메뉴 건너뛰기




Volumn 40, Issue 2, 2008, Pages 135-144

A unifying probabilistic framework for analyzing residual dipolar couplings

Author keywords

Inferential structure determination; Markov chain Monte Carlo; NMR structure determination; Protein structure; Residual dipolar couplings

Indexed keywords

ARTICLE; BIOINFORMATICS; CHEMICAL STRUCTURE; CONCEPTUAL FRAMEWORK; HISTOGRAM; MATHEMATICAL ANALYSIS; MEASUREMENT; METHODOLOGY; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROBABILITY; RESIDUAL DIPOLAR COUPLING; STRUCTURE ANALYSIS;

EID: 38349075835     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-007-9215-1     Document Type: Article
Times cited : (14)

References (37)
  • 1
    • 0037189885 scopus 로고    scopus 로고
    • Physical interpretation of residual dipolar couplings in neutral aligned media
    • Almond A, Axelsen JB (2002) Physical interpretation of residual dipolar couplings in neutral aligned media. J Am Chem Soc 124(34):9986-9987
    • (2002) J Am Chem Soc , vol.124 , Issue.34 , pp. 9986-9987
    • Almond, A.1    Axelsen, J.B.2
  • 2
    • 0037139443 scopus 로고    scopus 로고
    • Tracking alignment from the moment of inertia tensor (TRAMITE) of biomolecules in neutral dilute liquid crystal solutions
    • Azurmendi HF, Bush CA (2002) Tracking alignment from the moment of inertia tensor (TRAMITE) of biomolecules in neutral dilute liquid crystal solutions. J Am Chem Soc 124(11):2426-2427
    • (2002) J Am Chem Soc , vol.124 , Issue.11 , pp. 2426-2427
    • Azurmendi, H.F.1    Bush, C.A.2
  • 3
    • 0037215324 scopus 로고    scopus 로고
    • Weak alignment offers new NMR opportunities to study protein structure and dynamics
    • Bax A (2003) Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci 12:1-16
    • (2003) Protein Sci , vol.12 , pp. 1-16
    • Bax, A.1
  • 4
    • 25844506708 scopus 로고    scopus 로고
    • Weak alignment NMR: A hawk-eyed view on biomolecular structure
    • Bax A, Grishaev A (2005) Weak alignment NMR: A hawk-eyed view on biomolecular structure. Curr Opin Struct Biol 15:563-570
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 563-570
    • Bax, A.1    Grishaev, A.2
  • 5
    • 0034919243 scopus 로고    scopus 로고
    • Dipolar couplings in macromolecular structure determination
    • Bax A, Kontaxis G, Tjandra N (2001) Dipolar couplings in macromolecular structure determination. Methods Enzymol 339:127-174
    • (2001) Methods Enzymol , vol.339 , pp. 127-174
    • Bax, A.1    Kontaxis, G.2    Tjandra, N.3
  • 6
    • 0032012610 scopus 로고    scopus 로고
    • Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude
    • Clore GM, Gronenborn AM, Tjandra N (1998a) Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J Magn Reson 131:159-162
    • (1998) J Magn Reson , vol.131 , pp. 159-162
    • Clore, G.M.1    Gronenborn, A.M.2    Tjandra, N.3
  • 7
    • 0032113480 scopus 로고    scopus 로고
    • A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information
    • Clore GM, Bax A, Gronenborn AM (1998b) A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. J Magn Reson 133:216-221
    • (1998) J Magn Reson , vol.133 , pp. 216-221
    • Clore, G.M.1    Bax, A.2    Gronenborn, A.M.3
  • 8
    • 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
  • 9
    • 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
  • 10
    • 0021518209 scopus 로고
    • Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images
    • Geman S, Geman D (1984) Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE Trans PAMI 6(6):721-741
    • (1984) IEEE Trans PAMI , vol.6 , Issue.6 , pp. 721-741
    • Geman, S.1    Geman, D.2
  • 11
    • 25144471317 scopus 로고    scopus 로고
    • Bayesian estimation of Karplus parameters and torsion angles from three-bond scalar coupling constants
    • Habeck M, Rieping W, Nilges M (2005a) Bayesian estimation of Karplus parameters and torsion angles from three-bond scalar coupling constants. J Magn Reson 177:160-165
    • (2005) J Magn Reson , vol.177 , pp. 160-165
    • Habeck, M.1    Rieping, W.2    Nilges, M.3
  • 12
    • 28844442908 scopus 로고    scopus 로고
    • Bayesian inference applied to macromolecular structure determination
    • Habeck M, Nilges M, Rieping W (2005b) Bayesian inference applied to macromolecular structure determination. Phys Rev E 72:031912
    • (2005) Phys Rev E , vol.72 , pp. 031912
    • Habeck, M.1    Nilges, M.2    Rieping, W.3
  • 13
    • 18144399340 scopus 로고    scopus 로고
    • Replica-exchange Monte Carlo scheme for Bayesian data analysis
    • Habeck M, Nilges M, Rieping W (2005c) Replica-exchange Monte Carlo scheme for Bayesian data analysis. Phys Rev Lett 94:0181051-0181054
    • (2005) Phys Rev Lett , vol.94 , pp. 0181051-0181054
    • Habeck, M.1    Nilges, M.2    Rieping, W.3
  • 14
    • 32444439415 scopus 로고    scopus 로고
    • Weighting of experimental evidence in macromolecular structure determination
    • Habeck M, Rieping W, Nilges M (2006) Weighting of experimental evidence in macromolecular structure determination. Proc Natl Acad Sci USA 103:1756-1761
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 1756-1761
    • Habeck, M.1    Rieping, W.2    Nilges, M.3
  • 15
    • 0034685602 scopus 로고    scopus 로고
    • De novo determination of protein structure by NMR using orientational and long-range order restraints
    • Hus J-C, Marion D, Blackledge M (2000) De novo determination of protein structure by NMR using orientational and long-range order restraints. J Mol Biol 298:927-936
    • (2000) J Mol Biol , vol.298 , pp. 927-936
    • Hus, J.-C.1    Marion, D.2    Blackledge, M.3
  • 16
    • 0035925135 scopus 로고    scopus 로고
    • Determination of protein backbone structure using only residual dipolar couplings
    • Hus J-C, 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
  • 18
    • 84873751778 scopus 로고
    • An invariant form for the prior probability in estimation problems
    • Jeffreys H (1946) An invariant form for the prior probability in estimation problems. Proc R Soc A 186:453-461
    • (1946) Proc R Soc A , vol.186 , pp. 453-461
    • Jeffreys, H.1
  • 19
    • 12244297937 scopus 로고
    • Vicinal proton coupling in nuclear magnetic resonance
    • Karplus M (1963) Vicinal proton coupling in nuclear magnetic resonance. J Am Chem Soc 85:2870-2871
    • (1963) J Am Chem Soc , vol.85 , pp. 2870-2871
    • Karplus, M.1
  • 20
    • 3042691762 scopus 로고    scopus 로고
    • Residual dipolar couplings in NMR structure analysis
    • Lipsitz RS, Tjandra N (2004) Residual dipolar couplings in NMR structure analysis. Ann Rev Biophys Biomol Struct 33:387-412
    • (2004) Ann Rev Biophys Biomol Struct , vol.33 , pp. 387-412
    • Lipsitz, R.S.1    Tjandra, N.2
  • 21
    • 0033145058 scopus 로고    scopus 로고
    • Order matrix analysis of residual dipolar couplings using singular value decomposition
    • Losonczi JA, Andrec M, Fischer MWF, Prestegard JH (1999) Order matrix analysis of residual dipolar couplings using singular value decomposition. J Magn Reson 138:334-342
    • (1999) J Magn Reson , vol.138 , pp. 334-342
    • Losonczi, J.A.1    Andrec, M.2    Fischer, M.W.F.3    Prestegard, J.H.4
  • 22
    • 0032866940 scopus 로고    scopus 로고
    • Structural constraints from residual tensorial couplings in high resolution NMR without an explicit term for the alignment tensor
    • Moltke S, Grzesiek S (1999) Structural constraints from residual tensorial couplings in high resolution NMR without an explicit term for the alignment tensor. J Biomol NMR 15:77-82
    • (1999) J Biomol NMR , vol.15 , pp. 77-82
    • Moltke, S.1    Grzesiek, S.2
  • 24
    • 0031851289 scopus 로고    scopus 로고
    • New techniques in structural NMR - Anisotropic interactions
    • Prestegard J (1998) New techniques in structural NMR - anisotropic interactions. Nat Struct Biol 5(Suppl):517-522
    • (1998) Nat Struct Biol , vol.5 , Issue.SUPPL. , pp. 517-522
    • Prestegard, J.1
  • 25
    • 22144489530 scopus 로고    scopus 로고
    • Inferential structure determination
    • Rieping W, Habeck M, Nilges M (2005a) Inferential structure determination. Science 309:303-306
    • (2005) Science , vol.309 , pp. 303-306
    • Rieping, W.1    Habeck, M.2    Nilges, M.3
  • 26
    • 28044443150 scopus 로고    scopus 로고
    • Modeling errors in NOE data with a lognormal distribution improves the quality of NMR structures
    • Rieping W, Habeck M, Nilges M (2005b) Modeling errors in NOE data with a lognormal distribution improves the quality of NMR structures. J Am Chem Soc 27:16026-16027
    • (2005) J Am Chem Soc , vol.27 , pp. 16026-16027
    • Rieping, W.1    Habeck, M.2    Nilges, M.3
  • 27
    • 0035211996 scopus 로고    scopus 로고
    • An easy way to include weak alignment constraints into NMR structure calculations
    • Sass H-J, Musco G, Stahl SJ, Wingfield PT, Grzesiek S (2001) An easy way to include weak alignment constraints into NMR structure calculations. J Biomol NMR 21:275-280
    • (2001) J Biomol NMR , vol.21 , pp. 275-280
    • Sass, H.-J.1    Musco, G.2    Stahl, S.J.3    Wingfield, P.T.4    Grzesiek, S.5
  • 28
    • 0001123769 scopus 로고
    • High-resolution nuclear magnetic resonance spectra of orientated molecules
    • Saupe A, Englert G (1963) High-resolution nuclear magnetic resonance spectra of orientated molecules. Phys Rev Lett 11:462-464
    • (1963) Phys Rev Lett , vol.11 , pp. 462-464
    • Saupe, A.1    Englert, G.2
  • 29
    • 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
  • 30
    • 0030612335 scopus 로고    scopus 로고
    • Use of dipolar H1-N15 and H1-C13 couplings in the structure determination of magnetically oriented macromolecules in solution
    • Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A (1997) Use of dipolar H1-N15 and H1-C13 couplings in the structure determination of magnetically oriented macromolecules in solution. Nat Struct Biol 4:732-738
    • (1997) Nat Struct Biol , vol.4 , pp. 732-738
    • Tjandra, N.1    Omichinski, J.G.2    Gronenborn, A.M.3    Clore, G.M.4    Bax, A.5
  • 31
    • 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
  • 32
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 Å resolution
    • Vijay-Kumar S, Bugg CE, Cook WJ (1987) Structure of ubiquitin refined at 1.8 Å resolution. J Mol Biol 194(3):531-544
    • (1987) J Mol Biol , vol.194 , Issue.3 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3
  • 33
    • 0035743157 scopus 로고    scopus 로고
    • A maximum likelihood method for determining and R for sets of dipolar coupling data
    • Warren JJ, Moore PB (2001) A maximum likelihood method for determining and R for sets of dipolar coupling data. J Magn Reson 149:271-275
    • (2001) J Magn Reson , vol.149 , pp. 271-275
    • Warren, J.J.1    Moore, P.B.2
  • 34
    • 29944441649 scopus 로고    scopus 로고
    • Prediction of charge-induced molecular alignment: Residual dipolar couplings at pH 3 and alignment in surfactant liquid crystalline phases
    • Zweckstetter M (2006) Prediction of charge-induced molecular alignment: residual dipolar couplings at pH 3 and alignment in surfactant liquid crystalline phases. Eur Biophys J 35:170-180
    • (2006) Eur Biophys J , vol.35 , pp. 170-180
    • Zweckstetter, M.1
  • 35
    • 0034685436 scopus 로고    scopus 로고
    • Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR
    • Zweckstetter M, Bax AJ (2000) Prediction of sterically induced alignment in a dilute liquid crystalline phase: Aid to protein structure determination by NMR. J Am Chem Soc 122:3791-3792
    • (2000) J Am Chem Soc , vol.122 , pp. 3791-3792
    • Zweckstetter, M.1    Bax, A.J.2
  • 36
    • 0035996721 scopus 로고    scopus 로고
    • Evaluation of uncertainty in alignment tensors obtained from dipolar couplings
    • Zweckstetter M, Bax A (2002) Evaluation of uncertainty in alignment tensors obtained from dipolar couplings. J Biomol NMR 23:127-137
    • (2002) J Biomol NMR , vol.23 , pp. 127-137
    • Zweckstetter, M.1    Bax, A.2
  • 37
    • 2942653357 scopus 로고    scopus 로고
    • Prediction of charge-induced alignment of biomolecules dissolved in dilute liquid-crystalline phases
    • Zweckstetter M, Hummer G, Bax A (2004) Prediction of charge-induced alignment of biomolecules dissolved in dilute liquid-crystalline phases. Biophys J 86:3444-3460
    • (2004) Biophys J , vol.86 , pp. 3444-3460
    • Zweckstetter, M.1    Hummer, G.2    Bax, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.