NMR paper Practical aspects of NMR signal assignment in larger and challenging proteins.

		BioNMR > Educational resources > Journal club
[NMR paper] Practical aspects of NMR signal assignment in larger and challenging 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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

02-19-2014, 03:12 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

Practical aspects of NMR signal assignment in larger and challenging proteins.

Practical aspects of NMR signal assignment in larger and challenging proteins.

Related Articles Practical aspects of NMR signal assignment in larger and challenging proteins.

Prog Nucl Magn Reson Spectrosc. 2014 Apr;78C:47-75

Authors: Frueh DP

Abstract
NMR has matured into a technique routinely employed for studying proteins in near physiological conditions. However, applications to larger proteins are impeded by the complexity of the various correlation maps necessary to assign NMR signals. This article reviews the data analysis techniques traditionally employed for resonance assignment and describes alternative protocols necessary for overcoming challenges in large protein spectra. In particular, simultaneous analysis of multiple spectra may help overcome ambiguities or may reveal correlations in an indirect manner. Similarly, visualization of orthogonal planes in a multidimensional spectrum can provide alternative assignment procedures. We describe examples of such strategies for assignment of backbone, methyl, and nOe resonances. We describe experimental aspects of data acquisition for the related experiments and provide guidelines for preliminary studies. Focus is placed on large folded monomeric proteins and examples are provided for 37, 48, 53, and 81kDa proteins.

PMID: 24534088 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Progress in Nuclear Magnetic Resonance Spectroscopy. Practical aspects of NMR signal assignment in larger and challenging proteins Progress in Nuclear Magnetic Resonance Spectroscopy. Practical aspects of NMR signal assignment in larger and challenging proteins Publication date: Available online 15 December 2013 Source:Progress in Nuclear Magnetic Resonance Spectroscopy</br> Author(s): Dominique P Frueh</br> NMR has matured into a technique routinely employed for studying proteins in near physiological conditions. However, applications to larger proteins are impeded by the complexity of the various correlation maps necessary to assign NMR signals. This article reviews the data analysis...	nmrlearner	Journal club	0	12-15-2013 06:08 PM
Practical aspects of high-sensitivity multidimensional 13C MAS NMR spectroscopy of perdeuterated proteins Practical aspects of high-sensitivity multidimensional 13C MAS NMR spectroscopy of perdeuterated proteins April 2012 Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 217</br> </br> The double nucleus enhanced recoupling (DONER) experiment employs simultaneous irradiation of protons and deuterons to promote spin diffusion processes in a perdeuterated protein. This results in 4–5times higher sensitivity in 2D 13C–13C correlation experiments as compared to PDSD . Here, a quantitative comparison of PDSD, 1H-DARR, 2H-DARR, and 1H+ 2H DONER has been...	nmrlearner	Journal club	0	02-03-2013 10:13 AM
Expanding the utility of NMR restraints with paramagnetic compounds: Background and practical aspects Expanding the utility of NMR restraints with paramagnetic compounds: Background and practical aspects November 2011 Publication year: 2011 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 59, Issue 4</br> </br> Graphical abstract	nmrlearner	Journal club	0	12-15-2012 09:51 AM
Expanding the utility of NMR restraints with paramagnetic compounds: Background and practical aspects Expanding the utility of NMR restraints with paramagnetic compounds: Background and practical aspects November 2011 Publication year: 2011 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 59, Issue 4</br> </br> Graphical abstract	nmrlearner	Journal club	0	12-01-2012 06:10 PM
Practical Aspects of High-Sensitivity Multidimensional 13C MAS NMR Spectroscopy of Perdeuterated Proteins Practical Aspects of High-Sensitivity Multidimensional 13C MAS NMR Spectroscopy of Perdeuterated Proteins Publication year: 2012 Source:Journal of Magnetic Resonance</br> Ümit Akbey, Barth-Jan van Rossum, Hartmut Oschkinat</br> The double nucleus enhanced recoupling (DONER) experiment employs simultaneous irradiation of protons and deuterons to promote spin diffusion processes in a perdeuterated protein. This results in 4-5 times higher sensitivity in 2D 13C-13C correlation experiments as compared to PDSD. Here, a quantitative comparison of PDSD, 1H-DARR, 2H-DARR, and...	nmrlearner	Journal club	0	03-09-2012 09:16 AM
Expanding the utility of NMR restraints with paramagnetic compounds: Background and practical aspects Expanding the utility of NMR restraints with paramagnetic compounds: Background and practical aspects Publication year: 2011 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 59, Issue 4</br> Julia Koehler, Jens Meiler</br> Graphical Abstract http://ars.sciencedirect.com/content/image/1-s2.0-S0079656511000410-fx1.jpg Graphical abstract Highlights	nmrlearner	Journal club	0	03-09-2012 09:16 AM
Practical Aspects of High-Sensitivity MultidimensionalC MAS NMR Spectroscopy of Perdeuterated Proteins Practical Aspects of High-Sensitivity MultidimensionalC MAS NMR Spectroscopy of Perdeuterated Proteins Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 1 March 2012</br> ÜmitAkbey, Barth-Janvan Rossum, Hartmut*Oschkinat</br> Thedouble nucleus enhanced recoupling(DONER) experiment employs simultaneous irradiation of protons and deuterons to promote spin diffusion processes in a perdeuterated protein. This results in 4-5 times higher sensitivity in 2DC-C correlation experiments as compared to PDSD.Here, a quantitative comparison of PDSD,H-DARR,H-DARR,...	nmrlearner	Journal club	0	03-01-2012 11:03 PM
5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion 5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion Abstract Two novel 5D NMR experiments (CACONCACO, NCOCANCO) for backbone assignment of disordered proteins are presented. The pulse sequences exploit relaxation properties of the unstructured proteins and combine the advantages of 13C-direct detection, non-uniform sampling, and longitudinal relaxation optimization to maximize the achievable resolution and minimize the experimental time. The pulse sequences were successfully tested on the sample of partially disordered delta...	nmrlearner	Journal club	0	03-22-2011 07:32 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