NMR paper NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment.

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[NMR paper] NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment.

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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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NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment.

NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment.

NMR-based determination of the 3D structure of the ligand-protein interaction site without protein resonance assignment.

J Am Chem Soc. 2016 Mar 4;

Authors: Orts J, Wälti MA, Marsh M, Vera L, Gossert AD, Güntert P, Riek R

Abstract
Molecular replacement in X-ray crystallography is the prime method for establishing structure-activity relationships of pharmaceutically relevant molecules. Such an approach is not available for NMR. Here, we establish a comparable method, called NMR molecular replacement (NMR2). The method requires experimentally measured ligand intra-molecular NOEs and ligand-protein inter-molecular NOEs as well as a previously known receptor structure or model. Our findings demonstrate that NMR2 may open a new avenue for the fast and robust determination of the interaction site of ligand-protein complex- es at atomic resolution.

PMID: 26943491 [PubMed - as supplied by publisher]

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