BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 11-10-2010, 02:29 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,777
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default An introduction to NMR-based approaches for measuring protein dynamics.

An introduction to NMR-based approaches for measuring protein dynamics.

An introduction to NMR-based approaches for measuring protein dynamics.

Biochim Biophys Acta. 2010 Nov 5;

Authors: Kleckner IR, Foster MP

Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement.

PMID: 21059410 [PubMed - as supplied by publisher]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy.
Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy. Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy. J Biomol NMR. 2011 Mar 18; Authors: Bouvignies G, Vallurupalli P, Cordes MH, Hansen DF, Kay LE A method based on the Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated 'invisible' protein states that exchange...
nmrlearner Journal club 0 03-23-2011 05:41 PM
Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy
Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy Abstract A method based on the Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated â??invisibleâ?? protein states that exchange with a â??visibleâ?? ground state on the millisecond time-scale. The utility of the approach is demonstrated with an application to an I58D mutant of the Pfl6 Cro protein that undergoes exchange between the native, folded state and a cold...
nmrlearner Journal club 0 03-22-2011 07:32 PM
[NMR paper] Measuring pK(a) values in protein folding transition state ensembles by NMR spectrosc
Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy. Related Articles Measuring pK(a) values in protein folding transition state ensembles by NMR spectroscopy. J Am Chem Soc. 2005 Jun 29;127(25):8904-5 Authors: Tollinger M, Kay LE, Forman-Kay JD Protein folding kinetic data have been obtained for the marginally stable N-terminal SH3 domain of the Drosophila protein drk as a function of pH in order to investigate the electrostatic properties of Asp8 in the folding transition state ensemble. The slow exchange...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Leveraging structural approaches: applications of NMR-based screening and X-ray cryst
Leveraging structural approaches: applications of NMR-based screening and X-ray crystallography for inhibitor design. Related Articles Leveraging structural approaches: applications of NMR-based screening and X-ray crystallography for inhibitor design. J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):97-100 Authors: Moore J, Abdul-Manan N, Fejzo J, Jacobs M, Lepre C, Peng J, Xie X In the last several years, NMR strategies in drug discovery have evolved from a primarily structural focus to a set of technologies that are non-structural in nature but...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study
Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta. Related Articles Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta. J Am Chem Soc. 2003 Feb 19;125(7):1748-58 Authors: Choy WY, Shortle D, Kay LE NMR relaxation data on disordered proteins can provide insight into both structural and dynamic properties of these molecules. Because of chemical shift degeneracy in correlation spectra, detailed site-specific analyses of side chain dynamics...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Protein dynamics measurements by TROSY-based NMR experiments.
Protein dynamics measurements by TROSY-based NMR experiments. Related Articles Protein dynamics measurements by TROSY-based NMR experiments. J Magn Reson. 2000 Apr;143(2):423-6 Authors: Zhu G, Xia Y, Nicholson LK, Sze KH The described TROSY-based experiments for investigating backbone dynamics of proteins make it possible to elucidate internal motions in large proteins via measurements of T(1), T(2), and NOE of backbone (15)N nuclei. In our proposed sequences, the INEPT sequence is eliminated and the PEP sequence is replaced by the ST2-PT...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] Structure-based analysis of protein dynamics: comparison of theoretical results for h
Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Related Articles Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data. Proteins. 1999 Dec 1;37(4):654-67 Authors: Haliloglu T, Bahar I An analytical approach based on Gaussian network model (GNM) is proposed for predicting the rotational dynamics of proteins. The method, previously shown to successfully...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] Measuring protein self-association using pulsed-field-gradient NMR spectroscopy: appl
Measuring protein self-association using pulsed-field-gradient NMR spectroscopy: application to myosin light chain 2. Related Articles Measuring protein self-association using pulsed-field-gradient NMR spectroscopy: application to myosin light chain 2. J Biomol NMR. 1995 Nov;6(3):321-8 Authors: Dingley AJ, Mackay JP, Chapman BE, Morris MB, Kuchel PW, Hambly BD, King GF At the millimolar concentrations required for structural studies, NMR spectra of the calcium-binding protein myosin light chain 2 (MLC2) showed resonance line widths indicative...
nmrlearner Journal club 0 08-22-2010 03:50 AM



Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 10:19 AM.


Map