NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions.

		BioNMR > Educational resources > Journal club
NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions.

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

08-03-2011, 12:00 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions.

NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions.

NMR as a Unique Tool in Assessment and Complex Determination of Weak Protein-Protein Interactions.

Top Curr Chem. 2011 Aug 2;

Authors: Vinogradova O, Qin J

Protein-protein interactions are crucial for a wide variety of biological processes. These interactions range from high affinity (K (d) < nM) to very low affinity (K (d) > mM). While much is known about the nature of high affinity protein complexes, our knowledge about structural characteristics of weak protein-protein interactions (wPPIs) remains limited: in addition to the technical difficulties associated with their investigation, historically wPPIs used to be considered physiologically irrelevant. However, emerging evidence suggests that wPPIs, either in the form of intact protein complexes or as part of large molecular machineries, are fundamentally important for promoting rapid on/off switches of signal transduction, reversible cell-cell contacts, transient assembly/disassembly of signaling complexes, and enzyme-substrate recognition. Therefore an atomic-level elucidation of wPPIs is vital to understanding a cornucopia of diverse cellular events. Nuclear magnetic resonance (NMR) is famous for its unique abilities to study wPPIs and, by utilization of the new technical developments combined with sparse data based computational analysis, it now allows rapid identification and structural characterization of wPPIs. Here we present our perspective on the NMR methods employed.

PMID: 21809187 [PubMed - as supplied by publisher]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Biochemistry. 2011 Sep 26; Authors: Wang Q, Zhuravleva A, Gierasch LM Abstract Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods are needed that preserve these interactions...	nmrlearner	Journal club	0	09-30-2011 06:00 AM
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Biochemistry. 2011 Sep 26; Authors: Wang Q, Zhuravleva A, Gierasch LM Abstract Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods are needed that preserve these...	nmrlearner	Journal club	0	09-30-2011 05:59 AM
[NMR thesis] NMR Studies of Protein-DNA Interactions : Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions NMR Studies of Protein-DNA Interactions : Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions Sun, Yun (1992) NMR Studies of Protein-DNA Interactions : Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions. Dissertation (Ph.D.), California Institute of Technology. http://resolver.caltech.edu/CaltechTHESIS:09132011-160134197 More...	nmrlearner	NMR theses	0	09-16-2011 10:02 PM
13C-Labeled Heparan Sulfate Analogue as a Tool To Study Protein/Heparan Sulfate Interactions by NMR Spectroscopy: Application to the CXCL12? Chemokine 13C-Labeled Heparan Sulfate Analogue as a Tool To Study Protein/Heparan Sulfate Interactions by NMR Spectroscopy: Application to the CXCL12? Chemokine Ce?dric Laguri, Nicolas Sapay, Jean-Pierre Simorre, Bernhard Brutscher, Anne Imberty, Pierre Gans and Hugues Lortat-Jacob http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201753e/aop/images/medium/ja-2011-01753e_0006.gif Journal of the American Chemical Society DOI: 10.1021/ja201753e http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...	nmrlearner	Journal club	0	06-09-2011 01:32 AM
Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions. Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions. Structure, Dynamics, and Kinetics of Weak Protein-Protein Complexes from NMR Spin Relaxation Measurements of Titrated Solutions. Angew Chem Int Ed Engl. 2011 Mar 18; Authors: Salmon L, Ortega Roldan JL, Lescop E, Licinio A, van Nuland N, Jensen MR, Blackledge M	nmrlearner	Journal club	0	03-23-2011 05:41 PM
Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly. Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly. Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly. Sci China Life Sci. 2011 Feb;54(2):101-11 Authors: Feng W, Pan L, Zhang M NMR spectroscopy and X-ray crystallography are two premium methods for determining the atomic structures of macro-biomolecular complexes. Each method has unique strengths and...	nmrlearner	Journal club	0	02-15-2011 07:17 PM
[NMR paper] Spin labels as a tool to identify and characterize protein-ligand interactions by NMR Spin labels as a tool to identify and characterize protein-ligand interactions by NMR spectroscopy. Related Articles Spin labels as a tool to identify and characterize protein-ligand interactions by NMR spectroscopy. Chembiochem. 2002 Mar 1;3(2-3):167-73 Authors: Jahnke W NMR spectroscopy based discovery and optimization of lead compounds for a given molecular target requires the development of methods with maximum sensitivity and robustness. It is shown here that organic nitroxide radicals ("spin labels") can be used to boost the sensitivity...	nmrlearner	Journal club	0	11-24-2010 08:49 PM
[NMR paper] Determination of the NMR structure of the complex between U1A protein and its RNA pol Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element. Related Articles Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element. J Biomol NMR. 1998 Jan;11(1):59-84 Authors: Howe PW, Allain FH, Varani G, Neuhaus D RNA-protein recognition is critical to post-transcriptional regulation of gene expression, yet poorly understood at the molecular level. The relatively slow progress in understanding this important area of...	nmrlearner	Journal club	0	11-17-2010 11:06 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