Systems biology and physiology: between 2022 and 2023


Plasma membrane repair, blebbing and microvesiculation: parallels and relationships


A possible approach to computer simulation of the formation of platelet lamellipodia

Dear editors of the journal System Biology and Physiology! In our previous article [1], a computer model of actin polymerization during the growth of neutrophil pseudopodium was proposed. In this letter, we propose a variant of using the same computer model to describe the growth of platelet lamellipodia.


Analysis of the level of oxidative stress by assessing the damage to the plasma protein serum albumin under the influence of an oxidizing agent

Oxidative stress, which leads to oxidative modification of various macromolecules, including proteins, is now considered an important pathogenetic link in many diseases. In this work, oxidative damage to a blood plasma protein, bovine serum albumin BSA, under the action of an oxidizing agent, hydrogen peroxide H2O2, was studied by spectrofluorometric method. The H2O2 concentration-dependent quenching of the intrinsic fluorescence of BSA is shown. BSA fluorescence quenching constants in hydrogen peroxide solutions are calculated by mathematical modeling methods. The dependences found in the fluorescence quenching constants are explained both by oxidative damage to the microenvironment of BSA tryptophan residues and by changes in the native conformation of protein globules upon oxidative damage. More significant peroxide damage to BSA occurs at lower pH values due to the fact that H2O2, as an oxidizing agent, acts more strongly in an acidic environment. The registered quenching of the protein's own fluorescence when damaged by an oxidizing agent can be used as a medical method for assessing the level of oxidative stress in the body in the diagnosis of a number of diseases.

#oxidative stress#reactive oxygen species#free radicals#serum albumin#photobleaching#molecular dynamics

Cellular automaton modelling of platelet aggregation

Platelet aggregation plays an important role in hemostasis, as it prevents blood loss upon vessel wall disruption. Computational modelling is one of the useful approaches to study this system.  The use of a cellular automaton as a model makes it possible both to study the dynamics of individual aggregates and to investigate the behaviour of the system as a whole. The aim of this research is to study platelet aggregation using a model based on a cellular automaton. As a result, a model of platelet aggregation in the basic approximation and with flow condition was constructed. It was shown that under flow conditions, the most number of the aggregates are dimers and trimers, whereas aggregates of large sizes are much less presented.

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#platelet aggregation#mathematical modeling#cellular automaton

Annexin V: the membrane-binding protein with diverse functions

Annexin V is an eukaryotic protein from the annexin family which is able to reversibly bind to phospholipid membranes in a Ca2+-dependent manner. It possesses a complex mechanism of the membrane binding which includes the two-dimensional lattice formation from annexin V trimers and significant variation of the membrane structure. The precise functions of annexin V are largely unknown, however, its participation in the blood coagulation, membrane repair process and the Ca2+ channel activity is suggested. The usage of annexin V as a marker of phosphatidylserine-positive cells in in vitro and in vivo studies makes the understanding of the protein role in cellular processes critically important.

The current review is focused on the structure of annexin V and the mechanism and kinetics of its membrane binding. The lipid specificity and the multimerization process will be described. Finally, some of the proposed annexin V functions including inhibition of the blood coagulation and the Ca2+ transport activity will be discussed.

The annexin V structure. A. The view from the convex side. Magenta, N-terminal tail; blue, domain I; yellow, domain II; green, domain III; red, domain IV; orange, Ca2+ ions. In the center of annexin V the charged residues Asp280, Arg276, Asp92, Arg117, Glu112, Arg271 are represented. B. The view from the domain II. The convex and the concave sides are marked by black arrows. Ca2+-binding sites are located on the convex surface, N-terminal tail is on the concave side. Figures were created in VMD for the current review using the structure 1ANX [29] from PDB Data Bank. C. Annexin V from human (ANXA5_HUMAN) and from rat (ANXA5_RAT) sequences alignment. Residues that form the Ca2+-binding sites are highlighted in green and yellow for human and rat annexin V respectively. The alignment was done using the UniProt Align tool.
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#annexin A5#membrane interactions#calcium channel#inhibition of coagulation

Approaches to visualize microtubule dynamics in vitro

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#microtubules#light microscopy#atomic force microscopy#dynamic instability#tubulin#associated proteins

Mechanisms of Human Erythrocytes Volume Stabilization

Functional completeness of erythrocytes depends on high deformability of these cells, that allows them to pass through narrow tissue capillaries. The erythrocytes high deformability is provided due to maintenance of discoid shape with an optimal cell surface area to volume ratio. In its turn this ratio is maintained due to cell volume stabilization at a given cell surface area. In this work, using mathematical simulation, we studied role of Na/K-ATPase, calcium activated potassium channels and adenylate metabolism in human erythrocyte volume stabilization at increase in cell membrane permeability to cations. The simulation took into account a contribution of glycolytic metabolites and adenylates to cytoplasm osmotic pressure. It was shown that the presence in the cell of Na/K-ATPase and two opposite transmembrane gradients of Na+ and K+ ions provide a significantly improved cell volume stabilization at the increase in cell membrane permeability, compared with hypothetical cells, in which the osmotic balance between cell and extracellular compartment is provided due to a gradient of only one ion (Na+). In this case the erythrocyte volume deviates from the optimal value by less than 10% at change in cell membrane permeability from 50 to 200% of its normal value. In this case, however, the intracellular ion concentrations may change significantly (by several times). The adenylate metabolism system can provide an additional regulation of transport ATPases due to regulation of intracellular ATP levels. Under these conditions stabilization of steady-state values of intracellular ion concentrations (ion homeostasis) and of cell volume in the range of cell membrane permeability changes from 50 to 1500% of the normal value. In this case, however, the cell volume and intracellular ion concentrations may significantly deviate from the stabilized values during transitional processes. Simultaneous function of both, ion transport systems and adenylate metabolism allows to provide ion homeostasis and efficient erythrocyte volume stabilization (within 5% deviation from the optimal value) both in steady-state conditions and during transitional processes at increase in cell membrane permeability up to 10-15 times compared with the normal value.

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#red blood cells#metabolism#ion channel

Systems Biology and Physiology Reports in 2021: a yearly report

Dear All,

I am happy to greet all readers, editors, reviewers, staff members and publishers of SBPR on the eve of year 2022. I thank all of you for your efforts in creating this journal and making it work despite all the challenges faced by a new independent journal in the age dominated by huge publishers, research societies and citation systems. Please accept my best wishes for the year 2022 in your professional and personal undertakings!

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First year of open-access scientific journal publishing: our mishaps, our expectations, our plans for the bright future

In silico methods have become a versatile and effective tool for the studies of the natural phenomenon at multiple levels. However, unlike such fields as economics and physics, biology and physiology have always been slightly reluctant in acceptance of the novel systemic approaches. Since scientific articles are among the key metrics for the modern scientific society, the number of scientific journals, devoted to some topic, can be a good marker to evaluate the impact of this topic for the society. Indeed, there are esteemed journals, such as PLOS Computational Biology or Journal of Theoretical Biology, but they focus mainly on a common biological phenomenon, while questions of physiology and pathophysiology are often overlooked. On the other hand, the amount of work on computational biology is steadily growing with ~12000 works published in 2010 and ~28000 in 2020 with the keyword “computational model”, according to PubMed. With all this being said and our great experience in the different aspects of the field of computational physiology, our team has decided that it would be a mistake to lose an opportunity to cover this niche. Likewise, we, as a group of fellow scientists, at the end of 2019 decided to create our own venture and to launch our own scientific journal – Systems Biology and Physiology Reports (SBPReports) [1]. This publisher's would be an attempt to underline our first hectic year of the open access scientific publishing.

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