Nov 3 – 4, 2022
Europe/Prague timezone

An All-Atom Simulation Model of the Outer-Cell Interaction Network

Nov 3, 2022, 11:30 AM
atrium (IT4Innovations)



Studentská 6231/1B 708 00 Ostrava-Poruba
Keynote Users' talks Keynote I


Denys Biriukov (Institute of Organic Chemistry and Biochemistry of the CAS)


The extracellular space is a very dynamic and complex environment, especially above the plasma membrane. For decades, theoreticians and experimentalists have been trying to describe it piece by piece, i.e., grasp the idea of how cell membranes, proteins, and polysaccharides interact with each other. However, the complexity and functional length scales have made until now unfeasible to model a significant portion of the extracellular interaction network. The main limitations were the lack of computational power required for such simulations, the absence of uniform and accurate simulation models, and the large uncertainty of which molecular motifs should be modeled.
In our work, using the computational power provided by LUMI supercomputer via IT4Innovations together with recently improved all-atom molecular models of major classes of biomolecules, we modeled the outer-cell network on an unprecedented scale, combining in a single set of simulations all key components simultaneously (i.e., lipids, proteins, sugars, ions, and water) modeled at full atomic resolution. Our model but realistic systems, ranging from the lipid membranes with thoroughly detailed lipid composition to huge lipid membranes/glycocalyx complexes containing a wide variety of biologically relevant molecules, account for millions of atoms simulated at the microsecond timescale. The preliminary results include structural and interaction patterns present in such systems providing unique molecular insights into the organization and communication of biomacromolecules in realistic environments. Moreover, our large-scale molecular dynamics simulations offer the first of its kind opportunity to visualize in silico numerous biologically relevant processes at the atomic level.

Primary author

Denys Biriukov (Institute of Organic Chemistry and Biochemistry of the CAS)


Mr Miguel Riopedre (Institute of Organic Chemistry and Biochemistry of the CAS) Dr Hector Martinez-Seara (Institute of Organic Chemistry and Biochemistry of the CAS)

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