6AHL

Crystal Structure of HEWL in complex with Cinnamaldehyde (in the aroma form) after 5 hours under fibrillation conditions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cinnamaldehyde and Phenyl Ethyl Alcohol promote the entrapment of intermediate species of HEWL, as revealed by structural, kinetics and thermal stability studies.

Seraj, Z.Groves, M.R.Seyedarabi, A.

(2019) Sci Rep 9: 18615-18615

  • DOI: 10.1038/s41598-019-55082-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Numerous efforts have been directed towards investigating the different stages leading to the fibrillation process in neurodegenerative diseases and finding the factors modulating it. In this study, using a wide range of molecular techniques as well ...

    Numerous efforts have been directed towards investigating the different stages leading to the fibrillation process in neurodegenerative diseases and finding the factors modulating it. In this study, using a wide range of molecular techniques as well as fibrillation kinetics coupled with differential scanning fluorimetry (DSF) and crystal structure determination of HEWL treated with cinnamaldehyde (Cin) and Phenyl ethyl alcohol (PEA) in their aroma form during fibrillation, we were able to identify the binding positions of Cin and PEA in HEWL. Additionally, crystal structures were used to suggest residues Thr43, Asn44, Arg45 and Arg68 as a plausible 'hotspot' promoting entrapment of intermediate species in the process of fibril formation in HEWL. We were also able to use DSF to show that Cin can significantly decrease the thermal stability of HEWL, promoting the formation of partially unfolded intermediate species. In conclusion, our data led us to emphasize that compounds in their 'aroma form' can influence the structure and stability of protein molecules and suggest reconsideration of HEWL as a model protein for fibrillation studies related to neurodegenerative diseases based on the initial structure of the proteins, whether globular (HEWL) or intrinsically disordered.


    Organizational Affiliation

    Department of Biochemistry, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. a.seyedarabi@ut.ac.ir.,Department of Drug design, University of Groningen, Groningen, The Netherlands.,Department of Biochemistry, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
A
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CIN
Query on CIN

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A
4-CARBOXYCINNAMIC ACID
C10 H8 O4
HAEJSGLKJYIYTB-ZZXKWVIFSA-N
 Ligand Interaction
PGO
Query on PGO

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A
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.155 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.220α = 90.00
b = 78.220β = 90.00
c = 36.890γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2020-01-29
    Type: Database references