6CG3

Macrocyclic peptide derived from Abeta(17-36) - (ORN)LV(PHI)FAED(ORN)AII(2-nitrobenzylglycine)L(ORN)V

  • Classification: NEUROPEPTIDE
  • Organism(s): synthetic construct
  • Mutation(s): No 

  • Deposited: 2018-02-19 Released: 2018-05-16 
  • Deposition Author(s): Salveson, P.J., Nowick, J.S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Controlling the Oligomerization State of A beta-Derived Peptides with Light.

Salveson, P.J.Haerianardakani, S.Thuy-Boun, A.Kreutzer, A.G.Nowick, J.S.

(2018) J Am Chem Soc 140: 5842-5852

  • DOI: https://doi.org/10.1021/jacs.8b02658
  • Primary Citation of Related Structures:  
    6CG3, 6CG4, 6CG5

  • PubMed Abstract: 

    A key challenge in studying the biological and biophysical properties of amyloid-forming peptides is that they assemble to form heterogeneous mixtures of soluble oligomers and insoluble fibrils. Photolabile protecting groups have emerged as tools to control the properties of biomolecules with light. Blocking intermolecular hydrogen bonds that stabilize amyloid oligomers provides a general strategy to control the biological and biophysical properties of amyloid-forming peptides. In this paper we describe the design, synthesis, and characterization of macrocyclic β-hairpin peptides that are derived from amyloidogenic peptides and contain the N-2-nitrobenzyl photolabile protecting group. Each peptide contains two heptapeptide segments from Aβ 16-36 or Aβ 17-36 constrained into β-hairpins. The N-2-nitrobenzyl group is appended to the amide backbone of Gly 33 to disrupt the oligomerization of the peptides by disrupting intermolecular hydrogen bonds. X-ray crystallography reveals that N-2-nitrobenzyl groups can either block assembly into discrete oligomers or permit formation of trimers, hexamers, and dodecamers. Photolysis of the N-2-nitrobenzyl groups with long-wave UV light unmasks the amide backbone and alters the assembly and the biological properties of the macrocyclic β-hairpin peptides. SDS-PAGE studies show that removing the N-2-nitrobenzyl groups alters the assembly of the peptides. MTT conversion and LDH release assays show that decaging the peptides induces cytotoxicity. Circular dichroism studies and dye leakage assays with liposomes reveal that decaging modulates interactions of the peptides with lipid bilayers. Collectively, these studies demonstrate that incorporating N-2-nitrobenzyl groups into macrocyclic β-hairpin peptides provides a new strategy to probe the structures and the biological properties of amyloid oligomers.


  • Organizational Affiliation

    Department of Chemistry , University of California, Irvine , Irvine , California 92697-2025 , United States.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORN-LEU-VAL-PHI-PHE-ALA-GLU-ASP-ORN-ALA-ILE-ILE-EZY-LEU-ORN-VAL16synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
ORN
Query on ORN
A
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
PHI
Query on PHI
A
L-PEPTIDE LINKINGC9 H10 I N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.216 
  • Space Group: P 42 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.504α = 90
b = 47.504β = 90
c = 47.504γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097562

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence