Local and long range potentials for heparin-protein systems for coarse-grained simulations
Sergey Samsonov , Emilia Lubecka , Krzysztof Bojarski , Robert Ganzynkowicz , Józef Adam Liwo
AbstractHeparin belongs to glycosaminoglycans (GAGs), a class of periodic linear anionic polysaccharides, which are functionally important components of the extracellular matrix owing to their interactions with various protein targets. Heparin is known to be involved in many cell signaling processes, while the experimental data available for heparin are significantly more abundant than for other GAGs. At the same time, the length and conformational flexibility of the heparin represent major challenges for its theoretical analysis. Coarse-grained (CG) approaches, which enable us to extend the size- and time-scale by orders of magnitude owing to reduction of system representation, appear, therefore, to be useful in simulating these systems. In this work, by using umbrella-sampling molecular dynamics simulations, we derived and parameterized the CG backbone-local potentials of heparin chains and the orientational potentials for the interactions of heparin with amino acid side chains to be further included in the physics-based Unified Coarse-Grained Model of biological macromolecules. With these potentials, simulations of extracellular matrix processes where both heparin and multiple proteins participate will be possible.
|Journal series||Biopolymers, ISSN 0006-3525, (N/A 70 pkt)|
|Publication size in sheets||0.55|
|Keywords in English||heparin, physics-based unified coarse-grained model, potential of mean force, proteinglycosaminoglycan interactions, UNRES|
|ASJC Classification||; ; ; ;|
|Score||= 70.0, 02-10-2019, ArticleFromJournal|
|Publication indicators||= 0; : 2016 = 0.722; : 2017 = 1.99 (2) - 2017=2.165 (5)|
|Citation count*||2 (2019-10-19)|
* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.