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 09-22-2008, 12:00 AM
Junior Member
 
Join Date: Sep 2008
Posts: 2
Points: 24, Level: 1
Points: 24, Level: 1 Points: 24, Level: 1 Points: 24, Level: 1
Level up: 47%, 26 Points needed
Level up: 47% Level up: 47% Level up: 47%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 24
Downloads: 0
Uploads: 0
Default Investigation of the utility of selective methyl protonation for determination of membrane protein structures

Investigation of the utility of selective methyl protonation for determination of membrane protein structures
Steve C. C. Shih, Ileana Stoica and Natalie K. Goto
Journal of Biomolecular NMR; 2008; 42(1); pp 49-58

Abstract
Polytopic α-helical membrane proteins present one of the final frontiers for protein structural biology, with significant challenges causing severe under-representation in the protein structure databank. However, with the advent of hardware and methodology geared to the study of large molecular weight complexes, solution NMR is being increasingly considered as a tool for structural studies of these types of membrane proteins. One method that has the potential to facilitate these studies utilizes uniformly deuterated samples with protons reintroduced at one or two methyl groups of leucine, valine and isoleucine. In this work we demonstrate that in spite of the increased proportion of these amino acids in membrane proteins, the quality of structures that can be obtained from this strategy is similar to that obtained for all α-helical water soluble proteins. This is partly attributed to the observation that NOEs between residues within the transmembrane helix did not have an impact on structure quality. Instead the most important factors controlling structure accuracy were the strength of dihedral angle restraints imposed and the number of unique inter-helical pairs of residues constrained by NOEs. Overall these results suggest that the most accurate structures will arise from accurate identification of helical segments and utilization of inter-helical distance restraints from various sources to maximize the distribution of long-range restraints.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment
Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment Abstract Obtaining NMR assignments for slowly tumbling molecules such as detergent-solubilized membrane proteins is often compromised by low sensitivity as well as spectral overlap. Both problems can be addressed by amino-acid specific isotope labeling in conjunction with 15Nâ??1H correlation experiments. In this work an extended combinatorial selective in vitro labeling scheme is proposed that seeks to reduce the number of samples required for assignment. Including three...
nmrlearner Journal club 0 01-21-2012 06:26 PM
Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR.
Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR. Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR. J Magn Reson. 2011 Mar 17; Authors: Traaseth NJ, Veglia G We present a new method that combines carbonyl-selective labeling with frequency-selective heteronuclear recoupling to resolve the spectral overlap of magic angle spinning (MAS) NMR...
nmrlearner Journal club 0 04-13-2011 11:57 PM
Frequency-Selective Heteronuclear Dephasing and Selective Carbonyl Labeling to Deconvolute Crowded Spectra of Membrane Proteins By Magic Angle Spinning NMR
Frequency-Selective Heteronuclear Dephasing and Selective Carbonyl Labeling to Deconvolute Crowded Spectra of Membrane Proteins By Magic Angle Spinning NMR Publication year: 2011 Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 17 March 2011</br> Nathaniel J., Traaseth , Gianluigi, Veglia</br> We present a new method that combines carbonyl-selective labeling with frequency-selective heteronuclear recoupling to resolve the spectral overlap of magic angle spinning (MAS) NMR spectra of membrane proteins in fluid lipid membranes with broad lines and...
nmrlearner Journal club 0 03-18-2011 06:43 AM
[NMR paper] Evaluation of the utility of NMR structures determined from minimal NOE-based restrai
Evaluation of the utility of NMR structures determined from minimal NOE-based restraints for structure-based drug design, using MMP-1 as an example. Related Articles Evaluation of the utility of NMR structures determined from minimal NOE-based restraints for structure-based drug design, using MMP-1 as an example. Biochemistry. 2000 Nov 7;39(44):13365-75 Authors: Huang X, Moy F, Powers R The application of deuterium labeling and residual dipolar coupling constants in combination with other structural information has demonstrated the potential...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] NMR investigation of the multidrug transporter EmrE, an integral membrane protein.
NMR investigation of the multidrug transporter EmrE, an integral membrane protein. Related Articles NMR investigation of the multidrug transporter EmrE, an integral membrane protein. Eur J Biochem. 1998 Jun 15;254(3):610-9 Authors: Schwaiger M, Lebendiker M, Yerushalmi H, Coles M, Gröger A, Schwarz C, Schuldiner S, Kessler H EmrE is an Escherichia coli multidrug transport protein that confers resistance to a wide range of toxicants by active transport across the bacterial cell membrane. The highly hydrophobic polytopic integral membrane...
nmrlearner Journal club 0 11-17-2010 11:06 PM
[NMR paper] URPI: a utility program for planning selective protein double-labeling with 13C and 1
URPI: a utility program for planning selective protein double-labeling with 13C and 15N in NMR analyses. Related Articles URPI: a utility program for planning selective protein double-labeling with 13C and 15N in NMR analyses. J Magn Reson B. 1994 Jan;103(1):89-90 Authors: Shinagawa K, Ohya M, Wakamatsu K
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] URPI: a utility program for planning selective protein double-labeling with 13C and 1
URPI: a utility program for planning selective protein double-labeling with 13C and 15N in NMR analyses. Related Articles URPI: a utility program for planning selective protein double-labeling with 13C and 15N in NMR analyses. J Magn Reson B. 1994 Jan;103(1):89-90 Authors: Shinagawa K, Ohya M, Wakamatsu K
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Selective and extensive 13C labeling of a membrane protein for solid-state NMR invest
Selective and extensive 13C labeling of a membrane protein for solid-state NMR investigations. Related Articles Selective and extensive 13C labeling of a membrane protein for solid-state NMR investigations. J Biomol NMR. 1999 May;14(1):71-4 Authors: Hong M, Jakes K The selective and extensive 13C labeling of mostly hydrophobic amino acid residues in a 25 kDa membrane protein, the colicin Ia channel domain, is reported. The novel 13C labeling approach takes advantage of the amino acid biosynthetic pathways in bacteria and suppresses the...
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 - 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 01:50 AM.


Map