Proteins backbone dynamics

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... 

Clore GM, Schwieters CD (2004) Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein correspondence of dipolar coupling and heteronuclear relaxation measurements. Biochemistry 43(33) 10678-10691... 

Recent Developments in NMR Relaxation Studies that Probe Protein Backbone Dynamics... 

In this chapter, we describe mainly relaxation experiments to characterize protein backbone dynamics in solution. NMR spin-relaxation is a phenomenon in which perturbed magnetization is restored to statistical equilibrium by random fluctuations of local magnetic fields. The major local magnetic fields in diamagnetic proteins are generated by the amide dipolar interaction and chemical... 

Ishima R, Nagayama K (1995) Protein backbone dynamics revealed by quasi spectral density function analysis of amide N-15 nuclei. Biochemistry 34 3162-3171... 

Gaussian axial fluctuation (GAP) model for peptide plane reorientation about the C —axis, which was initially proposed to interpret spin relaxation derived order parameters [110], is useful to describe a common anisotropic component of protein backbone dynamics [111]. A complete three-dimensional GAP (3D GAP) analysis of local motion was conducted using an extensive set of RDCs from the third immunoglobin binding domain of streptococcal protein G (GB3) [112]. The averaged coupling is calculated by using Eq. (1.39), as a function of Oy and <7, and the amph-... 

V. Chevelkov, Y. Xue, R. Linser, N. Skrynnikov, B. Reif Comparison of sohd-state dipolar couplings and solution relaxation data provides insight into protein backbone dynamics,). Am. Chem. Soc. 132 (2010) 5015—5017. 

B. Vogeb, J. Ying, A. Grishaev, A. Bax, Limits on variations in protein backbone dynamics from precise measurements of scalar coupHngs, J. Am. Chem. Soc. 129 (2007) 9377-9385. 

In another related report on protein backbone dynamics NMR relaxation rates of amide N and carbonyl nuclei of the uniformly and N labelled ubiquitin were measured at different temperatures and field strengths in order to investigate the temperature dependence of overall rotational diffusion and local backbone motion. The results suggested that fast local motion... 

Several authors reported investigations of protein dynamics on the pico- and nano-second time scales. A standard approach to the protein backbone dynamics in this range is to measure N Ti, and NOE and to interpret the data using the Lipari-Szabo model-free approach, while or relaxation measurements provide information on the side-chain motions. The Lipari-Szabo order parameters can also be derived from MD simulations. Some authors compared the experimentally derived with the MD-derived counterparts. Smith and co-workers reported a study of this kind for the backbone of lysozyme from a bacteriophage and... 

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... 

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). 

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). 

Side-chain mobility is of particular interest because groups responsible for protein function are in many cases located in side chains rather than in the backbone. Gaining an insight into side-chain dynamics, therefore, could be necessary for understanding the relationship between protein dynamics and function. In contrast to protein backbone dy-... 

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. 

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