NMR paper Monitoring protein-metal binding by 19F NMR - a case study with the New Delhi metallo-?-lactamase 1.

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[NMR paper] Monitoring protein-metal binding by 19F NMR - a case study with the New Delhi metallo-?-lactamase 1.

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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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01-24-2021, 11:14 PM

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Monitoring protein-metal binding by 19F NMR - a case study with the New Delhi metallo-?-lactamase 1.

Related Articles Monitoring protein-metal binding by 19F NMR - a case study with the New Delhi metallo-?-lactamase 1.

RSC Med Chem. 2020 Mar 01;11(3):387-391

Authors: Rydzik AM, Brem J, Chandler SA, Benesch JLP, Claridge TDW, Schofield CJ

Abstract
19F NMR protein observed spectroscopy is evaluated as a method for analysing protein metal binding using the New Delhi metallo-?-lactamase 1. The results imply 19F NMR is useful for analysis of different metallated protein states and investigations on equilibrium states in the presence of inhibitors. One limitation is that 19F labelling may affect metal ion binding. The sensitive readout of changes in protein behaviour observed by 19F NMR spectra coupled with the broad scope of tolerated conditions (e.g. buffer variations) means 19F NMR should be further investigated for studying metal ion interactions and the inhibition of metallo-enzymes during drug discovery.

PMID: 33479644 [PubMed]

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