Probing molecular motion by NMR

Current Opinion in Structural Biology

Volumn 7, Issue 5, 1997, Pages 732-737

  Palmer III, Arthur G ^a  

^a 630 W 168th Street ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON 13; MEMBRANE PROTEIN; NITROGEN 15;

BIOPHYSICS; CARBON NUCLEAR MAGNETIC RESONANCE; CATALYSIS; CONFORMATION; DEUTERON NUCLEAR MAGNETIC RESONANCE; DIFFUSION; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR PROBE; MOTION; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; REVIEW;

EID: 0030778008     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80085-1     Document Type: Article

References (59)

1. 15N NMR relaxation measurements at two magnetic fields. J Biomol NMR. 8:1996;273-284.
2. 15N chemical shift anisotropy from quantitative measurement of relaxation interference effects. J Am Chem Soc. 118:1996;6986-6991.
3. Ross A, Czisch M, King GC. Systematic errors associated with the CPMG pulse sequence and their effect on motional analysis of biomolecules. J Magn Reson. 124:1997;355-365.
4. 2H-labeled proteins in solution. J Am Chem Soc. 117:1995;11536-11544.
5. 2D spin systems. J Magn Reson Ser B. 110:1996;213-218.
6. 15N relaxation data from the side chains of asparagine and glutamine residues in proteins. J Magn Reson Ser B. 107:1995;279-285.
7. 13C-relaxation studies of randomly fractionally labeled protein. Biochemistry. 35:1996;6116-6125.
8. 12C nuclei and random fractional deuteration to obtain isolated IS spin systems. A broad range of sidechain dynamics properties are observed, including millisecond motions that are proposed to contribute to the reactivity of the active-site disulfide bond. of outstanding interest.
9. 15N-labeled homeodomain and its DNA complex. J Am Chem Soc. 119:1997;3842-3843.
10. 13C-labelled proteins. J Biomol NMR. 7:1996;163-168.
11. 13CO longitudinal relaxation. J Biomol NMR. 7:1996;157-162.
12. Brüschweiler R, Liao X, Wright PE. Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling. Science. 268:1995;886-889.
13. 15N NMR relaxation. J Am Chem Soc. 117:1995;12562-12566.
14. 15N NMR relaxation. Biochemistry. 34:1995;5212-5223.
15. 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;4546-4559.
16. Schurr JM, Babcock HP, Fujimoto BS. A test of the model-free formulas. Effects of anisotropic rotational diffusion and dimerization. J Magn Reson Ser B. 105:1994;211-224.
17. 15N relaxation with monomer/dimer equilibration. J Mol Biol. 266:1997;173-194.
18. Brüschweiler R, Wright PE. NMR order parameters of biomolecules: a new analytical representation and application to the Gaussian axial fluctuation model. J Am Chem Soc. 116:1994;8426-8427.
19. Bremi T, Brüschweiler R, Ernst RR. A protocol for the interpretation of side-chain dynamics based on NMR relaxation: application to phenylalanines in antamanide. J Am Chem Soc. 119:1997;4272-4284.
20. 9k. J Am Chem Soc. 115:1993;9832-9833.
21. 2 measured by NMR relaxation methods and the local configurational entropy of proteins. of special interest.
22. Yang D, Kay LE. Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J Mol Biol. 263:1996;369-382 The relationship between order parameters derived from NMR spin relaxation experiments and the contribution to conformational entropy from picosecond/nanosecond timescale bond vector dynamics is evaluated using classical and quantum mechanical models of bond vector motions. The local entropies and order parameters calculated from a 1.12 ns molecular dynamics trajectory of E. coli ribonuclease H are reproduced by using a simple expression based on the diffusion-in-a-cone model. of special interest.
23. ex characterize the energetics of conformational fluctuations on picosecond/nanosecond and microsecond/millisecond timescales. of outstanding interest.
24. Peng J, Wagner G. Frequency spectrum of NH bonds in eglin c from spectral density mapping at multiple fields. Biochemistry. 34:1995;16733-16752.
25. 15N relaxation data exclusively. J Biomol NMR. 6:1995;153-162.
26. Phan IQH, Boyd J, Campbell ID. Dynamic studies of a fibronectin type I module pair at three frequencies: anisotropic modeling and direct determination of conformational exchange. J Biomol NMR. 8:1996;369-378.
27. 1 constant-relaxation-time NMR spectroscopy. J Am Chem Soc. 118:1996;911-912.
28. Ishima R, Nagayama K. Quasi-spectral density function analysis for nitrogen-15 nuclei in proteins. J Magn Reson Ser B. 108:1995;73-76.
29. N) that defines the rates for overall rotation and internal motions. of special interest.
30. 15N NMR relaxation parameters are used to characterize the backbone dynamics of the folded and denatured states of the N-terminal SH3 domain from the adapter protein drk in high salt or guanidinium chloride, respectively, at 14 and 30°C. The value of J(O) for the unfolded state of the domain indicates that residues in the middle of the protein sequence are considerably less mobile than those at the termini. The picosecond/nanosecond motions in the unfolded SH3 domain are affected to a greater extent by changes in temperature than in the folded state. of outstanding interest.
31. Feng Y, Klein BK, McWherter CA. Three-dimensional solution structure and backbone dynamics of a variant of human interleukin-3. J Mol Biol. 259:1996;524-541.
32. 15N spin relaxation data are measured to study the dynamic properties of the protein histidine kinase CheA from E. coli. The phosphotransfer P1 domain and the CheY-binding P2 domain reorient independently, and the linker region is highly flexible. Regulation of CheA autophosphorylation activity is proposed to depend on access of the mean position of kinase domain to the phosphotransfer domain. of special interest.
33. 15N NMR spectroscopy. Biochemistry. 34:1995;16608-16617.
34. Wikström M, Forsén S, Drakenberg T. Backbone dynamics of a domain of protein L which binds to immunoglobulin light chains. Eur J Biochem. 235:1996;543-548.
35. Mandel AM, Akke M, Palmer AG. Backbone dynamics of Escherichia coli ribonuclease HI: Correlations with structure and function in an active enzyme. J Mol Biol. 246:1995;144-163.
36. 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme. Biochemistry. 34:1995;4041-4055.
37. Pascal SM, Yamazaki T, Singer AU, Kay LE, Forman-Kay JD. Structural and dynamic characterization of the phosphotyrosine binding region of an Src homology 2 domain - phosphopeptide complex by NMR relaxation, proton exchange, and chemical shift approaches. Biochemistry. 34:1995;11353-11362.
38. 2H-enriched SH2 domain of phospholipase C γ1. Comparisons between the dynamic properties of the free protein and those of the complex with a phosphotyrosine-containing peptide indicate that the dynamic properties of residues in and C-terminal to the phosphotyrosine-binding site contribute differentially to binding affinity and specificity. of outstanding interest.
39. 2>0.8 but also exhibit conformational exchange on a microsecond/millisecond timescale. of special interest.
40. Frank MK, Clore GM, Gronenborn AM. Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy. Protein Sci. 4:1995;2605-2615.
41. 15N mainchain dynamics are compared for four forms of staphylococcal nuclease that have different stabilities. An increase in the proportion of residues with large-amplitude internal motions is observed as the stability of the folded state decreases. of special interest.
42. Farrow NA, Zhang O, Forman-Kay JD, Kay LE. Comparison of the backbone dynamics of a folded and an unfolded SH3 domain existing in equilibrium in aqueous buffer. Biochemistry. 34:1995;868-878.
43. 2 increase for seven residues and decrease for eight residues upon binding of the inhibitor, suggesting that changes in configurational entropy from the increased rigidity of some residues are partially compensated by the increased flexibility of others. of outstanding interest.
44. 1H exchange NMR measurements. Increased mobility and discrete disorder observed in the backbone of the unliganded protein may permit the entry of ligand into the binding cavity. of outstanding interest.
45. Olejniczak ET, Zhou M-M, Fesik SW. Changes in the NMR-derived motional parameters of the insulin receptor substrate 1 phosphotyrosine binding domain upon binding to an interleukin 4 receptor phosphopeptide. Biochemistry. 36:1997;4118-4124 The backbone dynamics of the insulin receptor substrate 1 phosphotyrosine-binding domain are characterized in the presence and absence of phosphotyrosine peptide. The changes in conformational flexibility observed are compared with published results for the SH2 domain of phospholipase C γ1. of outstanding interest.
46. 2 for the majority of the residues. of special interest.
47. 15N transverse relaxation measurements suggest that the loop between helix α1 and strand β1 is flexible on a picosecond/nanosecond timescale in the free protein but not in the protein bound to RNA. of special interest.
48. Berglund H, Baumann H, Knapp S, Ladenstein R, Härd T. Flexibility of an arginine side chain at a DNA - protein interface. J Am Chem Soc. 117:1995;12883-12884.
49. 15N spin relaxation. The loop between helices II and III becomes significantly more rigid upon complexation. of outstanding interest.
50. Epstein D, Benkovic SJ, Wright PE. Dynamics of the dihydrofolate reductase - folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features. Biochemistry. 34:1995;11037-11048.
51. 15N NMR relaxation measurements. Biochemistry. 32:1993;426-435.
52. Nicholson LK, Yamazaki T, Torchia DA, Grzesiek S, Bax A, Stahl S, Kaufman JD, Wingfield PT, Lam PYS, Jadhav PK, et al. Flexibility and function in HIV-1 protease. Nat Struct Biol. 2:1995;274-280.
53. 15N- NMR relaxation measurements. Eur J Biochem. 235:1996;629-640.
54. 15N-NMR relaxation measurements. Eur J Biochem. 230:1995;1014-1024.
55. Spitzfaden C, Grant RP, Mardon HJ, Campbell ID. Module - module interactions in the cell binding region of fibronectin: stability, flexibility and specificity. J Mol Biol. 265:1997;565-579 Thermodynamic and NMR spectroscopic techniques are used to investigate domain - domain interactions between the ninth and tenth type III domains of fibronectin. The relative contributions of specific domain - domain interactions, long-range nonspecific interactions, and excluded volume effects in constraining the relative motions and orientations of the domains are assessed. of special interest.
56. 15N lysine residues demonstrates that the interdomain linker is highly flexible. Rotational diffusion of the two domains appears uncorrelated. of special interest.
57. 15N relaxation rate constants on rotational diffusion anisotropy is used to refine the relative orientations of the α and α/β domains of Enzyme I by using a simulated annealing protocol. of outstanding interest.
58. 15N nuclear magnetic resonance relaxation measurements using the model-free approach and reduced spectral density mapping. Biochemistry. 36:1997;4015-4026.
59. Williams KA, Farrow NA, Deber CM, Kay LE. Structure and dynamics of bacteriophage IKe major coat protein in MPG micelles by solution NMR. Biochemistry. 35:1996;5145-5157.