NMR paper Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

		BioNMR > Educational resources > Journal club
[NMR paper] Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

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

07-12-2017, 12:48 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

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

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

Related Articles Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory.

J Am Chem Soc. 2017 Jul 10;:

Authors: Pritišanac I, Degiacomi MT, Alderson TR, Carneiro MG, Ab E, Siegal G, Baldwin AJ

Abstract
Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

PMID: 28691806 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory Iva Pritis?anac, Matteo T. Degiacomi, T. Reid Alderson, Marta G. Carneiro, Eiso AB, Gregg Siegal and Andrew J. Baldwin http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.6b11358/20170710/images/medium/ja-2016-11358e_0008.gif Journal of the American Chemical Society DOI: 10.1021/jacs.6b11358 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/VuC8AlNsrfs	nmrlearner	Journal club	0	07-11-2017 09:20 AM
[NMR paper] Bringing Dynamic Molecular Machines into Focus by Methyl-TROSY NMR. Bringing Dynamic Molecular Machines into Focus by Methyl-TROSY NMR. Related Articles Bringing Dynamic Molecular Machines into Focus by Methyl-TROSY NMR. Annu Rev Biochem. 2014 Jun 2;83:291-315 Authors: Rosenzweig R, Kay LE Abstract Large macromolecular assemblies, so-called molecular machines, are critical to ensuring proper cellular function. Understanding how proper function is achieved at the atomic level is crucial to advancing multiple avenues of biomedical research. Biophysical studies often include X-ray diffraction and...	nmrlearner	Journal club	0	06-07-2014 07:12 PM
Journal Highlight: Automatic assignment of 1H-NMR spectra of small molecules Journal Highlight: Automatic assignment of 1H-NMR spectra of small molecules http://www.spectroscopynow.com/common/images/thumbnails/1426b18dc06.jpgA novel data-evaluation procedure for the automatic atom to peak or multiplet assignment of 1H-NMR spectra of small molecules has been developed using a fast and robust expert system. Read the rest at Spectroscopynow.com	nmrlearner	General	0	11-18-2013 10:42 PM
TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra Abstract While NMR studies of proteins typically aim at structure, dynamics or interactions, resonance assignments represent in almost all cases the initial step of the analysis. With increasing complexity of the NMR spectra, for example due to decreasing extent of ordered structure, this task often becomes both difficult and time-consuming, and the recording of high-dimensional data with high-resolution may be essential. Random sampling of the evolution time space,...	nmrlearner	Journal club	0	07-20-2012 11:13 PM
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy Abstract Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ~1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic...	nmrlearner	Journal club	0	09-26-2011 06:42 AM
[NMR paper] A random graph approach to NMR sequential assignment. A random graph approach to NMR sequential assignment. Related Articles A random graph approach to NMR sequential assignment. J Comput Biol. 2005 Jul-Aug;12(6):569-83 Authors: Bailey-Kellogg C, Chainraj S, Pandurangan G Nuclear magnetic resonance (NMR) spectroscopy allows scientists to study protein structure, dynamics and interactions in solution. A necessary first step for such applications is determining the resonance assignment, mapping spectral data to atoms and residues in the primary sequence. Automated resonance assignment algorithms...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Use of graph theory for secondary structure recognition and sequential assignment in Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: application to HU protein from Bacillus stearothermophilus. Related Articles Use of graph theory for secondary structure recognition and sequential assignment in heteronuclear (13C, 15N) NMR spectra: application to HU protein from Bacillus stearothermophilus. Biopolymers. 1996 Nov;39(5):691-707 Authors: van Geerestein-Ujah EC, Mariani M, Vis H, Boelens R, Kaptein R A computer-assisted procedure, based upon a branch of...	nmrlearner	Journal club	0	08-22-2010 02:20 PM
[NMR paper] Graph-theoretical assignment of secondary structure in multidimensional protein NMR s Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: application to the lac repressor headpiece. Related Articles Graph-theoretical assignment of secondary structure in multidimensional protein NMR spectra: application to the lac repressor headpiece. J Biomol NMR. 1995 Jul;6(1):67-78 Authors: van Geerestein-Ujah EC, Slijper M, Boelens R, Kaptein R A novel procedure is presented for the automatic identification of secondary structures in proteins from their corresponding NOE data. The method uses a branch...	nmrlearner	Journal club	0	08-22-2010 03:41 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