NMR paper Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy.

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[NMR paper] Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy.

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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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07-30-2014, 10:22 AM

nmrlearner

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Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy.

Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy.

Related Articles Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy.

Proteins. 2014 Jul 26;

Authors: Gupta S, Bhattacharjya S

Abstract
The sterile alpha motif or SAM domain is one of the most frequently present protein interaction modules with diverse functional attributions. SAM domain of the Ste11 protein of budding yeast plays important roles in mitogen-activated protein kinase (MAPK) cascades. In the current study, urea-induced, at sub-denaturing concentrations, structural and dynamical changes of the Ste11 SAM domain have been investigated by NMR spectroscopy. Our study revealed that a number of residues from helix 1 and helix 5 of the Ste11 SAM domain display plausible alternate conformational states and largest chemical shift perturbations at low urea concentrations. Amide proton (H/D) exchange experiments indicated that helix 1, loop and helix 5 become more susceptible to solvent exchange with increased concentrations of urea. Notably, helix1 and helix5 are directly involved in binding interactions of the Ste11 SAM domain. Our data further demonstrate that the existence of alternate conformational states around the regions involved in dimeric interactions in native or near native conditions. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.

PMID: 25066357 [PubMed - as supplied by publisher]

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