NMR paper Present and future of NMR for RNA-protein complexes: A perspective of integrated structural biology.

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[NMR paper] Present and future of NMR for RNA-protein complexes: A perspective of integrated structural biology.

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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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03-25-2014, 11:49 AM

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Present and future of NMR for RNA-protein complexes: A perspective of integrated structural biology.

Present and future of NMR for RNA-protein complexes: A perspective of integrated structural biology.

Related Articles Present and future of NMR for RNA-protein complexes: A perspective of integrated structural biology.

J Magn Reson. 2014 Apr;241:126-36

Authors: Carlomagno T

Abstract
Nucleic acids are gaining enormous importance as key molecules in almost all biological processes. Most nucleic acids do not act in isolation but are generally associated with proteins to form high-molecular-weight nucleoprotein complexes. In this perspective article I focus on the structural studies of supra-molecular ribonucleoprotein (RNP) assemblies in solution by a combination of state-of-the-art TROSY-based NMR experiments and other structural biology techniques. I discuss ways how to combine sparse NMR data with low-resolution structural information from small-angle scattering, fluorescence and electron paramagnetic resonance spectroscopy to obtain the structure of large RNP particles by an integrated structural biology approach. In the last section I give a perspective for the study of RNP complexes by solid-state NMR.

PMID: 24656085 [PubMed - in process]

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