crystal structures of bovine beta-lactoglobulin in the orthorhombic space group C222(1). Structural differences between genetic variants A and B and features of the Tanford transit
    • Oliveira K.M., Valente-Mesquita V.L., Botelho M.M., Sawyer L., Ferreira S.T., and Polikarpov I. Crystal structures of bovine beta-lactoglobulin in the orthorhombic space group C222(1). Structural differences between genetic variants A and B and features of the Tanford transit. Eur. J. Biochem. 268 (2001) 477-483
    • (2001) Eur. J. Biochem. , vol.268 , pp. 477-483
    • Oliveira, K.M.1    Valente-Mesquita, V.L.2    Botelho, M.M.3    Sawyer, L.4    Ferreira, S.T.5    Polikarpov, I.6
  • 52
    • 35748982423 scopus 로고    scopus 로고
    • Analysis of X-ray and neutron scattering from biomacromolecular solutions
    • Petoukhov M.V., and Svergun D.I. Analysis of X-ray and neutron scattering from biomacromolecular solutions. Curr. Op. Str. Biol. 17 (2007) 562-571
    • (2007) Curr. Op. Str. Biol. , vol.17 , pp. 562-571
    • Petoukhov, M.V.1    Svergun, D.I.2
  • 58
    • 27144470266 scopus 로고    scopus 로고
    • Use-dependent inhibition of the skeletal muscle ryanodine receptor by the suramin analogue NF676
    • Wolner I., Kassack M.U., Ullmann H., Karel A., and Hohenegger M. Use-dependent inhibition of the skeletal muscle ryanodine receptor by the suramin analogue NF676. Br. J. Pharmacol. 146 (2005) 525-533
    • (2005) Br. J. Pharmacol. , vol.146 , pp. 525-533
    • Wolner, I.1    Kassack, M.U.2    Ullmann, H.3    Karel, A.4    Hohenegger, M.5
  • 59
    • 9644258969 scopus 로고    scopus 로고
    • Crystallization and preliminary X-ray diffraction analysis of suramin, a highly charged polysulfonated napthylurea, complexed with a myotoxic PLA2 from Bothrops asper venom
    • Murakami M.T., Gava L.M., Zela S.P., Arruda E.Z., Melo P.A., Gutierrez J.M., and Arni R.K. Crystallization and preliminary X-ray diffraction analysis of suramin, a highly charged polysulfonated napthylurea, complexed with a myotoxic PLA2 from Bothrops asper venom. Biochim. Biophys. Acta 1703 (2004) 83-85
    • (2004) Biochim. Biophys. Acta , vol.1703 , pp. 83-85
    • Murakami, M.T.1    Gava, L.M.2    Zela, S.P.3    Arruda, E.Z.4    Melo, P.A.5    Gutierrez, J.M.6    Arni, R.K.7
  • 60
    • 23844501931 scopus 로고    scopus 로고
    • Structural basis for antagonism by suramin of heparin binding to vaccinia complement protein
    • Ganesh V.K., Muthuvel S.K., Smith S.A., Kotwal G.J., and Murthy K.H.M. Structural basis for antagonism by suramin of heparin binding to vaccinia complement protein. Biochemistry 44 (2005) 10757-10765
    • (2005) Biochemistry , vol.44 , pp. 10757-10765
    • Ganesh, V.K.1    Muthuvel, S.K.2    Smith, S.A.3    Kotwal, G.J.4    Murthy, K.H.M.5
  • 61
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • Part 12 Sp. Iss. 1
    • Krissinel E., and Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr., D-Biol. Crystallogr. 60 (2004) 2256-2268 Part 12 Sp. Iss. 1
    • (2004) Acta Crystallogr., D-Biol. Crystallogr. , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 62
    • 0029185933 scopus 로고
    • CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
    • Svergun D., Barberato C., and Koch M.H.J. CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Cryst. (1995) 768-773
    • (1995) J. Appl. Cryst. , pp. 768-773
    • Svergun, D.1    Barberato, C.2    Koch, M.H.J.3


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