An NMR method to study protein-protein interactions.

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An NMR method to study protein-protein interactions.

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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:

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09-13-2011, 08:27 PM

nmrlearner

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An NMR method to study protein-protein interactions.

An NMR method to study protein-protein interactions.

An NMR method to study protein-protein interactions.

Methods Mol Biol. 2012;757:129-37

Authors: Nishida N, Shimada I

Abstract
Specific interactions between proteins are a fundamental process underlying the various biological events, such as cell-cell contacts, signal transduction, and gene expression. Therefore, the structural investigations of protein-protein interactions provide useful information for understanding these events. We describe an NMR method, termed the cross-saturation (CS) method, to determine the binding sites of protein complexes more precisely than conventional NMR methods. The CS method can determine the binding sites of a protein complex that undergoes fast exchange between the free and the bound states, regardless of the molecular size of the complex.

PMID: 21909911 [PubMed - in process]

Source: PubMed

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