I. B. Kovalenko
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View article: Features of the Electrostatic Interaction of Methylene Blue with the Protein Coat of Flaviviruses
Features of the Electrostatic Interaction of Methylene Blue with the Protein Coat of Flaviviruses Open
Among the many pharmacological properties of methylene blue, its antiviral activity against enveloped viruses, including flaviviruses, is well known. Flaviviruses pose a global threat to human health. This group of viruses includes Zika vi…
View article: Investigation of Porin-Dependent Translocation of Methylene Blue and Gentamicin through the Outer Membrane of Gram-Negative Bacteria Using Molecular Dynamics Methods
Investigation of Porin-Dependent Translocation of Methylene Blue and Gentamicin through the Outer Membrane of Gram-Negative Bacteria Using Molecular Dynamics Methods Open
The outer membrane of Gram-negative bacteria serves as a critical barrier to the permeability of antimicrobial compounds. Porin channels are believed to be the primary route for the penetration of hydrophilic molecules with a molecular wei…
View article: Exploring tubulin-paclitaxel binding modes through extensive molecular dynamics simulations
Exploring tubulin-paclitaxel binding modes through extensive molecular dynamics simulations Open
View article: Control of the force-bearing properties of microtubule-associated proteins via stalk/linker regions: insights from the NDC80 complex
Control of the force-bearing properties of microtubule-associated proteins via stalk/linker regions: insights from the NDC80 complex Open
Many microtubule-associated proteins (MAPs) function under mechanical loads. Among them, motor proteins and passive couplers link microtubules with other cytoskeletal filaments, membranous structures and diverse scaffolds to enable cell sh…
View article: The Impact of a Catalytic Site Mutation on the Shape and Mechanics of Tubulin Protofilaments
The Impact of a Catalytic Site Mutation on the Shape and Mechanics of Tubulin Protofilaments Open
Alpha-beta heterodimers of tubulin proteins serve as the building blocks of microtubules, which are key biopolymers forming one of the principal systems of the cellular cytoskeleton. A detailed study of these building blocks, as well as th…
View article: Plastocyanin and Cytochrome f Complex Structures Obtained by NMR, Molecular Dynamics, and AlphaFold 3 Methods Compared to Cryo-EM Data
Plastocyanin and Cytochrome f Complex Structures Obtained by NMR, Molecular Dynamics, and AlphaFold 3 Methods Compared to Cryo-EM Data Open
Plastocyanin is a small mobile protein that facilitates electron transfer through the formation of short-lived protein–protein complexes with cytochrome bf and photosystem 1. Due to the transient nature of plastocyanin–cytochrome f complex…
View article: Cationic Biocides Tend to Embed into the Inner Layer of the Model Outer Membrane Vesicles of Gram-negative Bacteria: Computational Insights
Cationic Biocides Tend to Embed into the Inner Layer of the Model Outer Membrane Vesicles of Gram-negative Bacteria: Computational Insights Open
The outer membrane vesicles (OMVs), produced by many pathogenic bacteria, play a significant role in bacterial pathogenesis. They promote bacterial resistance to antibiotics and act as natural protective barriers. The study of OMVs is esse…
View article: Patellar motion and dysfunction of its stabilizers in a biomechanical model of the knee joint
Patellar motion and dysfunction of its stabilizers in a biomechanical model of the knee joint Open
Aim. To develop a biomechanical model of the knee joint, including a detailed representation of the patellofemoral segment for the normal anatomy of bones, joints, ligaments and muscles, and study patellar movement during passive knee flex…
View article: Molecular dynamics of tubulin protofilaments and the effect of taxol on their bending deformation
Molecular dynamics of tubulin protofilaments and the effect of taxol on their bending deformation Open
Несмотря на широкое распространение и применение препаратов химиотерапии рака, остаются невыясненными молекулярные механизмы действия многих из них. Известно, что некоторые из этих препаратов, например таксол, оказывают влияние на динамику…
View article: Role of Charged Amino Acid Residues of Plastocyanin in Interaction with Cytochrome B6f Complex and Photosystem I of Higher Plants: A Study Using the Brownian Dynamics Method
Role of Charged Amino Acid Residues of Plastocyanin in Interaction with Cytochrome B6f Complex and Photosystem I of Higher Plants: A Study Using the Brownian Dynamics Method Open
Plastocyanin is an electron carrier protein in the electron transport chain of chloroplasts, carrying out the transfer of an electron from cytochrome f of the cytochrome b6f complex to photosystem I. Using the method of Brownian dynamics, …
View article: Interaction of Methylene Blue with Severe Acute Respiratory Syndrome Coronavirus 2 Envelope Revealed by Molecular Modeling
Interaction of Methylene Blue with Severe Acute Respiratory Syndrome Coronavirus 2 Envelope Revealed by Molecular Modeling Open
Methylene blue has multiple antiviral properties against Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2). The ability of methylene blue to inhibit different stages of the virus life cycle, both in light-independent and…
View article: High-Performance Computing of Microtubule Protofilament Dynamics by Means of All-Atom Molecular Modeling
High-Performance Computing of Microtubule Protofilament Dynamics by Means of All-Atom Molecular Modeling Open
Molecular dynamics (MD) simulation is a useful tool for understanding biological systems at the level of individual molecules and atoms. However, studying such massive biological systems as microtubules and even their constituent component…
View article: Analysis of Brownian and molecular dynamics trajectories of to reveal the mechanisms of protein-protein interactions
Analysis of Brownian and molecular dynamics trajectories of to reveal the mechanisms of protein-protein interactions Open
В работе предложен набор достаточно простых алгоритмов, который может быть применен для анализа широкого круга белок-белковых взаимодействий. В настоящей работе мы совместно используем методы броуновской и молекулярной динамики для описани…
View article: Design of a Molecular Dynamics Model for High-Performance Computing of Conformational Changes in Microtubule Protofilaments Associated with the Anticancer Drug Taxol
Design of a Molecular Dynamics Model for High-Performance Computing of Conformational Changes in Microtubule Protofilaments Associated with the Anticancer Drug Taxol Open
Molecular dynamics models of tubulin tetramers in complex with the anticancer drug taxol were created based on high-resolution spatial structures (PDB ID 3J6G). We tested performance of various computational architectures in molecular dyna…
View article: Opportunities and Challenges to Integrate Artificial Intelligence into Manufacturing Systems: Thoughts from a Panel Discussion
Opportunities and Challenges to Integrate Artificial Intelligence into Manufacturing Systems: Thoughts from a Panel Discussion Open
Rapid advances in artificial intelligence (AI) have the potential to significantly increase the productivity, quality, and profitability in future manufacturing systems. Traditional mass-production will give way to personalized production,…
View article: Insights into the Formation of Intermolecular Complexes of Fluorescent Probe 10-N-Nonyl Acridine Orange with Cardiolipin and Phosphatidylglycerol in Bacterial Plasma Membrane by Molecular Modeling
Insights into the Formation of Intermolecular Complexes of Fluorescent Probe 10-N-Nonyl Acridine Orange with Cardiolipin and Phosphatidylglycerol in Bacterial Plasma Membrane by Molecular Modeling Open
In this article, we used molecular dynamics (MD), one of the most common methods for simulations of membranes, to study the interaction of fluorescent membranotropic biological probe 10-N-nonyl acridine orange (NAO) with the bilayer, mimic…
View article: Calculation of Electrostatic Potential Field of Coronavirus S Proteins for Brownian Dynamics Simulations
Calculation of Electrostatic Potential Field of Coronavirus S Proteins for Brownian Dynamics Simulations Open
The Brownian dynamics method can give insight into the initial stages of the interaction of antiviral drug molecules with the structural components of bacteria or viruses. RAM of conventional personal computer allows calculation of Brownia…
View article: Molecular, Brownian, kinetic and stochastic models of the processes in photosynthetic membrane of green plants and microalgae
Molecular, Brownian, kinetic and stochastic models of the processes in photosynthetic membrane of green plants and microalgae Open
View article: Electrostatic Map of the SARS-CoV-2 Virion Specifies Binding Sites of the Antiviral Cationic Photosensitizer
Electrostatic Map of the SARS-CoV-2 Virion Specifies Binding Sites of the Antiviral Cationic Photosensitizer Open
Electrostatics is an important part of virus life. Understanding the detailed distribution of charges over the surface of a virus is important to predict its interactions with host cells, antibodies, drugs, and different materials. Using a…
View article: Interaction of cationic antiseptics with cardiolipin-containing model bacterial membranes
Interaction of cationic antiseptics with cardiolipin-containing model bacterial membranes Open
Plasma membrane is one of the major targets for cationic antiseptics (CA). The study was aimed to assess molecular effects of CAs of different chemical classes on cardiolipin-containing regions of bacterial plasma membranes. The study was …
View article: What Binds Cationic Photosensitizers Better: Brownian Dynamics Reveals Key Interaction Sites on Spike Proteins of SARS-CoV, MERS-CoV, and SARS-CoV-2
What Binds Cationic Photosensitizers Better: Brownian Dynamics Reveals Key Interaction Sites on Spike Proteins of SARS-CoV, MERS-CoV, and SARS-CoV-2 Open
We compared the electrostatic properties of the spike proteins (S-proteins) of three coronaviruses, SARS-CoV, MERS-CoV, and SARS-CoV-2, and their interactions with photosensitizers (PSs), octacationic octakis(cholinyl)zinc phthalocyanine (…
View article: α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics
α-tubulin tail modifications regulate microtubule stability through selective effector recruitment, not changes in intrinsic polymer dynamics Open
View article: The Photosensitizer Octakis(cholinyl)zinc Phthalocyanine with Ability to Bind to a Model Spike Protein Leads to a Loss of SARS-CoV-2 Infectivity In Vitro When Exposed to Far-Red LED
The Photosensitizer Octakis(cholinyl)zinc Phthalocyanine with Ability to Bind to a Model Spike Protein Leads to a Loss of SARS-CoV-2 Infectivity In Vitro When Exposed to Far-Red LED Open
Photodynamic inactivation of pathogenic microorganisms can be successfully used to eradicate pathogens in localized lesions, infected liquid media, and on various surfaces. This technique utilizes the photosensitizer (PS), light, and molec…
View article: Update on Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein-Protein Interactions
Update on Performance Analysis of Different Computational Architectures: Molecular Dynamics in Application to Protein-Protein Interactions Open
Molecular dynamics has proved itself as a powerful computer simulation method to study dynamics, conformational changes, and interactions of biological macromolecules and their complexes. In order to achieve the best performance and effici…
View article: Empirical Simulation of Redox Reactions between Proteins in Solution
Empirical Simulation of Redox Reactions between Proteins in Solution Open
Предложен простой эмпирический подход к описанию окислительно-восстановительных реакций между белковыми молекулами в моделях броуновской динамики.В основе подхода лежит предположение об экспоненциальной зависимости скорости переноса электр…
View article: Modeling the Movement of Kinetochore Complex Ndc80 along a Microtubule
Modeling the Movement of Kinetochore Complex Ndc80 along a Microtubule Open
Свойства взаимодействия хромосом с микротрубочками в митозе во многом зависят от характеристик контактов белкового комплекса NDC80 с тубулином.В данной работе с помощью методов молекулярной динамики было показано, что взаимодействие между …
View article: Sensitivity of antibiotic resistant coagulase-negative staphylococci to antiseptic piсloxydin in eye drops Vitabact
Sensitivity of antibiotic resistant coagulase-negative staphylococci to antiseptic piсloxydin in eye drops Vitabact Open
Background. Coagulase-negative staphylococci (CNS), primarily Staphylococcus epidermidis, predominate in the normal microflora of the eye. However, due to irrational antibiotic therapy, resistant strains are widely distributed among CNS. O…
View article: Microtubule protofilament bending characterization
Microtubule protofilament bending characterization Open
Работа посвящена анализу конформационных изменений в димерах и тетрамерах тубулина, в частности оценке изгиба составленных из них протофиламентов. В работе рассмотрено три недавно использованных подхода для оценки изгиба тубулиновых протоф…
View article: Brownian dynamics simulation of cytochrome c diffusion and binding with cytochrome c1 in mitochondrial crista
Brownian dynamics simulation of cytochrome c diffusion and binding with cytochrome c1 in mitochondrial crista Open
Cytochrome c (Cc) protein shuttles electrons from respiratory chain complex III — from cytochrome c1 (Cc1) subunit — to complex IV during oxidative phosphorylation, in intermembrane space of mitochondria and cristae lumen. With Leigh syndr…
View article: Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability
Mechanical properties of tubulin intra- and inter-dimer interfaces and their implications for microtubule dynamic instability Open
Thirteen tubulin protofilaments, made of αβ-tubulin heterodimers, interact laterally to produce cytoskeletal microtubules. Microtubules exhibit the striking property of dynamic instability, manifested in their intermittent growth and shrin…