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



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  
Unread 08-14-2010, 04:19 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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 Mapping of protein structural ensembles by chemical shifts

Abstract Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift prediction methods are optimized to predict the lowest energy ground state structure that is only weakly populated at physiological temperatures. An analysis of the data shows that a chemical shift prediction can be used as measure to define the minimum size of the structural bundle required for a faithful description of the structural ensemble.
  • Content Type Journal Article
  • DOI 10.1007/s10858-010-9438-4
  • Authors
    • Kumaran Baskaran, University of Regensburg Department of Biophysics and Physical Biochemistry 93040 Regensburg Federal Republic of Germany
    • Konrad Brunner, University of Regensburg Department of Biophysics and Physical Biochemistry 93040 Regensburg Federal Republic of Germany
    • Claudia E. Munte, University of Regensburg Department of Biophysics and Physical Biochemistry 93040 Regensburg Federal Republic of Germany
    • Hans Robert Kalbitzer, University of Regensburg Department of Biophysics and Physical Biochemistry 93040 Regensburg Federal Republic of Germany

Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
nmrlearner Journal club 0 02-11-2012 10:31 AM
Mapping allostery through the covariance analysis of NMR chemical shifts [Biophysics and Computational Biology]
Mapping allostery through the covariance analysis of NMR chemical shifts Selvaratnam, R., Chowdhury, S., VanSchouwen, B., Melacini, G.... Date: 2011-04-12 Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the propagation of allosteric signals between the end points often remain elusive. Here we show that the covariance analysis of NMR chemical...
nmrlearner Journal club 0 04-13-2011 01:15 AM
Mapping allostery through the covariance analysis of NMR chemical shifts.
Mapping allostery through the covariance analysis of NMR chemical shifts. Mapping allostery through the covariance analysis of NMR chemical shifts. Proc Natl Acad Sci U S A. 2011 Mar 28; Authors: Selvaratnam R, Chowdhury S, Vanschouwen B, Melacini G Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the...
nmrlearner Journal club 0 03-31-2011 06:24 PM
[NMR paper] Secondary structural effects on protein NMR chemical shifts.
Secondary structural effects on protein NMR chemical shifts. Related Articles Secondary structural effects on protein NMR chemical shifts. J Biomol NMR. 2004 Nov;30(3):233-44 Authors: Wang Y For an amino acid in protein, its chemical shift, delta(phi, psi)(s), is expressed as a function of its backbone torsion angles (phi and psi) and secondary state (s): delta(phi, psi)(s=deltaphi, psi)_coil+Deltadelta(phi, psi)_s), where delta(phi, psi)(coil) represents its chemical shift at coil state (s=coil); Delta delta(phi, psi)(s) (s=sheet or helix) is...
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initi
Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. Related Articles Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. Science. 1993 Jun 4;260(5113):1491-6 Authors: de Dios AC, Pearson JG, Oldfield E Recent theoretical developments permit the prediction of 1H, 13C, 15N, and 19F nuclear magnetic resonance chemical shifts in proteins and offer new ways of analyzing secondary and tertiary structure as well as for probing protein electrostatics. For 13C,...
nmrlearner Journal club 0 08-21-2010 11:53 PM
Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations
Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins. Related Articles Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins. Structure. 2010 Aug 11;18(8):923-933 Authors: Robustelli P, Kohlhoff K, Cavalli A, Vendruscolo M We introduce a procedure to determine the structures of proteins by incorporating NMR chemical shifts as structural restraints in molecular dynamics simulations. In this approach, the chemical shifts are expressed as differentiable...
nmrlearner Journal club 0 08-17-2010 03:36 AM
Use of chemical shifts for structural studies of nucleic acids
Use of chemical shifts for structural studies of nucleic acids Publication year: 2010 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 1 February 2010</br> Sik Lok, Lam , Lai Man, Chi</br> More...
nmrlearner Journal club 0 08-16-2010 03:50 AM
Structure-based protein NMR assignments using native structural ensembles
Structure-based protein NMR assignments using native structural ensembles Mehmet Serkan Apaydın, Vincent Conitzer and Bruce Randall Donald Journal of Biomolecular NMR; 2008; 40(4); pp 263-276 Abstract: An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure (“template”) for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange...
matthias Journal club 0 08-14-2008 12:54 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

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 02:38 PM.


Map