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 04-15-2015, 04:40 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,654
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 Optimizing nanodiscs and bicelles for solution NMR studies of two ?-barrel membrane proteins.

Optimizing nanodiscs and bicelles for solution NMR studies of two ?-barrel membrane proteins.

Related Articles Optimizing nanodiscs and bicelles for solution NMR studies of two ?-barrel membrane proteins.

J Biomol NMR. 2015 Apr;61(3-4):261-74

Authors: Kucharska I, Edrington TC, Liang B, Tamm LK

Abstract
Solution NMR spectroscopy has become a robust method to determine structures and explore the dynamics of integral membrane proteins. The vast majority of previous studies on membrane proteins by solution NMR have been conducted in lipid micelles. Contrary to the lipids that form a lipid bilayer in biological membranes, micellar lipids typically contain only a single hydrocarbon chain or two chains that are too short to form a bilayer. Therefore, there is a need to explore alternative more bilayer-like media to mimic the natural environment of membrane proteins. Lipid bicelles and lipid nanodiscs have emerged as two alternative membrane mimetics that are compatible with solution NMR spectroscopy. Here, we have conducted a comprehensive comparison of the physical and spectroscopic behavior of two outer membrane proteins from Pseudomonas aeruginosa, OprG and OprH, in lipid micelles, bicelles, and nanodiscs of five different sizes. Bicelles stabilized with a fraction of negatively charged lipids yielded spectra of almost comparable quality as in the best micellar solutions and the secondary structures were found to be almost indistinguishable in the two environments. Of the five nanodiscs tested, nanodiscs assembled from MSP1D1?H5 performed the best with both proteins in terms of sample stability and spectral resolution. Even in these optimal nanodiscs some broad signals from the membrane embedded barrel were severely overlapped with sharp signals from the flexible loops making their assignments difficult. A mutant OprH that had two of the flexible loops truncated yielded very promising spectra for further structural and dynamical analysis in MSP1D1?H5 nanodiscs.


PMID: 25869397 [PubMed - in process]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Optimizing nanodiscs and bicelles for solution NMR studies of two β-barrel membrane proteins
Optimizing nanodiscs and bicelles for solution NMR studies of two β-barrel membrane proteins Abstract Solution NMR spectroscopy has become a robust method to determine structures and explore the dynamics of integral membrane proteins. The vast majority of previous studies on membrane proteins by solution NMR have been conducted in lipid micelles. Contrary to the lipids that form a lipid bilayer in biological membranes, micellar lipids typically contain only a single hydrocarbon chain or two chains that are too short to form a bilayer. Therefore,...
nmrlearner Journal club 0 02-10-2015 10:56 AM
Solution NMR resonance assignment strategies for ?-barrel membrane proteins
Solution NMR resonance assignment strategies for ?-barrel membrane proteins Abstract Membrane proteins in detergent micelles are large and dynamic complexes that present challenges for solution NMR investigations such as spectral overlap and line broadening. In this study, multiple methods are introduced to facilitate resonance assignment of ?-barrel membrane proteins using Opa60 from Neisseria gonorrhoeae as a model system. Opa60 is an eight-stranded ?-barrel with long extracellular loops (~63% of the protein) that engage host receptors and induce engulfment of the bacterium. The NMR...
nmrlearner Journal club 0 07-27-2013 01:35 PM
Solution NMR resonance assignment strategies for ?-barrel membrane proteins
Solution NMR resonance assignment strategies for ?-barrel membrane proteins Abstract Membrane proteins in detergent micelles are large and dynamic complexes that present challenges for solution NMR investigations such as spectral overlap and line broadening. In this study, multiple methods are introduced to facilitate resonance assignment of ?-barrel membrane proteins using Opa60 from Neisseria gonorrhoeae as a model system. Opa60 is an eight-stranded ?-barrel with long extracellular loops (~63% of the protein) that engage host receptors and induce engulfment of the bacterium. The NMR...
nmrlearner Journal club 0 06-27-2013 02:10 PM
Solution NMR resonance assignment strategies for ?-barrel membrane proteins
Solution NMR resonance assignment strategies for ?-barrel membrane proteins Abstract Membrane proteins in detergent micelles are large and dynamic complexes that present challenges for solution NMR investigations such as spectral overlap and line broadening. In this study, multiple methods are introduced to facilitate resonance assignment of ?-barrel membrane proteins using Opa60 from Neisseria gonorrhoeae as a model system. Opa60 is an eight-stranded ?-barrel with long extracellular loops (~63% of the protein) that engage host receptors and induce engulfment of the bacterium. The NMR...
nmrlearner Journal club 0 06-27-2013 01:52 AM
[NMR paper] Solution NMR resonance assignment strategies for ?-barrel membrane proteins.
Solution NMR resonance assignment strategies for ?-barrel membrane proteins. Solution NMR resonance assignment strategies for ?-barrel membrane proteins. Protein Sci. 2013 Jun 10; Authors: Fox DA, Columbus L Abstract Membrane proteins in detergent micelles are large and dynamic complexes that present challenges for solution NMR investigations such as spectral overlap and line broadening. In this study, multiple methods are introduced to facilitate resonance assignment of ?-barrel membrane proteins using Opa60 from Neisseria...
nmrlearner Journal club 0 06-12-2013 11:42 AM
‘q-titration’ of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy
‘q-titration’ of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy Publication year: 2011 Source: Journal of Magnetic Resonance, Available online 25 October 2011</br> Woo Sung*Son, Sang Ho*Park, Henry J.*Nothnagel, George J.*Lu, Yan*Wang, ...</br> ‘q-titration’ refers to the systematic comparison of signal intensities in solution NMR spectra of uniformlyN labeled membrane proteins solubilized in micelles and isotropic bicelles as a function of the molar ratios (q) of the...
nmrlearner Journal club 0 10-26-2011 11:25 AM
Nanodiscs versus Macrodiscs for NMR of Membrane Proteins
Nanodiscs versus Macrodiscs for NMR of Membrane Proteins http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi201289c/aop/images/medium/bi-2011-01289c_0002.gif Biochemistry DOI: 10.1021/bi201289c http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/4XXVT7tcC8w More...
nmrlearner Journal club 0 09-30-2011 08:01 PM
Nanodiscs vs. Macrodiscs for NMR of Membrane Proteins.
Nanodiscs vs. Macrodiscs for NMR of Membrane Proteins. Nanodiscs vs. Macrodiscs for NMR of Membrane Proteins. Biochemistry. 2011 Sep 21; Authors: Park SH, Berkamp S, Cook GA, Chan MK, Viadiu H, Opella SJ Abstract It is challenging to find membrane mimics that stabilize the native structure, dynamics, and functions of membrane proteins. In a recent advance, nanodiscs have been shown to provide a bilayer environment compatible with solution NMR. Increasing the lipid to "belt" peptide ratio expands their diameter, slows their reorientation...
nmrlearner Journal club 0 09-23-2011 05:30 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 06:30 PM.


Map