NMR paper Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

		BioNMR > Educational resources > Journal club
[NMR paper] Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

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

09-03-2014, 11:44 AM

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

Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

Related Articles Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

Magn Reson Chem. 2014 Sep 1;

Authors: Reddy JG, Kumar D, Hosur RV

Abstract
Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments - (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH - which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins. Copyright © 2014 John Wiley & Sons, Ltd.

PMID: 25178811 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] High-dimensionality (13)C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins. High-dimensionality (13)C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins. Related Articles High-dimensionality (13)C direct-detected NMR experiments for the automatic assignment of intrinsically disordered proteins. J Biomol NMR. 2013 Nov 8; Authors: Bermel W, Felli IC, Gonnelli L, Ko?mi?ski W, Piai A, Pierattelli R, Zawadzka-Kazimierczuk A Abstract We present three novel exclusively heteronuclear 5D (13)C direct-detected NMR experiments, namely (H(N-flip)N)CONCACON, (HCA)CONCACON and...	nmrlearner	Journal club	0	11-11-2013 01:30 AM
[NMR paper] Reduced Dimensionality tailored HN(C)N Experiments for Facile Backbone Resonance Assignment of Proteins through Unambiguous Identification of Sequential HSQC Peaks Reduced Dimensionality tailored HN(C)N Experiments for Facile Backbone Resonance Assignment of Proteins through Unambiguous Identification of Sequential HSQC Peaks Publication date: Available online 8 October 2013 Source:Journal of Magnetic Resonance</br> Author(s): Dinesh Kumar</br> Two novel reduced dimensionality (RD) tailored HN(C)N experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments -referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH- exploit the linear combination of...	nmrlearner	Journal club	0	10-09-2013 05:31 AM
[NMR paper] Reduced dimensionality (4,3)D-hnCOCANH experiment: an efficient backbone assignment tool for NMR studies of proteins. Reduced dimensionality (4,3)D-hnCOCANH experiment: an efficient backbone assignment tool for NMR studies of proteins. Reduced dimensionality (4,3)D-hnCOCANH experiment: an efficient backbone assignment tool for NMR studies of proteins. J Struct Funct Genomics. 2013 Aug 27; Authors: Kumar D Abstract	nmrlearner	Journal club	0	08-29-2013 01:53 PM
Reduced dimensionality 3D HNCAN for unambiguous HN, CA and N assignment in proteins Reduced dimensionality 3D HNCAN for unambiguous HN, CA and N assignment in proteins Publication year: 2012 Source:Journal of Magnetic Resonance</br> Manoj Kumar Rout, Pushpa Mishra, Hanudatta S. Atreya, Ramakrishna V. Hosur</br> We present here an improvisation of HNN (Panchal, Bhavesh et al., 2001) called RD 3D HNCAN for backbone (HN, CA and 15N) assignment in both folded and unfolded proteins. This is a reduced dimensionality experiment which employs CA chemical shifts to improve dispersion. Distinct positive and negative peak patterns of various triplet segments...	nmrlearner	Journal club	0	03-09-2012 09:16 AM
Efficient sequential assignments in proteins with reduced dimensionality 3D HN(CA)NH Efficient sequential assignments in proteins with reduced dimensionality 3D HN(CA)NH Abstract We present reduced dimensionality (RD) 3D HN(CA)NH for efficient sequential assignment in proteins. The experiment correlates the 15N and 1H chemical shift of a residue (â??iâ??) with those of its immediate N-terminal (i â?? 1) and C-terminal (i + 1) neighbors and provides four-dimensional chemical shift correlations rapidly with high resolution. An assignment strategy is presented which combines the correlations observed in this experiment with amino acid type information obtained from 3D ...	nmrlearner	Journal club	0	01-09-2012 08:08 AM
Aliasing in reduced dimensionality NMR spectra: (3,2)D HNHA and (4,2)D HN(COCA)NH experiments as examples Aliasing in reduced dimensionality NMR spectra: (3,2)D HNHA and (4,2)D HN(COCA)NH experiments as examples Abstract Reduced dimensionality NMR spectra usually require very large spectral widths in the shared dimension. In this paper we show that aliasing can be introduced in reduced dimensionality NMR spectra either to decrease the acquisition time or increase the resolution of the experiments without losing information. The gains of introducing aliasing are illustrated with two examples, the (3,2)D HNHA and the (4,2)D HN(COCA)NH experiments. In both cases a reduction of the spectral...	nmrlearner	Journal club	0	01-09-2011 12:46 PM
[NMR paper] NMR analysis of in vitro-synthesized proteins without purification: a high-throughput NMR analysis of in vitro-synthesized proteins without purification: a high-throughput approach. Related Articles NMR analysis of in vitro-synthesized proteins without purification: a high-throughput approach. FEBS Lett. 2002 Jul 31;524(1-3):159-62 Authors: Guignard L, Ozawa K, Pursglove SE, Otting G, Dixon NE A cell-free protein expression system was established that provides protein samples of adequate concentration and purity for direct NMR analysis. The Escherichia coli peptidyl-prolyl cis-trans isomerase PpiB was expressed in this system...	nmrlearner	Journal club	0	11-24-2010 08:58 PM
[NMR paper] Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignm Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment. Related Articles Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment. Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8009-14 Authors: Szyperski T, Yeh DC, Sukumaran DK, Moseley HN, Montelione GT A suite of reduced-dimensionality (13)C,(15)N,(1)H-triple-resonance NMR experiments is presented for rapid and complete protein resonance assignment. Even when using short measurement times, these experiments allow one to retain...	nmrlearner	Journal club	0	11-24-2010 08:49 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