NMR paper Analysis of slow interdomain motion of macromolecules using NMR relaxation data.

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[NMR paper] Analysis of slow interdomain motion of macromolecules using NMR relaxation data.

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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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11-19-2010, 08:32 PM

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Analysis of slow interdomain motion of macromolecules using NMR relaxation data.

Analysis of slow interdomain motion of macromolecules using NMR relaxation data.

Related Articles Analysis of slow interdomain motion of macromolecules using NMR relaxation data.

J Am Chem Soc. 2001 May 2;123(17):3953-9

Authors: Baber JL, Szabo A, Tjandra N

The interpretation of NMR relaxation data for macromolecules possessing slow interdomain motions is considered. It is shown how the "extended model-free approach" can be used to analyze (15)N backbone relaxation data acquired at three different field strengths for Xenopus Ca(2+)-ligated calmodulin. This protein is comprised of two domains connected by two rigid helices joined by a flexible segment. It is possible to uniquely determine all "extended model-free" parameters without any a priori assumptions regarding their magnitudes by simultaneously least-squares fitting the relaxation data measured at two different magnetic fields. It is found that the two connecting helices (and consequently the domains) undergo slow motions relative to the conformation in which the two helices are parallel. The time scales and amplitudes of these "wobbling" motions are characterized by effective correlation times and squared-order parameters of approximately 3 ns and 0.7, respectively. These values are consistent with independent estimates indicating that this procedure provides a useful first-order description of complex internal motions in macromolecules despite neglecting the coupling of overall and interdomain motions.

PMID: 11457145 [PubMed - indexed for MEDLINE]

Source: PubMed

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