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 07-15-2017, 05:05 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,969
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 Unraveling the meaning of chemical shifts in protein NMR

Unraveling the meaning of chemical shifts in protein NMR

Publication date: Available online 15 July 2017
Source:Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Author(s): Mark V. Berjanskii, David S. Wishart

Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.







More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] A robust algorithm for optimizing protein structures with NMR chemical shifts.
A robust algorithm for optimizing protein structures with NMR chemical shifts. Related Articles A robust algorithm for optimizing protein structures with NMR chemical shifts. J Biomol NMR. 2015 Sep 7; Authors: Berjanskii M, Arndt D, Liang Y, Wishart DS Abstract Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts....
nmrlearner Journal club 0 09-09-2015 11:49 AM
[NMR images] NMR spectrum shows the chemical shifts of hydrogen atoms in a protein ...
http://publications.nigms.nih.gov/structlife/images/ch3_nmr3.gif 31/05/2014 1:57:48 PM GMT NMR spectrum shows the chemical shifts of hydrogen atoms in a protein ... More...
nmrlearner NMR pictures 0 05-31-2014 01:57 PM
[NMR paper] Unraveling the interaction between the LPS O-antigen of Burkholderia anthina and the 5D8 monoclonal antibody by using a multidisciplinary chemical approach, with synthesis, NMR, and molecular modeling methods.
Unraveling the interaction between the LPS O-antigen of Burkholderia anthina and the 5D8 monoclonal antibody by using a multidisciplinary chemical approach, with synthesis, NMR, and molecular modeling methods. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary-Button_120x27px_FullText.gif Related Articles Unraveling the interaction between the LPS O-antigen of Burkholderia anthina and the 5D8 monoclonal antibody by using a multidisciplinary chemical approach, with synthesis, NMR, and molecular modeling methods....
nmrlearner Journal club 0 03-04-2014 06:37 PM
Interpreting Protein Structural Dynamics from NMR Chemical Shifts
Interpreting Protein Structural Dynamics from NMR Chemical Shifts Paul Robustelli, Kate A. Stafford and Arthur G. Palmer http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja300265w/aop/images/medium/ja-2012-00265w_0003.gif Journal of the American Chemical Society DOI: 10.1021/ja300265w http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/AvG321E_RMU
nmrlearner Journal club 0 03-28-2012 09:28 PM
Unraveling the 13C NMR Chemical Shiftsin Single-Walled Carbon Nanotubes: Dependence on Diameter and ElectronicStructure
Unraveling the 13C NMR Chemical Shiftsin Single-Walled Carbon Nanotubes: Dependence on Diameter and ElectronicStructure Chaiwat Engtrakul, Veronica M. Irurzun, Erica L. Gjersing, Josh M. Holt, Brian A. Larsen, Daniel E. Resasco and Jeffrey L. Blackburn http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja211181q/aop/images/medium/ja-2011-11181q_0004.gif Journal of the American Chemical Society DOI: 10.1021/ja211181q http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/k6jE1qN8glA
nmrlearner Journal club 0 02-29-2012 10:20 AM
4D prediction of protein 1H chemical shifts
4D prediction of protein 1H chemical shifts Abstract A 4D approach for protein 1H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6??7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Hα and HN shifts, respectively. However, for individual proteins...
nmrlearner Journal club 0 01-09-2011 12:46 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
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...
nmrlearner Journal club 0 08-14-2010 04:19 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 - 2017, 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 09:35 AM.


Map