메뉴 건너뛰기




Volumn 6, Issue 4, 2007, Pages 946-963

Finding protein-protein interaction patterns by contact map matching

Author keywords

BPTI; Contact maps; Protein protein interactions; Serine proteases

Indexed keywords

APROTININ; CHYMOTRYPSIN; KALLIKREIN; MATRIPTASE; PROTEIN; SERINE PROTEINASE; THROMBIN; TRYPSIN;

EID: 37349059302     PISSN: None     EISSN: 16765680     Source Type: Journal    
DOI: None     Document Type: Conference Paper
Times cited : (14)

References (30)
  • 2
    • 21844455282 scopus 로고    scopus 로고
    • Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases
    • Bobofchak KM, Pineda AO, Mathews FS and Di Cera E (2005). Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases. J. Biol. Chem. 280: 25644-25650.
    • (2005) J. Biol. Chem , vol.280 , pp. 25644-25650
    • Bobofchak, K.M.1    Pineda, A.O.2    Mathews, F.S.3    Di Cera, E.4
  • 3
    • 0034925093 scopus 로고    scopus 로고
    • Computational analysis of binding of P1 variants to trypsin
    • Brandsdal BO, Aqvist J and Smalas AO (2001). Computational analysis of binding of P1 variants to trypsin. Protein Sci. 10: 1584-1595.
    • (2001) Protein Sci , vol.10 , pp. 1584-1595
    • Brandsdal, B.O.1    Aqvist, J.2    Smalas, A.O.3
  • 4
    • 33746268441 scopus 로고    scopus 로고
    • Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin
    • Brandsdal BO, Smalas AO and Aqvist J (2006). Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin. Proteins 64: 740-748.
    • (2006) Proteins , vol.64 , pp. 740-748
    • Brandsdal, B.O.1    Smalas, A.O.2    Aqvist, J.3
  • 5
    • 0026967479 scopus 로고
    • A survey of image registration techniques
    • Brown LG (1992). A survey of image registration techniques. ACM Comput. Surv. 24: 325-376.
    • (1992) ACM Comput. Surv , vol.24 , pp. 325-376
    • Brown, L.G.1
  • 6
    • 0024280501 scopus 로고
    • Dissecting the catalytic triad of a serine protease
    • Carter P and Wells JA (1988). Dissecting the catalytic triad of a serine protease. Nature 332: 564-568.
    • (1988) Nature , vol.332 , pp. 564-568
    • Carter, P.1    Wells, J.A.2
  • 7
    • 0034602930 scopus 로고    scopus 로고
    • High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence
    • Czapinska H, Otlewski J, Krzywda S, Sheldrick GM, et al. (2000). High-resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence. J. Mol. Biol. 295: 1237-1249.
    • (2000) J. Mol. Biol , vol.295 , pp. 1237-1249
    • Czapinska, H.1    Otlewski, J.2    Krzywda, S.3    Sheldrick, G.M.4
  • 10
    • 0015935205 scopus 로고
    • The charge relay system in chymotrypsin and chymotrypsinogen
    • Fersht AR and Sperling J (1973). The charge relay system in chymotrypsin and chymotrypsinogen. J. Mol. Biol. 74: 137-149.
    • (1973) J. Mol. Biol , vol.74 , pp. 137-149
    • Fersht, A.R.1    Sperling, J.2
  • 11
    • 0036882394 scopus 로고    scopus 로고
    • Serine protease mechanism and specificity
    • Hedstrom L (2002). Serine protease mechanism and specificity. Chem. Rev. 102: 4501-4524.
    • (2002) Chem. Rev , vol.102 , pp. 4501-4524
    • Hedstrom, L.1
  • 12
    • 0033574398 scopus 로고    scopus 로고
    • The crystal structures of the complexes between bovine beta-trypsin and ten P1 variants of BPTI
    • Helland R, Otlewski J, Sundheim O, Dadlez M, et al. (1999). The crystal structures of the complexes between bovine beta-trypsin and ten P1 variants of BPTI. J. Mol. Biol. 287: 923-942.
    • (1999) J. Mol. Biol , vol.287 , pp. 923-942
    • Helland, R.1    Otlewski, J.2    Sundheim, O.3    Dadlez, M.4
  • 13
    • 0023131408 scopus 로고
    • Similarity and dissimilarity in the stereogeometry of the active sites of thrombin, trypsin, plasmin and glandular kallikrein
    • Hijikata-Okunomiya A, Okamoto S, Kikumoto R, Tamao Y, et al. (1987). Similarity and dissimilarity in the stereogeometry of the active sites of thrombin, trypsin, plasmin and glandular kallikrein. Thromb. Res. 45: 451-462.
    • (1987) Thromb. Res , vol.45 , pp. 451-462
    • Hijikata-Okunomiya, A.1    Okamoto, S.2    Kikumoto, R.3    Tamao, Y.4
  • 14
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito T, Chiba T, Ozawa R, Yoshida M, et al. (2001). A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98: 4569-4574.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3    Yoshida, M.4
  • 15
    • 0017324044 scopus 로고
    • Serine proteases: Structure and mechanism of catalysis
    • Kraut J (1977). Serine proteases: structure and mechanism of catalysis. Annu. Rev. Biochem. 46: 331-358.
    • (1977) Annu. Rev. Biochem , vol.46 , pp. 331-358
    • Kraut, J.1
  • 16
    • 0033612211 scopus 로고    scopus 로고
    • Interscaffolding additivity: Binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases
    • Krowarsch D, Dadlez M, Buczek O, Krokoszynska I, et al. (1999). Interscaffolding additivity: binding of P1 variants of bovine pancreatic trypsin inhibitor to four serine proteases. J. Mol. Biol. 289: 175-186.
    • (1999) J. Mol. Biol , vol.289 , pp. 175-186
    • Krowarsch, D.1    Dadlez, M.2    Buczek, O.3    Krokoszynska, I.4
  • 17
    • 70350674995 scopus 로고
    • On the shortest spanning subtree of a graph and the traveling salesman problem
    • Kruskal JB Jr (1956). On the shortest spanning subtree of a graph and the traveling salesman problem. Proc. Am. Math. Soc. 7: 48-50.
    • (1956) Proc. Am. Math. Soc , vol.7 , pp. 48-50
    • Kruskal Jr, J.B.1
  • 18
    • 0342445397 scopus 로고    scopus 로고
    • What can the structures of enzyme-inhibitor complexes tell us about the structures of enzyme substrate complexes?
    • Laskowski M Jr and Qasim MA (2000). What can the structures of enzyme-inhibitor complexes tell us about the structures of enzyme substrate complexes? Biochim. Biophys. Acta 1477: 324-337.
    • (2000) Biochim. Biophys. Acta , vol.1477 , pp. 324-337
    • Laskowski Jr, M.1    Qasim, M.A.2
  • 19
    • 0001239782 scopus 로고    scopus 로고
    • Interaction of standard mechanism, canonical protein inhibitors with serine proteinases
    • Protein-Protein Recognition, the Frontiers in Molecular Biology, Kleanthous C, ed, Oxford University Press, New York
    • Laskowski M Jr, Qasim MA and Lu SM (2000). Interaction of standard mechanism, canonical protein inhibitors with serine proteinases. In: Protein-Protein Recognition, the Frontiers in Molecular Biology Series (Kleanthous C, ed.). Oxford University Press, New York, 228-279.
    • (2000) Series , pp. 228-279
    • Laskowski Jr, M.1    Qasim, M.A.2    Lu, S.M.3
  • 20
    • 0032008619 scopus 로고    scopus 로고
    • A survey of medical image registration
    • Maintz JB and Viergever MA (1998). A survey of medical image registration. Med. Image Anal. 2: 1-36.
    • (1998) Med. Image Anal , vol.2 , pp. 1-36
    • Maintz, J.B.1    Viergever, M.A.2
  • 21
    • 4544344689 scopus 로고    scopus 로고
    • STING contacts: A web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces
    • Mancini AL, Higa RH, Oliveira A, Dominiquini F, et al. (2004). STING contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces. Bioinformatics 20: 2145-2147.
    • (2004) Bioinformatics , vol.20 , pp. 2145-2147
    • Mancini, A.L.1    Higa, R.H.2    Oliveira, A.3    Dominiquini, F.4
  • 22
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T and Chothia C (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540.
    • (1995) J. Mol. Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 23
    • 0028914722 scopus 로고
    • Structural basis of substrate specificity in the serine proteases
    • Perona JJ and Craik CS (1995). Structural basis of substrate specificity in the serine proteases. Protein Sci. 4: 337-360.
    • (1995) Protein Sci , vol.4 , pp. 337-360
    • Perona, J.J.1    Craik, C.S.2
  • 25
    • 13044272912 scopus 로고    scopus 로고
    • Automated analysis of interatomic contacts in proteins
    • Sobolev V, Sorokine A, Prilusky J, Abola EE, et al. (1999). Automated analysis of interatomic contacts in proteins. Bioinformatics 15: 327-332.
    • (1999) Bioinformatics , vol.15 , pp. 327-332
    • Sobolev, V.1    Sorokine, A.2    Prilusky, J.3    Abola, E.E.4
  • 26
    • 2242428041 scopus 로고    scopus 로고
    • Ab initio QM/MM dynamics simulation of the tetrahedral intermediate of serine proteases: Insights into the active site hydrogen-bonding network
    • Topf M, Várnai P and Richards WG (2002). Ab initio QM/MM dynamics simulation of the tetrahedral intermediate of serine proteases: insights into the active site hydrogen-bonding network. J. Am. Chem. Soc. 124: 14780-14788.
    • (2002) J. Am. Chem. Soc , vol.124 , pp. 14780-14788
    • Topf, M.1    Várnai, P.2    Richards, W.G.3
  • 28
    • 0034886313 scopus 로고    scopus 로고
    • X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate
    • Wilmouth RC, Edman K, Neutze R, Wright PA, et al. (2001). X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate. Nat. Struct. Biol. 8: 689-694.
    • (2001) Nat. Struct. Biol , vol.8 , pp. 689-694
    • Wilmouth, R.C.1    Edman, K.2    Neutze, R.3    Wright, P.A.4
  • 29
    • 0032606105 scopus 로고    scopus 로고
    • Sequence to structure alignment in comparative modeling using PrISM
    • Yang AS and Honig B (1999). Sequence to structure alignment in comparative modeling using PrISM. Proteins 3: 66-72.
    • (1999) Proteins , vol.3 , pp. 66-72
    • Yang, A.S.1    Honig, B.2
  • 30
    • 0027325129 scopus 로고
    • Families and the structural relatedness among globular proteins
    • Yee DP and Dill KA (1993). Families and the structural relatedness among globular proteins. Protein Sci. 2: 884-899.
    • (1993) Protein Sci , vol.2 , pp. 884-899
    • Yee, D.P.1    Dill, K.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.