NMR paper Targeting a dark excited state of HIV-1 nucleocapsid by anti-retroviral thioesters revealed by NMR.

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[NMR paper] Targeting a dark excited state of HIV-1 nucleocapsid by anti-retroviral thioesters revealed by NMR.

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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

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NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

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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

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NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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01-19-2018, 08:57 PM

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Targeting a dark excited state of HIV-1 nucleocapsid by anti-retroviral thioesters revealed by NMR.

Related Articles Targeting a dark excited state of HIV-1 nucleocapsid by anti-retroviral thioesters revealed by NMR.

Angew Chem Int Ed Engl. 2018 Jan 18;:

Authors: Deshmukh L, Tugarinov V, Appella DH, Clore GM

Abstract
HIV-1 nucleocapsid (NCp7) is a two Cys2HisCys zinc knuckle (N-Zn and C-Zn) protein that plays a key role in viral replication. Here we characterize NCp7 conformational dynamics by NMR relaxation dispersion and chemical exchange saturation transfer measurements. While the N-Zn knuckle is conformationally stable, the C-Zn knuckle interconverts on the millisecond time scale between the major state, in which the zinc is coordinated by three cysteines and a histidine, and two folded minor species (with populations around 1%) in which one of the coordination bonds (Cys413-S?---Zn or His421-N?2---Zn) is hydrolysed. These findings explain why anti-retroviral thioesters specifically disrupt the C-Zn knuckle by initial acylation of Cys413, and show that transient, sparsely-populated ('dark'), excited states of proteins can present effective targets for rational drug design.

PMID: 29345807 [PubMed - as supplied by publisher]

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