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 06-27-2018, 05:55 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 Assigning methyl resonances for protein solution-state NMR studies

Assigning methyl resonances for protein solution-state NMR studies

Publication date: Available online 26 June 2018
Source:Methods

Author(s): Scott D. Gorman, Debashish Sahu, Kathleen F. O'Rourke, David D. Boehr

Solution-state NMR is an important tool for studying protein structure and function. The ability to probe methyl groups has helped to substantially expand the scope of proteins accessible by NMR spectroscopy, including facilitating study of proteins and complexes greater than 100 kDa in size. While the toolset for studying protein structure and dynamics by NMR continues to expand, a major rate-limiting step in these studies is the initial resonance assignments, especially for larger (> 50 kDa) proteins. In this practical review, we present strategies for efficiently isotopically labeling proteins, delineate NMR pulse sequences that can be used to determine methyl resonance assignments in the presence and absence of backbone assignments, and outline computational methods for NMR data analysis. We use our experiences from assigning methyl resonances for the aromatic biosynthetic enzymes tryptophan synthase and chorismate mutase to provide advice for all stages of experimental set-up and data analysis.







More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Assignment of methyl NMR resonances of a 52*kDa protein with residue-specific 4D correlation maps.
Assignment of methyl NMR resonances of a 52*kDa protein with residue-specific 4D correlation maps. Related Articles Assignment of methyl NMR resonances of a 52*kDa protein with residue-specific 4D correlation maps. J Biomol NMR. 2015 May 8; Authors: Mishra SH, Frueh DP Abstract Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method...
nmrlearner Journal club 0 05-10-2015 03:50 AM
Assignment of methyl NMR resonances of a 52Â*kDa protein with residue-specific 4D correlation maps
Assignment of methyl NMR resonances of a 52Â*kDa protein with residue-specific 4D correlation maps Abstract Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method that facilitates assignment of methyl resonances from assigned amide groups. Calculating the covariance between sensitive methyl and amide 3D spectra, each providing correlations to Cα and Cβ...
nmrlearner Journal club 0 05-07-2015 03:04 PM
Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins
Methyl-specific isotopic labeling: a molecular tool box for solution NMR studies of large proteins Publication date: June 2015 Source:Current Opinion in Structural Biology, Volume 32</br> Author(s): Rime Kerfah , Michael J Plevin , Remy Sounier , Pierre Gans , Jerome Boisbouvier</br> Nuclear magnetic resonance (NMR) spectroscopy is a uniquely powerful tool for studying the structure, dynamics and interactions of biomolecules at atomic resolution. In the past 15 years, the development of new isotopic labeling strategies has opened the possibility of exploiting...
nmrlearner Journal club 0 04-14-2015 01:24 PM
[NMR paper] Specific (13)C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies.
Specific (13)C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies. Specific (13)C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies. J Magn Reson. 2015 Jan 6;252C:10-19 Authors: Fasshuber HK, Demers JP, Chevelkov V, Giller K, Becker S, Lange A Abstract Here we present an isotopic labeling strategy to easily obtain unambiguous long-range...
nmrlearner Journal club 0 01-28-2015 05:28 PM
Specific 13C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies
Specific 13C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies Publication date: Available online 6 January 2015 Source:Journal of Magnetic Resonance</br> Author(s): Hannes Klaus Fasshuber , Jean-Philippe Demers , Veniamin Chevelkov , Karin Giller , Stefan Becker , Adam Lange</br> Here we present an isotopic labeling strategy to easily obtain unambiguous long-range distance restraints in protein solid-state NMR studies. The method is based on the inclusion of two...
nmrlearner Journal club 0 01-07-2015 11:26 AM
[NMR paper] Combination of (15)N reverse labeling and afterglow spectroscopy for assigning membrane protein spectra by magic-angle-spinning solid-state NMR: application to the multidrug resistance protein EmrE.
Combination of (15)N reverse labeling and afterglow spectroscopy for assigning membrane protein spectra by magic-angle-spinning solid-state NMR: application to the multidrug resistance protein EmrE. Related Articles Combination of (15)N reverse labeling and afterglow spectroscopy for assigning membrane protein spectra by magic-angle-spinning solid-state NMR: application to the multidrug resistance protein EmrE. J Biomol NMR. 2013 Mar 29; Authors: Banigan JR, Gayen A, Traaseth NJ Abstract Magic-angle-spinning (MAS) solid-state NMR...
nmrlearner Journal club 0 03-30-2013 12:59 PM
[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
[NMR paper] Solution studies of staphylococcal nuclease H124L. 1. Backbone 1H and 15N resonances
Solution studies of staphylococcal nuclease H124L. 1. Backbone 1H and 15N resonances and secondary structure of the unligated enzyme as identified by three-dimensional NMR spectroscopy. Related Articles Solution studies of staphylococcal nuclease H124L. 1. Backbone 1H and 15N resonances and secondary structure of the unligated enzyme as identified by three-dimensional NMR spectroscopy. Biochemistry. 1992 Jan 28;31(3):911-20 Authors: Wang JF, Mooberry ES, Walkenhorst WF, Markley JL The backbone 1H and 15N resonances of unligated staphylococcal...
nmrlearner Journal club 0 08-21-2010 11:41 PM


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 04:36 AM.


Map