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 11-29-2014, 04:09 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,906
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 NMR Studies of Dynamic Biomolecular Conformational Ensembles

NMR Studies of Dynamic Biomolecular Conformational Ensembles


Publication date: Available online 28 November 2014
Source:Progress in Nuclear Magnetic Resonance Spectroscopy

Author(s): Dennis A. Torchia

Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: “Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?” This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA.
Graphical abstract








More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Proc Natl Acad Sci U S A. 2014 Oct 13; Authors: Baxa MC, Haddadian EJ, Jumper JM, Freed KF, Sosnick TR Abstract The loss of conformational entropy is a major contribution in the thermodynamics of protein folding. However, accurate determination of the quantity...
nmrlearner Journal club 0 10-15-2014 10:58 AM
NMR-Based Conformational Ensembles Explain pH-Gated Opening and Closing of OmpG Channel
NMR-Based Conformational Ensembles Explain pH-Gated Opening and Closing of OmpG Channel Tiandi Zhuang, Christina Chisholm, Min Chen and Lukas K. Tamm http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja408206e/aop/images/medium/ja-2013-08206e_0011.gif Journal of the American Chemical Society DOI: 10.1021/ja408206e http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/UcxM_KhEqyU
nmrlearner Journal club 0 10-01-2013 11:15 PM
[NMR paper] NMR-based Conformational Ensembles Explain pH-Gated Opening and Closing of OmpG Channel.
NMR-based Conformational Ensembles Explain pH-Gated Opening and Closing of OmpG Channel. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles NMR-based Conformational Ensembles Explain pH-Gated Opening and Closing of OmpG Channel. J Am Chem Soc. 2013 Sep 10; Authors: Zhuang T, Chisholm C, Chen M, Tamm LK Abstract The outer membrane protein G (OmpG) is a monomeric 33 kDa 14-stranded ?-barrel membrane protein functioning as a non-specific porin for the uptake of...
nmrlearner Journal club 0 09-12-2013 11:02 PM
[NMR paper] Conformational Ensembles in GPCR Activation.
Conformational Ensembles in GPCR Activation. Related Articles Conformational Ensembles in GPCR Activation. Cell. 2013 Jan 31;152(3):385-6 Authors: Vardy E, Roth BL Abstract Recent advances in G-protein-coupled receptor structural biology have provided only limited insight into the active conformations of these key signaling molecules. A paper from Nygaard et*al. reveals the dynamic nature of GPCRs along the activation pathway by complementing NMR experiments with ultralong-timescale molecular dynamics simulations.
nmrlearner Journal club 0 02-05-2013 09:51 PM
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles Abstract The combination of the wide availability of protein backbone and side-chain NMR chemical shifts with advances in understanding of their relationship to protein structure makes these parameters useful for the assessment of structural-dynamic protein models. A new chemical shift predictor (PPM) is introduced, which is solely based on physicalâ??chemical contributions to the chemical shifts for both the protein backbone and methyl-bearing amino-acid side chains. To...
nmrlearner Journal club 0 09-15-2012 09:04 AM
[NMR paper] Conformational and dynamic differences between N-ras P21 bound to GTPgammaS and to GM
Conformational and dynamic differences between N-ras P21 bound to GTPgammaS and to GMPPNP as studied by NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Conformational and dynamic differences between N-ras P21 bound to GTPgammaS and to GMPPNP as studied by NMR. Biochemistry. 1997 Apr 22;36(16):5045-52 Authors: Hu JS, Redfield AG Heteronuclear-edited proton-detected NMR methods are used to study the nucleotide-dependent conformational changes between the GMPPNP form of human N-ras P21...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] Conformational studies of microcystin-LR using NMR spectroscopy and molecular dynamic
Conformational studies of microcystin-LR using NMR spectroscopy and molecular dynamics calculations. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Conformational studies of microcystin-LR using NMR spectroscopy and molecular dynamics calculations. Biochemistry. 1996 Mar 12;35(10):3197-205 Authors: Trogen GB, Annila A, Eriksson J, Kontteli M, Meriluoto J, Sethson I, Zdunek J, Edlund U NMR spectroscopy in aqueous and dimethyl sulfoxide/water solutions is used to determine the...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] NMR characterization of partially folded and unfolded conformational ensembles of pro
NMR characterization of partially folded and unfolded conformational ensembles of proteins. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles NMR characterization of partially folded and unfolded conformational ensembles of proteins. Biopolymers. 1999;51(3):191-207 Authors: Barbar E Studies of unfolded and partially folded proteins provide important insight into the initiation and process of protein folding. This review focuses on the...
nmrlearner Journal club 0 08-21-2010 04:03 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 12:44 PM.


Map