3RFJ

Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

Summary for 3RFJ

• Entry DOI: 10.2210/pdb3rfj/pdb
• Related: 3RFS
• Descriptor: Internalin B, repeat modules, Variable lymphocyte receptor, SULFATE ION (3 entities in total)
• Functional Keywords: lrr, protein binding, plasma
• Biological source: Listeria monocytogenes (marine lamprey); More
• Total number of polymer chains: 1
• Total formula weight: 31419.40

Authors

Kim, H.J.,Cheong, H.K.,Jeon, Y.H. (deposition date: 2011-04-06, release date: 2012-03-14, Last modification date: 2024-11-06)

Primary citation

Lee, S.C.,Park, K.,Han, J.,Lee, J.J.,Kim, H.J.,Hong, S.,Heu, W.,Kim, Y.J.,Ha, J.S.,Lee, S.G.,Cheong, H.K.,Jeon, Y.H.,Kim, D.,Kim, H.S.
Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering
Proc.Natl.Acad.Sci.USA, 109:3299-3304, 2012

PubMed Abstract: Repeat proteins have recently been of great interest as potential alternatives to immunoglobulin antibodies due to their unique structural and biophysical features. We here present the development of a binding scaffold based on variable lymphocyte receptors, which are nonimmunoglobulin antibodies composed of Leucine-rich repeat modules in jawless vertebrates, by module engineering. A template scaffold was first constructed by joining consensus repeat modules between the N- and C-capping motifs of variable lymphocyte receptors. The N-terminal domain of the template scaffold was redesigned based on the internalin-B cap by analyzing the modular similarity between the respective repeat units using a computational approach. The newly designed scaffold, termed "Repebody," showed a high level of soluble expression in bacteria, displaying high thermodynamic and pH stabilities. Ease of molecular engineering was shown by designing repebodies specific for myeloid differentiation protein-2 and hen egg lysozyme, respectively, by a rational approach. The crystal structures of designed repebodies were determined to elucidate the structural features and interaction interfaces. We demonstrate general applicability of the scaffold by selecting repebodies with different binding affinities for interleukin-6 using phage display.

PubMed: 22328160
DOI: 10.1073/pnas.1113193109

Experimental method

X-RAY DIFFRACTION (1.78 Å)