A CD2-based model of yeast α-agglutinin elucidates solution properties and binding characteristics

A. Grigorescu, M. H. Chen, H. Zhao, P. C. Kahn, P. N. Lipke

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

We have previously shown that the Saccharomyces cerevisiae cell adhesion protein α-agglutinin has sequence characteristics of immunoglobulin-like proteins and have successfully modeled residues 200-325, based on the structure of immunoglobulin variable-type domains. Alignments matching residues 20-200 of α-agglutinin with domains I and II of members of the CD2/CD4 subfamily of the immunoglobulin superfamily showed >80% conservation of key residues despite low sequence similarity overall. Three-dimensional models of two α-agglutinin domains constructed on the basis of these alignments were shown to conform to peptide mapping data and biophysical properties of α-agglutinin. In addition, the residue volume and surface accessibility characteristics of these models resembled those of the well-packed structures of related proteins. Residue-by-residue analysis showed that packing and accessibility anomalies were largely confined to glycosylated and protease-susceptible loop regions of the domains. Surface accessibility of hydrophobic residues was typical of proteins with extensive domain interactions, a finding compatible with the hydrodynamic properties of α-agglutinin and the hydrophobic nature of binding to its peptide ligand a-agglutinin. The procedures used to align the α-agglutinin sequence and test the quality of the model may be applicable to other proteins, especially those that resist crystallization because of extensive glycosylation.

Original languageEnglish (US)
Pages (from-to)105-113
Number of pages9
JournalIUBMB Life
Volume50
Issue number2
DOIs
StatePublished - 2000

Keywords

  • Cell adhesion protein
  • Homology model
  • Immunoglobulin superfamily
  • Peptide mapping
  • Residue volume
  • Saccharomyces cerevisiae
  • Surface accessibility

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics
  • Clinical Biochemistry
  • Cell Biology

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