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 02-21-2007, 04:52 PM
Junior Member
 
Join Date: Jul 2005
Posts: 7
Points: 104, Level: 2
Points: 104, Level: 2 Points: 104, Level: 2 Points: 104, Level: 2
Level up: 8%, 46 Points needed
Level up: 8% Level up: 8% Level up: 8%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 104
Downloads: 0
Uploads: 0
Default Structural biology: Molecular machinery in action

News and Views


Nature 445, 609 (8 February 2007) | doi:10.1038/nature05566; Published online 21 January 2007

Structural biology: Molecular machinery in action


Ad Bax and Dennis A. Torchia

Abstract

Nuclear magnetic resonance is the best way to study motion in proteins, but it could be applied only to small systems. This limitation has been overcome to reveal the dynamics of a large protein complex.



THE ORIGINAL PAPER is here!!



Nature 445, 618-622 (8 February 2007) | doi:10.1038/nature05512; Received 28 July 2006; Accepted 6 December 2006; Published online 21 January 2007

Quantitative dynamics and binding studies of the 20S proteasome by NMR

Remco Sprangers and Lewis E. Kay

Figure


Departments of Biochemistry, Medical Genetics and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada

Abstract

The machinery used by the cell to perform essential biological processes is made up of large molecular assemblies. One such complex, the proteasome, is the central molecular machine for removal of damaged and misfolded proteins from the cell. Here we show that for the 670-kilodalton 20S proteasome core particle it is possible to overcome the molecular weight limitations that have traditionally hampered quantitative nuclear magnetic resonance (NMR) spectroscopy studies of such large systems. This is achieved by using an isotope labelling scheme where isoleucine, leucine and valine methyls are protonated in an otherwise highly deuterated background in concert with experiments that preserve the lifetimes of the resulting NMR signals. The methodology has been applied to the 20S core particle to reveal functionally important motions and interactions by recording spectra on complexes with molecular weights of up to a megadalton. Our results establish that NMR spectroscopy can provide detailed insight into supra-molecular structures over an order of magnitude larger than those routinely studied using methodology that is generally applicable.
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR tweet] Frontiers of Nuclear Magnetic Resonance in Molecular Biology (UCLA Symposia on Molecular and Cellular Biology, ... http://amzn.to/hLhUP1
Frontiers of Nuclear Magnetic Resonance in Molecular Biology (UCLA Symposia on Molecular and Cellular Biology, ... http://amzn.to/hLhUP1 Published by Caritaxg55 (Carita Calvano) on 2011-04-19T22:01:24Z Source: Twitter
nmrlearner Twitter NMR 0 04-19-2011 10:11 PM
[NMR900 blog] NMR paper in Nature Structural & Molecular Biology
NMR paper in Nature Structural & Molecular Biology L.A. Freiburger, O.M. Baettig, T. Sprules, A.M. Berghuis, K. Auclair, A.K. Mittermaier, "Competing allosteric mechanisms modulate substrate binding in a dimeric enzyme," Nature Structural & Molecular Biology (2011) online. http://dx.doi.org/10.1038/nsmb.1978 https://blogger.googleusercontent.com/tracker/8663203727601106205-794484937251380301?l=nmr900.blogspot.com Read complete story on NMR900 blog
nmrlearner News from NMR blogs 0 02-11-2011 08:31 AM
Postdoctoral Position in Molecular and Structural Biology, Chemistry Department, Univ
Postdoctoral Position in Molecular and Structural Biology, Chemistry Department, University of Calif - University of California Davis - Davis, CA, United States A postdoctoral position in molecular and structural biology is available immediately to study structure-activity relationships (SAR by NMR) and drug design for the microbial protein FtsZ, an important target for antibiotics drugs. The goal of the study will be to clone and prepare functional fragments and mutants of FtsZ that will be used in NMR s... More...
nmrlearner Job marketplace 0 08-26-2010 04:54 AM
Postdoctoral Position in Molecular and Structural Biology
Postdoctoral Position in Molecular and Structural Biology A postdoctoral position in molecular and structural biology is available immediately to study structure-activity relationships (SAR by NMR) and drug design for the microbial protein FtsZ, an important target for antibiotic drugs. The goal of the study will be to clone and prepare functional fragments and mutants of FtsZ that will be used in NMR structural studies of protein-drug complexes. Specific experience in molecular biology/cloning techniques, site-specific mutagenesis, expression and p… More...
nmrlearner Job marketplace 0 08-19-2010 02:44 AM
Institute of Genetics and Molecular and Cellular Biology
Sorry everybody, I posted this in the wrong section. The thread I was actually trying to make can be found here: http://www.bionmr.com/board/showthread.php?p=848
Louis Journal club 0 09-17-2008 08:39 PM
Protein NMR Techniques (Methods in Molecular Biology) - David G. Reid (1997)
Protein NMR Techniques (Methods in Molecular Biology) Edited by David G. Reid (1997) Amazon book description First Sentence: There are numerous modern, and older but nonetheless valuable, textbooks that should be consulted for an introduction to the basic principles and practices of nuclear magnetic resonance (NMR) in chemistry (including volumes devoted primarily to exchanging systems, nuclei less familiar to the organic chemist, and solids), biochemistry, including parts of recent volumes in this series, and drug discovery. Book Info: 419 pages. SmithKline Beecham...
Shannon Books 0 08-20-2008 08:51 PM
Postdoctoral Position in Molecular Medicine and Structural Biology - University of Iowa
Hello. The University of Iowa are looking for a post-doc (advertised on naturejobs.com) """ Description The Department of Anatomy and Cell Biology and Center for Gene Therapy at the University of Iowa is looking for Postdoctoral Scholar interested in pursuing a career investing molecular mechanisms of redox-mediated neurodegenerative diseases and the development of pharmacologic and gene based therapies. Successful candidates should have a strong biochemical background in protein structure including: NMR, X-ray crystallography, and/or Mass Spectrometry. Projects will focus on...
sharim Job marketplace 0 08-11-2008 12:12 PM
NMR in Molecular Biology 2005, ESF Conference
ESF Research Conference on NMR in Molecular Biology, 2005 EuroConference on Structural Genomics: Structure, Dynamics and Interactions of Biomolecules Backagården, Höör (near Malmö), Sweden, 20-25 August 2005 NMR has become an important tool in molecular and structural biology. From the new information obtained in the total genomic sequences of a number of organisms, it is clear that structural biology has to deal with not only the three-dimensional structures of
nmrlearner Conferences 0 04-07-2005 07:15 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 04:36 AM.


Map