[ASAP] Solution Structure Ensembles of the Open and Closed Forms of the ~130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR

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[ASAP] Solution Structure Ensembles of the Open and Closed Forms of the ~130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and 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

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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06-07-2023, 11:06 AM

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[ASAP] Solution Structure Ensembles of the Open and Closed Forms of the ~130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR

[ASAP] Solution Structure Ensembles of the Open and Closed Forms of the ~130 kDa Enzyme I via AlphaFold Modeling, Coarse Grained Simulations, and NMR

Sergey L. Sedinkin, Daniel Burns, Divyanshu Shukla, Davit A. Potoyan, and Vincenzo Venditti

Journal of the American Chemical Society
DOI: 10.1021/jacs.3c03425

Source: Journal of the American Chemical Society

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