4GLN

Crystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21/n

Summary for 4GLN

• Entry DOI: 10.2210/pdb4gln/pdb
• Related: 3QTK 4GLS 4GLU
• Descriptor: D-RFX001, Vascular endothelial growth factor A (3 entities in total)
• Functional Keywords: heterochiral protein-protein complex, d-protein antagonist, growth factor-inhibitor complex, growth factor/inhibitor
• Biological source: synthetic construct ; More
• Total number of polymer chains: 4
• Total formula weight: 36649.11

Authors

Mandal, K.,Uppalapati, M.,Ault-Riche, D.,Kenney, J.,Lowitz, J.,Sidhu, S.,Kent, S.B.H. (deposition date: 2012-08-14, release date: 2012-09-05, Last modification date: 2024-11-27)

Primary citation

Mandal, K.,Uppalapati, M.,Ault-Riche, D.,Kenney, J.,Lowitz, J.,Sidhu, S.S.,Kent, S.B.
Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography.
Proc.Natl.Acad.Sci.USA, 109:14779-14784, 2012

PubMed Abstract: Total chemical synthesis was used to prepare the mirror image (D-protein) form of the angiogenic protein vascular endothelial growth factor (VEGF-A). Phage display against D-VEGF-A was used to screen designed libraries based on a unique small protein scaffold in order to identify a high affinity ligand. Chemically synthesized D- and L- forms of the protein ligand showed reciprocal chiral specificity in surface plasmon resonance binding experiments: The L-protein ligand bound only to D-VEGF-A, whereas the D-protein ligand bound only to L-VEGF-A. The D-protein ligand, but not the L-protein ligand, inhibited the binding of natural VEGF(165) to the VEGFR1 receptor. Racemic protein crystallography was used to determine the high resolution X-ray structure of the heterochiral complex consisting of {D-protein antagonist + L-protein form of VEGF-A}. Crystallization of a racemic mixture of these synthetic proteins in appropriate stoichiometry gave a racemic protein complex of more than 73 kDa containing six synthetic protein molecules. The structure of the complex was determined to a resolution of 1.6 Å. Detailed analysis of the interaction between the D-protein antagonist and the VEGF-A protein molecule showed that the binding interface comprised a contact surface area of approximately 800 Å(2) in accord with our design objectives, and that the D-protein antagonist binds to the same region of VEGF-A that interacts with VEGFR1-domain 2.

PubMed: 22927390
DOI: 10.1073/pnas.1210483109

Experimental method

X-RAY DIFFRACTION (1.6 Å)