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 11-24-2010, 09:01 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,135
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 Simultaneous assignment and structure determination of a membrane protein from NMR or

Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints.

Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints.

Protein Sci. 2003 Mar;12(3):403-11

Authors: Marassi FM, Opella SJ

A solid-state NMR approach for simultaneous resonance assignment and three-dimensional structure determination of a membrane protein in lipid bilayers is described. The approach is based on the scattering, hence the descriptor "shotgun," of (15)N-labeled amino acids throughout the protein sequence (and the resulting NMR spectra). The samples are obtained by protein expression in bacteria grown on media in which one type of amino acid is labeled and the others are not. Shotgun NMR short-circuits the laborious and time-consuming process of obtaining complete sequential assignments prior to the calculation of a protein structure from the NMR data by taking advantage of the orientational information inherent to the spectra of aligned proteins. As a result, it is possible to simultaneously assign resonances and measure orientational restraints for structure determination. A total of five two-dimensional (1)H/(15)N PISEMA (polarization inversion spin exchange at the magic angle) spectra, from one uniformly and four selectively (15)N-labeled samples, were sufficient to determine the structure of the membrane-bound form of the 50-residue major pVIII coat protein of fd filamentous bacteriophage. Pisa (polarity index slat angle) wheels are an essential element in the process, which starts with the simultaneous assignment of resonances and the assembly of isolated polypeptide segments, and culminates in the complete three-dimensional structure of the protein with atomic resolution. The principles are also applicable to weakly aligned proteins studied by solution NMR spectroscopy. [The structure we determined for the membrane-bound form of the Fd bacteriophage pVIII coat protein has been deposited in the Protein Data Bank as PDB file 1MZT.]

PMID: 12592011 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra
AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra Publication year: 2011 Source: Journal of Magnetic Resonance, Available online 8 October 2011</br> Ye*Tian, Charles D.*Schwieters, Stanley J.*Opella, Francesca M.*Marassi</br> AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between...
nmrlearner Journal club 0 10-10-2011 06:27 AM
[NMR paper] NMR structure determination of a membrane protein with two transmembrane helices in m
NMR structure determination of a membrane protein with two transmembrane helices in micelles: MerF of the bacterial mercury detoxification system. Related Articles NMR structure determination of a membrane protein with two transmembrane helices in micelles: MerF of the bacterial mercury detoxification system. Biochemistry. 2005 Apr 5;44(13):5196-206 Authors: Howell SC, Mesleh MF, Opella SJ The three-dimensional backbone structure of a membrane protein with two transmembrane helices in micelles was determined using solution NMR methods that...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Simultaneous assignment and structure determination of protein backbones by using NMR
Simultaneous assignment and structure determination of protein backbones by using NMR dipolar couplings. Related Articles Simultaneous assignment and structure determination of protein backbones by using NMR dipolar couplings. Angew Chem Int Ed Engl. 2004 Jun 28;43(26):3479-81 Authors: Jung YS, Sharma M, Zweckstetter M
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Membrane protein structure determination using solid-state NMR.
Membrane protein structure determination using solid-state NMR. Related Articles Membrane protein structure determination using solid-state NMR. Methods Mol Biol. 2004;278:403-73 Authors: Watts A, Straus SK, Grage SL, Kamihira M, Lam YH, Zhao X Solid-state NMR is emerging as a method for resolving structural information for large biomolecular complexes, such as membrane-embedded proteins. In principle, there is no molecular weight limit to the use of the approach, although the complexity and volume of data is still outside complete assignment...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] Protein NMR structure determination with automated NOE assignment using the new softw
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. Related Articles Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol. 2002 May 24;319(1):209-27 Authors: Herrmann T, Güntert P, Wüthrich K Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Membrane protein structure determination by solid state NMR.
Membrane protein structure determination by solid state NMR. Related Articles Membrane protein structure determination by solid state NMR. Nat Prod Rep. 1999 Aug;16(4):419-23 Authors: Watts A, Burnett IJ, Glaubitz C, Gröbner G, Middleton DA, Spooner PJ, Watts JA, Williamson PT
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] Determination of membrane protein structure by rotational resonance NMR: bacteriorhod
Determination of membrane protein structure by rotational resonance NMR: bacteriorhodopsin. Related Articles Determination of membrane protein structure by rotational resonance NMR: bacteriorhodopsin. Science. 1991 Feb 15;251(4995):783-6 Authors: Creuzet F, McDermott A, Gebhard R, van der Hoef K, Spijker-Assink MB, Herzfeld J, Lugtenburg J, Levitt MH, Griffin RG Rotationally resonant magnetization exchange, a new nuclear magnetic resonance (NMR) technique for measuring internuclear distances between like spins in solids, was used to determine...
nmrlearner Journal club 0 08-21-2010 11:16 PM
Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bo
Simultaneous Structure and Dynamics of a Membrane Protein using REDCRAFT: Membrane-bound form of Pf1 Coat Protein Publication year: 2010 Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 30 July 2010</br> Paul, Shealy , Mikhail, Simin , Sang Ho, Park , Stanley J., Opella , Homayoun, Valafar</br> A strategy for simultaneous study of the structure and internal dynamics of a membrane protein is described using the REDCRAFT algorithm. The membrane-bound form of the Pf1 major coat protein (mbPf1) was used as an example. First, synthetic data is...
nmrlearner Journal club 0 08-15-2010 12:32 AM


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 05:33 AM.


Map