Different approaches to study protein surface fractality are considered. An approach based on analysis of surface versus molecular weight dependence is shown to be an informative tool for investigation of protein surface behaviour. An evidence for protein surface fractality, obtained with the use of this analysis from the data of both NMR measurements in protein solutions and computer analysis of protein structures, is presented. Obtained value of fractal dimension of protein surface (ds congruent to 2.2) is in a good agreement with the results of conventional approach (with variation of yardstick length) to protein surface fractality. A conclusion is made that surface enlargement due to the rise of protein molecular weight is accompanied by the increase of maximum scale of irregularities on protein surface. Possible effect of surface fractality on hydrodynamic characteristics of protein molecules in solution is discussed.
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
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...
nmrlearner
Journal club
0
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...
nmrlearner
Journal club
0
05-28-2011 06:50 PM
[NMR paper] Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic cal
Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR.
Related Articles Interpretation 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...
nmrlearner
Journal club
0
11-24-2010 08:49 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...
nmrlearner
Journal club
0
11-17-2010 11:15 PM
[NMR paper] An approach to global fold determination using limited NMR data from larger proteins
An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types.
An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types.
J Biomol NMR. 1996 Oct;8(3):360-8
Authors: Smith BO, Ito Y, Raine A, Teichmann S, Ben-Tovim L, Nietlispach D, Broadhurst RW, Terada T, Kelly M, Oschkinat H, Shibata T, Yokoyama S, Laue ED
A combination of calculation and experiment is used to demonstrate that the global fold of...
nmrlearner
Journal club
0
08-22-2010 02:20 PM
[NMR paper] Simulation of NMR data from oriented membrane proteins: practical information for exp
Simulation of NMR data from oriented membrane proteins: practical information for experimental design.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Simulation of NMR data from oriented membrane proteins: practical information for experimental design.
Biophys J. 1993 Oct;65(4):1460-9
Authors: Sanders CR, Schwonek JP
Several hundred solid state NMR...
nmrlearner
Journal club
0
08-22-2010 03:01 AM
Theory
Theory2D NMR
Introduction to (high resolution) multidimensional solution NMR spectroscopy. Description of line-shapes, product operator formalism, phase-cycling, pulsed field gradients and relaxation. By James Keeler. Also contains the full text of "EMBO Course: Il Ciocco" lecture notes.
Applications for measuring scalar and residual dipolar couplings in proteins
By Perttu Permi. The entire paper and dissertation is available in pdf format.
Biomolecular structure determination by using solid state NMR spectroscopy
Solid state NMR methodology for structure determination of uniformly...
Surface fractality of proteins from theory and NMR data.
Linear Mode
