NMR paper Diffusion NMR spectroscopy: folding and aggregation of domains in p53.

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[NMR paper] Diffusion NMR spectroscopy: folding and aggregation of domains in p53.

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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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12-01-2010, 06:56 PM

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Diffusion NMR spectroscopy: folding and aggregation of domains in p53.

Diffusion NMR spectroscopy: folding and aggregation of domains in p53.

Related Articles Diffusion NMR spectroscopy: folding and aggregation of domains in p53.

Chembiochem. 2005 Sep;6(9):1550-65

Authors: Dehner A, Kessler H

Protein interactions and aggregation phenomena are probably amongst the most ubiquitous types of interactions in biological systems; they play a key role in many cellular processes. The ability to identify weak intermolecular interactions is a unique feature of NMR spectroscopy. In recent years, pulsed-field gradient NMR spectroscopy has become a convenient method to study molecular diffusion in solution. Since the diffusion coefficient of a certain molecule under given conditions correlates with its effective molecular weight, size, and shape, it is evident that diffusion can be used to map intermolecular interactions or aggregation events. Complex models can be derived from comparison of experimental diffusion data with those predicted by hydrodynamic simulations. In this review, we will give an introduction to pulsed-field gradient NMR spectroscopy and the hydrodynamic properties of proteins and peptides. Furthermore, we show examples for applying these techniques to a helical peptide and its hydrophobic oligomerization, as well as to the dimerization behavior and folding of p53.

PMID: 16138303 [PubMed - indexed for MEDLINE]

Source: PubMed

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