NMR paper A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.

		BioNMR > Educational resources > Journal club
[NMR paper] A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.

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

11-14-2014, 08:33 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,188

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

A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.

A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.

Related Articles A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.

Proteins. 2014 Nov 12;

Authors: Rossi P, Shi L, Liu G, Barbieri CM, Lee HW, Grant TD, Luft JR, Xiao R, Acton TB, Snell EH, Montelione GT, Baker D, Lange OF, Sgourakis NG

Abstract
Oligomeric proteins are important targets for structure determination in solution. While in most cases the fold of individual subunits can be determined experimentally, or predicted by homology-based methods, protein-protein interfaces are challenging to determine de novo using conventional NMR structure determination protocols. Here we focus on a member of the bet-V1 superfamily, Aha1 from Colwellia psychrerythraea. This family displays a broad range of crystallographic interfaces none of which can be reconciled with the NMR and SAXS data collected for Aha1. Unlike conventional methods relying on a dense network of experimental restraints, the sparse data are used to limit conformational search during optimization of a physically realistic energy function. This work highlights a new approach for studying minor conformational changes due to structural plasticity within a single dimeric interface in solution. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

PMID: 25388768 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Structure-based drug design: NMR-based approach for ligand-protein interactions. Structure-based drug design: NMR-based approach for ligand-protein interactions. Related Articles Structure-based drug design: NMR-based approach for ligand-protein interactions. Drug Discov Today Technol. 2006;3(3):241-5 Authors: Zhang X, Tang H, Ye C, Liu M Abstract The realization of the powerfulness in analyzing ligand-protein interactions at the atomic resolution has made NMR techniques increasingly attractive in drug discovery and development. With some significant new method developments during the past few years,...	nmrlearner	Journal club	0	07-06-2014 08:28 PM
[NMR paper] Using a Fragment-Based Approach To Target Protein-Protein Interactions. Using a Fragment-Based Approach To Target Protein-Protein Interactions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2250-98-WileyOnlineLibrary-Button_120x27px_FullText.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-2251-04-WileyOnlineLibrary-Button_120x27px_FullTextFree.gif Related Articles Using a Fragment-Based Approach To Target Protein-Protein Interactions. Chembiochem. 2013 Jan 23; Authors: Scott DE, Ehebauer MT, Pukala T, Marsh M, Blundell TL, Venkitaraman AR, Abell C, Hyvönen M ...	nmrlearner	Journal club	0	02-03-2013 10:19 AM
[BMNRC community] CS-ROSETTA: System for chemical shifts based protein structure prediction using ROSETTA CS-ROSETTA: System for chemical shifts based protein structure prediction using ROSETTA http://spin.niddk.nih.gov/bax/ http://condor.bmrb.wisc.edu/bbee/rosetta/	nmrlearner	News from other NMR forums	0	07-12-2011 08:26 PM
Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements. Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements. Rapid identification of protein-protein interfaces for the construction of a complex model based on multiple unassigned signals by using time-sharing NMR measurements. J Struct Biol. 2011 Apr 9; Authors: Kodama Y, Reese ML, Shimba N, Ono K, Kanamori E, Dötsch V, Noguchi S, Fukunishi Y, Suzuki EI, Shimada I, Takahashi H Protein-protein interactions are necessary for various cellular...	nmrlearner	Journal club	0	04-20-2011 07:15 PM
[NMR paper] NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: implications for protein folding initiation. Related Articles NMR and SAXS characterization of the denatured state of the chemotactic protein CheY: implications for protein folding initiation. Protein Sci. 2001 Jun;10(6):1100-12 Authors: Garcia P, Serrano L, Durand D, Rico M, Bruix M The denatured state of a double mutant of the chemotactic protein CheY (F14N/V83T) has been analyzed in the presence of 5 M urea, using small angle X-ray scattering (SAXS) and...	nmrlearner	Journal club	0	11-19-2010 08:32 PM
[NMR paper] MS/NMR: a structure-based approach for discovering protein ligands and for drug desig MS/NMR: a structure-based approach for discovering protein ligands and for drug design by coupling size exclusion chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. Related Articles MS/NMR: a structure-based approach for discovering protein ligands and for drug design by coupling size exclusion chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy. Anal Chem. 2001 Feb 1;73(3):571-81 Authors: Moy FJ, Haraki K, Mobilio D, Walker G, Powers R, Tabei K, Tong H, Siegel MM A protocol is described...	nmrlearner	Journal club	0	11-19-2010 08:32 PM
[NMR paper] An approach to protein homology modelling based on an ensemble of NMR structures: app An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein. Related Articles An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein. Protein Eng. 1995 Jul;8(7):615-25 Authors: Adzhubei AA, Laughton CA, Neidle S A new approach has been developed to reduce multiple protein structures obtained from NMR structure analysis to a smaller number of representative structures which still reflect the structural diversity of...	nmrlearner	Journal club	0	08-22-2010 03:41 AM
NMR primer: an HSQC-based approach NMR primer: an HSQC-based approach Bio-NMR basics with vector animations More...	nmrlearner	General	0	08-16-2010 03:50 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