Illuminating an invisible state of the HIV-1 capsid protein CTD dimer using 19F NMR and weighted ensemble simulations

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Illuminating an invisible state of the HIV-1 capsid protein CTD dimer using 19F NMR and weighted ensemble simulations

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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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Illuminating an invisible state of the HIV-1 capsid protein CTD dimer using 19F NMR and weighted ensemble simulations

Illuminating an invisible state of the HIV-1 capsid protein CTD dimer using 19F NMR and weighted ensemble simulations

Darian T. YangLillian T. ChongAngela M. GronenbornaMolecular Biophysics and Structural Biology Graduate Program, University of Pittsburgh and Carnegie Mellon University, Pittsburgh, PA 15260bDepartment of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260cDepartment of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260...
Date:

Proceedings of the National Academy of Sciences, Volume 122, Issue 8, February 2025.
SignificanceProtein conformational dynamics are critical for understanding biological function. To derive atomic-resolution details of an alternate, “invisible” dimeric state of the HIV-1 capsid protein C-terminal domain (CTD), we used19F NMR and ... Read More

PNAS:
Number: 8
Volume: 122

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