Phylogenetic analysis and homology modelling of Paracentrotus lividus nectin

Mol Divers. 2010 Nov;14(4):653-65. doi: 10.1007/s11030-009-9203-3. Epub 2009 Nov 12.

Abstract

The extracellular matrix protein Pl-nectin, a 210-kDa homodimer originally purified from sea urchin eggs, plays a crucial role in cell adhesion and embryonic morphogenesis. The compiled cDNA sequence, obtained by RT-PCR primer walking and 3' RACE, identified a 984aa product containing a 23aa signal peptide and including all six internal peptides identified by protein microsequencing. The protein is a new member of the galactose-binding protein superfamily as it consists of six 151-156aa-long tandemly repeated domains (D1-D6), homologous to the discoidin-like domains, also known as F5/8-type C domains. Based on homology modelling, we present a three-dimensional structure (3D) for D5, identified as the prototype domain. The molecular modelling of the assembled Pl-nectin homodimer accounts for a Pl-nectin quaternary structure composed of two 105-kDa C-shaped monomers linked by a S-S bridge. The presence of an LDT motif between the first and the second exposed loops of the D2 domain suggests the binding of Pl-nectin to an integrin receptor. Altogether, the in silico analysis described here is consistent with previous biochemical reports and offers a basis for predictions to be experimentally tested.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Cell Adhesion Molecules / genetics*
  • Computational Biology / methods
  • Computer Simulation
  • Embryo, Nonmammalian
  • Models, Molecular
  • Molecular Sequence Data
  • Nectins
  • Paracentrotus / embryology
  • Paracentrotus / genetics*
  • Phylogeny*
  • Sequence Homology*

Substances

  • Cell Adhesion Molecules
  • Nectins