4WPB

Vascular endothelial growth factor in complex with alpha/beta-VEGF-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Targeting diverse protein-protein interaction interfaces with alpha / beta-peptides derived from the Z-domain scaffold.

Checco, J.W.Kreitler, D.F.Thomas, N.C.Belair, D.G.Rettko, N.J.Murphy, W.L.Forest, K.T.Gellman, S.H.

(2015) Proc.Natl.Acad.Sci.USA 112: 4552-4557

  • DOI: 10.1073/pnas.1420380112

  • PubMed Abstract: 
  • Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. Here, we describe a strategy for designing oligomers containi ...

    Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. Here, we describe a strategy for designing oligomers containing both α- and β-amino acid residues ("α/β-peptides") that mimic several peptides derived from the three-helix bundle "Z-domain" scaffold. We show that α/β-peptides derived from a Z-domain peptide targeting vascular endothelial growth factor (VEGF) can structurally and functionally mimic the binding surface of the parent peptide while exhibiting significantly decreased susceptibility to proteolysis. The tightest VEGF-binding α/β-peptide inhibits the VEGF165-induced proliferation of human umbilical vein endothelial cells. We demonstrate the versatility of this strategy by showing how principles underlying VEGF signaling inhibitors can be rapidly extended to produce Z-domain-mimetic α/β-peptides that bind to two other protein partners, IgG and tumor necrosis factor-α. Because well-established selection techniques can identify high-affinity Z-domain derivatives from large DNA-encoded libraries, our findings should enable the design of biostable α/β-peptides that bind tightly and specifically to diverse targets of biomedical interest. Such reagents would be useful for diagnostic and therapeutic applications.


    Organizational Affiliation

    Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706 gellman@chem.wisc.edu wlmurphy@wisc.edu forest@bact.wisc.edu.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705;,Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706; gellman@chem.wisc.edu wlmurphy@wisc.edu forest@bact.wisc.edu.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53705; Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, WI 53705; and gellman@chem.wisc.edu wlmurphy@wisc.edu forest@bact.wisc.edu.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor A
A, B
102Homo sapiensMutation(s): 0 
Gene Names: VEGFA (VEGF)
Find proteins for P15692 (Homo sapiens)
Go to Gene View: VEGFA
Go to UniProtKB:  P15692
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
alpha/beta-VEGF-1
C, D
40N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  6 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
C, D
NON-POLYMERH2 N

--

B3D
Query on B3D
C, D
PEPTIDE-LIKEC5 H9 N O4ASP
AIB
Query on AIB
C, D
L-PEPTIDE LINKINGC4 H9 N O2ALA
XPC
Query on XPC
C, D
peptide-likeC5 H10 N2 O2

--

3FB
Query on 3FB
C, D
NON-POLYMERC10 H13 N O2

--

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

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.100α = 90.00
b = 78.400β = 102.80
c = 56.500γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM056414
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM008349

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release
  • Version 1.1: 2015-04-29
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2017-10-11
    Type: Data collection