NMR paper NMR Spectroscopy Approach to Study the Structure, Orientation, and Mechanism of the Multidrug Exporter EmrE.

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[NMR paper] NMR Spectroscopy Approach to Study the Structure, Orientation, and Mechanism of the Multidrug Exporter EmrE.

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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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11-28-2017, 04:45 PM

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NMR Spectroscopy Approach to Study the Structure, Orientation, and Mechanism of the Multidrug Exporter EmrE.

NMR Spectroscopy Approach to Study the Structure, Orientation, and Mechanism of the Multidrug Exporter EmrE.

NMR Spectroscopy Approach to Study the Structure, Orientation, and Mechanism of the Multidrug Exporter EmrE.

Methods Mol Biol. 2018;1700:83-96

Authors: Leninger M, Traaseth NJ

Abstract
Multidrug exporters are a class of membrane proteins that remove antibiotics from the cytoplasm of bacteria and in the process confer multidrug resistance to the organism. This chapter outlines the sample preparation and optimization of oriented solid-state NMR experiments applied to the study of structure and dynamics for the model transporter EmrE from the small multidrug resistance (SMR) family.

PMID: 29177827 [PubMed - in process]

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