Article
Engineering, Environmental
Mingshan Zhang, Wenhui Li, Zhehui Jin
Summary: Molecular dynamic simulations reveal that deprotonated cyclohexanoic acid and heptanoic acid exhibit different interaction modes with water in pristine and hydroxylated carbon nanopores, which play a crucial role in the removal of NAs by activated carbons.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Materials Science, Multidisciplinary
Leon A. Smook, Guido C. Ritsema van Eck, Sissi de Beer
Summary: Coating sensor surfaces with end-anchored immiscible polymers can significantly increase the sensitivity of vapor sensors at low concentrations, forming surface-bound polymer blends that can concentrate vapors, reaching sorption enhancements of more than one order of magnitude.
ACS APPLIED POLYMER MATERIALS
(2021)
Article
Chemistry, Medicinal
Emmanuel E. Moutoussamy, Hanif M. Khan, Mary F. Roberts, Anne Gershenson, Christophe Chipot, Nathalie Reuter
Summary: This study calculated the binding free energy between a peripheral membrane protein and a phospholipid bilayer using a computational method, and compared it with experimental results. The mechanism of the protein's disengagement from the lipid bilayer during interaction separation was also investigated.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Multidisciplinary
Miguel de la Puente, Rolf David, Axel Gomez, Damien Laage
Summary: The acidity at the air-water interface decreases compared to the bulk, but is higher below the interface. This has important implications for environmental and biochemical processes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Medicinal
Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai
Summary: A new strategy for accurately predicting binding free energies of medium-sized protein-protein complexes within the microsecond timescale is introduced in this article. This strategy combines an ergodic-sampling algorithm known as Gaussian-accelerated molecular dynamics (GaMD) with a geometrical route that uses geometrical restraints to facilitate the physical separation of the binding partners. Numerical applications demonstrate the effectiveness of this strategy with low errors in binding free energy calculations for various protein-protein complexes. Compared to the classical geometrical route, this new strategy shows improved convergence properties and robustness, making it suitable for studying recognition-association phenomena in physical, biological, and medicinal chemistry.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Medicinal
Haohao Fu, Christophe Chipot, Xueguang Shao, Wensheng Cai
Summary: A new strategy for predicting binding free energies of protein-protein complexes is introduced in this article. By combining an ergodic-sampling algorithm with a geometrical route, accurate calculations can be achieved within the microsecond timescale. The strategy reduces computational cost and human effort, and has shown good convergence properties and robustness for protein-protein complexes. Numerical applications have demonstrated low errors for various protein complexes. The strategy has broad applications in physical, biological, and medicinal chemistry.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Min Liu, Huashan Liu, Hailong Peng
Summary: Surface-induced phenomena, such as dynamic acceleration, surface anchoring, and orientational wetting, were studied in this report through classic molecular dynamics simulations on the free-standing surface of imidazolium-based ionic liquids. The presence of significant orientational wetting on the [C(10)mim][PF6] surface was observed, with the wetting strength showing a diverging tendency. The study also connected the results to the dynamics in bulk liquids, highlighting the importance of collective dynamics in the bulk on orientational wetting and surface dynamics in the ionic liquids.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Takamasa Saito, Eita Shoji, Masaki Kubo, Takao Tsukada, Gota Kikugawa, Donatas Surblys
Summary: This study evaluated the affinity between a surface-modified inorganic solid and an organic solvent by calculating the work of adhesion at the interface. Results showed that the surface coverage of the modifier affected the work of adhesion, with solvent molecules penetrating the modification layer at high coverage, increasing the adhesion.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Computer Science, Interdisciplinary Applications
Rodrigo Ochoa, Miguel A. Soler, Alessandro Laio, Pilar Cossio
Summary: PARCE is an open source Protocol for Amino acid Refinement through Computational Evolution, which efficiently explores novel sequences with potential better affinities towards targets using random mutations, molecular dynamics simulations, and multiple scoring functions. This protocol offers a new method for the computational design of peptides and proteins as binders for diagnosis and therapeutics.
COMPUTER PHYSICS COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Tainah Dorina Marforio, Alessandro Calza, Edoardo Jun Mattioli, Francesco Zerbetto, Matteo Calvaresi
Summary: The study quantitatively investigated the interactions between twenty proteinogenic amino acids and C-60 using molecular dynamics simulations. It was found that the conserved amino acid backbone and the contribution from amino acid side chains played key roles in the binding, with influences from van der Waals, hydrophobic, and polar solvation interactions. The presence of C-60 led to specific configurations and geometric structures in the interacting residues and amino acid backbone.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Engineering, Chemical
Gonzalo R. Quezada, Roberto E. Rozas, Pedro G. Toledo
Summary: The adsorption of partially hydrolyzed polyacrylamide (HPAM) on quartz surfaces is influenced by salts and surface charge under conditions of high salt and wide pH range, primarily achieved via salt bridges.
MINERALS ENGINEERING
(2021)
Article
Chemistry, Physical
Tan Hu, Zhuo Zhang, Meital Reches
Summary: The study designed a self-standing superhydrophobic material through the self-assembly of a functionalized aromatic amino acid. The material exhibited fibrous structures and showed high mechanical strength and resistance to enzymatic degradation.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2024)
Article
Chemistry, Physical
Monika Michaelis, Massimo Delle Piane, Dirk Rothenstein, Carole C. Perry, Lucio Colombi Ciacchi
Summary: In this study, four challenges hindering the understanding of ZnO/biomolecule interfaces at the atomic scale were overcome. The adsorption free energies predicted showed remarkable agreement with experimental measurements, revealing the mechanism of interactions between ZnO surface and amino acids.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Gerhard Koenig, Benjamin Ries, Philippe H. Huenenberger, Sereina Riniker
Summary: Alchemical free energy calculations often require intermediate states along a coupling parameter lambda to ensure phase space overlap for converged results. The lambda-EDS scheme combines minimum variance pathway and EDS methods to improve sampling efficiency, allowing larger steps along the alchemical pathway and eliminating the need for soft-core potentials.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Multidisciplinary
Da-Shiuan Chiou, Yu-Chun Chuang, Chung-Kai Chang, Cheng-Hsun Hsu, Li-Chiang Lin, Dun-Yen Kang
Summary: This paper presents a novel methodology for obtaining free energy profiles and self-diffusivity of gases in crystalline microporous materials, using X-ray diffraction on powder samples instead of single crystal samples. The experimental results obtained using this approach for CO2 and CH4 diffusion properties in a metal-organic framework, CAU-10-H, match those obtained through molecular simulations. This XRD-based methodology can be applied in the design of MOFs for membrane gas separation.
Review
Chemistry, Physical
Daniel Espiritu, Anna K. Gribkova, Shubhangi Gupta, Alexey K. Shaytan, Anna R. Panchenko
Summary: Cancer involves the interplay between the genome and epigenome at the cellular level, with nucleosomes playing a crucial role. Mutations, changes in expression, and slicing of histones can affect epigenetic dysregulation and carcinogenesis. The differential expression of histone variants and isoforms is linked to cancer phenotypes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Multidisciplinary Sciences
Grigoriy A. Armeev, Anastasiia S. Kniazeva, Galina A. Komarova, Mikhail P. Kirpichnikov, Alexey K. Shaytan
Summary: Nucleosomes tightly wrap around 147 DNA base pairs with an octamer of histone proteins, and their dynamics enable DNA unwrapping and sliding. Molecular dynamics simulations revealed functional modes of nucleosome dynamics such as DNA breathing, unwrapping, twisting, and sliding. This study highlights the importance of nucleosomal DNA dynamics in chromatin conformational variability and the effects of chromatin modifications.
NATURE COMMUNICATIONS
(2021)
Article
Anatomy & Morphology
Dmitry Bagrov, Grigory S. Glukhov, Andrey Moiseenko, Maria G. Karlova, Daniil S. Litvinov, Petr A. Zaitsev, Liubov Kozlovskaya, Anna A. Shishova, Anastasia A. Kovpak, Yury Y. Ivin, Anastasia N. Piniaeva, Alexey S. Oksanich, Viktor P. Volok, Dmitry Osolodkin, Aydar A. Ishmukhametov, Alexey M. Egorov, Konstantin Shaitan, Mikhail P. Kirpichnikov, Olga S. Sokolova
Summary: This study characterized the beta-propiolactone inactivated SARS-CoV-2 virions using TEM and AFM, finding that samples prepared using SEC and IEC retained more spikes on the surface and the S proteins were in the pre-fusion conformation. Analytical TEM showed that the inactivated virions retained nucleic acid, demonstrating their potential as a vaccine candidate.
MICROSCOPY RESEARCH AND TECHNIQUE
(2022)
Article
Virology
Marine E. Bozdaganyan, Konstantin V. Shaitan, Mikhail P. Kirpichnikov, Olga S. Sokolova, Philipp S. Orekhov
Summary: This study analyzed the diversity of neutralizing antibody epitopes in the receptor-binding domain (RBD) of SARS-CoV-2 S-protein and assessed the effects of single and multiple mutations on its binding affinity to antibodies and the human ACE2 receptor. The results indicate that multiple mutations may lead to broader antigenic escape, while natural mutations tend to reduce binding affinity to antibodies.
Article
Polymer Science
Andrei A. Dudun, Elizaveta A. Akoulina, Vsevolod A. Zhuikov, Tatiana K. Makhina, Vera V. Voinova, Nikita V. Belishev, Dolgor D. Khaydapova, Konstantin V. Shaitan, Garina A. Bonartseva, Anton P. Bonartsev
Summary: This study investigated the effect of various cultivation conditions on alginate biosynthesis using Azotobacter vinelandii 12 and studied the physicochemical properties of the produced bacterial alginate. The study demonstrated the applicability of bacterial alginate for tissue engineering and showed that high molecular weight and high acetylation level alginate had low cytotoxicity.
Review
Chemistry, Multidisciplinary
Philipp S. Orekhov, Marine E. Bozdaganyan, Natalia Voskoboynikova, Armen Y. Mulkidjanian, Maria G. Karlova, Anna Yudenko, Alina Remeeva, Yury L. Ryzhykau, Ivan Gushchin, Valentin I. Gordeliy, Olga S. Sokolova, Heinz-Juergen Steinhoff, Mikhail P. Kirpichnikov, Konstantin V. Shaitan
Summary: Amphiphilic copolymers with alternating hydrophilic and hydrophobic units can extract membrane proteins directly from lipid membranes, forming nanoparticles suitable for various spectroscopy and biophysical techniques. Copolymer-encased nanolipoparticles have proven to be important in structural biology applications such as cryo-electron microscopy.
Article
Materials Science, Multidisciplinary
Meng Luo, Konstantin Shaitan, Xiaoyan Qu, Anton P. Bonartsev, Bo Lei
Summary: Rare earth-based biomaterials possess representative optical/magnetic properties and special biological properties, which make them potential candidates for wound healing and skin tissue regeneration. Inorganic-organic hybrid rare earth-based biomaterials demonstrate promising applications in wound healing and repair.
APPLIED MATERIALS TODAY
(2022)
Correction
Biophysics
Yu. M. Efremov, D. V. Bagrov, M. P. Kirpichnikov, K. V. Shaitan
COLLOIDS AND SURFACES B-BIOINTERFACES
(2022)
Review
Oncology
Anton P. Bonartsev, Bo Lei, Margarita S. Kholina, Ksenia A. Menshikh, Dmitriy S. Svyatoslavov, Svetlana I. Samoylova, Mikhail Y. Sinelnikov, Vera V. Voinova, Konstantin V. Shaitan, Mikhail P. Kirpichnikov, Igor V. Reshetov
Summary: The use of bioengineering methods for experimental modeling of cancer, particularly head and neck squamous cell carcinomas (HNSCC), shows great promise for testing novel anticancer drugs and diagnostics. Various bioengineering techniques have been developed to model HNSCC tumors, including genetic engineering, exposure experiments, cell culture methods, microfluidics, and cell co-culture. These models can contribute to the development of new approaches for the diagnosis, prevention, and treatment of HNSCC.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2022)
Article
Polymer Science
Roman Chernozem, Igor O. Pariy, Artem Pryadko, Anton P. Bonartsev, Vera V. Voinova, Vsevolod A. Zhuikov, Tatiana K. Makhina, Garina A. Bonartseva, Konstantin Shaitan, Vladimir V. Shvartsman, Doru C. Lupascu, Konstantin N. Romanyuk, Andrei L. Kholkin, Roman A. Surmenev, Maria A. Surmeneva
Summary: Comprehensive research has revealed that the thermal behavior, molecular structure, and crystalline structure of PHB and PHB-HV films are influenced by their thickness, molecular weight, and 3-HV content. Increasing film thickness leads to increased isotropic crystal orientation, while decreasing PHB molecular weight results in a reduced number of piezoactive domains. The addition of 3-HV in PHB-HV causes anisotropy in the crystalline structure and decreases melting temperature and degree of crystallinity. Furthermore, increasing 3-HV content improves the smoothness of PHB-HV films.
Review
Virology
Aleksandr V. Kudriavtsev, Anna V. Vakhrusheva, Valery N. Novoseletsky, Marine E. Bozdaganyan, Konstantin V. Shaitan, Mikhail P. Kirpichnikov, Olga S. Sokolova
Summary: The evolution and emergence of new mutations in viruses, such as the Omicron strain of SARS-CoV-2, impact their transmissibility and pathogenicity. This evolution may be influenced by the virus adapting to therapeutic agents and escaping vaccine-induced and natural immunity. Understanding and monitoring the key mutations that contribute to immune escape and high receptor affinity in Omicron can inform vaccine and therapeutic development to control the direction of the COVID-19 pandemic.
Article
Polymer Science
Viktoryia Kulikouskaya, Viktoryia V. Nikalaichuk, Anton P. Bonartsev, Elizaveta A. Akoulina, Nikita Belishev, Irina Demianova, Dariana Chesnokova, Tatiana K. Makhina, Garina A. Bonartseva, Konstantin Shaitan, Kseniya S. Hileuskaya, Vera V. Voinova
Summary: Surface morphology plays a crucial role in cell attachment and proliferation. Different films with microstructured surfaces made of biodegradable polymers, poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-co-HV), of varying molecular weights were investigated. The study found that stem cells exhibit different behaviors depending on the surface morphology of the films.
Article
Biochemistry & Molecular Biology
Andrey Moiseenko, Dmitry Bagrov, Mikhail F. Vorovitch, Victoria Uvarova, Maxim M. Veselov, Anastasia Kashchenko, Alla L. Ivanova, Dmitry Osolodkin, Alexey M. Egorov, Aydar A. Ishmukhametov, Konstantin Shaitan, Olga S. Sokolova
Summary: This article provides a detailed analysis of the size and structure of the inactivated TBEV vaccine strain, using multiple analytical methods. The results show the monodispersity of the particles and their similarity in size, as well as the presence of specific protein molecules and RNA.
Article
Biochemistry & Molecular Biology
Irina I. Zharkova, Aleksey V. Volkov, Aleksandr A. Muraev, Tatiana K. Makhina, Vera V. Voinova, Valentina M. Ryabova, Yulia V. Gazhva, Alena S. Kashirina, Aleksandra V. Kashina, Garina A. Bonartseva, Vsevolod A. Zhuikov, Konstantin V. Shaitan, Mikhail P. Kirpichnikov, Sergey Yu. Ivanov, Anton P. Bonartsev
Summary: The biocompatibility of scaffolds in tissue engineering is still an urgent problem. A porous scaffold with a special design was used to guide cell growth and tissue development. Two types of structures were obtained from poly(3-hydroxybutyrate) (PHB) using a salt leaching technique. These scaffolds were suitable for the cultivation of rat mesenchymal stem cells and 3T3 fibroblasts in vitro, and they caused moderate inflammation and the formation of a fibrous capsule when implanted in older rats. A conduit made from PHB/PHBV tube with the scaffold-2 as a filler allowed soft connective tissue sprouting without any visible inflammatory processes when implanted in older rats.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Nanoscience & Nanotechnology
Artyom S. A. Pryadko, Yulia R. Mukhortova, Roman V. Chernozem, Igor Pariy, Svetlana I. Alipkina, Irina I. Zharkova, Andrey A. Dudun, Vsevolod A. Zhuikov, Anastasia M. Moisenovich, Garina A. Bonartseva, Vera V. Voinova, Dariana V. Chesnokova, Alexey A. Ivanov, Daria Yu. Travnikova, Konstantin V. Shaitan, Anton P. Bonartsev, Dmitry V. Wagner, Lada E. Shlapakova, Roman A. Surmenev, Maria A. Surmeneva
Summary: Magnetically responsive composite polymer scaffolds have great potential for various biomedical applications. In this study, electrospun composite scaffolds made of polyhydroxybutyrate (PHB) and magnetite (Fe3O4) particles were investigated for their degradation properties and mechanical characteristics. The results showed that particle size and surface functionalization affected the mechanical properties of the scaffolds, and the composite scaffolds exhibited biocompatibility and promoted cell proliferation.
ACS APPLIED BIO MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Michal Novotny, Matus Dubecky, Frantisek Karlicky
Summary: This paper investigates the accuracy of different DFT-based computational approaches in calculating the equilibrium lattice constants and exfoliation energy of hexagonal boron nitride (h-BN). The results are compared with experiments and reference QMC calculations to evaluate the accuracy of these computational methods.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Luigi Crisci, Federico Coppola, Alessio Petrone, Nadia Rega
Summary: The charge transfer dynamics in asymmetrically substituted indenotetracene molecules upon photo-excitation were investigated using real-time time-dependent density functional theory simulations. The study found that the electron-donating character of the substituents affects the overall electronic energy spacing and ultrafast charge transfer dynamics.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Vasilii Korotenko, Hendrik Zipse
Summary: The stability of various radicals and molecules has been studied using different theoretical methods, and good correlations between theoretical calculations and experimental results have been found. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have also been investigated.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
Article
Chemistry, Multidisciplinary
Oleg Egorov, Michael Rey, Dominika Viglaska, Andrei V. Nikitin
Summary: In this work, the rovibrational energy levels of four isotopologues of methylene were calculated using a new accurate ab initio potential energy surface. The accuracy of the calculations was improved by considering scalar relativistic effects, DBOC, and high-order electronic correlations. For the first time, all available experimental rovibrational transitions were reproduced with high accuracy, without any empirical corrections.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2024)
