6IAM

Modulating Protein-Protein Interactions with Visible Light Peptide Backbone Switches


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Modulating Protein-Protein Interactions with Visible-Light-Responsive Peptide Backbone Photoswitches.

Albert, L.Penalver, A.Djokovic, N.Werel, L.Hoffarth, M.Ruzic, D.Xu, J.Essen, L.O.Nikolic, K.Dou, Y.Vazquez, O.

(2019) Chembiochem 20: 1417-1429

  • DOI: https://doi.org/10.1002/cbic.201800737
  • Primary Citation of Related Structures:  
    6IAM

  • PubMed Abstract: 

    Life relies on a myriad of carefully orchestrated processes, in which proteins and their direct interplay ultimately determine cellular function and disease. Modulation of this complex crosstalk has recently attracted attention, even as a novel therapeutic strategy. Herein, we describe the synthesis and characterization of two visible-light-responsive peptide backbone photoswitches based on azobenzene derivatives, to exert optical control over protein-protein interactions (PPI). The novel peptidomimetics undergo fast and reversible isomerization with low photochemical fatigue under alternatively blue-/green-light irradiation cycles. Both bind in the nanomolar range to the protein of interest. Importantly, the best peptidomimetic displays a clear difference between isomers in its protein-binding capacity and, in turn, in its potential to inhibit enzymatic activity through PPI disruption. In addition, crystal structure determination, docking and molecular dynamics calculations allow a molecular interpretation and open up new avenues in the design and synthesis of future photoswitchable PPI modulators.


  • Organizational Affiliation

    Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5306Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens)
Explore P61964 
Go to UniProtKB:  P61964
GTEx:  ENSG00000196363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61964
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SER-ALA-ARG-ALA-XY5-VAL-HIS-LEU-ARG-LYS-SER-ALA12Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 54Homo sapiensMutation(s): 0 
Gene Names: SUMO1P1SUMO5UBL2UBL6
UniProt
Find proteins for G2XKQ0 (Homo sapiens)
Explore G2XKQ0 
Go to UniProtKB:  G2XKQ0
Entity Groups  
UniProt GroupG2XKQ0
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.526α = 90
b = 46.56β = 107.22
c = 66.168γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2019-06-12
    Changes: Data collection, Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations