NMR paper Solvent interaction of a Hsp70 chaperone substrate-binding domain investigated with w

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[NMR paper] Solvent interaction of a Hsp70 chaperone substrate-binding domain investigated with w

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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, 09:16 PM

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Solvent interaction of a Hsp70 chaperone substrate-binding domain investigated with w

Solvent interaction of a Hsp70 chaperone substrate-binding domain investigated with water-NOE NMR experiments.

Related Articles Solvent interaction of a Hsp70 chaperone substrate-binding domain investigated with water-NOE NMR experiments.

Biochemistry. 2003 Sep 30;42(38):11100-8

Authors: Cai S, Stevens SY, Budor AP, Zuiderweg ER

The interaction of solvent of the substrate binding domain of the bacterial heat shock 70 chaperone protein DnaK was studied in its apo form and with bound hydrophobic substrate peptide, using refined nuclear magnetic resonance experiments. Distinct differences between the two states of the protein were observed. According to our data, the apo form interacts more extensively with solvent than the peptide-bound form. Significantly, the open hydrophobic substrate binding cleft of DnaK in the apo form is found to contain several molecules of water which are displaced by the binding of the hydrophobic substrate, the peptide NRLLLTG. The solvent in the hydrophobic cleft has a residence time longer than 400 ps. It is predicted that the displacement of this trapped water must contribute to the binding free energy of the natural hydrophobic substrates of this class of protein-folding chaperone proteins.

PMID: 14503860 [PubMed - indexed for MEDLINE]

Source: PubMed

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