Automated protein NMR structure determination in solution.

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Automated protein NMR structure determination in solution.

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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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09-14-2010, 02:03 PM

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Automated protein NMR structure determination in solution.

Automated protein NMR structure determination in solution.

Automated protein NMR structure determination in solution.

Methods Mol Biol. 2010;673:95-127

Authors: Gronwald W, Kalbitzer HR

The main drawback of protein NMR spectroscopy today is still the extensive amount of time required for solving a single structure. The main bottleneck in this respect is the manual evaluation of the experimental spectra. A clear solution to this challenge is the development of automated methods for this purpose. At the current stage of development, this goal has been almost or in a few cases fully reached for favorable cases such as well-behaved, stably folding smaller proteins below the 25 kDa range. For larger and/or more difficult molecules, the input of a human expert is still required. However, even here, automated routines will substantially speed up the structure determination process. In this report, we will summarize recent developments in this field and especially emphasize practical aspects important for a successful automated protein structure determination in solution. An important aspect closely related to structure determination is structure validation. Therefore, we devote a section to automated approaches for this topic.

PMID: 20835795 [PubMed - in process]

Source: PubMed

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