NMR paper Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.

		BioNMR > Educational resources > Journal club
[NMR paper] Cobalt-based paramagnetic probe to study RNA-protein interactions by 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

03-07-2017, 08:54 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,178

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

Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.

Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.

Related Articles Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.

J Inorg Biochem. 2017 Feb 24;170:202-208

Authors: Seebald LM, DeMott CM, Ranganathan S, Asare-Okai PN, Glazunova A, Chen A, Shekhtman A, Royzen M

Abstract
Paramagnetic resonance enhancement (PRE) is an NMR technique that allows studying three-dimensional structures of RNA-protein complexes in solution. RNA strands are typically spin labeled using nitroxide reagents, which provide minimal perturbation to the native structure. The current work describes an alternative approach, which is based on a Co(2+)-based probe that can be covalently attached to RNA in the vicinity of the protein's binding site using 'click' chemistry. Similar to nitroxide spin labels, the transition metal based probe is capable of attenuating NMR signal intensities from protein residues localized

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR Publication date: Available online 24 February 2017 Source:Journal of Inorganic Biochemistry</br> Author(s): Leah M. Seebald, Christopher M. DeMott, Srivathsan Ranganathan, Papa Nii Asare Okai, Anastasia Glazunova, Alan Chen, Alexander Shekhtman, Maksim Royzen</br> Paramagnetic resonance enhancement (PRE) is an NMR technique that allows studying three-dimensional structures of RNA-protein complexes in solution. RNA strands are typically spin labeled using nitroxide reagents,...	nmrlearner	Journal club	0	02-25-2017 06:21 AM
An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe. An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe. An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe. J Biomol NMR. 2011 Sep 17; Authors: Saio T, Ogura K, Shimizu K, Yokochi M, Burke TR, Inagaki F Abstract A nuclear magnetic resonance-based ligand screening strategy utilizing a paramagnetic lanthanide probe is presented. By fixing a paramagnetic lanthanide ion to a target protein, a pseudo-contact shift (PCS) and a paramagnetic relaxation...	nmrlearner	Journal club	0	09-20-2011 03:10 PM
An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe Abstract A nuclear magnetic resonance-based ligand screening strategy utilizing a paramagnetic lanthanide probe is presented. By fixing a paramagnetic lanthanide ion to a target protein, a pseudo-contact shift (PCS) and a paramagnetic relaxation enhancement (PRE) can be observed for both the target protein and its bound ligand. Based on PRE and PCS information, the bound ligand is then screened from the compound library and the structure of the ligandâ??protein complex is determined. PRE is an...	nmrlearner	Journal club	0	09-20-2011 05:02 AM
[NMR paper] Oxygen as a paramagnetic probe of membrane protein structure by cysteine mutagenesis Oxygen as a paramagnetic probe of membrane protein structure by cysteine mutagenesis and (19)F NMR spectroscopy. Related Articles Oxygen as a paramagnetic probe of membrane protein structure by cysteine mutagenesis and (19)F NMR spectroscopy. J Am Chem Soc. 2002 Feb 27;124(8):1778-81 Authors: Luchette PA, Prosser RS, Sanders CR Oxygen solubility increases toward the hydrophobic interior of membranes. Using NMR, this O(2) solubility gradient gives rise to an exquisite range of position-dependent paramagnetic effects at partial pressures of 100...	nmrlearner	Journal club	0	11-24-2010 08:49 PM
[NMR paper] Probing the surface of a sweet protein: NMR study of MNEI with a paramagnetic probe. Probing the surface of a sweet protein: NMR study of MNEI with a paramagnetic probe. Related Articles Probing the surface of a sweet protein: NMR study of MNEI with a paramagnetic probe. Protein Sci. 2001 Aug;10(8):1498-507 Authors: Niccolai N, Spadaccini R, Scarselli M, Bernini A, Crescenzi O, Spiga O, Ciutti A, Di Maro D, Bracci L, Dalvit C, Temussi PA The design of safe sweeteners is very important for people who are affected by diabetes, hyperlipemia, and caries and other diseases that are linked to the consumption of sugars. Sweet...	nmrlearner	Journal club	0	11-19-2010 08:44 PM
[NMR paper] Paramagnetic NMR Spectroscopy of Cobalt(II) and Copper(II) Derivatives of Pseudomonas Paramagnetic NMR Spectroscopy of Cobalt(II) and Copper(II) Derivatives of Pseudomonas aeruginosa His46Asp Azurin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Paramagnetic NMR Spectroscopy of Cobalt(II) and Copper(II) Derivatives of Pseudomonas aeruginosa His46Asp Azurin. Inorg Chem. 1997 Sep 24;36(20):4567-4570 Authors: Vila AJ, Ramirez BE, Di Bilio AJ, Mizoguchi TJ, Richards JH, Gray HB NMR spectra of paramagnetic Co(II) and Cu(II) derivatives of Pseudomonas aeruginosa His46Asp...	nmrlearner	Journal club	0	08-22-2010 05:08 PM
[NMR paper] Paramagnetic cobalt and nickel derivatives of Alcaligenes denitrificans azurin and it Paramagnetic cobalt and nickel derivatives of Alcaligenes denitrificans azurin and its M121Q mutant. A 1H NMR study. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Paramagnetic cobalt and nickel derivatives of Alcaligenes denitrificans azurin and its M121Q mutant. A 1H NMR study. Biochemistry. 1996 Feb 13;35(6):1810-9 Authors: Salgado J, JimÃ©nez HR, Moratal JM, Kroes S, Warmerdam GC, Canters GW Using cobalt or nickel to replace copper in native azurin allows one to fingerprint the...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[NMR paper] 1H-NMR study of a cobalt-substituted blue copper protein: Pseudomonas aeruginosa Co(I 1H-NMR study of a cobalt-substituted blue copper protein: Pseudomonas aeruginosa Co(II)-azurin. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles 1H-NMR study of a cobalt-substituted blue copper protein: Pseudomonas aeruginosa Co(II)-azurin. Eur J Biochem. 1995 Jul 15;231(2):358-69 Authors: Salgado J, JimÃ©nez HR, Donaire A, Moratal JM Substitution of copper by cobalt in blue copper proteins gives a paramagnetic metalloderivative...	nmrlearner	Journal club	0	08-22-2010 03:50 AM

« 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