NMR paper Rapid NMR assignments of proteins using optimized combinatorial selective unlabeling.

		BioNMR > Educational resources > Journal club
[NMR paper] Rapid NMR assignments of proteins using optimized combinatorial selective unlabeling.

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

12-15-2015, 08:09 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

Rapid NMR assignments of proteins using optimized combinatorial selective unlabeling.

Rapid NMR assignments of proteins using optimized combinatorial selective unlabeling.

Rapid NMR assignments of proteins using optimized combinatorial selective unlabeling.

Chembiochem. 2015 Dec 10;

Authors: Atreya HS, Dubey A, Jaipuria G, Kadumuri RV, Vadrevu R

Abstract
A new approach for rapid resonance assignments in proteins based on amino acid selective unlabeling is presented. The method involves choosing a set of multiple amino acid types for selective unlabeling and identifying specific tri-peptides surrounding the labeled residues using two-dimensional (2D) NMR spectra in a combinatorial manner. It is shown that a 2D [15N-1H] HSQC spectrum along with two 2D spectra can yield ~50% assignments directly. The methodology is applicable to deuterated proteins and was applied to two systems: an intrinsically disordered protein (12 kDa) and 29 kDa (268 residues) ?-subunit of Escherichia coli tryptophan synthase, presenting a challenging case with spectral overlaps and missing peaks. Taken together, the method can augment conventional approaches and/or will be useful for applications such as identifying active-site residues, residues involved in ligand binding or protein-protein interactions even prior to complete resonance assignments.

PMID: 26662553 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Amino Acid Selective Unlabeling in Protein NMR Spectroscopy. Amino Acid Selective Unlabeling in Protein NMR Spectroscopy. Related Articles Amino Acid Selective Unlabeling in Protein NMR Spectroscopy. Methods Enzymol. 2015;565:167-189 Authors: Prasanna C, Dubey A, Atreya HS Abstract Three-dimensional structure determination of proteins by NMR requires the acquisition of multidimensional spectra followed by assignment of chemical shifts to the respective nuclei. In order to speed up this process, resonances corresponding to individual amino acid types are often selectively identified...	nmrlearner	Journal club	0	11-19-2015 05:22 PM
[NMR paper] Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide. Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide. Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide. J Biomol NMR. 2015 Mar 28; Authors: Oktaviani NA, Risør MW, Lee YH, Megens RP, de Jong DH, Otten R, Scheek RM, Enghild JJ, Nielsen NC, Ikegami T, Mulder FA Abstract Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by...	nmrlearner	Journal club	0	03-31-2015 07:17 PM
Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide Abstract Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T 1 relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form...	nmrlearner	Journal club	0	03-27-2015 11:59 PM
Amino acid selective unlabeling for sequence specific resonance assignments in proteins Amino acid selective unlabeling for sequence specific resonance assignments in proteins Abstract Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative...	nmrlearner	Journal club	1	03-20-2012 12:42 AM
Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment Abstract Obtaining NMR assignments for slowly tumbling molecules such as detergent-solubilized membrane proteins is often compromised by low sensitivity as well as spectral overlap. Both problems can be addressed by amino-acid specific isotope labeling in conjunction with 15Nâ??1H correlation experiments. In this work an extended combinatorial selective in vitro labeling scheme is proposed that seeks to reduce the number of samples required for assignment. Including three...	nmrlearner	Journal club	0	01-21-2012 06:26 PM
Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR. Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR. Frequency-selective heteronuclear dephasing and selective carbonyl labeling to deconvolute crowded spectra of membrane proteins by magic angle spinning NMR. J Magn Reson. 2011 Mar 17; Authors: Traaseth NJ, Veglia G We present a new method that combines carbonyl-selective labeling with frequency-selective heteronuclear recoupling to resolve the spectral overlap of magic angle spinning (MAS) NMR...	nmrlearner	Journal club	0	04-13-2011 11:57 PM
[NMR paper] A combinatorial selective labeling method for the assignment of backbone amide NMR re A combinatorial selective labeling method for the assignment of backbone amide NMR resonances. Related Articles A combinatorial selective labeling method for the assignment of backbone amide NMR resonances. J Am Chem Soc. 2004 Apr 28;126(16):5020-1 Authors: Parker MJ, Aulton-Jones M, Hounslow AM, Craven CJ A combinatorial selective labeling (CSL) method is presented for the assignment of backbone amide NMR resonances, which has a particular application in the identification of protein-ligand interaction sites. The method builds on the dual...	nmrlearner	Journal club	0	11-24-2010 09:51 PM
[NMR paper] Selective 'unlabeling' of amino acids in fractionally 13C labeled proteins: an approa Selective 'unlabeling' of amino acids in fractionally 13C labeled proteins: an approach for stereospecific NMR assignments of CH3 groups in Val and Leu residues. Related Articles Selective 'unlabeling' of amino acids in fractionally 13C labeled proteins: an approach for stereospecific NMR assignments of CH3 groups in Val and Leu residues. J Biomol NMR. 2001 Mar;19(3):267-72 Authors: Atreya HS, Chary KV A novel methodology for stereospecific NMR assignments of methyl (CH3) groups of Val and Leu residues in fractionally 13C-labeled proteins is...	nmrlearner	Journal club	0	11-19-2010 08:32 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