7Q5I

A glucose-based molecular rotor probes the catalytic site of glycogen phosphorylase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.158 

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This is version 2.2 of the entry. See complete history


Literature

A glucose-based molecular rotor inhibitor of glycogen phosphorylase as a probe of cellular enzymatic function.

Minadakis, M.P.Mavreas, K.F.Neofytos, D.D.Paschou, M.Kogkaki, A.Athanasiou, V.Mamais, M.Veclani, D.Iatrou, H.Venturini, A.Chrysina, E.D.Papazafiri, P.Gimisis, T.

(2022) Org Biomol Chem 20: 2407-2423

  • DOI: https://doi.org/10.1039/d1ob02211c
  • Primary Citation of Related Structures:  
    7Q5I

  • PubMed Abstract: 

    Molecular rotors belong to a family of fluorescent compounds characterized as molecular switches, where a fluorescence on/off signal signifies a change in the molecule's microenvironment. Herein, the successful synthesis and detailed study of ( E )-2-cyano-3-( p -(dimethylamino)phenyl)- N -(β-D-glucopyranosyl)acrylamide (RotA), is reported. RotA was found to be a strong inhibitor of rabbit muscle glycogen phosphorylase (RMGP b ), that binds at the catalytic site of the enzyme. RotA's interactions with the residues lining the catalytic site of RMGP b were determined by X-ray crystallography. Spectroscopic studies coupled with theoretical calculations proved that RotA is a molecular rotor. When bound in the catalytic channel of RMGP b , it behaved as a light switch, generating a strong fluorescence signal, allowing utilization of RotA as a probe that locates glycogen phosphorylase (GP). RotA, mono-, di- and per-acetylated derivatives, as well as nanoparticles with RotA encapsulated in polyethylene glycol-poly-L-histidine, were used in live cell fluorescence microscopy imaging to test the delivery of RotA through the plasma membrane of HepG2 and A431 cells, with the nanoparticles providing the best results. Once in the intracellular milieu, RotA exhibits remarkable colocalization with GP and significant biological effects, both in cell growth and inhibition of GP.


  • Organizational Affiliation

    Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece. gimisis@chem.uoa.gr.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle formA [auth AAA]843Oryctolagus cuniculusMutation(s): 0 
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
LLP
Query on LLP
A [auth AAA]L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.158 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.602α = 90
b = 128.602β = 90
c = 116.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGreeceMIS 5002550
European CommissionEuropean UnionProject ID: 653706
Other governmentGreeceMIS 5048135

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 2.0: 2022-03-09
    Changes: Advisory, Atomic model, Data collection, Non-polymer description, Structure summary
  • Version 2.1: 2022-03-30
    Changes: Database references
  • Version 2.2: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description