Evaluation of competing J domain:Hsp70 complex models in light of existing mutational and NMR data [Letters (Online Only)]

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Evaluation of competing J domain:Hsp70 complex models in light of existing mutational and NMR data [Letters (Online Only)]

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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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03-27-2012, 08:41 PM

nmrlearner

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Evaluation of competing J domain:Hsp70 complex models in light of existing mutational and NMR data [Letters (Online Only)]

Evaluation of competing J domain:Hsp70 complex models in light of existing mutational and NMR data [Letters (Online Only)]

Sousa, R., Jiang, J., Lafer, E. M., Hinck, A. P., Wang, L., Taylor, A. B., Maes, E. G....
Date: 2012-03-27

The work by Ahmad et al. (1) presented an NMR-based model for a bacterial DnaJ J domain:DnaK(Hsp70):ADP complex that differs from our crystal structure of a disulfide-linked bovine Hsc70:auxilin J domain complex (2). The work by Ahmad et al. (1) claimed that their model can better account for published mutational data, that their model is in better agreement with a previous NMR study of a bacterial DnaJ J domain:DnaK complex (3), and that the cross-link in our structure renders it irrelevant for understanding J domain:Hsp70 interactions or mechanism. However, bacterial DnaK and mammalian Hsc70 bind J proteins very differently. Bacterial... Read More

PNAS:
Number: 13
Volume: 109

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