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 12-21-2013, 03:15 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 Resonance assignments of a membrane protein in phospholipid bilayers by combining multiple strategies of oriented sample solid-state NMR.

Resonance assignments of a membrane protein in phospholipid bilayers by combining multiple strategies of oriented sample solid-state NMR.

Related Articles Resonance assignments of a membrane protein in phospholipid bilayers by combining multiple strategies of oriented sample solid-state NMR.

J Biomol NMR. 2013 Dec 20;

Authors: Lu GJ, Opella SJ

Abstract
Oriented sample solid-state NMR spectroscopy can be used to determine the three-dimensional structures of membrane proteins in magnetically or mechanically aligned lipid bilayers. The bottleneck for applying this technique to larger and more challenging proteins is making resonance assignments, which is conventionally accomplished through the preparation of multiple selectively isotopically labeled samples and performing an analysis of residues in regular secondary structure based on Polarity Index Slant Angle (PISA) Wheels and Dipolar Waves. Here we report the complete resonance assignment of the full-length mercury transporter, MerF, an 81-residue protein, which is challenging because of overlapping PISA Wheel patterns from its two trans-membrane helices, by using a combination of solid-state NMR techniques that improve the spectral resolution and provide correlations between residues and resonances. These techniques include experiments that take advantage of the improved resolution of the MSHOT4-Pi4/Pi pulse sequence; the transfer of resonance assignments through frequency alignment of heteronuclear dipolar couplings, or through dipolar coupling correlated isotropic chemical shift analysis; (15)N/(15)N dilute spin exchange experiments; and the use of the proton-evolved local field experiment with isotropic shift analysis to assign the irregular terminal and loop regions of the protein, which is the major "blind spot" of the PISA Wheel/Dipolar Wave method.


PMID: 24356892 [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
[NMR paper] Aggregation and dynamics of oligocholate transporters in phospholipid bilayers revealed by solid-state NMR spectroscopy.
Aggregation and dynamics of oligocholate transporters in phospholipid bilayers revealed by solid-state NMR spectroscopy. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Aggregation and dynamics of oligocholate transporters in phospholipid bilayers revealed by solid-state NMR spectroscopy. Langmuir. 2012 Dec 11;28(49):17071-8 Authors: Wang T, Widanapathirana L, Zhao Y, Hong M Abstract Macrocycles made of cholate building blocks were previously found to...
nmrlearner Journal club 0 05-22-2013 04:43 PM
Tertiary Structural Models for a Three Helix Membrane Protein in*a Bilayer Environment from Oriented Sample Solid State NMR Data
Tertiary Structural Models for a Three Helix Membrane Protein in*a Bilayer Environment from Oriented Sample Solid State NMR Data 29 January 2013 Publication year: 2013 Source:Biophysical Journal, Volume 104, Issue 2, Supplement 1</br> </br> </br> </br></br>
nmrlearner Journal club 0 02-03-2013 10:13 AM
Improved 1H amide resonance line narrowing in oriented sample solid-state NMR of membrane proteins in phospholipid bilayers
Improved 1H amide resonance line narrowing in oriented sample solid-state NMR of membrane proteins in phospholipid bilayers July 2012 Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 220</br> </br> We demonstrate 1H amide resonance line widths
nmrlearner Journal club 0 02-03-2013 10:13 AM
Magic Angle Spinning and Oriented Sample Solid-State NMR Structural Restraints Combine for Influenza A M2 Protein Functional Insights
Magic Angle Spinning and Oriented Sample Solid-State NMR Structural Restraints Combine for Influenza A M2 Protein Functional Insights Thach V. Can, Mukesh Sharma, Ivan Hung, Peter L. Gor’kov, William W. Brey and Timothy A. Cross http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja3004039/aop/images/medium/ja-2012-004039_0004.gif Journal of the American Chemical Society DOI: 10.1021/ja3004039 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/xappAmN-wb8
nmrlearner Journal club 0 05-25-2012 07:14 PM
Improved 1H Amide Resonance Line Narrowing in Oriented Sample Solid-state NMR of Membrane Proteins in Phospholipid Bilayers
Improved 1H Amide Resonance Line Narrowing in Oriented Sample Solid-state NMR of Membrane Proteins in Phospholipid Bilayers Publication year: 2012 Source:Journal of Magnetic Resonance</br> George J. Lu, Sang Ho Park, Stanley J. Opella</br> We demonstrate 1H amide resonance line widths
nmrlearner Journal club 0 04-26-2012 08:10 PM
Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers
Multidimensional oriented solid-state NMR experiments enable the sequential assignment of uniformly 15N labeled integral membrane proteins in magnetically aligned lipid bilayers Abstract Oriented solid-state NMR is the most direct methodology to obtain the orientation of membrane proteins with respect to the lipid bilayer. The method consists of measuring 1H-15N dipolar couplings (DC) and 15N anisotropic chemical shifts (CSA) for membrane proteins that are uniformly aligned with respect to the membrane bilayer. A significant advantage of this approach is that tilt and azimuthal...
nmrlearner Journal club 0 10-10-2011 06:27 AM
[NMR paper] Hydration-optimized oriented phospholipid bilayer samples for solid-state NMR structu
Hydration-optimized oriented phospholipid bilayer samples for solid-state NMR structural studies of membrane proteins. Related Articles Hydration-optimized oriented phospholipid bilayer samples for solid-state NMR structural studies of membrane proteins. J Magn Reson. 2003 Mar;161(1):64-9 Authors: Marassi FM, Crowell KJ The preparation of oriented, hydration-optimized lipid bilayer samples, for NMR structure determination of membrane proteins, is described. The samples consist of planar phospholipid bilayers, containing membrane proteins, that...
nmrlearner Journal club 0 11-24-2010 09:01 PM
Lipid-Protein Correlations in Nanoscale Phospholipid Bilayers by Solid-State NMR.
Lipid-Protein Correlations in Nanoscale Phospholipid Bilayers by Solid-State NMR. Lipid-Protein Correlations in Nanoscale Phospholipid Bilayers by Solid-State NMR. Biochemistry. 2010 Aug 30; Authors: Kijac A, Shih AY, Nieuwkoop AJ, Schulten K, Sligar SG, Rienstra CM Nanodiscs are an example of discoidal nanoscale lipid/protein particles that have been extremely useful for the biochemical and biophysical characterization of membrane proteins. They are discoidal lipid bilayer fragments encircled and stabilized by two amphipathic helical...
nmrlearner Journal club 0 09-02-2010 03:58 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 04:34 PM.


Map