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 11-12-2013, 03:52 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 Visualizing Side-chains of Invisible Protein Conformers by Solution NMR.

Visualizing Side-chains of Invisible Protein Conformers by Solution NMR.

Related Articles Visualizing Side-chains of Invisible Protein Conformers by Solution NMR.

J Mol Biol. 2013 Nov 7;

Authors: Bouvignies G, Vallurupalli P, Kay LE

Abstract
Sparsely populated and transiently formed protein conformers can play key roles in many biochemical processes. Understanding the structure function paradigm requires, therefore, an atomic resolution description of these rare states. Yet they are difficult to study because they cannot be observed using standard biophysical techniques. In the past decade NMR methods have been developed for structural studies of these elusive conformers, focusing primarily on backbone (1)H, (15)N and (13)C nuclei. Here we extend the methodology to include side-chains by developing a (13)C-based Chemical Exchange Saturation Transfer experiment for the assignment of side-chain aliphatic (13)C chemical shifts in uniformly (13)C labeled proteins. A pair of applications is provided, involving the folding of ?-sheet Fyn SH3 and ?-helical FF domains. Over 96% and 89% of the side-chain (13)C chemical shifts for excited states corresponding to the unfolded conformation of the Fyn SH3 domain and a folding intermediate of the FF domain, respectively, have been obtained, providing insight into side-chain packing and dynamics.


PMID: 24211467 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Visualizing Side-chains of Invisible Protein Conformers by Solution NMR
Visualizing Side-chains of Invisible Protein Conformers by Solution NMR Publication date: Available online 8 November 2013 Source:Journal of Molecular Biology</br> Author(s): Guillaume Bouvignies , Pramodh Vallurupalli , Lewis E. Kay</br> Sparsely populated and transiently formed protein conformers can play key roles in many biochemical processes. Understanding the structure function paradigm requires, therefore, an atomic resolution description of these rare states. Yet they are difficult to study because they cannot be observed using standard biophysical...
nmrlearner Journal club 0 11-08-2013 01:42 PM
Interactions of protein side chains with RNA defined with REDOR solid state NMR.
Interactions of protein side chains with RNA defined with REDOR solid state NMR. Interactions of protein side chains with RNA defined with REDOR solid state NMR. J Biomol NMR. 2011 Sep 25; Authors: Huang W, Varani G, Drobny GP Abstract Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived...
nmrlearner Journal club 0 09-30-2011 06:00 AM
Interactions of protein side chains with RNA defined with REDOR solid state NMR.
Interactions of protein side chains with RNA defined with REDOR solid state NMR. Interactions of protein side chains with RNA defined with REDOR solid state NMR. J Biomol NMR. 2011 Sep 25; Authors: Huang W, Varani G, Drobny GP Abstract Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived...
nmrlearner Journal club 0 09-30-2011 05:59 AM
Interactions of protein side chains with RNA defined with REDOR solid state NMR
Interactions of protein side chains with RNA defined with REDOR solid state NMR Abstract Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived peptides have been obtained by solution NMR, but only a small number of intermolecular NOEs could be identified unambiguously, preventing the determination of a complete structure. Here we show that a...
nmrlearner Journal club 0 09-27-2011 07:04 AM
[NMR paper] NMR assignment of protein side chains using residue-correlated labeling and NOE spect
NMR assignment of protein side chains using residue-correlated labeling and NOE spectra. Related Articles NMR assignment of protein side chains using residue-correlated labeling and NOE spectra. J Magn Reson. 2003 Dec;165(2):237-47 Authors: Mueller GA, Kirby TW, DeRose EF, London RE A new approach for the isotopic labeling of proteins is proposed that aims to facilitate side chain resonance assignments. Residue-correlated (RC) labeling is achieved by the expression of a protein on a medium containing a mixture of labeled, e.g., amino acids,...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] The effects of mutations on motions of side-chains in protein L studied by 2H NMR dyn
The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. Related Articles The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. J Mol Biol. 2003 Jun 6;329(3):551-63 Authors: Millet O, Mittermaier A, Baker D, Kay LE Recently developed 2H spin relaxation experiments are applied to study the dynamics of methyl-containing side-chains in the B1 domain of protein L and in a pair of point mutants of the domain, F22L and A20V. X-ray and...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N r
Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme. Related Articles Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme. J Am Chem Soc. 2001 Feb 7;123(5):967-75 Authors: Mulder FA, Skrynnikov NR, Hon B, Dahlquist FW, Kay LE A new NMR experiment is presented for...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide
Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide spin label and two-dimensional NMR study. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide spin label and two-dimensional NMR study. J Biol Chem. 1999 Mar 26;274(13):8411-20 Authors: Yuan T, Ouyang H, Vogel HJ Binding of calcium to calmodulin (CaM) causes a conformational...
nmrlearner Journal club 0 08-21-2010 04:03 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 08:56 AM.


Map