5AGW

Bcl-2 alpha beta-1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.695 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Alpha Beta Peptide Foldamers Targeting Intracellular Protein-Protein Interactions with Activity on Living Cells

Checco, J.W.Lee, E.F.Evangelista, M.Sleebs, N.Rodgers, K.Pettikiriarachchi, A.Kershaw, N.Eddinger, G.A.Belair, D.G.Wilson, J.L.Eller, C.H.Raines, R.T.Murphy, W.L.Smith, B.J.Gellman, S.H.Fairlie, W.D.

(2015) J.Am.Chem.Soc. 137: 11365

  • DOI: 10.1021/jacs.5b05896
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peptides can be developed as effective antagonists of protein-protein interactions, but conventional peptides (i.e., oligomers of l-α-amino acids) suffer from significant limitations in vivo. Short half-lives due to rapid proteolytic degradation and ...

    Peptides can be developed as effective antagonists of protein-protein interactions, but conventional peptides (i.e., oligomers of l-α-amino acids) suffer from significant limitations in vivo. Short half-lives due to rapid proteolytic degradation and an inability to cross cell membranes often preclude biological applications of peptides. Oligomers that contain both α- and β-amino acid residues ("α/β-peptides") manifest decreased susceptibility to proteolytic degradation, and when properly designed these unnatural oligomers can mimic the protein-recognition properties of analogous "α-peptides". This report documents an extension of the α/β-peptide approach to target intracellular protein-protein interactions. Specifically, we have generated α/β-peptides based on a "stapled" Bim BH3 α-peptide, which contains a hydrocarbon cross-link to enhance α-helix stability. We show that a stapled α/β-peptide can structurally and functionally mimic the parent stapled α-peptide in its ability to enter certain types of cells and block protein-protein interactions associated with apoptotic signaling. However, the α/β-peptide is nearly 100-fold more resistant to proteolysis than is the parent stapled α-peptide. These results show that backbone modification, a strategy that has received relatively little attention in terms of peptide engineering for biomedical applications, can be combined with more commonly deployed peripheral modifications such as side chain cross-linking to produce synergistic benefits.


    Organizational Affiliation

    The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
A, B
166Homo sapiensMutation(s): 0 
Gene Names: BCL2, BCL2L1 (BCL2L, BCLX)
Find proteins for P10415 (Homo sapiens)
Go to Gene View: BCL2
Go to UniProtKB:  P10415
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
BCL-2-LIKE PROTEIN 11
C, D
22Homo sapiensMutation(s): 5 
Gene Names: BCL2L11 (BIM)
Find proteins for O43521 (Homo sapiens)
Go to Gene View: BCL2L11
Go to UniProtKB:  O43521
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
AJE
Query on AJE
C, D
L-PEPTIDE LINKINGC9 H14 N2 O5

--

MH8
Query on MH8
C, D
L-peptide linkingC8 H15 N O2

--

XCP
Query on XCP
C, D
peptide-likeC6 H11 N O2

--

ACE
Query on ACE
C, D
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.695 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.673α = 90.00
b = 87.673β = 90.00
c = 107.480γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references