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 Rating: Thread Rating: 2 votes, 5.00 average. Display Modes
  #1  
Unread 04-05-2017, 02:30 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,165
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 Nanodiscs and Solution NMR: preparation, application and challenges.

Nanodiscs and Solution NMR: preparation, application and challenges.

Related Articles Nanodiscs and Solution NMR: preparation, application and challenges.

Nanotechnol Rev. 2017 Feb;6(1):111-126

Authors: Puthenveetil R, Nguyen K, Vinogradova O

Abstract
Nanodiscs provide an excellent system for the structure-function investigation of membrane proteins. Its direct advantage lies in presenting a water soluble form of an otherwise hydrophobic molecule, making it amenable to a plethora of solution techniques. Nuclear Magnetic Resonance is one such high resolution approach that looks at the structure and dynamics of a protein with atomic level precision. Recently, there has been a breakthrough in making nanodiscs more susceptible for structure determination by solution NMR, yet it still remains to become the preferred choice for a membrane mimetic. In this practical review, we provide a general discourse on nanodisc and its application to solution NMR. We also offer potential solutions to remediate the technical challenges associated with nanodisc preparation and the choice of proper experimental set-ups. Along with discussing several structural applications, we demonstrate an alternative use of nanodiscs for functional studies, where we investigated the phosphorylation of a cell surface receptor, Integrin. This is the first successful manifestation of observing activated receptor phosphorylation in nanodiscs through NMR. We additionally present an on-column method for nanodisc preparation with multiple strategies and discuss the potential use of alternative nanoscale phospholipid bilayer systems like SMA lipid discs and Saposin-A lipoprotein discs.


PMID: 28373928 [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
[NMR paper] Smaller*Nanodiscs are Suitable for Studying Protein Lipid Interactions by Solution NMR.
Smaller*Nanodiscs are Suitable for Studying Protein Lipid Interactions by Solution NMR. Related Articles Smaller*Nanodiscs are Suitable for Studying Protein Lipid Interactions by Solution NMR. Protein J. 2015 May 17; Authors: Wang X, Mu Z, Li Y, Bi Y, Wang Y Abstract Phospholipid bilayer nanodiscs, a newly developed model membrane system, provides "native-like" membrane environment for membrane protein studies. Nanodiscs assembled by membrane scaffold protein and phospholipid bilayer, with defined sizes that can be accurately...
nmrlearner Journal club 0 05-20-2015 10:27 AM
[NMR paper] 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...
nmrlearner Journal club 0 04-15-2015 04:40 PM
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
[NMR paper] Solution-NMR Characterization of Outer-Membrane Protein A from E. coli in Lipid Bilayer Nanodiscs and Detergent Micelles.
Solution-NMR Characterization of Outer-Membrane Protein A from E. coli in Lipid Bilayer Nanodiscs and Detergent Micelles. Related Articles Solution-NMR Characterization of Outer-Membrane Protein A from E. coli in Lipid Bilayer Nanodiscs and Detergent Micelles. Chembiochem. 2014 Apr 1; Authors: Suac L, Horst R, Wthrich K Abstract X-ray crystallography and solution NMR of detergent-reconstituted OmpA (outer membrane protein A from E. coli) had shown that this protein forms an eight-stranded transmembrane ?-barrel, but only...
nmrlearner Journal club 0 04-03-2014 12:59 PM
[NMR paper] Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs.
Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution NMR spectroscopic characterization of human VDAC-2 in detergent micelles and lipid bilayer nanodiscs. Biochim Biophys Acta. 2012 Jun;1818(6):1562-9 Authors: Yu TY, Raschle T, Hiller S, Wagner G Abstract Three isoforms of the human voltage-dependent anion channel (VDAC), located...
nmrlearner Journal club 0 04-04-2013 08:50 PM
[NMR paper] Optimization of the design and preparation of nanoscale phospholipid bilayers for its application to solution NMR.
Optimization of the design and preparation of nanoscale phospholipid bilayers for its application to solution NMR. Optimization of the design and preparation of nanoscale phospholipid bilayers for its application to solution NMR. Proteins. 2013 Feb 21; Authors: Puthenveetil R, Vinogradova O Abstract Despite arduous efforts and recent technological developments structural investigation of integral membrane proteins remains a challenge. The primary deterrents include difficulties with their expression, low inherent solubility and various...
nmrlearner Journal club 0 02-26-2013 06:35 PM
Preparation of a functional GABARAP-lipid conjugate in nanodiscs and its investigation by solution NMR spectroscopy.
Preparation of a functional GABARAP-lipid conjugate in nanodiscs and its investigation by solution NMR spectroscopy. Preparation of a functional GABARAP-lipid conjugate in nanodiscs and its investigation by solution NMR spectroscopy. Chembiochem. 2010 Sep 24;11(14):1967-70 Authors: Ma P, Mohrlder J, Schwarten M, Stoldt M, Singh SK, Hartmann R, Pacheco V, Willbold D
nmrlearner Journal club 0 01-21-2011 01:22 AM
[NMR paper] Escherichia coli diacylglycerol kinase: a case study in the application of solution N
Escherichia coli diacylglycerol kinase: a case study in the application of solution NMR methods to an integral membrane protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Escherichia coli diacylglycerol kinase: a case study in the application of solution NMR methods to an integral membrane protein. Biophys J. 1997 Jun;72(6):2688-701 Authors: Vinogradova O,...
nmrlearner Journal club 0 08-22-2010 03:31 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 - 2020, 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 11:37 AM.


Map