NMR paper An Approach to NMR Assignment of Intrinsically Disordered Proteins.

		BioNMR > Educational resources > Journal club
[NMR paper] An Approach to NMR Assignment of Intrinsically Disordered 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

02-03-2015, 12:16 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,713

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

An Approach to NMR Assignment of Intrinsically Disordered Proteins.

An Approach to NMR Assignment of Intrinsically Disordered Proteins.

An Approach to NMR Assignment of Intrinsically Disordered Proteins.

Chemphyschem. 2015 Jan 30;

Authors: Goradia N, Wiedemann C, Herbst C, Görlach M, Heinemann SH, Ohlenschläger O, Ramachandran R

Abstract
An efficient approach to NMR assignments in intrinsically disordered proteins is presented, making use of the good dispersion of cross peaks observed in [(15) N,(13) C']- and [(13) C',(1) H(N) ]-correlation spectra. The method involves the simultaneous collection of {3D (H)NCO(CAN)H and 3D (HACA)CON(CA)HA} spectra for backbone assignments via sequential H(N) and H(?) correlations and {3D (H)NCO(CACS)HS and 3D (HS)CS(CA)CO(N)H} spectra for side-chain (1) H and (13) C assignments, employing sequential (1) H data acquisitions with direct detection of both the amide and aliphatic protons. The efficacy of the approach for obtaining resonance assignments with complete backbone and side-chain chemical shifts is demonstrated experimentally for the 61-residue [(13) C,(15) N]-labelled peptide of a voltage-gated potassium channel protein of the Kv1.4 channel subunit. The general applicability of the approach for the characterisation of moderately sized globular proteins is also demonstrated.

PMID: 25639453 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
â??CON-CONâ?? assignment strategy for highly flexible intrinsically disordered proteins â??CON-CONâ?? assignment strategy for highly flexible intrinsically disordered proteins Abstract Intrinsically disordered proteins (IDPs) are a class of highly flexible proteins whose characterization by NMR spectroscopy is complicated by severe spectral overlaps. The development of experiments designed to facilitate the sequence-specific assignment procedure is thus very important to improve the tools for the characterization of IDPs and thus to be able to focus on IDPs of increasing size and complexity. Here, we present and describe the...	nmrlearner	Journal club	0	10-21-2014 11:31 PM
New 13C-detected experiments for the assignment of intrinsically disordered proteins New 13C-detected experiments for the assignment of intrinsically disordered proteins Abstract NMR assignment of intrinsically disordered proteins (IDPs) by conventional HN-detected methods is hampered by the small dispersion of the amide protons chemical shifts and exchange broadening of amide proton signals. Therefore several alternative assignment strategies have been proposed in the last years. Attempting to seize that dispersion of 13Câ?² and 15N chemical shifts holds even in IDPs, we recently proposed two 13C-detected experiments to directly...	nmrlearner	Journal club	0	06-19-2014 10:21 PM
[NMR paper] A reduced dimensionality NMR pulse sequence and an efficient protocol for unambiguous assignment in intrinsically disordered proteins. A reduced dimensionality NMR pulse sequence and an efficient protocol for unambiguous assignment in intrinsically disordered proteins. Related Articles A reduced dimensionality NMR pulse sequence and an efficient protocol for unambiguous assignment in intrinsically disordered proteins. J Biomol NMR. 2014 May 23; Authors: Reddy JG, Hosur RV Abstract Resonance assignment in intrinsically disordered proteins poses a great challenge because of poor chemical shift dispersion in most of the nuclei that are commonly monitored....	nmrlearner	Journal club	0	05-24-2014 04:50 PM
[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] Highly efficient NMR assignment of intrinsically disordered proteins: application to B- and T cell receptor domains. Highly efficient NMR assignment of intrinsically disordered proteins: application to B- and T cell receptor domains. Related Articles Highly efficient NMR assignment of intrinsically disordered proteins: application to B- and T cell receptor domains. PLoS One. 2013;8(5):e62947 Authors: Isaksson L, Mayzel M, Saline M, Pedersen A, Rosenlöw J, Brutscher B, Karlsson BG, Orekhov VY Abstract We present an integrated approach for efficient characterization of intrinsically disordered proteins. Batch cell-free expression, fast data acquisition,...	nmrlearner	Journal club	0	05-15-2013 03:12 PM
An assignment of intrinsically disordered regions of proteins based on NMR structures An assignment of intrinsically disordered regions of proteins based on NMR structures January 2013 Publication year: 2013 Source:Journal of Structural Biology, Volume 181, Issue 1</br> </br> Intrinsically disordered proteins (IDPs) do not adopt stable three-dimensional structures in physiological conditions, yet these proteins play crucial roles in biological phenomena. In most cases, intrinsic disorder manifests itself in segments or domains of an IDP, called intrinsically disordered regions (IDRs), but fully disordered IDPs also exist. Although IDRs can be detected as...	nmrlearner	Journal club	0	02-03-2013 10:13 AM
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. Bioinformatics. 2011 Mar 3; Authors: Tamiola K, Mulder FA SUMMARY: We describe here the ncIDP-assign extension for the popular NMR assignment programme SPARKY, which aids in the sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The assignment plugin greatly facilitates the effective matching of a set of...	nmrlearner	Journal club	0	03-05-2011 01:02 PM
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins Abstract Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing 15N, 13Câ?² and 1HN spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially 15N and 13Câ?² spins offer superior chemical shift dispersion in comparison to 13CÎ± and 13CÎ² spins. However, HN-detected experiments...	nmrlearner	Journal club	0	01-29-2011 05:31 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