NMR paper Using pseudocontact shifts and residual dipolar couplings as exact NMR restraints for the determination of protein structural ensembles.

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[NMR paper] Using pseudocontact shifts and residual dipolar couplings as exact NMR restraints for the determination of protein structural ensembles.

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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

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NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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Using pseudocontact shifts and residual dipolar couplings as exact NMR restraints for the determination of protein structural ensembles.

Using pseudocontact shifts and residual dipolar couplings as exact NMR restraints for the determination of protein structural ensembles.

Using pseudocontact shifts and residual dipolar couplings as exact NMR restraints for the determination of protein structural ensembles.

Biochemistry. 2015 Dec 1;

Authors: Camilloni C, Vendruscolo M

Abstract
Nuclear magnetic resonance (NMR) spectroscopy provides detailed information about the struc-ture and dynamics of proteins by exploiting the conformational dependence of the magnetic properties of certain atomic nuclei. The mapping between NMR measurements and molecular structures, however, often requires approximated descriptions based on the fitting of a number of parameters, thus reducing the quality of the information available from the experiments. To im-prove on this limitation we show here that it is possible to use pseudocontact shifts and residual dipolar couplings measured in the presence of paramagnetic metal ions as 'exact' NMR re-straints, i.e. where NMR measurements are translated into structural restraints without free pa-rameters. We implement this strategy by using a replica-averaging method and illustrate its appli-cation by calculating an ensemble of structures representing the dynamics of the two-domain pro-tein calmodulin.

PMID: 26624789 [PubMed - as supplied by publisher]

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