Biological Molecular Dynamics Simulations 2.0

PN 3-11

Project Description

The project aims to promote molecular dynamics simulation of biological systems to the next level in three steps. At first, force field parameters of diverse post-translational modifications will be established both at all-atom and at coarse-grained resolution. The biological impact on molecular level of those post-translational modifications will be investigated on sample applications including cellular signalling events and interactions among bio(macro)molecules in cancerogenous cells. Next, a methodology for constant pH molecular dynamic simulations (both all-atom and coarse-grained) will be extended to diverse charged groups including titratable post-translational modification. This will allow for unravelling the role of charge adaptation in biological processes including protein insertion into cellular membranes, signal propagation within a cell, transmembrane transport and aggregation of biomolecules. In the last task a novel resolution conversion method will be developed based on automated generation of the mapping files by using machine learning and chemical information included e.g. in the original all- atom resolution. Therefore, the simulation system will be able to alter the resolution of the description between atomistic and coarse-grained resolution of diverse granularity in an automated manner thus sparing user-required time and avoiding user-induced errors. This technique will interconnect MD methods of diverse resolution by enabling sequential multiscaling MD simulations. However, not being restricted to biological systems, the fine-grading method will complement coarse graining techniques by a feedback control enabling a quality check of the newly established coarse-grained representation by its conversion back to higher level of resolution and control of the properties against experimental and other simulational data.

Project Information

Project Number PN 3-11
Project Name Biological Molecular Dynamics Simulations 2.0
Project Duration January 2021 - June 2024
Project Leader Kristyna Pluhackova
Project Members Viktoria Korn, PhD Researcher
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