An accurate determination of the overall rotation of a protein plays a crucial role in the investigation of its internal motions by NMR. In the present work, an innovative approach to the determination of the protein rotational correlation time tau(R) from the heteronuclear relaxation data is proposed. The approach is based on a joint fit of relaxation data acquired at several viscosities of a protein solution. The method has been tested on computer simulated relaxation data as compared to the traditional tau(R) determination method from T(1)/T(2) ratio. The approach has been applied to ribonuclease barnase from Bacillus amyloliquefaciens dissolved in an aqueous solution and deuterated glycerol as a viscous component. The resulting rotational correlation time of 5.56 +/- 0.01 ns and other rotational diffusion tensor parameters are in good agreement with those determined from T(1)/T(2) ratio.
Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data
Microsecond Time-Scale Conformational Exchange in Proteins: Using Long Molecular Dynamics Trajectory To Simulate NMR Relaxation Dispersion Data
Yi Xue, Joshua M. Ward, Tairan Yuwen, Ivan S. Podkorytov and Nikolai R. Skrynnikov
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja206442c/aop/images/medium/ja-2011-06442c_0001.gif
Journal of the American Chemical Society
DOI: 10.1021/ja206442c
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/NvRRKHU2H3k
nmrlearner
Journal club
0
01-28-2012 05:27 AM
[NMR paper] Effective rotational correlation times of proteins from NMR relaxation interference.
Effective rotational correlation times of proteins from NMR relaxation interference.
Related Articles Effective rotational correlation times of proteins from NMR relaxation interference.
J Magn Reson. 2006 Jan;178(1):72-6
Authors: Lee D, Hilty C, Wider G, Wüthrich K
Knowledge of the effective rotational correlation times, tauc, for the modulation of anisotropic spin-spin interactions in macromolecules subject to Brownian motion in solution is of key interest for the practice of NMR spectroscopy in structural biology. The value of tauc enables...
nmrlearner
Journal club
0
12-01-2010 06:56 PM
[NMR paper] Rapid protein fold determination using unassigned NMR data.
Rapid protein fold determination using unassigned NMR data.
Related Articles Rapid protein fold determination using unassigned NMR data.
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15404-9
Authors: Meiler J, Baker D
Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs),...
nmrlearner
Journal club
0
11-24-2010 09:16 PM
[NMR paper] Sampling of protein dynamics in nanosecond time scale by 15N NMR relaxation and self-
Sampling of protein dynamics in nanosecond time scale by 15N NMR relaxation and self-diffusion measurements.
Related Articles Sampling of protein dynamics in nanosecond time scale by 15N NMR relaxation and self-diffusion measurements.
J Biomol Struct Dyn. 1999 Aug;17(1):157-74
Authors: Orekhov VY, Korzhnev DM, Pervushin KV, Hoffmann E, Arseniev AS
This paper presents a procedure for detection of intermediate nanosecond internal dynamics in globular proteins. The procedure uses 1H-15N relaxation measurements at several spectrometer frequencies...
nmrlearner
Journal club
0
11-18-2010 08:31 PM
[NMR paper] Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurem
Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurements.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Rotational dynamics of calcium-free calmodulin studied by 15N-NMR relaxation measurements.
Eur J Biochem. 1995 Jun 15;230(3):1014-24
Authors: Tjandra N, Kuboniwa H, Ren H, Bax A
The backbone motions of calcium-free Xenopus calmodulin have been characterized by measurements of the 15N...
nmrlearner
Journal club
0
08-22-2010 03:41 AM
[NMR paper] Determination of membrane protein structure by rotational resonance NMR: bacteriorhod
Determination of membrane protein structure by rotational resonance NMR: bacteriorhodopsin.
Related Articles Determination of membrane protein structure by rotational resonance NMR: bacteriorhodopsin.
Science. 1991 Feb 15;251(4995):783-6
Authors: Creuzet F, McDermott A, Gebhard R, van der Hoef K, Spijker-Assink MB, Herzfeld J, Lugtenburg J, Levitt MH, Griffin RG
Rotationally resonant magnetization exchange, a new nuclear magnetic resonance (NMR) technique for measuring internuclear distances between like spins in solids, was used to determine...
nmrlearner
Journal club
0
08-21-2010 11:16 PM
[NMR paper] Relaxation data in NMR structure determination: model calculations for the lysozyme-G
Relaxation data in NMR structure determination: model calculations for the lysozyme-Gd3+ complex.
Related Articles Relaxation data in NMR structure determination: model calculations for the lysozyme-Gd3+ complex.
Proteins. 1991;10(2):117-29
Authors: Sutcliffe MJ, Dobson CM
The effect of including paramagnetic relaxation data as additional restraints in the determination of protein tertiary structures from NMR data has been explored by a systematic series of model calculations. The system used for testing the method was the 2.0 A resolution...
nmrlearner
Journal club
0
08-21-2010 11:16 PM
[NMR paper] Assessing potential bias in the determination of rotational correlation times of prot
Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation.
Related Articles Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation.
J Biomol NMR. 1999 Feb;13(2):101-12
Authors: Lee AL, Wand AJ
The various factors that influence the reliable and efficient determination of the correlation time describing molecular reorientation of proteins by NMR relaxation methods are examined. Nuclear Overhauser effects, spin-lattice, and spin-spin relaxation...