8BQP

Hen Egg-White Lysozyme (HEWL) complexed with methyl-functionalised Anderson-Evans polyoxometalate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Fine-tuning non-covalent interactions between hybrid metal-oxo clusters and proteins.

Lentink, S.Salazar Marcano, D.E.Moussawi, M.A.Vandebroek, L.Van Meervelt, L.Parac-Vogt, T.N.

(2023) Faraday Discuss 244: 21-38

  • DOI: https://doi.org/10.1039/d2fd00161f
  • Primary Citation of Related Structures:  
    8BQP, 8BQQ, 8BQR, 8BQT

  • PubMed Abstract: 

    Interactions between the protein Hen Egg White Lysozyme (HEWL) and three different hybrid Anderson-Evans polyoxometalate clusters - AE-NH2 (δ-[MnMo 6 O 18 {(OCH 2 ) 3 CNH 2 } 2 ] 3- ), AE-CH3 (δ-[MnMo 6 O 18 {(OCH 2 ) 3 CCH 3 } 2 ] 3- ) and AE-Biot (δ-[MnMo 6 O 18 {(OCH 2 ) 3 CNHCOC 9 H 15 N 2 OS} 2 ] 3- ) - were studied via tryptophan fluorescence spectroscopy and single crystal X-ray diffraction. Quenching of tryptophan fluorescence was observed in the presence of all three hybrid polyoxometalate clusters (HPOMs), but the extent of quenching and the binding affinity were greatly dependent on the nature of the organic groups attached to the cluster. Control experiments further revealed the synergistic effect of the anionic polyoxometalate core and organic ligands towards enhanced protein interactions. Furthermore, the protein was co-crystallised with each of the three HPOMs, resulting in four different crystal structures, thus allowing for the binding modes of HPOM-protein interactions to be investigated with near-atomic precision. All crystal structures displayed a unique mode of binding of the HPOMs to the protein, with both functionalisation and the pH of the crystallisation conditions influencing the interactions. From the crystal structures, it was determined that HPOM-protein non-covalent complexes formed through a combination of electrostatic attraction between the polyoxometalate cluster and positively charged surface regions of HEWL, and direct and water-mediated hydrogen bonds with both the metal-oxo inorganic core and the functional groups of the ligand, where possible. Hence, functionalisation of metal-oxo clusters shows great potential in tuning their interactions with proteins, which is of interest for several biomedical applications.


  • Organizational Affiliation

    Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven 3001, Belgium. tatjana.vogt@kuleuven.be.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysozyme C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.24 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.388α = 90
b = 76.388β = 90
c = 36.981γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - Flanders (FWO)Belgium1183021N
Research Foundation - Flanders (FWO)Belgium1279721N
Research Foundation - Flanders (FWO)Belgium11A3517N
Research Foundation - Flanders (FWO)BelgiumG0E4717N
KU LeuvenBelgiumC14/19/076

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-05-10
    Changes: Database references
  • Version 1.2: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.3: 2024-02-07
    Changes: Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary