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Volumn 45, Issue 3, 2009, Pages 265-281

High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations

Author keywords

Nuclear magnetic resonance; Nuclear overhauser effect assignment; Packing; Residual dipolar coupling; Structure determination

Indexed keywords

RNA POLYMERASE II; UBIQUITIN;

EID: 70350344265     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-009-9366-3     Document Type: Article
Times cited : (36)

References (53)
  • 1
    • 0035695158 scopus 로고    scopus 로고
    • Protein backbone structure determination using only residual dipolar couplings from one ordering medium
    • Andrec M, Du P, Levy RM (2004) Protein backbone structure determination using only residual dipolar couplings from one ordering medium. J Biomol NMR 21:335-347
    • (2004) J Biomol NMR , vol.21 , pp. 335-347
    • Andrec, M.1    Du, P.2    Levy, R.M.3
  • 2
    • 0033677333 scopus 로고    scopus 로고
    • The NOESY Jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data
    • Bailey-Kellogg C, Widge A, Kelley JJ, Berardi MJ, Bushweller JH, Donald BR (2000) The NOESY Jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. J Comput Biol 7(3-4):537-558
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 537-558
    • Bailey-Kellogg, C.1    Widge, A.2    Kelley, J.J.3    Berardi, M.J.4    Bushweller, J.H.5    Donald, B.R.6
  • 4
    • 0343459675 scopus 로고
    • The program XEASY for computer-supported NMR spectral analysis of biological macromolecules
    • Bartels C, Xia T, Billeter M, Güntert P, Wüthrich K (1995) The program XEASY for computer-supported NMR spectral analysis of biological macromolecules. J Biomol NMR 6:1-10
    • (1995) J Biomol NMR , vol.6 , pp. 1-10
    • Bartels, C.1    Xia, T.2    Billeter, M.3    Güntert, P.4    Wüthrich, K.5
  • 5
    • 33847338933 scopus 로고    scopus 로고
    • Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase η
    • Bomar MG, Pai M, Tzeng S, Li S, Zhou P (2007) Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase η. EMBO Rep 8:247-251
    • (2007) EMBO Rep , vol.8 , pp. 247-251
    • Bomar, M.G.1    Pai, M.2    Tzeng, S.3    Li, S.4    Zhou, P.5
  • 6
    • 70350287841 scopus 로고
    • X-PLOR, Version 3.1: A system for X-ray crystallography and NMR
    • Brünger AT (1992) X-PLOR, Version 3.1: A system for X-ray crystallography and NMR. J Am Chem Soc
    • (1992) J Am Chem Soc
    • Brünger, A.T.1
  • 7
    • 0031721689 scopus 로고    scopus 로고
    • The hierarchical organization of molecular structure computations
    • Chen CC, Singh JP, Altman RB (1998) The hierarchical organization of molecular structure computations. J Comput Biol 5:409-422
    • (1998) J Comput Biol , vol.5 , pp. 409-422
    • Chen, C.C.1    Singh, J.P.2    Altman, R.B.3
  • 8
    • 0038663223 scopus 로고    scopus 로고
    • PACES: Protein sequential assignment by computer-assisted exhaustive search
    • Coggins BE, Zhou P (2003) PACES: Protein sequential assignment by computer-assisted exhaustive search. J Biomol NMR 26:93-111
    • (2003) J Biomol NMR , vol.26 , pp. 93-111
    • Coggins, B.E.1    Zhou, P.2
  • 9
    • 55949122794 scopus 로고    scopus 로고
    • High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN
    • Coggins BE, Zhou P (2008) High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN. J Biomol NMR 42: 225-239
    • (2008) J Biomol NMR , vol.42 , pp. 225-239
    • Coggins, B.E.1    Zhou, P.2
  • 10
    • 0032528033 scopus 로고    scopus 로고
    • Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase
    • Cornilescu G, Marquardt JL, Ottiger M, Bax A (1998) Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc 120:6836-6837
    • (1998) J Am Chem Soc , vol.120 , pp. 6836-6837
    • Cornilescu, G.1    Marquardt, J.L.2    Ottiger, M.3    Bax, A.4
  • 11
    • 0033003335 scopus 로고    scopus 로고
    • Protein backbone angle restraints from searching a database for chemical shift and sequence homology
    • Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289-302
    • (1999) J Biomol NMR , vol.13 , pp. 289-302
    • Cornilescu, G.1    Delaglio, F.2    Bax, A.3
  • 12
    • 3242886389 scopus 로고    scopus 로고
    • MolProbity: Structure validation and all-atom contact analysis for nucleic acids and their complexes
    • Davis IW, Murray LW, Richardson JS, Richardson DC (2004) MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32:W615-W619
    • (2004) Nucleic Acids Res , vol.32
    • Davis, I.W.1    Murray, L.W.2    Richardson, J.S.3    Richardson, D.C.4
  • 14
    • 0034620764 scopus 로고    scopus 로고
    • Protein structure determination using molecular fragment replacement and NMR dipolar couplings
    • Delaglio F, Kontaxis G, Bax A (2000) Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J Am Chem Soc 122:2142-2143
    • (2000) J Am Chem Soc , vol.122 , pp. 2142-2143
    • Delaglio, F.1    Kontaxis, G.2    Bax, A.3
  • 15
    • 67650473269 scopus 로고    scopus 로고
    • Automated NMR assignment and protein structure determination using sparse dipolar coupling constraints
    • Donald BR, Martin J (2009) Automated NMR assignment and protein structure determination using sparse dipolar coupling constraints. Prog NMR Spectrosc 55(2):101-127
    • (2009) Prog NMR Spectrosc , vol.55 , Issue.2 , pp. 101-127
    • Donald, B.R.1    Martin, J.2
  • 16
    • 51749107733 scopus 로고    scopus 로고
    • Automated amino acid side-chain NMR assignment of proteins using (13)C- and (15)N-resolved 3D [(1)H, (1)H]-NOESY
    • Fiorito F, Herrmann T, Damberger F, Wüthrich K (2008) Automated amino acid side-chain NMR assignment of proteins using (13)C- and (15)N-resolved 3D [(1)H, (1)H]-NOESY. J Biomol NMR 42:23-33
    • (2008) J Biomol NMR , vol.42 , pp. 23-33
    • Fiorito, F.1    Herrmann, T.2    Damberger, F.3    Wüthrich, K.4
  • 17
    • 0034388123 scopus 로고    scopus 로고
    • Rapid determination of protein folds using residual dipolar couplings
    • Fowler CA, Tian F, Al-Hashimi HM, Prestegard JH (2000) Rapid determination of protein folds using residual dipolar couplings. J Mol Biol 304:447-460
    • (2000) J Mol Biol , vol.304 , pp. 447-460
    • Fowler, C.A.1    Tian, F.2    Al-Hashimi, H.M.3    Prestegard, J.H.4
  • 18
    • 46449106372 scopus 로고    scopus 로고
    • The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
    • Georgiev I, Lilien RH, Donald BR (2008) The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. J Comput Chem 29:1527-1542
    • (2008) J Comput Chem , vol.29 , pp. 1527-1542
    • Georgiev, I.1    Lilien, R.H.2    Donald, B.R.3
  • 20
    • 4344698912 scopus 로고    scopus 로고
    • Automated NMR protein structure determination
    • Güntert P (2003) Automated NMR protein structure determination. Prog Nucl Magn Reson Spectrosc 43:105-125
    • (2003) Prog Nucl Magn Reson Spectrosc , vol.43 , pp. 105-125
    • Güntert, P.1
  • 23
    • 0036308102 scopus 로고    scopus 로고
    • Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA
    • Herrmann T, Güntert P, Wuüthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319(1):209-227
    • (2002) J Mol Biol , vol.319 , Issue.1 , pp. 209-227
    • Herrmann, T.1    Güntert, P.2    Wuüthrich, K.3
  • 24
    • 31944451135 scopus 로고    scopus 로고
    • A topology-constrained distance network algorithm for protein structure determination from NOESY data
    • Huang YJ, Tejero R, Powers R, Montelione GT (2006) A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins Struct Funct Bioinform 62(3):587-603
    • (2006) Proteins Struct Funct Bioinform , vol.62 , Issue.3 , pp. 587-603
    • Huang, Y.J.1    Tejero, R.2    Powers, R.3    Montelione, G.T.4
  • 25
    • 0035925135 scopus 로고    scopus 로고
    • Determination of protein backbone structure using only residual dipolar couplings
    • Hus JC, Marion D, Blackledge M (2001) Determination of protein backbone structure using only residual dipolar couplings. J Am Chem Soc 123:1541-1542
    • (2001) J Am Chem Soc , vol.123 , pp. 1541-1542
    • Hus, J.C.1    Marion, D.2    Blackledge, M.3
  • 26
    • 56749158755 scopus 로고    scopus 로고
    • 16-Fold Degeneracy of peptide plane orientations from residual dipolar couplings: Analytical treatment and implications for protein structure determination
    • Hus JC, Salmon L, Bouvignies G, Lotze J, Blackledge M, Brüschweiler R (2008) 16-Fold Degeneracy of peptide plane orientations from residual dipolar couplings: Analytical treatment and implications for protein structure determination. J Am Chem Soc 130:15927-15937
    • (2008) J Am Chem Soc , vol.130 , pp. 15927-15937
    • Hus, J.C.1    Salmon, L.2    Bouvignies, G.3    Lotze, J.4    Blackledge, M.5    Brüschweiler, R.6
  • 28
    • 2442528145 scopus 로고
    • Distance metrics for comparing shapes in the plane
    • In: Donald BR, Kapur D, Mundy J (eds) Academic Press, New York
    • Huttenlocher DP, Kedem K (1992) Distance metrics for comparing shapes in the plane. In: Donald BR, Kapur D, Mundy J (eds) Symbolic and numerical computation for artificial intelligence. Academic Press, New York, pp 201-219
    • (1992) Symbolic and Numerical Computation for Artificial Intelligence , pp. 201-219
    • Huttenlocher, D.P.1    Kedem, K.2
  • 29
    • 34249765651 scopus 로고
    • NMRView: A computer program for the visualization and analysis of NMR data
    • Johnson BA, Blevins RA (1994) NMRView: A computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603-614
    • (1994) J Biomol NMR , vol.4 , pp. 603-614
    • Johnson, B.A.1    Blevins, R.A.2
  • 30
    • 2442717620 scopus 로고    scopus 로고
    • Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments
    • Kuszewski J, Schwieters CD, Garrett DS, Byrd RA, Tjandra N, Clore GM (2004) Completely automated, highly error-tolerant macromolecular structure determination from multidimensional nuclear overhauser enhancement spectra and chemical shift assignments. J Am Chem Soc 126(20):6258-6273
    • (2004) J Am Chem Soc , vol.126 , Issue.20 , pp. 6258-6273
    • Kuszewski, J.1    Schwieters, C.D.2    Garrett, D.S.3    Byrd, R.A.4    Tjandra, N.5    Clore, G.M.6
  • 31
    • 1842555458 scopus 로고    scopus 로고
    • An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments
    • Langmead C, Donald B (2004) An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments. J Biomol NMR 29(2):111-138
    • (2004) J Biomol NMR , vol.29 , Issue.2 , pp. 111-138
    • Langmead, C.1    Donald, B.2
  • 32
    • 29144448731 scopus 로고    scopus 로고
    • Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1
    • Li M, Phatnani HP, Guan Z, Sage H, Greenleaf AL, Zhou P (2005) Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1. Proc Natl Acad Sci 102:17636-17641
    • (2005) Proc Natl Acad Sci , vol.102 , pp. 17636-17641
    • Li, M.1    Phatnani, H.P.2    Guan, Z.3    Sage, H.4    Greenleaf, A.L.5    Zhou, P.6
  • 33
    • 0037316363 scopus 로고    scopus 로고
    • ARIA: Automated NOE assignment and NMR structure calculation
    • Linge JP, Habeck M, Rieping W, Nilges M (2003) ARIA: Automated NOE assignment and NMR structure calculation. Bioinformatics 19(2):315-316
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 315-316
    • Linge, J.P.1    Habeck, M.2    Rieping, W.3    Nilges, M.4
  • 35
    • 0031304082 scopus 로고    scopus 로고
    • Automated combined assignment of NOESY spectra and three-dimensional protein structure determination
    • Mumenthaler C, Güntert P, Braun W, Wüthrich K (1997) Automated combined assignment of NOESY spectra and three-dimensional protein structure determination. J Biomol NMR 10(4):351-362
    • (1997) J Biomol NMR , vol.10 , Issue.4 , pp. 351-362
    • Mumenthaler, C.1    Güntert, P.2    Braun, W.3    Wüthrich, K.4
  • 36
    • 0032042263 scopus 로고    scopus 로고
    • Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra
    • Ottiger M, Delaglio F, Bax A (1998) Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J Magn Reson 138:373-378
    • (1998) J Magn Reson , vol.138 , pp. 373-378
    • Ottiger, M.1    Delaglio, F.2    Bax, A.3
  • 38
    • 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
    • Potluri S, Yan AK, Chou JJ, Donald BR, Bailey-Kellogg C (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
    • (2006) Proteins , vol.65 , pp. 203-219
    • Potluri, S.1    Yan, A.K.2    Chou, J.J.3    Donald, B.R.4    Bailey-Kellogg, C.5
  • 39
    • 33845925822 scopus 로고    scopus 로고
    • A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers
    • Potluri S, Yan AK, Donald BR, Bailey-Kellogg C (2007) A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers. Protein Sci 16:69-81
    • (2007) Protein Sci , vol.16 , pp. 69-81
    • Potluri, S.1    Yan, A.K.2    Donald, B.R.3    Bailey-Kellogg, C.4
  • 40
    • 22144489530 scopus 로고    scopus 로고
    • Inferential structure determination
    • Rieping W, Habeck M, Nilges M (2005) Inferential structure determination. Science 309:303-306
    • (2005) Science , vol.309 , pp. 303-306
    • Rieping, W.1    Habeck, M.2    Nilges, M.3
  • 41
    • 44949209342 scopus 로고    scopus 로고
    • De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media
    • Ruan K, Briggman KB, Tolman JR (2008) De novo determination of internuclear vector orientations from residual dipolar couplings measured in three independent alignment media. J Biomol NMR 41:61-76
    • (2008) J Biomol NMR , vol.41 , pp. 61-76
    • Ruan, K.1    Briggman, K.B.2    Tolman, J.R.3
  • 42
    • 0033636451 scopus 로고    scopus 로고
    • Assessment of molecular structure using frame-independent orientational restraints derived from residual dipolar couplings
    • Skrynnikov NR, Kay LE (2000) Assessment of molecular structure using frame-independent orientational restraints derived from residual dipolar couplings. J Biomol NMR 18(3):239-252
    • (2000) J Biomol NMR , vol.18 , Issue.3 , pp. 239-252
    • Skrynnikov, N.R.1    Kay, L.E.2
  • 43
    • 0035965759 scopus 로고    scopus 로고
    • A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones
    • Tian F, Valafar H, Prestegard JH. (2001) A dipolar coupling based strategy for simultaneous resonance assignment and structure determination of protein backbones. J Am Chem Soc 123:11791-11796
    • (2001) J Am Chem Soc , vol.123 , pp. 11791-11796
    • Tian, F.1    Valafar, H.2    Prestegard, J.H.3
  • 44
    • 0030722243 scopus 로고    scopus 로고
    • Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium
    • Tjandra N, Bax A (1997) Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278:1111-1114
    • (1997) Science , vol.278 , pp. 1111-1114
    • Tjandra, N.1    Bax, A.2
  • 45
    • 0029050883 scopus 로고
    • Nuclear magnetic dipole interactions in field-oriented proteins: Information for structure determination in solution
    • Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH (1995) Nuclear magnetic dipole interactions in field-oriented proteins: Information for structure determination in solution. Proc Natl Acad Sci USA 92:9279-9283
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 9279-9283
    • Tolman, J.R.1    Flanagan, J.M.2    Kennedy, M.A.3    Prestegard, J.H.4
  • 46
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 A resolution
    • Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 A resolution. J Mol Biol 194:531-544
    • (1987) J Mol Biol , vol.194 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 48
    • 14044272802 scopus 로고    scopus 로고
    • Analysis of a systematic search-based algorithm for determining protein backbone structure from a minimal number of residual dipolar couplings
    • In: Stanford, CA (August 2004) PMID: 16448025
    • Wang L, Donald BR (2004a) Analysis of a systematic search-based algorithm for determining protein backbone structure from a minimal number of residual dipolar couplings. In: Proceedings of The IEEE computational systems bioinformatics conference (CSB), Stanford, CA (August 2004), pp 319-330, PMID: 16448025
    • (2004) Proceedings of The IEEE Computational Systems Bioinformatics Conference (CSB) , pp. 319-330
    • Wang, L.1    Donald, B.R.2
  • 49
    • 3042719896 scopus 로고    scopus 로고
    • Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure
    • Wang L, Donald BR (2004b) Exact solutions for internuclear vectors and backbone dihedral angles from NH residual dipolar couplings in two media, and their application in a systematic search algorithm for determining protein backbone structure. J Biomol NMR 29(3):223-242
    • (2004) J Biomol NMR , vol.29 , Issue.3 , pp. 223-242
    • Wang, L.1    Donald, B.R.2
  • 50
    • 33745497536 scopus 로고    scopus 로고
    • An efficient and accurate algorithm for assigning nuclear overhauser effect restraints using a rotamer library ensemble and residual dipolar couplings
    • In: Stanford, CA (August 2005) PMID: 16447976
    • Wang L, Donald BR (2005) An efficient and accurate algorithm for assigning nuclear overhauser effect restraints using a rotamer library ensemble and residual dipolar couplings. In: The IEEE computational systems bioinformatics conference (CSB), Stanford, CA (August 2005), pp 189-202, PMID: 16447976
    • (2005) The IEEE Computational Systems Bioinformatics Conference (CSB) , pp. 189-202
    • Wang, L.1    Donald, B.R.2
  • 51
    • 33846263054 scopus 로고    scopus 로고
    • A polynomial-time algorithm for de novo protein backbone structure determination from NMR data
    • Wang L, Mettu R, Donald BR (2006) A polynomial-time algorithm for de novo protein backbone structure determination from NMR data. J Comput Biol 13(7):1276-1288
    • (2006) J Comput Biol , vol.13 , Issue.7 , pp. 1276-1288
    • Wang, L.1    Mettu, R.2    Donald, B.R.3
  • 52
    • 0036180645 scopus 로고    scopus 로고
    • Exact solutions for chemical bond orientations from residual dipolar couplings
    • Wedemeyer WJ, Rohl CA, Scheraga HA (2002) Exact solutions for chemical bond orientations from residual dipolar couplings. J Biomol NMR 22:137-151
    • (2002) J Biomol NMR , vol.22 , pp. 137-151
    • Wedemeyer, W.J.1    Rohl, C.A.2    Scheraga, H.A.3
  • 53
    • 69249224514 scopus 로고    scopus 로고
    • A Hausdorff-based NOE assignment algorithm using protein backbone determined from residual dipolar couplings and rotamer patterns
    • In: Stanford CA ISBN 1752-7791. PMID: 19122773
    • Zeng J, Tripathy C, Zhou P, Donald BR (2008) A Hausdorff-based NOE assignment algorithm using protein backbone determined from residual dipolar couplings and rotamer patterns. In: Proceedings of the 7th annual international conference on computational systems bioinformatics, Stanford CA, pp 169-181. ISBN 1752-7791. PMID: 19122773
    • (2008) Proceedings of the 7th Annual International Conference on Computational Systems Bioinformatics , pp. 169-181
    • Zeng, J.1    Tripathy, C.2    Zhou, P.3    Donald, B.R.4


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