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Volumn 20, Issue 4, 2012, Pages 718-728

Detection of spatial correlations in protein structures and molecular complexes

Author keywords

[No Author keywords available]

Indexed keywords

DNA; FERREDOXIN; MONOMER; OLIGOMER; OXIDOREDUCTASE; POLYPEPTIDE;

EID: 84859379149     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2012.01.024     Document Type: Article
Times cited : (58)

References (47)
  • 2
    • 77958056909 scopus 로고    scopus 로고
    • Structural classification of proteins and structural genomics: New insights into protein folding and evolution
    • A. Andreeva, and A.G. Murzin Structural classification of proteins and structural genomics: new insights into protein folding and evolution Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 2010 1190 1197
    • (2010) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. , vol.66 , pp. 1190-1197
    • Andreeva, A.1    Murzin, A.G.2
  • 4
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 resolution
    • N. Ban, P. Nissen, J. Hansen, P.B. Moore, and T.A. Steitz The complete atomic structure of the large ribosomal subunit at 2.4 resolution Science 289 2000 905 920
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 7
    • 73649156890 scopus 로고
    • Physical principles in the construction of regular viruses
    • D.L. Caspar, and A. Klug Physical principles in the construction of regular viruses Cold Spring Harb. Symp. Quant. Biol. 27 1962 1 24
    • (1962) Cold Spring Harb. Symp. Quant. Biol. , vol.27 , pp. 1-24
    • Caspar, D.L.1    Klug, A.2
  • 8
    • 72449163474 scopus 로고    scopus 로고
    • Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism
    • 10.1016/j.jsb.2009.08.006 Published online August 15, 2009
    • Y.-Y. Chen, T.-P. Ko, W.-H. Chen, L.-P. Lo, C.-H. Lin, and A.H.-J. Wang Conformational changes associated with cofactor/substrate binding of 6-phosphogluconate dehydrogenase from Escherichia coli and Klebsiella pneumoniae: Implications for enzyme mechanism J. Struct. Biol. 169 2010 25 35 10.1016/j.jsb.2009.08.006 Published online August 15, 2009
    • (2010) J. Struct. Biol. , vol.169 , pp. 25-35
    • Chen, Y.-Y.1    Ko, T.-P.2    Chen, W.-H.3    Lo, L.-P.4    Lin, C.-H.5    Wang, A.H.-J.6
  • 9
    • 0035827346 scopus 로고    scopus 로고
    • Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution
    • P. Cramer, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution Science 292 2001 1863 1876
    • (2001) Science , vol.292 , pp. 1863-1876
    • Cramer, P.1    Bushnell, D.A.2    Kornberg, R.D.3
  • 11
    • 0037122805 scopus 로고    scopus 로고
    • X-ray structure of a ClC chloride channel at 3.0 reveals the molecular basis of anion selectivity
    • R. Dutzler, E.B. Campbell, M. Cadene, B.T. Chait, and R. MacKinnon X-ray structure of a ClC chloride channel at 3.0 reveals the molecular basis of anion selectivity Nature 415 2002 287 294
    • (2002) Nature , vol.415 , pp. 287-294
    • Dutzler, R.1    Campbell, E.B.2    Cadene, M.3    Chait, B.T.4    MacKinnon, R.5
  • 12
    • 0029988488 scopus 로고    scopus 로고
    • Structure of bordetella pertussis virulence factor P.69 pertactin
    • P. Emsley, I.G. Charles, N.F. Fairweather, and N.W. Isaacs Structure of Bordetella pertussis virulence factor P.69 pertactin Nature 381 1996 90 92
    • (1996) Nature , vol.381 , pp. 90-92
    • Emsley, P.1    Charles, I.G.2    Fairweather, N.F.3    Isaacs, N.W.4
  • 13
    • 0022412307 scopus 로고
    • The structure of a T = 1 icosahedral empty particle from southern bean mosaic virus
    • J.W. Erickson, A.M. Silva, M.R. Murthy, I. Fita, and M.G. Rossmann The structure of a T = 1 icosahedral empty particle from southern bean mosaic virus Science 229 1985 625 629
    • (1985) Science , vol.229 , pp. 625-629
    • Erickson, J.W.1    Silva, A.M.2    Murthy, M.R.3    Fita, I.4    Rossmann, M.G.5
  • 14
    • 0030334647 scopus 로고    scopus 로고
    • Optimum superimposition of protein structures: Ambiguities and implications
    • Z.K. Feng, and M.J. Sippl Optimum superimposition of protein structures: ambiguities and implications Fold. Des. 1 1996 123 132
    • (1996) Fold. Des. , vol.1 , pp. 123-132
    • Feng, Z.K.1    Sippl, M.J.2
  • 15
    • 79953904501 scopus 로고    scopus 로고
    • Biochemical and structural characterization of lysophosphatidic acid binding by a humanized monoclonal antibody
    • J.K. Fleming, J.M. Wojciak, M.-A. Campbell, and T. Huxford Biochemical and structural characterization of lysophosphatidic acid binding by a humanized monoclonal antibody J. Mol. Biol. 408 2011 462 476
    • (2011) J. Mol. Biol. , vol.408 , pp. 462-476
    • Fleming, J.K.1    Wojciak, J.M.2    Campbell, M.-A.3    Huxford, T.4
  • 17
    • 77957352833 scopus 로고    scopus 로고
    • Jmol - A paradigm shift in crystallographic visualization
    • R.M. Hanson Jmol - a paradigm shift in crystallographic visualization J. Appl. Crystallogr. 43 2010 1250 1260
    • (2010) J. Appl. Crystallogr. , vol.43 , pp. 1250-1260
    • Hanson, R.M.1
  • 18
    • 66549119395 scopus 로고    scopus 로고
    • Advances and pitfalls of protein structural alignment
    • H. Hasegawa, and L. Holm Advances and pitfalls of protein structural alignment Curr. Opin. Struct. Biol. 19 2009 341 348
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 341-348
    • Hasegawa, H.1    Holm, L.2
  • 19
    • 46449139197 scopus 로고    scopus 로고
    • Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site
    • R. Janowski, T. Auerbach-Nevo, and M.S. Weiss Bacterioferritin from Mycobacterium smegmatis contains zinc in its di-nuclear site Protein Sci. 17 2008 1138 1150
    • (2008) Protein Sci. , vol.17 , pp. 1138-1150
    • Janowski, R.1    Auerbach-Nevo, T.2    Weiss, M.S.3
  • 20
    • 0021724242 scopus 로고
    • Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 resolution
    • T.A. Jones, and L. Liljas Structure of satellite tobacco necrosis virus after crystallographic refinement at 2.5 resolution J. Mol. Biol. 177 1984 735 767
    • (1984) J. Mol. Biol. , vol.177 , pp. 735-767
    • Jones, T.A.1    Liljas, L.2
  • 23
    • 0026717535 scopus 로고
    • Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp
    • X.P. Kong, R. Onrust, M. O'Donnell, and J. Kuriyan Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp Cell 69 1992 425 437
    • (1992) Cell , vol.69 , pp. 425-437
    • Kong, X.P.1    Onrust, R.2    O'Donnell, M.3    Kuriyan, J.4
  • 24
    • 0028618183 scopus 로고
    • Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA
    • T.S. Krishna, X.P. Kong, S. Gary, P.M. Burgers, and J. Kuriyan Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA Cell 79 1994 1233 1243
    • (1994) Cell , vol.79 , pp. 1233-1243
    • Krishna, T.S.1    Kong, X.P.2    Gary, S.3    Burgers, P.M.4    Kuriyan, J.5
  • 25
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • E. Krissinel, and K. Henrick Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr. D Biol. Crystallogr. 60 2004 2256 2268
    • (2004) Acta Crystallogr. D Biol. Crystallogr. , vol.60 , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 28
    • 67649869968 scopus 로고    scopus 로고
    • MM-align: A quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming
    • 10.1093/nar/gkp318
    • S. Mukherjee, and Y. Zhang MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming Nucleic Acids Res. 37 2009 e83 10.1093/nar/gkp318
    • (2009) Nucleic Acids Res. , vol.37 , pp. 83
    • Mukherjee, S.1    Zhang, Y.2
  • 29
    • 79959948293 scopus 로고    scopus 로고
    • Biological insights from topology independent comparison of protein 3D structures
    • 10.1093/nar/gkr348
    • M.N. Nguyen, and M.S. Madhusudhan Biological insights from topology independent comparison of protein 3D structures Nucleic Acids Res. 39 2011 e94 10.1093/nar/gkr348
    • (2011) Nucleic Acids Res. , vol.39 , pp. 94
    • Nguyen, M.N.1    Madhusudhan, M.S.2
  • 32
    • 33747478692 scopus 로고    scopus 로고
    • Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism
    • M.A. Schumacher, E. Karamooz, A. Zíková, L. Trantírek, and J. Lukes Crystal structures of T. brucei MRP1/MRP2 guide-RNA binding complex reveal RNA matchmaking mechanism Cell 126 2006 701 711
    • (2006) Cell , vol.126 , pp. 701-711
    • Schumacher, M.A.1    Karamooz, E.2    Zíková, A.3    Trantírek, L.4    Lukes, J.5
  • 33
    • 0020475392 scopus 로고
    • On the problem of comparing protein structures. Development and applications of a new method for the assessment of structural similarities of polypeptide conformations
    • M.J. Sippl On the problem of comparing protein structures. Development and applications of a new method for the assessment of structural similarities of polypeptide conformations J. Mol. Biol. 156 1982 359 388
    • (1982) J. Mol. Biol. , vol.156 , pp. 359-388
    • Sippl, M.J.1
  • 34
    • 40749148575 scopus 로고    scopus 로고
    • On distance and similarity in fold space
    • M.J. Sippl On distance and similarity in fold space Bioinformatics 24 2008 872 873
    • (2008) Bioinformatics , vol.24 , pp. 872-873
    • Sippl, M.J.1
  • 35
    • 66549127349 scopus 로고    scopus 로고
    • Fold space unlimited
    • URL
    • Sippl, M.J. (2009). Fold space unlimited. Curr. Opin. Struct. Biol. 19, 312-320. URL http://dx.doi.org/10.1016/j.sbi.2009.03.010.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 312-320
    • Sippl, M.J.1
  • 36
    • 0026051059 scopus 로고
    • Superposition of three-dimensional objects: A fast and numerically stable algorithm for the calculation of the matrix of optimal rotation
    • M.J. Sippl, and H. Stegbuchner Superposition of three-dimensional objects: a fast and numerically stable algorithm for the calculation of the matrix of optimal rotation Comput. Chem. 15 1991 73 78
    • (1991) Comput. Chem. , vol.15 , pp. 73-78
    • Sippl, M.J.1    Stegbuchner, H.2
  • 37
    • 38849092210 scopus 로고    scopus 로고
    • A note on difficult structure alignment problems
    • URL
    • Sippl, M.J., and Wiederstein, M. (2008). A note on difficult structure alignment problems. Bioinformatics 24, 426-427. URL http://dx.doi.org/10.1093/ bioinformatics/btm622.
    • (2008) Bioinformatics , vol.24 , pp. 426-427
    • Sippl, M.J.1    Wiederstein, M.2
  • 40
    • 67849124338 scopus 로고    scopus 로고
    • COPS - A novel workbench for explorations in fold space
    • Web Server Issue
    • S.J. Suhrer, M. Wiederstein, M. Gruber, and M.J. Sippl COPS - a novel workbench for explorations in fold space Nucleic Acids Res. 37 Web Server issue 2009 W539 W544
    • (2009) Nucleic Acids Res. , vol.37
    • Suhrer, S.J.1    Wiederstein, M.2    Gruber, M.3    Sippl, M.J.4
  • 41
    • 0034710671 scopus 로고    scopus 로고
    • A deeply knotted protein structure and how it might fold
    • W.R. Taylor A deeply knotted protein structure and how it might fold Nature 406 2000 916 919
    • (2000) Nature , vol.406 , pp. 916-919
    • Taylor, W.R.1
  • 43
    • 66549127972 scopus 로고    scopus 로고
    • Nothing about protein structure classification makes sense except in the light of evolution
    • R.E. Valas, S. Yang, and P.E. Bourne Nothing about protein structure classification makes sense except in the light of evolution Curr. Opin. Struct. Biol. 19 2009 329 334
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 329-334
    • Valas, R.E.1    Yang, S.2    Bourne, P.E.3
  • 45
    • 38849202435 scopus 로고    scopus 로고
    • Effect of N-terminal residues on the structural stability of recombinant horse L-chain apoferritin in an acidic environment
    • K. Yoshizawa, Y. Mishima, S.-Y. Park, J.G. Heddle, J.R.H. Tame, K. Iwahori, M. Kobayashi, and I. Yamashita Effect of N-terminal residues on the structural stability of recombinant horse L-chain apoferritin in an acidic environment J. Biochem. 142 2007 707 713
    • (2007) J. Biochem. , vol.142 , pp. 707-713
    • Yoshizawa, K.1    Mishima, Y.2    Park, S.-Y.3    Heddle, J.G.4    Tame, J.R.H.5    Iwahori, K.6    Kobayashi, M.7    Yamashita, I.8
  • 46
    • 79955867558 scopus 로고    scopus 로고
    • Atomic model of CPV reveals the mechanism used by this single-shelled virus to economically carry out functions conserved in multishelled reoviruses
    • X. Yu, P. Ge, J. Jiang, I. Atanasov, and Z.H. Zhou Atomic model of CPV reveals the mechanism used by this single-shelled virus to economically carry out functions conserved in multishelled reoviruses Structure 19 2011 652 661
    • (2011) Structure , vol.19 , pp. 652-661
    • Yu, X.1    Ge, P.2    Jiang, J.3    Atanasov, I.4    Zhou, Z.H.5
  • 47
    • 77951912692 scopus 로고    scopus 로고
    • 3.3 cryo-em structure of a nonenveloped virus reveals a priming mechanism for cell entry
    • X. Zhang, L. Jin, Q. Fang, W.H. Hui, and Z.H. Zhou 3.3 cryo-em structure of a nonenveloped virus reveals a priming mechanism for cell entry Cell 141 2010 472 482
    • (2010) Cell , vol.141 , pp. 472-482
    • Zhang, X.1    Jin, L.2    Fang, Q.3    Hui, W.H.4    Zhou, Z.H.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.