Volume 41, Nº 5-6 (2024)

The review examines the history of the emergence, development, and achievements of the Rhodopsin project, organized by Yu.A. Ovchinnikov in 1973. The current state of some issues related to the structure and function of retinal-containing proteins – types I and II rhodopsins – is also presented.

The superfamily of membrane proteins known as P-loop channels encompasses potassium, sodium, and calcium channels, as well as TRP channels and ionotropic glutamate receptors. An increasing number of crystal and cryo-EM structures are uncovering both general and specific features of these channels. Fundamental folding principles, the arrangement of structural segments, key residues that influence ionic selectivity, gating, and binding sites for toxins and medically relevant ligands have now been firmly established. The advent of AlphaFold2 (AF2) models represents another significant step in computationally predicting protein structures. Comparison of experimental P-loop channel structures with their corresponding AF2 models shows consistent folding patterns in experimentally resolved regions. Despite this remarkable progress, many crucial structural details, particularly important for predicting the outcomes of mutations and designing new medically relevant ligands, remain unresolved. Certain methodological challenges currently hinder the direct assessment of such details. Until the next methodological breakthrough occurs, a promising approach to analyzing ion channel structures in greater depth involves integrating various experimental and theoretical methods.

Illuminated giant cells of Characeae comprise alternating areas with H⁺ pump activity and zones with high conductivity for H⁺/OH^–, which create counter-directed H⁺ flows between the medium and the cytoplasm. In areas where H⁺ enters the cell, the pH on the surface (pH_o) increases to pH 10, while the cytoplasmic pH (pH_c) decreases. The lack of the permeant substrate of photosynthesis (CO₂) and the acidic pH_c shift in the region of external alkaline zones redirect electron transport in chloroplasts from CO₂-dependent (assimilatory) pathway to O₂ reduction. This electron transport route is associated with an increase in thylakoid membrane ΔpH and an enhanced nonphotochemical quenching (NPQ) of chlorophyll excitations, which underlies strict coordination between nonuniform distributions of pH_o and photosynthetic activity in resting cells. When the action potential (AP) is generated, the longitudinal pH profile is temporarily smoothed out, while the heterogeneity of the distribution of NPQ and PSII photochemical activity (YII) sharply increases. The damping of the pHo profile is due to the suppression of the H⁺ pump and passive H⁺ conductance under the influence of an almost 100-fold increase in the cytoplasmic of Ca²⁺ level ([Ca²⁺]_c) during AP. The increase in [Ca²⁺]_c stimulates photoreduction of O₂ in chloroplasts under external alkaline zones and, at the same time, arrests the cytoplasmic streaming, which causes the accumulation of excess amounts of H₂O₂ in the cytoplasm in areas of intense production of this metabolite, with a weak effect on areas of CO₂ assimilation. These changes enhance the nonuniform distribution of cell photosynthesis and account for the long-term oscillations of chlorophyll fluorescence F_m' and the quantum efficiency of linear electron flow in microscopic cell areas after the AP generation.

Sterol biosynthesis has evolved early in the history of eukaryotes. In most animals, as well as in primitive fungi, the main sterol is cholesterol. During the process of evolution, fungi acquired the ability to synthesize ergosterol. The pathway of its biosynthesis is more complex than the one of cholesterol biosynthesis. However, the evolutionary choice of most fungi was ergosterol, and the reason for this choice is still debated. In the majority of the works on this issue, the choice of most fungi is associated with the transition to life on land, and, consequently, the danger of cell dehydration. In our review we oppose this point of view. Probably, compared to cholesterol, ergosterol has more pronounced antioxidant properties. Indeed, the presence of three double bonds in the structure of the ergostеrol molecule, as compared to one in cholesterol, relatively increases the likelihood of interaction with reactive oxygen species. Perhaps, the transition to life on land required additional antioxidant protection. Due to the aforementioned structural differences, the molecule of cholesterol is apparently more flexible than that of ergosterol. Experimental data indicate that this feature provides greater membrane flexibility as compared to fungal membranes, as well as a greater ability to compensate for disturbances in the packing of membrane phospholipids. Presumably, for animal cells these qualities turned out to be relatively more important than antioxidant ones, which predetermined their evolutionary choice of sterol.

The paper overviews the results of computational studies of the molecular mechanisms underlying the adaptation of model cell membranes taking place during their interaction with proteins and peptides. We discuss changes in the structural and dynamic parameters of the water–lipid environment, the hydrophobic/hydrophilic organization of the lipid bilayer surface (the so-called “mosaicity”), etc. Taken together, these effects are called the “membrane response” (MR) and constitute the most important ability of the cell membranes to respond specifically and consistently to the incorporation of extraneous agents, primarily proteins and peptides, and their subsequent functioning. The results of the authors’ long-term research in the field of molecular modeling of MR processes with various spatial and temporal characteristics are described, from the effects of binding of individual lipid molecules to proteins to changes in the integral macroscopic parameters of membranes. The bulk of the results were obtained using the “dynamic molecular portrait” approach developed by the authors. The biological role of the observed phenomena and potential ways of rationally designing artificial membrane systems with specified MR characteristics are discussed. This, in turn, is important for targeted changes in the activity profile of proteins and peptides exerting action on biomembranes, not least as promising pharmacological agents.