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Volumn 285, Issue 2, 1999, Pages 727-740

Influence of internal dynamics on accuracy of protein NMR structures: Derivation of realistic model distance data from a long molecular dynamics trajectory

Author keywords

Molecular dynamics; NMR; NOE; Solution structure; Structure accuracy

Indexed keywords

PROTON;

EID: 0344791680     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2323     Document Type: Article
Times cited : (36)

References (60)
  • 1
    • 0029044470 scopus 로고
    • NMR cross relaxation investigated by molecular dynamics simulation: A case study of ubiquitin in solution
    • Abseher R., Lüdemann S., Schreiber H., Steinhauser O. NMR cross relaxation investigated by molecular dynamics simulation: a case study of ubiquitin in solution. J. Mol. Biol. 249:1995;604-624.
    • (1995) J. Mol. Biol. , vol.249 , pp. 604-624
    • Abseher, R.1    Lüdemann, S.2    Schreiber, H.3    Steinhauser, O.4
  • 2
    • 0032101346 scopus 로고    scopus 로고
    • Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap
    • Abseher R., Horstink L., Hilbers C. W., Nilges M. Essential spaces defined by NMR structure ensembles and molecular dynamics simulation show significant overlap. Proteins: Struct. Funct. Genet. 31:1998;370-382.
    • (1998) Proteins: Struct. Funct. Genet. , vol.31 , pp. 370-382
    • Abseher, R.1    Horstink, L.2    Hilbers, C.W.3    Nilges, M.4
  • 4
    • 0026795399 scopus 로고
    • Determination of a high-quality nuclear magnetic resonance solution structure of the bovine pancreatic trypsin inhibitor and comparison with three crystal structures
    • Berndt K., Güntert P., Orbons L., Wüthrich K. Determination of a high-quality nuclear magnetic resonance solution structure of the bovine pancreatic trypsin inhibitor and comparison with three crystal structures. J. Mol. Biol. 227:1993;757-775.
    • (1993) J. Mol. Biol. , vol.227 , pp. 757-775
    • Berndt, K.1    Güntert, P.2    Orbons, L.3    Wüthrich, K.4
  • 6
    • 0029022355 scopus 로고
    • Conformational variability of solution nuclear magnetic resonance structures
    • Bonvin A. M. J. J., Brünger A. T. Conformational variability of solution nuclear magnetic resonance structures. J. Mol. Biol. 250:1995a;80-93.
    • (1995) J. Mol. Biol. , vol.250 , pp. 80-93
    • Bonvin, A.M.J.J.1    Brünger, A.T.2
  • 7
    • 0029693351 scopus 로고
    • Do NOE distances contain enough distance information to access the relative populations of multi-conformer structures?
    • Bonvin A. M. J. J., Brünger A. T. Do NOE distances contain enough distance information to access the relative populations of multi-conformer structures? J. Biomol. NMR. 5:1995b;72-76.
    • (1995) J. Biomol. NMR , vol.5 , pp. 72-76
    • Bonvin, A.M.J.J.1    Brünger, A.T.2
  • 9
    • 84988057883 scopus 로고
    • Spatially constrained minimization of macromolecules
    • Bruccoleri R. E., Karplus M. Spatially constrained minimization of macromolecules. J. Comput. Chem. 7:1986;165-175.
    • (1986) J. Comput. Chem. , vol.7 , pp. 165-175
    • Bruccoleri, R.E.1    Karplus, M.2
  • 10
    • 0024250301 scopus 로고
    • Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison
    • Brünger A., Karplus M. Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison. Proteins: Struct. Funct. Genet. 4:1988;148-156.
    • (1988) Proteins: Struct. Funct. Genet. , vol.4 , pp. 148-156
    • Brünger, A.1    Karplus, M.2
  • 12
    • 0030791762 scopus 로고    scopus 로고
    • X-ray crystallography and NMR reveal complementary views of structure and dynamics
    • Brünger A. X-ray crystallography and NMR reveal complementary views of structure and dynamics. Nature Struct. Biol. 4:1997;S862-S865.
    • (1997) Nature Struct. Biol. , vol.4
    • Brünger, A.1
  • 13
    • 0027918891 scopus 로고
    • Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation
    • Brünger A. T., Clore G. M., Gronenborn A. M., Saffrich R., Nilges M. Assessing the quality of solution nuclear magnetic resonance structures by complete cross-validation. Science. 261:1993;328-331.
    • (1993) Science , vol.261 , pp. 328-331
    • Brünger, A.T.1    Clore, G.M.2    Gronenborn, A.M.3    Saffrich, R.4    Nilges, M.5
  • 14
    • 0026734453 scopus 로고
    • Normal modes and NMR order parameters in proteins
    • Brüschweiler R. Normal modes and NMR order parameters in proteins. J. Am. Chem. Soc. 114:1992;5341-5344.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 5341-5344
    • Brüschweiler, R.1
  • 15
    • 0001767250 scopus 로고
    • Influence of rapid intramolecular motion on NMR cross-relaxation rates. a molecular dynamics study of antamanide in solution
    • Brüschweiler R., Roux B., Blackledge M., Griesinger C., Karplus M., Ernst R. Influence of rapid intramolecular motion on NMR cross-relaxation rates. a molecular dynamics study of antamanide in solution. J. Am. Chem. Soc. 114:1992;2289-2302.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 2289-2302
    • Brüschweiler, R.1    Roux, B.2    Blackledge, M.3    Griesinger, C.4    Karplus, M.5    Ernst, R.6
  • 18
  • 19
    • 0025046144 scopus 로고
    • Deviation from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins
    • Clore G., Szabo A., Bax A., Kay L., Driscoll P., Gronenborn A. Deviation from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. Chem. Soc. 112:1990;4989-4991.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 4989-4991
    • Clore, G.1    Szabo, A.2    Bax, A.3    Kay, L.4    Driscoll, P.5    Gronenborn, A.6
  • 20
    • 0027172878 scopus 로고
    • Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy [published erratum appears in J.Mol.Biol. (1994) Mar 25;237 (2):243]
    • Clore G. M., Robien M. A., Gronenborn A. M. Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy [published erratum appears in J.Mol.Biol. (1994) Mar 25;237 (2):243]. J. Mol. Biol. 231:1993;82-102.
    • (1993) J. Mol. Biol. , vol.231 , pp. 82-102
    • Clore, G.M.1    Robien, M.A.2    Gronenborn, A.M.3
  • 21
    • 0029366730 scopus 로고
    • Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor
    • Fadel A. R., Jin D. Q., Montelione G. T., Levy R. M. Crankshaft motions of the polypeptide backbone in molecular dynamics simulations of human type-alpha transforming growth factor. J. Biomol. NMR. 6:1995;221-225.
    • (1995) J. Biomol. NMR , vol.6 , pp. 221-225
    • Fadel, A.R.1    Jin, D.Q.2    Montelione, G.T.3    Levy, R.M.4
  • 22
    • 0027991494 scopus 로고
    • Determination of the backbone mobility of ribonuclease T1 and its 2′GMP complex using molecular dynamics simulations and NMR relaxation data
    • Fushman D., Ohlenschläger O., Rüterjans H. Determination of the backbone mobility of ribonuclease T1 and its 2′GMP complex using molecular dynamics simulations and NMR relaxation data. J. Biol. Struct. Dynam. 11:1994;1377-1402.
    • (1994) J. Biol. Struct. Dynam. , vol.11 , pp. 1377-1402
    • Fushman, D.1    Ohlenschläger, O.2    Rüterjans, H.3
  • 23
    • 0001249550 scopus 로고
    • Nonexponential relaxation of rotating three-spin systems in molecules of a liquid
    • Hubbard P. S. Nonexponential relaxation of rotating three-spin systems in molecules of a liquid. J. Chem. Phys. 52:1970;563-568.
    • (1970) J. Chem. Phys. , vol.52 , pp. 563-568
    • Hubbard, P.S.1
  • 24
    • 0020997912 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W., Sander C. A solution for the best rotation to relate two sets of vectors. Biopolymers. 22:1983;2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 25
    • 0029334378 scopus 로고
    • Dynamic modelling of a helical peptide in solution using NMR data: Multiple conformations and multi-spin effects
    • Kemmink J., Scheek R. M. Dynamic modelling of a helical peptide in solution using NMR data: multiple conformations and multi-spin effects. J. Biomol. NMR. 5:1995;33-40.
    • (1995) J. Biomol. NMR , vol.5 , pp. 33-40
    • Kemmink, J.1    Scheek, R.M.2
  • 26
    • 0024435205 scopus 로고
    • A dynamic model for the structure of acyl carrier protein in solution
    • Kim Y., Prestegard J. H. A dynamic model for the structure of acyl carrier protein in solution. Biochemistry. 28:1989;8792-8797.
    • (1989) Biochemistry , vol.28 , pp. 8792-8797
    • Kim, Y.1    Prestegard, J.H.2
  • 27
    • 44949290542 scopus 로고
    • Calculation of the nuclear Overhauser effect and the determination of proton-proton distances in the presence of internal motion
    • Koning T. M. G., Boelens R., Kaptein R. Calculation of the nuclear Overhauser effect and the determination of proton-proton distances in the presence of internal motion. J. Magn. Reson. 90:1990;111-123.
    • (1990) J. Magn. Reson. , vol.90 , pp. 111-123
    • Koning, T.M.G.1    Boelens, R.2    Kaptein, R.3
  • 28
    • 0026244229 scopus 로고
    • Molscript: A program to produce both detailed and schematic plots of protein structures
    • Kraulis P. Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
    • (1991) J. Appl. Crystallog. , vol.24 , pp. 946-950
    • Kraulis, P.1
  • 29
    • 0023053635 scopus 로고
    • Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics
    • Kuriyan J., Petsko G. A., Levi R. M., Karplus M. Effect of anisotropy and anharmonicity on protein crystallographic refinement. An evaluation by molecular dynamics. J. Mol. Biol. 190:1986;227-254.
    • (1986) J. Mol. Biol. , vol.190 , pp. 227-254
    • Kuriyan, J.1    Petsko, G.A.2    Levi, R.M.3    Karplus, M.4
  • 30
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski R. A., MacArthur M. W., Moss D. S., Thornton J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-291.
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 31
  • 32
    • 0024094768 scopus 로고
    • Accurate simulation of protein dynamics in solution
    • Levitt M., Sharon R. Accurate simulation of protein dynamics in solution. Proc. Natl Acad. Sci. USA. 85:1988;7557-7561.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 7557-7561
    • Levitt, M.1    Sharon, R.2
  • 33
    • 33845553743 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
    • Lipari G., Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104:1982;4546-4558.
    • (1982) J. Am. Chem. Soc. , vol.104 , pp. 4546-4558
    • Lipari, G.1    Szabo, A.2
  • 34
    • 0019960215 scopus 로고
    • Protein dynamics and NMR relaxatoin: Comparison of simulations with experiment
    • Lipari G., Szabo A., Levy R. Protein dynamics and NMR relaxatoin: comparison of simulations with experiment. Nature. 300:1982;197-198.
    • (1982) Nature , vol.300 , pp. 197-198
    • Lipari, G.1    Szabo, A.2    Levy, R.3
  • 35
    • 0024795316 scopus 로고
    • The effects of truncating long-range forces on protein dynamics
    • Loncharich R. J., Brooks B. R. The effects of truncating long-range forces on protein dynamics. Proteins: Struct. Funct. Genet. 6:1989;32-45.
    • (1989) Proteins: Struct. Funct. Genet. , vol.6 , pp. 32-45
    • Loncharich, R.J.1    Brooks, B.R.2
  • 36
    • 84977303841 scopus 로고
    • The geometry of the reactive site of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors
    • Marquart M., Walter J., Deisenhofer J., Bode W., Huber R. The geometry of the reactive site of the peptide groups in trypsin, trypsinogen and its complexes with inhibitors. Acta Crystallog. sect. B. 39:1983;480-487.
    • (1983) Acta Crystallog. Sect. B , vol.39 , pp. 480-487
    • Marquart, M.1    Walter, J.2    Deisenhofer, J.3    Bode, W.4    Huber, R.5
  • 37
    • 0347988396 scopus 로고    scopus 로고
    • Ambiguous NOEs and automated NOESY assignment
    • Nilges M., O'Donoghue S. I. Ambiguous NOEs and automated NOESY assignment. Prog. NMR Spectrosc. 32:1998;107-139.
    • (1998) Prog. NMR Spectrosc. , vol.32 , pp. 107-139
    • Nilges, M.1    O'Donoghue, S.I.2
  • 38
    • 0021754836 scopus 로고
    • Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of Lysozyme
    • Olejniczak E. T., Dobson C. M., Karplus M., Levy R. M. Motional averaging of proton nuclear Overhauser effects in proteins. Predictions from a molecular dynamics simulation of Lysozyme. J. Am. Chem. Soc. 106:1984;1923-1930.
    • (1984) J. Am. Chem. Soc. , vol.106 , pp. 1923-1930
    • Olejniczak, E.T.1    Dobson, C.M.2    Karplus, M.3    Levy, R.M.4
  • 39
    • 0030778008 scopus 로고    scopus 로고
    • Probing molecular motion by NMR
    • Palmer A. G. III. Probing molecular motion by NMR. Curr. Opin. Struct. Biol. 7:1997;732-737.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 732-737
    • Palmer A.G. III1
  • 40
    • 2442460927 scopus 로고
    • Molecular dynamics analysis of NMR-relaxation in a zinc-finger peptide
    • Palmer A. G. III, Case D. A. Molecular dynamics analysis of NMR-relaxation in a zinc-finger peptide. J. Am. Chem. Soc. 114:1992;9067-9075.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 9067-9075
    • Palmer A.G. III1    Case, D.A.2
  • 41
    • 0025778738 scopus 로고
    • Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA
    • Pearlman D. A., Kollman P. A. Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA. J. Mol. Biol. 220:1991;457-479.
    • (1991) J. Mol. Biol. , vol.220 , pp. 457-479
    • Pearlman, D.A.1    Kollman, P.A.2
  • 42
    • 0030877076 scopus 로고    scopus 로고
    • Accuracy and precision of NMR relaxation experiments and md simulations for characterizing protein dynamics
    • Philippopoulos M., Mandel A. M., Palmer A. G. III, Lim C. Accuracy and precision of NMR relaxation experiments and md simulations for characterizing protein dynamics. Proteins: Struct. Funct. Genet. 28:1997;481-493.
    • (1997) Proteins: Struct. Funct. Genet. , vol.28 , pp. 481-493
    • Philippopoulos, M.1    Mandel, A.M.2    Palmer A.G. III3    Lim, C.4
  • 43
    • 0026559517 scopus 로고
    • Internal motional averaging and three-dimensional structure determination by nuclear magnetic resonance
    • Post C. B. Internal motional averaging and three-dimensional structure determination by nuclear magnetic resonance. J. Mol. Biol. 224:1992;1087-1101.
    • (1992) J. Mol. Biol. , vol.224 , pp. 1087-1101
    • Post, C.B.1
  • 44
    • 0019322641 scopus 로고
    • Carbon-13 nuclear magnetic resonance relaxation studies of internal mobility of the polypeptide chain in basic pancreatic trypsin inhibitor and a selectively reduced analogue
    • Richarz R., Nagayama K., Wüthrich K. Carbon-13 nuclear magnetic resonance relaxation studies of internal mobility of the polypeptide chain in basic pancreatic trypsin inhibitor and a selectively reduced analogue. Biochemistry. 19:1980;5189-5196.
    • (1980) Biochemistry , vol.19 , pp. 5189-5196
    • Richarz, R.1    Nagayama, K.2    Wüthrich, K.3
  • 45
    • 33646940952 scopus 로고
    • Numerical-integration of Cartesian equations of motion of a system with constraints - molecular dynamics of N-alkanes
    • Ryckaert J., Ciocotti G., Berendsen H. Numerical-integration of Cartesian equations of motion of a system with constraints - molecular dynamics of N-alkanes. J. Comput. Phys. 23:1977;327-341.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.1    Ciocotti, G.2    Berendsen, H.3
  • 46
    • 0028294214 scopus 로고
    • Translational and rotational diffusion of proteins
    • Smith P. E., van Gunsteren W. F. Translational and rotational diffusion of proteins. J. Mol. Biol. 236:1994;629-636.
    • (1994) J. Mol. Biol. , vol.236 , pp. 629-636
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 47
    • 84986534166 scopus 로고
    • New spherical-cutoff methods for long-range forces in macromolecular simulation
    • Steinbach P. J., Brooks B. B. New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comp. Chem. 15:1994;667-683.
    • (1994) J. Comp. Chem. , vol.15 , pp. 667-683
    • Steinbach, P.J.1    Brooks, B.B.2
  • 49
    • 0000437307 scopus 로고
    • Time-dependent distance restraints in molecular dynamics simulations
    • Torda A. E., Scheek R. M., van Gunsteren W. F. Time-dependent distance restraints in molecular dynamics simulations. Chem. Phys. Letters. 157:1989;289-294.
    • (1989) Chem. Phys. Letters , vol.157 , pp. 289-294
    • Torda, A.E.1    Scheek, R.M.2    Van Gunsteren, W.F.3
  • 50
    • 36749110658 scopus 로고
    • Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances
    • Tropp J. Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: the effect of fluctuating internuclear distances. J. Chem. Phys. 72:1980;6035-6043.
    • (1980) J. Chem. Phys. , vol.72 , pp. 6035-6043
    • Tropp, J.1
  • 51
    • 0029075795 scopus 로고
    • The essential dynamics of thermolysin: Confirmation of the hinge-bending motion and comparison of simulations in vacuum and water
    • van Aalten D. M., Amadei A., Linssen A. B., Eijsink V. G., Vriend G., Berendsen H. J. The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water. Proteins: Struct. Funct. Genet. 22:1995;45-54.
    • (1995) Proteins: Struct. Funct. Genet. , vol.22 , pp. 45-54
    • Van Aalten, D.M.1    Amadei, A.2    Linssen, A.B.3    Eijsink, V.G.4    Vriend, G.5    Berendsen, H.J.6
  • 52
    • 0028674385 scopus 로고
    • Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data
    • van Gunsteren W. F., Brunne R. M., Gros P., van Schaik R. C., Schiffer C. A., Torda A. E. Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data. Methods Enzymol. 261:1994;619-654.
    • (1994) Methods Enzymol. , vol.261 , pp. 619-654
    • Van Gunsteren, W.F.1    Brunne, R.M.2    Gros, P.3    Van Schaik, R.C.4    Schiffer, C.A.5    Torda, A.E.6
  • 53
    • 36849105774 scopus 로고
    • Effect of internal rotation on angular correlation functions
    • Wallach D. Effect of internal rotation on angular correlation functions. J. Chem. Phys. 47:1967;5258-5268.
    • (1967) J. Chem. Phys. , vol.47 , pp. 5258-5268
    • Wallach, D.1
  • 55
    • 0026511587 scopus 로고
    • Toward a dynamical structure of DNA: Comparison of theoretical and experimental noe intensities
    • Withka J. M., Swaminathan S., Srinivasan J., Beveridge D. L., Bolton P. H. Toward a dynamical structure of DNA: comparison of theoretical and experimental noe intensities. Science. 255:1992;597-599.
    • (1992) Science , vol.255 , pp. 597-599
    • Withka, J.M.1    Swaminathan, S.2    Srinivasan, J.3    Beveridge, D.L.4    Bolton, P.H.5
  • 56
    • 0021603710 scopus 로고
    • Structure of bovine pancreatic trypsin inhibitor. results of joint neutron and X-ray refinement of crystal form ii
    • Wlodawer A., Walter J., Huber R., Sjolin L. Structure of bovine pancreatic trypsin inhibitor. results of joint neutron and X-ray refinement of crystal form ii. J. Mol. Biol. 180:1984;301-329.
    • (1984) J. Mol. Biol. , vol.180 , pp. 301-329
    • Wlodawer, A.1    Walter, J.2    Huber, R.3    Sjolin, L.4
  • 58
    • 84989068920 scopus 로고
    • 13C spin relaxation studies of the basic pancreatic trypsin inhibitor
    • 13C spin relaxation studies of the basic pancreatic trypsin inhibitor. Org. Magn. Res. 8:1976;532-535.
    • (1976) Org. Magn. Res. , vol.8 , pp. 532-535
    • Wüthrich, K.1    Baumann, R.2
  • 59
    • 0028232369 scopus 로고
    • An assessment of the precision and accuracy of protein structures determined by NMR: Dependence on distance errors
    • Zhao D., Jardetzky O. An assessment of the precision and accuracy of protein structures determined by NMR: dependence on distance errors. J. Mol. Biol. 239:1994;601-607.
    • (1994) J. Mol. Biol. , vol.239 , pp. 601-607
    • Zhao, D.1    Jardetzky, O.2
  • 60
    • 36049058132 scopus 로고
    • Statistical error due to finite time averaging in computer experiments
    • Zwanzig R., Ailawadi N. K. Statistical error due to finite time averaging in computer experiments. Phys. Rev. 182:1969;280-283.
    • (1969) Phys. Rev. , vol.182 , pp. 280-283
    • Zwanzig, R.1    Ailawadi, N.K.2


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