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In silico analysis of the two tandem somatomedin B domains of ENPP1 reveals hints on the homodimerization of the protein
Author(s) -
Bellacchio Emanuele
Publication year - 2012
Publication title -
journal of cellular physiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.529
H-Index - 174
eISSN - 1097-4652
pISSN - 0021-9541
DOI - 10.1002/jcp.24058
Subject(s) - tandem , molecular dynamics , docking (animal) , in silico , transmembrane domain , transmembrane protein , tandem repeat , monomer , chemistry , biophysics , protein–protein interaction , membrane , protein structure , biochemistry , biology , materials science , computational chemistry , receptor , medicine , nursing , organic chemistry , genome , composite material , gene , polymer
The homodimerization of ENPP1 is mediated by the two somatomedin B (SMB) domains of the protein through a mechanism that is yet unknown at the atomistic level. The tandem arrangement of these domains without an intermediate spacer implies their possible packing into a functional assembly, which we explored by rigid docking. To exclude potential bias in the docking search we assessed the absence of flexible protein regions by evaluating the normalized B‐factors calculated from the Cα atom displacements derived from molecular dynamics simulations. After filtering the docking results exploiting the criterion that residues located at the inter‐domain interfaces are more conserved than non‐interface residues, the resulting best model of the tandem SMB domains revealed the presence of two large conserved surface patches not engaged in the inter‐domain contact. The largest patch is flat and contains all the invariant positively charged residues characterized by fully solvent‐exposed side chains within the tandem SMB domains, suggesting as a possible role its interaction with the negative phospholipids on the cell surface. We envisage that an ENPP1 monomer bound to the cell membrane via the transmembrane segment can also interact with the cell surface through the largest conserved patch favoring a specific geometry of the tandem SMB module on the cell that optimally exposes the second conserved patch for the symmetric interaction with another membrane‐bound ENPP1 monomer, finally promoting the homodimerization. Biological implications of this model and insights into the effects of the K173Q variant associated with insulin resistance and related abnormalities are presented. J. Cell. Physiol. 227: 3566–3574, 2012. © 2012 Wiley Periodicals, Inc.