Related ArticlesInterpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR.
J Biomol NMR. 2002 Jun;23(2):139-50
Authors: Bernadó P, García de la Torre J, Pons M
HYDRONMR is an implementation of state of the art hydrodynamic modeling to calculate the spectral density functions for NH or C(alpha)-H vectors in a rigid protein structure starting from an atomic level representation. Thus HYDRONMR can be used to predict NMR relaxation times from a rigid model and to compare them with the experimental results. HYDRONMR contains a single adjustable parameter, the atomic element radius. A protocol to determine the value that gives the best agreement between calculated and experimental T1/T2 values is described. For most proteins, the value of the atomic element radius ranges between 2.8 A and 3.8 A with a distribution centered at 3.3 A. Deviations from the usual range towards larger values are associated to aggregation in several proteins. Deviations to lower values may be related to large-scale motions or inappropriate model structures. If the average structure is correct, deviations between experimental T1/T2 values and those calculated with HYDRONMR can be used to distinguish residues affected by anisotropic motion from those that are involved in chemical exchange.
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins
Abstract Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was...
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06-06-2011 12:53 AM
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins.
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins.
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and ?s motion of proteins.
J Biomol NMR. 2011 May 27;
Authors: Bieri M, d'Auvergne EJ, Gooley PR
Investigation of protein dynamics on the ps-ns and ?s-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying...
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05-28-2011 06:50 PM
[NMR paper] Thermodynamic interpretation of protein dynamics from NMR relaxation measurements.
Thermodynamic interpretation of protein dynamics from NMR relaxation measurements.
Related Articles Thermodynamic interpretation of protein dynamics from NMR relaxation measurements.
Protein Pept Lett. 2005 Apr;12(3):235-40
Authors: Spyracopoulos L
Protein dynamics and thermodynamics can be characterized through measurements of relaxation rates of side chain (2)H and (13)C, and backbone (15)N nuclei using NMR spectroscopy. The rates reflect protein motions on timescales from picoseconds to milliseconds. Backbone and methyl side chain NMR...
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11-25-2010 08:21 PM
[NMR paper] Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on B
Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations.
Related Articles Interpretation of NMR relaxation properties of Pin1, a two-domain protein, based on Brownian dynamic simulations.
J Biomol NMR. 2004 May;29(1):21-35
Authors: Bernadó P, Fernandes MX, Jacobs DM, Fiebig K, García de la Torre J, Pons M
Many important proteins contain multiple domains connected by flexible linkers. Inter-domain motion is suggested to play a key role in many processes involving molecular recognition....
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11-24-2010 09:51 PM
[NMR paper] New approaches to the dynamic interpretation and prediction of NMR relaxation data fr
New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins.
Related Articles New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins.
Curr Opin Struct Biol. 2003 Apr;13(2):175-83
Authors: Brüschweiler R
NMR relaxation experiments of isotopically labeled proteins provide a wealth of information on reorientational global and local dynamics on nanosecond and subnanosecond timescales for folded and nonfolded proteins in solution. Recent methodological advances in the...
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11-24-2010 09:01 PM
[NMR paper] HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structu
HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.
Related Articles HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations.
J Magn Reson. 2000 Nov;147(1):138-46
Authors: García de la Torre J, Huertas ML, Carrasco B
The heteronuclear NMR relaxation of globular proteins depends on the anisotropic rotational diffusion tensor. Using our previous developments for prediction of hydrodynamic properties of arbitrarily...
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11-19-2010 08:29 PM
[NMR paper] Hydrodynamic radii of native and denatured proteins measured by pulse field gradient
Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques.
Related Articles Hydrodynamic radii of native and denatured proteins measured by pulse field gradient NMR techniques.
Biochemistry. 1999 Dec 14;38(50):16424-31
Authors: Wilkins DK, Grimshaw SB, Receveur V, Dobson CM, Jones JA, Smith LJ
Pulse field gradient NMR methods have been used to determine the effective hydrodynamic radii of a range of native and nonnative protein conformations. From these experimental data, empirical relationships...
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11-18-2010 08:31 PM
[NMR paper] 3D NMR experiments for measuring 15N relaxation data of large proteins: application t
3D NMR experiments for measuring 15N relaxation data of large proteins: application to the 44 kDa ectodomain of SIV gp41.
Related Articles 3D NMR experiments for measuring 15N relaxation data of large proteins: application to the 44 kDa ectodomain of SIV gp41.
J Magn Reson. 1998 Dec;135(2):368-72
Authors: Caffrey M, Kaufman J, Stahl SJ, Wingfield PT, Gronenborn AM, Clore GM
A suite of 3D NMR experiments for measuring 15N-¿1H¿ NOE, 15N T1, and 15N T1rho values in large proteins, uniformly labeled with 15N and 13C, is presented. These...
Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic cal
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