Backbone dynamics

Barbate G, Ikura M, Kay L E, Pastor R W and Bax A 1992 Backbone dynamics of calmodulin studied by N relaxation using inverse detected two-dimensional NMR spectroscopy the central helix is flexible S/oefrem/sf/ y 31 5269-78... 

Tjandra N, Szabo A and Bax A 1996 Protein backbone dynamics and N-15 chemical shift anisotropy from quantitative measurement of relaxation interference effected. Am. Chem. Soc. 118 6986-91... 

Baryshnikova OK, Sykes BD (2006) Backbone dynamics of SDF-lalpha determined by NMR interpretation in the presence of monomer-dimer equilibrium. Protein Sci 15 2568-2578 Becker EB, Bonni A (2004) Cell cycle regulation of neuronal apoptosis in development and disease. Prog Neurobiol 72 1-25... 

NMRrelaxation and diffusion experiments provide important insights into both the internal molecular dynamics and the overall hydrodynamic behavior of unfolded and partly folded states. Local variations in backbone dynamics are correlated with propensities for local compaction of the polypeptide chain that results in constriction of backbone motions (Eliezer et al., 1998, 2000). This can occur through formation of... 

Backbone dynamics are most commonly investigated by measurement of 15N T and T% relaxation times and the fyH -15N NOE in uniformly 15N-labeled protein. To circumvent problems associated with the limited dispersion of the NMR spectra of unfolded proteins, the relaxation and NOE data are generally measured using 2D HSQC-based methods (Farrow et al., 1994 Palmer et al., 1991). 

NMR techniques are unique in their ability to resolve internal dynamics with site-specific probes. Backbone dynamics may be derived from relaxation data of 15N nuclei. Relaxation data are conveniently measured in experiments that utilize [15N,1H]-HSQC-derived pulse sequences and hence can be performed within less than a week of total instrument time with a 1 mM sample (at one field). The underlying principle of the measurement is described in Chapt. 12 and has also been recently reviewed by Palmer [91]. 

D11/Dj, from 1 to 10. Symbols correspond to synthetic experimental data generated assuming overall tumbling with rc = 5 ns and various degrees of anisotropy as indicated. Model-free parameters typical of restricted local backbone dynamics in protein core, S2=0.87, T oc =20 ps, were used to describe the effect of local motions. The H resonance frequency was set to 600 MHz. The solid lines correspond to the right-hand-side expression in Eq. (10). 

Feng Y., Klein B.K., and McWherter C.A. (1996), Three-dimensional solution structure and backbone dynamics of a variant of human interleukin-3,./. Mol. Biol. 259, 524-541. 

COMPARISON BETWEEN BACKBONE DYNAMICS AND SUBSTITUENT GROUP ROTATION... 

The backbone dynamics of 4-oxalocrotonate tautomerase, a 41-kDa homo-hexamer with 62 residues per subunit, and its complex with a substrate analogue have been analyzed by the model-free formalism.60 Binding of the analogue freezes the motion of some of the backbone NH vectors in the active site, leading to a loss of entropy (Chapter 2). 

Fan, P., Li, M., Brodsky, B., and Baum, J. (1993). Backbone dynamics of (Pro-Hyp-Gly) 10 and a designed collagen-like triple-helical peptide by 15N NMR relaxation and hydrogen-exchange measurements. Biochemistry 32, 13299-13309. 

Columbus, L., and Hubbell, W. L. (2004). Mapping backbone dynamics in solution with site-directed spin labeling GCN4—58 bZip free and bound to DNA. Biochemistry 43,... 

Renisio, J. G., Perez, J., Czisch, M., et al. (2002) Solution structure and backbone dynamics of an antigen-free heavy chain variable domain (VHH) from Llama. Proteins 47, 546-555. 

Hill, R.B., Bracken, C., DeGrado, W. F., and Palmer, A. G. Ill (2000) Molecular motion and protein folding characterization of the backbone dynamics and folding equilibrium ofa2D using, 3C NMR spin relaxation,... 

Kay, L.E., Torchia, D. A., and Bax, A. (1989) Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy application to Staphylococcal nuclease, Biochemistry 28, 8972-8979. 

Shaw, G.L, Davis, B., Keeler, J., Fersht, A. (1995) Backbone dynamics of chymotrypsin inhibitor 2 effect of breaking the active site bond and its implications for the mechanism of inhibition of serin proteases, Biochemistry 34, 2225-2233. 

Loh, A. P., Guo, W., Nicholson, L. K., and Oswald, R. E. (1999). Backbone dynamics of inactive, active, and effector-bound Gdc42Hs from measurements of N relaxation parameters at multiple field strengths. Biochem. 38, 12547-12557. 

Schutkowski M, Bernhardt A, Zhou XZ, Shen M, Reimer U, Rahfeld JU, Lu KP, Fischer G (1998) Role of phosphorylation in determining the backbone dynamics of the serine/threonine-proUne motif and Pinl substrate recognition. Biochemistry 37 5566-5575 Selkoe DJ (2001) Alzheimer s disease results from the cerebral accumulation and cytotoxicity of amyloid beta-protein. J Alzheimers Dis 3 75-80... 

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