메뉴 건너뛰기




Volumn 18, Issue 11, 2011, Pages 1507-1523

A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs

Author keywords

algorithms; computational molecular biology; protein structure

Indexed keywords

BACTERIAL PROTEIN; DIACYLGLYCEROL KINASE; DISULFIDE; ESCHERICHIA COLI PROTEIN; IGG FC BINDING PROTEIN, STREPTOCOCCUS; IGG FC-BINDING PROTEIN, STREPTOCOCCUS; MULTIPROTEIN COMPLEX;

EID: 80955123900     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0173     Document Type: Article
Times cited : (7)

References (37)
  • 1
    • 0033631450 scopus 로고    scopus 로고
    • Molecular symmetry as an aid to geometry determination in ligand protein complexes
    • Al-Hashimi, H. M., Bolon, P. J., and Prestegard, J. H. 2000. Molecular symmetry as an aid to geometry determination in ligand protein complexes. J. Magn. Reson. 142, 153-158.
    • (2000) J. Magn. Reson. , vol.142 , pp. 153-158
    • Al-Hashimi, H.M.1    Bolon, P.J.2    Prestegard, J.H.3
  • 2
    • 66149097825 scopus 로고    scopus 로고
    • Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA
    • Bardiaux, B., Bernard, A., Rieping, W., et al. 2009. Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA. Proteins 75, 569-585.
    • (2009) Proteins , vol.75 , pp. 569-585
    • Bardiaux, B.1    Bernard, A.2    Rieping, W.3
  • 4
    • 0034725409 scopus 로고    scopus 로고
    • Determination of the relative orientation of the two halves of the domain-swapped dimer of cyanovirin-N in solution using dipolar couplings and rigid body minimization
    • DOI 10.1021/ja000858o
    • Bewley, C. A., and Clore, G. M. 2000. Determination of the relative orientation of the two halves of the domain-swapped dimer of cyanovirin-N in solution using dipolar couplings and rigid body minimization. J. Am. Chem. Soc. 122, 6009-6016. (Pubitemid 30451105)
    • (2000) Journal of the American Chemical Society , vol.122 , Issue.25 , pp. 6009-6016
    • Bewley, C.A.1    Clore, G.M.2
  • 5
    • 0141569110 scopus 로고    scopus 로고
    • A protein contortionist: Core mutations of GB1 that induce dimerization and domain swapping
    • DOI 10.1016/S0022-2836(03)00928-8
    • Byeon, I.-J. L., Louis, J. M., and Gronenborn, A. M. 2003. A protein contortionist: core mutations of GB1 that induce dimerization and domain swapping. J. Mol. Biol. 333, 141-152. (Pubitemid 37153271)
    • (2003) Journal of Molecular Biology , vol.333 , Issue.1 , pp. 141-152
    • Byeon, I.-J.L.1    Louis, J.M.2    Gronenborn, A.M.3
  • 6
    • 62649153772 scopus 로고    scopus 로고
    • Computational structure-based redesign of enzyme activity
    • Chen, C.-Y., Georgiev, I., Anderson, A. C., et al. 2009. Computational structure-based redesign of enzyme activity. Proc. Natl. Acad. Sci. USA 106, 3764-3769.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 3764-3769
    • Chen, C.-Y.1    Georgiev, I.2    Anderson, A.C.3
  • 7
    • 67650473269 scopus 로고    scopus 로고
    • Automated NMR assignment and protein structure determination using sparse dipolar coupling constraints
    • Donald, B. R., and Martin, J. 2009. Automated NMR assignment and protein structure determination using sparse dipolar coupling constraints. Prog. Nucl. Magn. Reson. Spectrosc. 55, 101-127.
    • (2009) Prog. Nucl. Magn. Reson. Spectrosc. , vol.55 , pp. 101-127
    • Donald, B.R.1    Martin, J.2
  • 8
    • 77956377719 scopus 로고    scopus 로고
    • Predicting resistance mutations using protein design algorithms
    • Frey, K. M., Georgiev, I., Donald, B. R., et al. 2010. Predicting resistance mutations using protein design algorithms. Proc. Natl. Acad. Sci. USA 107, 13707-13712.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 13707-13712
    • Frey, K.M.1    Georgiev, I.2    Donald, B.R.3
  • 10
    • 0001798952 scopus 로고    scopus 로고
    • Arrangements
    • Goodman, J. E., and O'Rourke, J., eds, 2nd ed. CRC Press, Boca Raton, FL
    • Halperin, D. 1997. Arrangements, 529-562. In Goodman, J. E., and O'Rourke, J., eds. Handbook of Discrete and Computational Geometry, 2nd ed. CRC Press, Boca Raton, FL.
    • (1997) Handbook of Discrete and Computational Geometry , pp. 529-562
    • Halperin, D.1
  • 11
    • 84896756067 scopus 로고    scopus 로고
    • Two-Dimensional Arrangements in CGAL and Adaptive Point Location for Parametric Curves
    • Algorithm Engineering
    • Hanniel, I., and Halperin, D. 2000. Two-dimensional arrangements in CGAL and adaptive point location for parametric curves. Lect. Notes Comput. Sci. 1982, 171-182. (Pubitemid 33322471)
    • (2001) Lect. Notes Comput. Sci. , Issue.1982 , pp. 171-182
    • Hanniel, I.1    Halperin, D.2
  • 13
    • 0000165109 scopus 로고
    • Isotope-filtered 2D NMR of a protein-peptide complex: Study of a skeletal muscle myosin light chain kinase fragment bound to calmodulin
    • Ikura, M., and Bax, A. 1992. Isotope-filtered 2D NMR of a protein-peptide complex: study of a skeletal muscle myosin light chain kinase fragment bound to calmodulin. J. Am. Chem. Soc. 114, 2433-2440.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 2433-2440
    • Ikura, M.1    Bax, A.2
  • 14
    • 0024988099 scopus 로고
    • Four-dimensional heteronuclear triple-resonance NMR spectroscopy of interleukin-1 beta in solution
    • Kay, L. E., Clore, G. M., Bax, A., et al. 1990. Four-dimensional heteronuclear triple-resonance NMR spectroscopy of interleukin-1 beta in solution. Science 249, 411-414.
    • (1990) Science , vol.249 , pp. 411-414
    • Kay, L.E.1    Clore, G.M.2    Bax, A.3
  • 15
    • 0037419802 scopus 로고    scopus 로고
    • GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information
    • DOI 10.1021/ja028197d
    • Kim, S., and Szyperski, T. 2003. GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. J. Am. Chem. Soc. 125, 1385-1393. (Pubitemid 36159850)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.5 , pp. 1385-1393
    • Kim, S.1    Szyperski, T.2
  • 17
    • 80955127823 scopus 로고    scopus 로고
    • Novel x-ray structure of the YkuJ protein from Bacillus subtilis. Northeast structural genomics target SR360
    • Kuzin, A., Abashidze, M., Forouhar, F., et al. 2005. Novel x-ray structure of the YkuJ protein from Bacillus subtilis. Northeast Structural Genomics target SR360. Northeast Structural Genomics Consortium.
    • (2005) Northeast Structural Genomics Consortium
    • Kuzin, A.1    Abashidze, M.2    Forouhar, F.3
  • 18
    • 46249083761 scopus 로고    scopus 로고
    • Assembly reflects evolution of protein complexes
    • DOI 10.1038/nature06942, PII NATURE06942
    • Levy, E. D., Erba, E. B., Robinson, C. V., et al. 2008. Assembly reflects evolution of protein complexes. Nature 453, 1262-1265. (Pubitemid 351913589)
    • (2008) Nature , vol.453 , Issue.7199 , pp. 1262-1265
    • Levy, E.D.1    Erba, E.B.2    Robinson, C.V.3    Teichmann, S.A.4
  • 20
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang, J., Woodward, C., and Edelsbrunner, H. 1998b. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 7, 1884-1897. (Pubitemid 28432430)
    • (1998) Protein Science , vol.7 , Issue.9 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 21
    • 0033145058 scopus 로고    scopus 로고
    • Order Matrix Analysis of Residual Dipolar Couplings Using Singular Value Decomposition
    • Losonczi, J. A., Andrec, M., Fischer, M. W. F., et al. 1999. Order matrix analysis of residual dipolar couplings using singular value decomposition. J. Magn. Reson. 138, 334-342. (Pubitemid 129608294)
    • (1999) Journal of Magnetic Resonance , vol.138 , Issue.2 , pp. 334-342
    • Losonczi, J.A.1    Andrec, M.2    Fischer, M.W.F.3    Prestegard, J.H.4
  • 22
    • 0001081820 scopus 로고
    • Three-dimensional heteronuclear NMR of nitrogen-15 labeled proteins
    • Marion, D., Kay, L. E., Sparks, S. W., et al. 1989. Three-dimensional heteronuclear NMR of nitrogen-15 labeled proteins. J. Am. Chem. Soc. 111, 1515-1517.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 1515-1517
    • Marion, D.1    Kay, L.E.2    Sparks, S.W.3
  • 23
    • 79956216314 scopus 로고    scopus 로고
    • A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers
    • Martin, J. W., Yan, A. K., Bailey-Kellogg, C., et al. 2011. A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers. Protein Sci. 20, 970-985.
    • (2011) Protein Sci. , vol.20 , pp. 970-985
    • Martin, J.W.1    Yan, A.K.2    Bailey-Kellogg, C.3
  • 27
    • 33748271512 scopus 로고    scopus 로고
    • Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing
    • DOI 10.1002/prot.21091
    • Potluri, S., Yan, A. K., Chou, J. J., et al. 2006. Structure determination of symmetric homo-oligomers by a complete search of symmetry configuration space, using NMR restraints and van der Waals packing. Proteins 65, 203-219. (Pubitemid 44320629)
    • (2006) Proteins: Structure, Function and Genetics , vol.65 , Issue.1 , pp. 203-219
    • Potluri, S.1    Yan, A.K.2    Chou, J.J.3    Donald, B.R.4    Bailey-Kellogg, C.5
  • 28
    • 33845925822 scopus 로고    scopus 로고
    • A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers
    • DOI 10.1110/ps.062427307
    • Potluri, S., Yan, A. K., Donald, B. R., et al. 2007. A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Protein Sci. 16, 69-81. (Pubitemid 46036499)
    • (2007) Protein Science , vol.16 , Issue.1 , pp. 69-81
    • Potluri, S.1    Yan, A.K.2    Donald, B.R.3    Bailey-Kellogg, C.4
  • 29
    • 0002702652 scopus 로고
    • Embeddability of weighted graphs in k-space is strongly NP-hard
    • Saxe, J. 1979. Embeddability of weighted graphs in k-space is strongly NP-hard. Proc. 17th Allerton Conf. Commun. Control Comput. 480-489.
    • (1979) Proc. 17th Allerton Conf. Commun. Control Comput. , pp. 480-489
    • Saxe, J.1
  • 30
    • 38749106195 scopus 로고    scopus 로고
    • Structure and mechanism of the M2 proton channel of influenza A virus
    • DOI 10.1038/nature06531, PII NATURE06531
    • Schnell, J. R., and Chou, J. J. 2008. Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451, 591-595. (Pubitemid 351186272)
    • (2008) Nature , vol.451 , Issue.7178 , pp. 591-595
    • Schnell, J.R.1    Chou, J.J.2
  • 31
    • 0013293280 scopus 로고    scopus 로고
    • The Xplor-NIH NMR molecular structure determination package
    • Schwieters, C. D., Kuszewski, J. J., Tjandra, N., et al. 2003. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160, 65-73.
    • (2003) J. Magn. Reson. , vol.160 , pp. 65-73
    • Schwieters, C.D.1    Kuszewski, J.J.2    Tjandra, N.3
  • 32
    • 67649908268 scopus 로고    scopus 로고
    • Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase
    • Van Horn, W. D., Kim, H.-J., Ellis, C. D., et al. 2009. Solution nuclear magnetic resonance structure of membrane-integral diacylglycerol kinase. Science 324, 1726-1729.
    • (2009) Science , vol.324 , pp. 1726-1729
    • Van Horn, W.D.1    Kim, H.-J.2    Ellis, C.D.3
  • 33
    • 2642620234 scopus 로고    scopus 로고
    • AmbiPack: A systematic algorithm for packing of macromolecular structures with ambigous distance constraints
    • DOI 10.1002/(SICI)1097-0134(19980701)32:1<26::AID-PROT5>3.0.CO;2-C
    • Wang, C.-S. E., Lozano-Pérez, T., and Tidor, B. 1998. AmbiPack: a systematic algorithm for packing of macromolecular structures with ambiguous distance constraints. Proteins 32, 26-42. (Pubitemid 28313250)
    • (1998) Proteins: Structure, Function and Genetics , vol.32 , Issue.1 , pp. 26-42
    • Wang, C.-S.E.1    Lozano-Perez, T.2    Tidor, B.3
  • 34
    • 71449091133 scopus 로고    scopus 로고
    • Solution structure and functional analysis of the influenza B proton channel
    • Wang, J., Pielak, R. M., McClintock, M. A., et al. 2009. Solution structure and functional analysis of the influenza B proton channel. Nat. Struct. Mol. Biol. 16, 1267-1271.
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 1267-1271
    • Wang, J.1    Pielak, R.M.2    McClintock, M.A.3
  • 35
    • 33846263054 scopus 로고    scopus 로고
    • A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data
    • DOI 10.1089/cmb.2006.13.1267
    • Wang, L., Mettu, R. R., and Donald, B. R. 2006. A polynomial-time algorithm for de novo protein backbone structure determination from nuclear magnetic resonance data. J. Comput. Biol. 13, 1267-1288. (Pubitemid 46100693)
    • (2006) Journal of Computational Biology , vol.13 , Issue.7 , pp. 1267-1288
    • Wang, L.1    Mettu, R.R.2    Donald, B.R.3
  • 36
    • 43049118964 scopus 로고    scopus 로고
    • RDC-assisted modeling of symmetric protein homo-oligomers
    • DOI 10.1110/ps.073395108
    • Wang, X., Bansal, S., Jiang, M., et al. 2008. RDC-assisted modeling of symmetric protein homo-oligomers. Protein Sci. 17, 899-907. (Pubitemid 351629584)
    • (2008) Protein Science , vol.17 , Issue.5 , pp. 899-907
    • Wang, X.1    Bansal, S.2    Jiang, M.3    Prestegard, J.H.4
  • 37
    • 3042621274 scopus 로고    scopus 로고
    • The progress of membrane protein structure determination
    • DOI 10.1110/ps.04712004
    • White, S. H. 2004. The progress of membrane protein structure determination. Protein Sci. 13, 1948-1949. (Pubitemid 38822136)
    • (2004) Protein Science , vol.13 , Issue.7 , pp. 1948-1949
    • White, S.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.