Implementation of the UNRES/SUGRES-1P Coarse-Grained Model of Heparin for Simulating Protein/Heparin Interactions

Abstract

Heparin is a natural highly sulfated unbranched periodic polysaccharide that plays a critical role in regulating various cellular events through interactions with its protein targets such as growth factors and cytokines. Although all-atom simulations of heparin-containing systems provide valuable insights into their structural and dynamical properties, long chains of heparin participate in many biologically relevant processes at much bigger scales and longer times than the ones which all-atom MD is able to effectively deal with. Among these processes is the establishment of chemokine gradients, amyloidogenesis, or collagen network organization. To address this limitation, coarse-grained models simplify these systems by reducing the number of degrees of freedom, allowing for the efficient exploration of structural changes within protein/heparin complexes. We introduce and validate the accuracy of a new coarse-grained physics-based model designed for studying protein/heparin interactions, which has been incorporated into the UNRES software package. The effective energy functions from UNRES and SUGRES-1P have been employed for the protein and heparin components, respectively. A good agreement between the obtained coarse-grained simulation results and experimental data confirms the suitability of the combined coarse-grained UNRES and SUGRES-1P model for in silico analysis of complex biological phenomena involving heparin, spanning time scales and molecular system sizes not attainable by conventional atomistic molecular dynamics simulations.