NMR paper Structure determination of protein complexes by NMR.

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[NMR paper] Structure determination of protein complexes by NMR.

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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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11-24-2010, 09:25 PM

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Structure determination of protein complexes by NMR.

Structure determination of protein complexes by NMR.

Related Articles Structure determination of protein complexes by NMR.

Methods Mol Biol. 2004;278:255-88

Authors: Nietlispach D, Mott HR, Stott KM, Nielsen PR, Thiru A, Laue ED

This chapter describes nuclear magnetic resonance (NMR) methods that can be used to determine the structures of protein complexes. Many of these techniques are also applicable to other systems (e.g., protein-nucleic acid complexes). In the first section, we discuss methodologies for optimizing the sample conditions for the study of complexes. This is followed by a description of the methods that can be used to map interfaces when a full structure determination of the complex is not appropriate or not possible. We then describe experimental approaches for resonance assignment in complexes, these are essentially the same as those for isolated proteins. Subheading 6. describes the different types of so-called X-filtered NMR experiments that have been devised to separate and selectively observe either inter- or intramolecular structural information. These filtered NMR experiments are then exploited in the experimental strategies for structure determination of either protein complexes or homodimeric proteins. This is followed by a description of the calculation of their structures. Finally, we present case studies from three projects carried out in our laboratory, where we successfully used the methods presented in this chapter.

PMID: 15318000 [PubMed - indexed for MEDLINE]

Source: PubMed

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