NMR paper Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.

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[NMR paper] Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.

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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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06-15-2016, 11:12 PM

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Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.

Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.

Related Articles Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation.

J Phys Chem Lett. 2016 Jun 14;

Authors: Salvi N, Abyzov A, Blackledge M

Abstract
Intrinsically disordered proteins (IDPs) access highly diverse ensembles of conformations in their functional states. Although this plasticity is essential to their function, little is known about the dynamics underlying interconversion between accessible states. Nuclear Magnetic Resonance (NMR) relaxation rates contain a wealth of information about motion in IDPs, but the dynamic nature of IDPs complicates their interpretation. We present a novel framework in which Molecular Dynamics (MD) simulations are used in combination with experimental 15N relaxation measurements to characterize the ensemble of dynamic processes contributing to the observed rates. By accounting for the dynamic averaging present in the different conformational states sampled by the equilibrium ensemble, we are able to accurately describe both dynamic timescales and conformational sampling. The method is robust, systematically improving agreement with independent experimental relaxation data, irrespective of the actively targeted rates, and suggesting interdependence of motions occurring on timescales varying over three orders of magnitude.

PMID: 27300592 [PubMed - as supplied by publisher]

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