Decorin Core Protein (Decoron) Shape Complements Collagen Fibril Surface Structure and Mediates Its Binding
Open Access
- 15 September 2009
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 4 (9), e7028
- https://doi.org/10.1371/journal.pone.0007028
Abstract
Decorin is the archetypal small leucine rich repeat proteoglycan of the vertebrate extracellular matrix (ECM). With its glycosaminoglycuronan chain, it is responsible for stabilizing inter-fibrillar organization. Type I collagen is the predominant member of the fibrillar collagen family, fulfilling both organizational and structural roles in animal ECMs. In this study, interactions between decoron (the decorin core protein) and binding sites in the d and e1 bands of the type I collagen fibril were investigated through molecular modeling of their respective X-ray diffraction structures. Previously, it was proposed that a model-based, highly curved concave decoron interacts with a single collagen molecule, which would form extensive van der Waals contacts and give rise to strong non-specific binding. However, the large well-ordered aggregate that is the collagen fibril places significant restraints on modes of ligand binding and necessitates multi-collagen molecular contacts. We present here a relatively high-resolution model of the decoron-fibril collagen complex. We find that the respective crystal structures complement each other well, although it is the monomeric form of decoron that shows the most appropriate shape complementarity with the fibril surface and favorable calculated energies of interaction. One molecule of decoron interacts with four to six collagen molecules, and the binding specificity relies on a large number of hydrogen bonds and electrostatic interactions, primarily with the collagen motifs KXGDRGE and AKGDRGE (d and e1 bands). This work helps us to understand collagen-decorin interactions and the molecular architecture of the fibrillar ECM in health and disease.Keywords
This publication has 45 references indexed in Scilit:
- Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of VertebratesJournal of Biological Chemistry, 2008
- Collagen fibril architecture, domain organization, and triple-helical conformation govern its proteolysisProceedings of the National Academy of Sciences of the United States of America, 2008
- The Decorin Sequence SYIRIADTNIT Binds Collagen Type IPublished by Elsevier BV ,2007
- Cartilage elasticity resides in shape module decoran and aggrecan sumps of damping fluid: implications in osteoarthrosisThe Journal of Physiology, 2006
- Microfibrillar structure of type I collagen in situProceedings of the National Academy of Sciences of the United States of America, 2006
- Scalable molecular dynamics with NAMDJournal of Computational Chemistry, 2005
- Light and X-ray Scattering Show Decorin to Be a Dimer in SolutionPublished by Elsevier BV ,2003
- VMD: Visual molecular dynamicsJournal of Molecular Graphics, 1996
- Characterization and interactions of a fragment of the core protein of the small proteoglycan (PGII) from bovine tendonBiochemical and Biophysical Research Communications, 1987
- A role for disulphide bridges in the protein core in the interaction of proteodermatan sulphate and collagenBiochemical and Biophysical Research Communications, 1986