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 06-29-2005, 04:25 AM
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

The Origin of Protein Sidechain Order Parameter Distributions
Robert B. Best, Jane Clarke, and Martin Karplus
J. Am. Chem. Soc.; 2004; 126(25) pp 7734 - 7735


Abstract:

Previous work by Wand et al. (Nature 2001, 411, 501-504) showed that the NMR order parameters characterizing the amplitude of motion of protein side chains seemed to form a multimodal distribution. At the time, no detailed explanation of this at the molecular level was offered, yet three "classes" of motion were inferred. We have analyzed a larger published data set and found that, although the distribution is multimodal, the evidence for three classes is weak. More significantly, we have been able to provide a simple physical explanation for the distributions based on the results of molecular dynamics simulations. This result will aid in the interpretation of data from NMR dynamics experiments.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy Abstract Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ~1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic...
nmrlearner Journal club 0 09-26-2011 06:42 AM
[MWClarkson blog] Alternative side-chain structures from methyl CPMG
Alternative side-chain structures from methyl CPMG http://www.researchblogging.org/public/citation_icons/rb2_large_gray.pngAs I have mentioned before on this blog, the use of tools like CS-ROSETTA holds the promise of determining protein structures using only the chemical shifts of its backbone atoms. In addition to potentially making NOEs and RDCs redundant, this technology allows biologists to determine the conformations of minor members of the structural ensemble, which are very difficult to obtain using conventional approaches in population-dominated techniques like NMR and X-ray...
nmrlearner News from NMR blogs 0 06-21-2011 03:31 AM
[Question from NMRWiki Q&A forum] RDCs di-Methyl lysine
RDCs di-Methyl lysine We are interested in studying di-methyl lysine, given that in most cases the two methyl groups are equivalent and each have the three protons, how much and if so what, information could you realistically get from RDCs on the Di- methyl signals? Check if somebody has answered this question on NMRWiki QA forum
nmrlearner News from other NMR forums 0 03-30-2011 09:11 PM
[NMR paper] Amino acid-type edited NMR experiments for methyl-methyl distance measurement in 13C-
Amino acid-type edited NMR experiments for methyl-methyl distance measurement in 13C-labeled proteins. Related Articles Amino acid-type edited NMR experiments for methyl-methyl distance measurement in 13C-labeled proteins. J Am Chem Soc. 2004 Aug 11;126(31):9584-91 Authors: Van Melckebeke H, Simorre JP, Brutscher B New NMR experiments are presented for the measurement of methyl-methyl distances in (13)C-labeled proteins from a series of amino acid-type separated 2D or 3D NOESY spectra. Hadamard amino acid-type encoding of the proximal methyl...
nmrlearner Journal club 0 11-24-2010 10:01 PM
A simple strategy for 13C,1H labeling at the Ile-γ2 methyl position in highly deuter
A simple strategy for 13C,1H labeling at the Ile-γ2 methyl position in highly deuterated proteins Abstract A straightforward approach for the production of highly deuterated proteins labeled with 13C and 1H at Ile-γ2 methyl positions is described. The utility of the methodology is illustrated with an application involving the half proteasome (360 kDa). High quality 2D Ile 13Cγ2,1Hγ2 HMQC data sets, exploiting the methyl-TROSY principle, are recorded with excellent sensitivity and resolution, that compare favorably with Ile 13Cδ1,1Hδ1 spectra. This labeling scheme adds to a growing...
nmrlearner Journal club 0 10-20-2010 06:50 AM
[NMR paper] NMR studies of the methionine methyl groups in calmodulin.
NMR studies of the methionine methyl groups in calmodulin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR studies of the methionine methyl groups in calmodulin. FEBS Lett. 1995 Jun 12;366(2-3):104-8 Authors: Siivari K, Zhang M, Palmer AG, Vogel HJ Calmodulin (CaM) is a ubiquitous Ca(2+)-binding protein that can regulate a wide variety of cellular events. The protein contains 9 Met out of a total of 148 amino acid residues. The binding of Ca2+ to CaM induces...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Stereospecific assignments of the leucine methyl resonances in the 1H NMR spectrum of
Stereospecific assignments of the leucine methyl resonances in the 1H NMR spectrum of Lactobacillus casei dihydrofolate reductase. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Stereospecific assignments of the leucine methyl resonances in the 1H NMR spectrum of Lactobacillus casei dihydrofolate reductase. FEBS Lett. 1993 Mar 1;318(2):177-80 Authors: Ostler G, Soteriou A, Moody CM, Khan JA, Birdsall B, Carr MD, Young DW, Feeney J A general method is described for the...
nmrlearner Journal club 0 08-21-2010 11:53 PM
Quiz 1 - NMR Methyl methanoate
Quiz 1 - NMR Methyl methanoate More...
nmrlearner NMR bookmarks 0 08-19-2010 02:34 PM



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 06:14 AM.


Map