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 11-19-2010, 08:32 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,697
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 Toward direct determination of conformations of protein building units from multidime

Toward direct determination of conformations of protein building units from multidimensional NMR experiments part II: a theoretical case study of formyl-L-valine amide.

Related Articles Toward direct determination of conformations of protein building units from multidimensional NMR experiments part II: a theoretical case study of formyl-L-valine amide.

Chemistry. 2001 Mar 2;7(5):1069-83

Authors: Perczel A, Császár AG

Chemical shielding anisotropy tensors have been determined for all twenty-seven characteristic conformers of For-L-Val-NH2 using the GIAO-RHF formalism with the 6-31 + G* and TZ2P basis sets. The individual chemical shifts and their conformational averages have been compared to their experimental counterparts taken from the BioMagnetic Resonance Bank (BMRB). At the highest level of theory applied, for all nuclei but the amide proton, deviations between statistically averaged theoretical and experimental chemical shifts are as low as 1-3%. Correlated chemical shift plots of selected nuclei, as function of the respective phi, psi, chi1, and chi2 torsional angles, have been generated. On two-dimensional chemical shift-chemical shift plots, for example, 1H(NH)-15N(NH) and 15N(NH)-13Calpha, regions corresponding to major conformational clusters have been identified, providing a basis for the quantitative identification of conformers from NMR shift data. Experimental NMR resonances of nuclei of valine residues have been deduced from 18 selected proteins, resulting in 93 1Halpha-13Calpha chemical shift pairs. These experimental results have been compared to relevant ab initio values revealing remarkable correlation between the two sets of data. Correlations of 1Halpha and 13Calpha values with backbone conformational parameters (phi and psi) have also been found for all pairs (e.g. 1Halpha/phi and 13Calpha/phi) but 1Halpha/psi. Overall, the appealing idea of establishing backbone folding of proteins by employing chemical shift information alone, obtained from selected multiple-pulse NMR experiments (e.g. 2D-HSQC, 2D-HMQC, and 3D-HNCA), has received further support.

PMID: 11303866 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Direct NMR Observationand pKa Determination of the Asp102 Side Chain in a SerineProtease
Direct NMR Observationand pKa Determination of the Asp102 Side Chain in a SerineProtease Paul Everill, James L. Sudmeier and William W. Bachovchin http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja210091q/aop/images/medium/ja-2011-10091q_0008.gif Journal of the American Chemical Society DOI: 10.1021/ja210091q http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/k51DxgP9CaI
nmrlearner Journal club 0 01-24-2012 07:54 PM
High-Pressure Protein Crystallography and NMR to Explore Protein Conformations.
High-Pressure Protein Crystallography and NMR to Explore Protein Conformations. High-Pressure Protein Crystallography and NMR to Explore Protein Conformations. Annu Rev Biophys. 2010 Jul 21; Authors: Collins MD, Kim CU, Gruner SM High-pressure methods for solving protein structures by X-ray crystallography and NMR are maturing. These techniques are beginning to impact our understanding of thermodynamic and structural features that define not only the protein's native conformation, but also the higher free energy conformations. The ability of...
nmrlearner Journal club 0 02-02-2011 02:40 AM
[NMR paper] Direct determination of the interleukin-6 binding epitope of the interleukin-6 recept
Direct determination of the interleukin-6 binding epitope of the interleukin-6 receptor by NMR spectroscopy. Related Articles Direct determination of the interleukin-6 binding epitope of the interleukin-6 receptor by NMR spectroscopy. J Biol Chem. 2004 Jan 2;279(1):571-6 Authors: Schwantner A, Dingley AJ, Ozbek S, Rose-John S, Grötzinger J All cytokines belonging to the interleukin-6 (IL-6)-type family of cytokines utilize receptors that have a modular build of several immunoglobulin-like and fibronectin type III-like domains. Characteristic...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Active conformations of glycosaminoglycans. NMR determination of the conformation of
Active conformations of glycosaminoglycans. NMR determination of the conformation of heparin sequences complexed with antithrombin and fibroblast growth factors in solution. Related Articles Active conformations of glycosaminoglycans. NMR determination of the conformation of heparin sequences complexed with antithrombin and fibroblast growth factors in solution. Semin Thromb Hemost. 2002 Aug;28(4):325-34 Authors: Hricovíni M, Guerrini M, Bisio A, Torri G, Naggi A, Casu B Binding to proteins usually induces perturbation of nuclear magnetic...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Determination of solution conformations of PrP106-126, a neurotoxic fragment of prion
Determination of solution conformations of PrP106-126, a neurotoxic fragment of prion protein, by 1H NMR and restrained molecular dynamics. Related Articles Determination of solution conformations of PrP106-126, a neurotoxic fragment of prion protein, by 1H NMR and restrained molecular dynamics. Eur J Biochem. 1999 Dec;266(3):1192-201 Authors: Ragg E, Tagliavini F, Malesani P, Monticelli L, Bugiani O, Forloni G, Salmona M Experimental two-dimensional 1H NMR data have been obtained for PrP106-128 under the following solvent conditions:...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] Direct determination of changes of interdomain orientation on ligation: use of the or
Direct determination of changes of interdomain orientation on ligation: use of the orientational dependence of 15N NMR relaxation in Abl SH(32). Related Articles Direct determination of changes of interdomain orientation on ligation: use of the orientational dependence of 15N NMR relaxation in Abl SH(32). Biochemistry. 1999 Aug 10;38(32):10225-30 Authors: Fushman D, Xu R, Cowburn D The relative orientation and motions of domains within many proteins are key to the control of multivalent recognition, or the assembly of protein-based cellular...
nmrlearner Journal club 0 11-18-2010 08:31 PM
[Stan NMR blog] Systems of Units of Measurements
Systems of Units of Measurements Collection of references and links to measurement units. More...
nmrlearner News from NMR blogs 0 08-21-2010 06:14 PM
[Stan NMR blog] Tables of SI Units and Prefixes
Tables of SI Units and Prefixes Includes basic, derived, accepted and deprecated units. More...
nmrlearner News from NMR blogs 0 08-21-2010 06:14 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 05:15 PM.


Map