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 05-01-2018, 10:20 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 Resolving biomolecular motion and interactions by R2 and R1? Relaxation Dispersion NMR.

Resolving biomolecular motion and interactions by R2 and R1? Relaxation Dispersion NMR.

Related Articles Resolving biomolecular motion and interactions by R2 and R1? Relaxation Dispersion NMR.

Methods. 2018 Apr 25;:

Authors: Walinda E, Morimoto D, Sugase K

Abstract
Among the tools of structural biology, NMR spectroscopy is unique in that it not only derives a static three-dimensional structure, but also provides an atomic-level description of the local fluctuations and global dynamics around this static structure. A battery of NMR experiments is now available to probe the motions of proteins and nucleic acids over the whole biologically relevant timescale from picoseconds to hours. Here we focus on one of these methods, relaxation dispersion, which resolves dynamics on the micro- to millisecond timescale. Key biological processes that occur on this timescale include enzymatic catalysis, ligand binding, and local folding. In other words, relaxation-dispersion-resolved dynamics are often closely related to the function of the molecule and therefore highly interesting to the structural biochemist. With an astounding sensitivity of ~0.5%, the method detects low-population excited states that are invisible to any other biophysical method. The kinetics of the exchange between the ground state and excited states are quantified in the form of the underlying exchange rate, while structural information about the invisible excited state is obtained in the form of its chemical shift. Lastly, the population of the excited state can be derived. This diversity in the information that can be obtained makes relaxation dispersion an excellent method to study the detailed mechanisms of conformational transitions and molecular interactions. Here we describe the two branches of relaxation dispersion, R2 and R1?, discussing their applicability, similarities, and differences, as well as recent developments in pulse sequence design and data processing.


PMID: 29704666 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Journal Highlight: Nuclear magnetic relaxation dispersion of murine tissue for development of T1 (R1) dispersion contrast imaging
Journal Highlight: Nuclear magnetic relaxation dispersion of murine tissue for development of T1 (R1) dispersion contrast imaging http://www.spectroscopynow.com/common/images/thumbnails/160a8525b7b.jpgThe spin–lattice relaxation rate (R1) dispersion of murine tissues from 0.24 mT to 3 T has been assessed using a combination of ex vivo and in vivo spin–lattice relaxation rate measurements on murine tissue. Read the rest at Spectroscopynow.com
nmrlearner General 0 01-02-2018 02:29 AM
[NMR paper] High resolution NMR study of T? magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide.
High resolution NMR study of T? magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--link.aip.org-jhtml-linkto.gif Related Articles High resolution NMR study of T? magnetic relaxation dispersion. IV. Proton relaxation in amino acids and Met-enkephalin pentapeptide. J Chem Phys. 2014 Oct 21;141(15):155101 Authors: Pravdivtsev AN, Yurkovskaya AV, Vieth HM, Ivanov KL Abstract Nuclear Magnetic Relaxation Dispersion...
nmrlearner Journal club 0 10-06-2015 10:39 PM
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation Justin L. Lorieau, John M. Louis and Ad Bax http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2045309/aop/images/medium/ja-2011-045309_0004.gif Journal of the American Chemical Society DOI: 10.1021/ja2045309 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/2aIqfWmdIn4
nmrlearner Journal club 0 08-23-2011 05:30 AM
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation.
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation. Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation. J Am Chem Soc. 2011 Aug 17; Authors: Lorieau JL, Louis JM, Bax A Abstract Biological membranes present a highly fluid environment and integration of proteins within such membranes is itself highly dynamic: proteins diffuse laterally within the plane of the membrane, and rotationally about the normal vector of this plane. We...
nmrlearner Journal club 0 08-19-2011 02:56 PM
Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study
Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study Dmitry M. Korzhnev, Robert M. Vernon, Tomasz L. Religa, Alexandar L. Hansen, David Baker, Alan R. Fersht and Lewis E. Kay http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja203686t/aop/images/medium/ja-2011-03686t_0002.gif Journal of the American Chemical Society DOI: 10.1021/ja203686t http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner Journal club 0 06-29-2011 04:45 AM
Non-Native Interactions in the FF Domain Folding Pathway From an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study.
Non-Native Interactions in the FF Domain Folding Pathway From an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study. Non-Native Interactions in the FF Domain Folding Pathway From an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study. J Am Chem Soc. 2011 Jun 6; Authors: Korzhnev DM, Vernon RM, Religa TL, Hansen AL, Baker D, Fersht AR, Kay LE Several all-helical single-domain proteins have been shown to fold rapidly (us timescale) to a compact...
nmrlearner Journal club 0 06-07-2011 11:05 AM
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins
relaxGUI: a new software for fast and simple NMR relaxation data analysis and calculation of ps-ns and μs motion of proteins Abstract Investigation of protein dynamics on the ps-ns and μs-ms timeframes provides detailed insight into the mechanisms of enzymes and the binding properties of proteins. Nuclear magnetic resonance (NMR) is an excellent tool for studying protein dynamics at atomic resolution. Analysis of relaxation data using model-free analysis can be a tedious and time consuming process, which requires good knowledge of scripting procedures. The software relaxGUI was...
nmrlearner Journal club 0 06-06-2011 12:53 AM
[NMR paper] Analysis of slow interdomain motion of macromolecules using NMR relaxation data.
Analysis of slow interdomain motion of macromolecules using NMR relaxation data. Related Articles Analysis of slow interdomain motion of macromolecules using NMR relaxation data. J Am Chem Soc. 2001 May 2;123(17):3953-9 Authors: Baber JL, Szabo A, Tjandra N The interpretation of NMR relaxation data for macromolecules possessing slow interdomain motions is considered. It is shown how the "extended model-free approach" can be used to analyze (15)N backbone relaxation data acquired at three different field strengths for Xenopus Ca(2+)-ligated...
nmrlearner Journal club 0 11-19-2010 08:32 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 08:34 AM.


Map