NMR paper Seeing the invisible by paramagnetic and diamagnetic NMR.

		BioNMR > Educational resources > Journal club
[NMR paper] Seeing the invisible by paramagnetic and diamagnetic NMR.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-22-2013, 03:09 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,175

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Seeing the invisible by paramagnetic and diamagnetic NMR.

Seeing the invisible by paramagnetic and diamagnetic NMR.

Related Articles Seeing the invisible by paramagnetic and diamagnetic NMR.

Biochem Soc Trans. 2013 Dec 1;41(6):1343-1354

Authors: Clore GM

Abstract
Sparsely populated transient states of proteins and their complexes play an important role in many biological processes including protein-protein and protein-DNA recognition, allostery, conformational selection, induced fit and self-assembly. These states are difficult to study as their low population and transient nature makes them effectively invisible to conventional structural and biophysical techniques. In the present article, I summarize recent NMR developments in our laboratory, including the use of paramagnetic relaxation enhancement, lifetime line broadening and dark-state exchange saturation transfer spectroscopy, that have permitted such sparsely populated states to be detected, characterized and, in some instances, visualized. I illustrate the application of these methods to the elucidation of mechanisms whereby transcription factors locate their specific target sites within an overwhelming sea of non-specific DNA, to the characterization of encounter complexes in protein-protein recognition, to large-scale interdomain motions involved in ligand binding, and to the interaction of monomeric amyloid ?-peptide with the surface of amyloid protofibrils and the internal cavity surface of the chaperonin GroEL.

PMID: 24256222 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Visualizing Side-chains of Invisible Protein Conformers by Solution NMR. Visualizing Side-chains of Invisible Protein Conformers by Solution NMR. Related Articles Visualizing Side-chains of Invisible Protein Conformers by Solution NMR. J Mol Biol. 2013 Nov 7; Authors: Bouvignies G, Vallurupalli P, Kay LE Abstract Sparsely populated and transiently formed protein conformers can play key roles in many biochemical processes. Understanding the structure function paradigm requires, therefore, an atomic resolution description of these rare states. Yet they are difficult to study because they cannot be observed using...	nmrlearner	Journal club	0	11-12-2013 03:52 PM
Visualizing Side-chains of Invisible Protein Conformers by Solution NMR Visualizing Side-chains of Invisible Protein Conformers by Solution NMR Publication date: Available online 8 November 2013 Source:Journal of Molecular Biology</br> Author(s): Guillaume Bouvignies , Pramodh Vallurupalli , Lewis E. Kay</br> Sparsely populated and transiently formed protein conformers can play key roles in many biochemical processes. Understanding the structure function paradigm requires, therefore, an atomic resolution description of these rare states. Yet they are difficult to study because they cannot be observed using standard biophysical...	nmrlearner	Journal club	0	11-08-2013 01:42 PM
Invisible touch: What's the matter? Invisible touch: What's the matter? http://www.spectroscopynow.com/common/images/thumbnails/13f37676ba6.jpgAn explanation as to why we cannot detect 85 percent of the predicted mass of the universe has emerged from fundamental particle research carried out in the 1930s. US physicists have now proposed that dark matter, may be composed of Majorana fermions, which are anapoles with a doughnut-shaped electromagnetic field invisible to any known detector technology. Read the rest at Spectroscopynow.com	nmrlearner	General	0	06-15-2013 08:18 AM
[Question from NMRWiki Q&A forum] Diamagnetic contamination Diamagnetic contamination How to determine diamagnetic contamination in PRE experiments.In what extent it will effect the Gamma2 values? Check if somebody has answered this question on NMRWiki QA forum	nmrlearner	News from other NMR forums	0	12-14-2012 08:57 PM
Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation. Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation. Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation. Protein Sci. 2011 Feb;20(2):229-46 Authors: Clore GM Sparsely populated states of macromolecules, characterized by short lifetimes and high free-energies relative to the predominant ground state, often play a key role in many biological, chemical, and biophysical processes. In this review, we briefly summarize various new developments in NMR...	nmrlearner	Journal club	0	06-04-2011 11:26 AM
Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy. Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy. Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy. J Biomol NMR. 2011 Mar 18; Authors: Bouvignies G, Vallurupalli P, Cordes MH, Hansen DF, Kay LE A method based on the Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated 'invisible' protein states that exchange...	nmrlearner	Journal club	0	03-23-2011 05:41 PM
[NMR paper] Probing copper2+ binding to the prion protein using diamagnetic nickel2+ and 1H NMR: Probing copper2+ binding to the prion protein using diamagnetic nickel2+ and 1H NMR: the unstructured N terminus facilitates the coordination of six copper2+ ions at physiological concentrations. Related Articles Probing copper2+ binding to the prion protein using diamagnetic nickel2+ and 1H NMR: the unstructured N terminus facilitates the coordination of six copper2+ ions at physiological concentrations. J Mol Biol. 2005 Mar 11;346(5):1393-407 Authors: Jones CE, Klewpatinond M, Abdelraheim SR, Brown DR, Viles JH The prion protein (PrP) is a...	nmrlearner	Journal club	0	11-24-2010 11:14 PM
[NMR paper] PASE (PAramagnetic signals enhancement): a new method for NMR study of paramagnetic p PASE (PAramagnetic signals enhancement): a new method for NMR study of paramagnetic proteins. Related Articles PASE (PAramagnetic signals enhancement): a new method for NMR study of paramagnetic proteins. J Magn Reson. 1998 Sep;134(1):154-7 Authors: Bondon A, Mouro C A new method for NMR spectra acquisition of paramagnetic proteins is described, based on the simple use of homonuclear broadband decoupling of the diamagnetic region. Several advantages are associated with this method which was applied to one-dimensional spectra, to 1D...	nmrlearner	Journal club	0	11-17-2010 11:15 PM

« Previous Thread | Next 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