NMR paper Plastocyanin and Cytochrome f Complex Structures Obtained by NMR, Molecular Dynamics, and AlphaFold 3 Methods Compared to Cryo-EM Data

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[NMR paper] Plastocyanin and Cytochrome f Complex Structures Obtained by NMR, Molecular Dynamics, and AlphaFold 3 Methods Compared to Cryo-EM Data

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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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10-26-2024, 11:30 PM

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Plastocyanin and Cytochrome f Complex Structures Obtained by NMR, Molecular Dynamics, and AlphaFold 3 Methods Compared to Cryo-EM Data

Plastocyanin and Cytochrome f Complex Structures Obtained by NMR, Molecular Dynamics, and AlphaFold 3 Methods Compared to Cryo-EM Data

Plastocyanin is a small mobile protein that facilitates electron transfer through the formation of short-lived protein-protein complexes with cytochrome bf and photosystem 1. Due to the transient nature of plastocyanin-cytochrome f complex, the lack of a long-lived tight complex makes it impossible to determine its structure by X-ray diffraction analysis. Up to today, a number of slightly different structures of such complexes have been obtained by experimental and computer methods. Now,...

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