In the present study, we functionally analyzed the c.67A>T (p.Met23Leu) missense-mutation in the KCNE2 gene of potassium channel Kv11.1 complementary subunit identified in a patient with asymptomatic QT interval prolongation on electrocardiogram. We artificially introduced this substitution into the plasmid encoding the KCNE2 subunit and expressed the mutant gene in Chinese hamster ovary cells together with the wild-type Kv11.1 channel gene to evaluate the effect of the mutation on IKR current parameters. We used a comprehensive approach including the study of the integrated IKr current using whole-cell patch clamp method. The study showed that the c.67A>T mutation (p.Met23Leu) is a gain-of-function type, but the current density carried by Kv11.1 channels is significantly reduced. Fluorescence microscopy showed impaired trafficking of a channel coexpressed with the mutant subunit to the cell surface. We applied molecular modeling to examine the location of the mutant subunit relative to the membrane.

The experimentally obtained structures of 48 ACE 2 receptor complexes with RBD of the S protein of the SARS-CoV and SARS-CoV-2 coronaviruses (including mutant forms of the latter) were evaluated, for which the dissociation constants were calculated. To predict the binding affinity, the ProBAN neural network algorithm developed by the authors earlier was used, as well as a number of other Gibbs free energy estimation algorithms: Prodigy, FoldX, DFIRE, and RosettaDock. A comparison of the evaluation results showed that ProBAN demonstrated the best prediction quality (Pearson correlation coefficient was 0.56 and the mean absolute error was 0.7 kcal/mol). The results we obtained suggested a better quality of affinity prediction for other protein–protein complexes as well. Information about the studied complexes and the prediction results are available in the repository at the link: https://github.com/EABogdanova/ProBAN_RBD-ACE2 .

The paper reports an example of a successful upgrade of the JEOL JEM-2100 analytical transmission electron microscope to a low-resolution cryo-electron microscope, which can be used to optimize sample preparation and to assess preparation quality. As a result of the instrument upgrade, it is possible to obtain subnanometer resolution of protein molecule reconstructions (within 8 Å). The role of graphene and amorphous carbon substrates in preventing the effect of preferential orientation of protein particles in a frozen sample is discussed.

The study involved the fabrication of films with different roughness and scaffolds made of poly-3-hydroxybutyrate using various methods. Chaotic and oriented scaffolds with varying fiber thickness were obtained through the electrospinning method, depending on the polymer concentration and electrospinning parameters. Films with different surface roughness were obtained using spin coating and self-assembly methods. It was demonstrated that the varying microstructure of the surface does not affect the growth of mesenchymal stem cells over the course of 1 week; however, it does influence the morphology of the adhered cells.

The article briefly reviews the history of the development of ideas about the dynamics of proteins and other biopolymers and notes the significant contribution of V.I. Goldansky in organizing and conducting these studies in Russia. The modern development of earlier ideas about the dynamics of biopolymers and protein folding is discussed. It is shown that folding is not an isolated problem and is related to the fundamental dynamic properties of linear polymers in the condensed phase. Analytical methods using approaches based on multidimensional geometry show that the viscosity of the medium is one of the most important factors that determines the rules for the movement of a representative point along the ultramultidimensional potential energy surface (PES). These rules lead to the concentration of trajectories in those regions of the configuration space of a macromolecule that correspond to relatively smooth PES regions, which is important for understanding the reasons for the stability of the results of calculations of large systems using the molecular dynamics (MD) method, despite the fundamental inaccuracy in determining the available force fields. This article also briefly describes a new approach to determine and study the properties of a multidimensional PES, which is based on the features of the topology of the configuration space of linear polymers (and biopolymers), symmetry with respect to permutations of identical chain links, and Morse theory for studying the topography of multidimensional surfaces. Under certain conditions, this approach gives observable analytical results for the topography of the PES and the free energy surface (FES) of a macromolecule and makes it possible to relate the rather heterogeneous results of experiments on protein folding from a unified point of view. At the same time, a new formulation appears for a number of fundamental and controversial issues related to the physical laws of the formation of living systems. In particular, a connection is traced between the temperature regime on the planet and the chemical realization of the energy of nonvalent interactions in a macromolecule, which are necessary for the formation of unique spatial structures of biopolymers.

This paper demonstrates an example of a successful upgrade of a JEOL JEM-2100 analytical transmission electron microscope to a low-resolution cryo-electron microscope designed for routine tasks of sample preparation and quality evaluation. As a result of the upgrade, the instrument allows the subnanometer resolution of protein molecule reconstructions (within 8 Å). The influence of graphene and amorphous carbon support films to prevent the effect of preferred orientation of protein particles in the frozen sample is discussed.

The current state of the protein folding problem and other biopolymers folding is discussed. The concept of a multidimensional potential energy surface and free energy surface for linear polymers is detailed, taking into account the topology of the configuration space and the presence of symmetry elements with respect to the rearrangement of identical monomer units. The presence of kinematic connections for conformational movements in a viscous medium leads to a tendency for the formation of helical structures of linear polymers. The dynamic effects of viscosity also lead to an almost uniform distribution of energy dissipation rates across the nodes of the chain. The combination of free energy surface topography and viscosity effects provides a physical basis for advancing folding theory toward interpreting a variety of experimental observations and elucidating principles of amino acid code formation for 3D protein structures. The relationship between the denaturation temperature of the folded state of the biopolymer and the energy of nonvalent interactions between monomers in the chain is analyzed.

Binding affinity is an important characteristic of protein-protein interactions, and its determination is important for the development of drugs and biotechnological preparations. This paper presents an algorithm based on convolutional neural networks that predicts the value of the dissociation constant in protein-protein complexes based on their spatial structure, as well as data processing and augmentation methods.

In this work we purified Shaker ion channel using two alternative techniques – the detergent-based (CHAPS) and styrene-maleic acid copolymer lipid particles (XIRAN-based). Using XIRAN-based technique, we can obtain higher yield of purified protein. We used atomic force microscopy and transmission electron microscopy methods to visualize the purified single molecules. Atomic force microscopy allows measuring the diameter of the single molecules but does not reveal any high-resolution details. The sizes of individual Shaker molecules isolated by the two purification methods were close to each other.

Для изучения структурных особенностей остановленных элонгационных комплексов, формирующихся в ходе транскрипции нуклеосом РНК-полимеразой 2, предложено использовать подход, основанный на измерении эффективности фёрстеровского резонансного переноса энергии в полиакриламидном геле после разделения интермедиатов транскрипции методом электрофореза. Флуоресцентно-меченые нуклеосомы были получены путем введения пары флуорофоров (донора и акцептора) в соседние супервитки нуклеосомной ДНК. Остановленные элонгационные комплексы формировали, проводя транскрипцию нуклеосом в присутствии ограниченного набора нуклеозидтрифосфатов. Сравнительный анализ эффективности фёрстеровского резонансного переноса энергии для свободных нуклеосом и полученных на их основе элонгационных комплексов с РНК-полимеразой 2 выявил изменение структуры нуклеосом в составе элонгационных комплексов. Показано, что элонгационные комплексы с одинаковой длиной РНК могут существовать в различных конформационных состояниях.

The effects of two types of symmetry for linear polymers are considered: spatial symmetry with respect to translations and rotation of the macromolecule as a whole in a homogeneous viscous medium, and symmetry with respect to permutations of identical monomer units (or sections of the polymer chain with the same chemical structure) in the chain. It is shown that, in a homogeneous viscous medium, for a macromolecule with rigid bonds during relaxation folding, the conservation law is obeyed—the sum of the rotation velocity vectors around torsion angles is equal to zero. Symmetry with respect to permutations of identical monomer units in the polymer chain under certain conditions leads to the formation of energy funnels with the minimal frustration which correspond to helical or multihelical 3D-structures of polymer chain. In this case, there exist the deepest central funnel and less deep satellite funnels, which all are separated from each other by energy barriers. This topography of the energy funnel corresponds to a number of effects that are observed in the kinetics of protein folding (a volcano-like profile of the free energy surface, the sensitivity of protein refolding to denaturing steps, etc.). When calculating the topography of the free energy surface, the characteristic temperature parameter T0 arises and this is defined as potential energy gain due to chain folding per one conformational degree of freedom. It is shown that at T > 0.26 T0, the spatial structure of the folded polymer is destroyed. The parameter T0 and the denaturation temperature in the system under consideration arise from the basic mathematical principles of the arrangement of energy landscapes in the configuration space of torsion angles with the topology of a multidimensional torus and symmetry considerations regarding the permutation of identical monomer units. At biopolymer denaturation temperatures, for example, on the order of 60°C, this ratio leads to an estimate of the energy of nonvalent bonds of monomers on the order of 2.5 kcal/mol per one conformational degree of freedom, which is very similar to hydrogen bonds in aqueous medium. The two types of symmetries under study and their influence on the dynamics of macromolecules and the topography of the energy landscapes of linear polymers can occur simultaneously under certain conditions. The effects that come with it may provide additional information about the prebiological physicochemical evolution of macromolecules in association with the formation of a pool of linear polymers with unique spatial structures.

Цитоскелетные белки септины участвуют во многих клеточных процессах, изменение их экспрессии является маркером онкологических заболеваний. В связи с этим септины могут являться потенциальной мишенью при воздействии на раковые клетки. Для поиска новых малых молекул, влияющих на структурную организацию септиновых филаментов, был проведен виртуальный скрининг библиотеки соединений базы данных PubChem и выбрано наиболее аффинное вещество из всех - флавоноид процианидин В3. С помощью молекулярного моделирования показано, что процианидин В3 взаимодействует с мономером септина SEPT9 в важной для связывания ГТФ области G1- и G4-мотивов и предотвращает димеризацию септиновых мономеров. Следовательно, процианидин В3 может рассматриваться как перспективное соединение для воздействия на структуру септиновых филаментов раковых клеток.

We studied the effect of porous composite scaffolds based on poly(3-hydroxybutyrate) (PHB) loaded with simvastatin on the growth and differentiation of mesenchymal stem cells. The scaffolds have a suitable microstructure (porosity and pore size) and physicochemical properties to support the growth of mesenchymal stem cells. Scaffold loading with simvastatin suppressed cell growth and increased alkaline phosphatase activity, which can attest to their osteoinductive properties.

One of the current problems in regenerative medicine is the search for new approaches for skin restoration. A promising area is the use of biocompatible materials. Such constructs can serve as the basis for biomedical products designed to replace damaged tissue or function as wound dressings. In this work, photopolymerized films based on silk fibroin and methacrylated gelatin (F-MG) were created. An in vitro study revealed that the use of films as a substrate for the cultivation of NIH 3T3 fibroblasts and HaCaT keratinocytes leads to a change in the kinetics of cell growth. According to the MTT assay, the fibroblasts’ proliferation rate was lower on photopolymerized films, while that for keratinocytes was higher compared to culture plastic. The effect of the obtained films on skin regeneration was investigated in vivo in a model of a full-thickness wound of mouse skin. The use of F-MG films as wound dressings contributed to faster wound healing and more complete recovery of the skin structure compared to control (use of gauze). Animals of the experimental group exhibited the formation of hair follicles and the reduction of the scar area after 28 days.