Article
Biochemical Research Methods
Anja Conev, Mauricio Menegatti Rigo, Didier Devaurs, Andre Faustino Fonseca, Hussain Kalavadwala, Martiela Vaz de Freitas, Cecilia Clementi, Geancarlo Zanatta, Dinler Amaral Antunes, Lydia E. Kavraki
Summary: Proteins are dynamic macromolecules that play vital roles in cells, and understanding their conformational landscapes is crucial for understanding their function. Our new approach, EnGens, provides a unified framework for generating and analyzing representative protein conformational ensembles from available structural datasets. These representative ensembles can be used for various downstream tasks such as protein-ligand docking, protein dynamics modeling, and analysis of mutations.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Polymer Science
Jingjie Su, Tingting Sun, Yan Wang, Yu Shen
Summary: Molecular dynamics simulation was used to explore the effect of electric field on the structure of Glucagon-like Peptide-2 (GLP-2). The stable α-helix structure of GLP-2 was unwound and transformed into an unstable Turn and Coil structure under the electric field. The degree of unwinding was not linearly related to the electric field intensity, with a maximum at E = 0.5 V/nm. Under weak electric fields, the secondary structure of GLP-2 became looser and chain entropy increased. At a certain electric field strength, the electric force of charged residues reached equilibrium, leading to reduced residue freedom, decreased entropy, increased enthalpy, and enhanced interaction between adjacent residues.
Article
Chemistry, Physical
Sohang Kundu, Nancy Makri
Summary: This study proposes a new algorithm, SMatQCPI, for simulating the interaction between a quantum system and its environment in nonadiabatic dynamics. The algorithm eliminates the tensor storage requirements and achieves high efficiency in challenging regimes of incoherent dynamics by driving quantum paths with classical trajectories.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Wendi Luo, Xiaocui Fang, Chen Wang, Yanlian Yang, Bin Tu, Qiaojun Fang
Summary: Peptide-modified delivery systems have great potential in improving targeting specificity, biocompatibility, and stability. However, designing a peptide-decorated surface with specific function remains challenging due to a lack of understanding of the interactions between surface-bound peptide ligands and their receptors.
Article
Polymer Science
Qun Zhang, Dongqing Shao, Peng Xu, Zhouting Jiang
Summary: This study investigated the effect of pulsed and oscillating electric fields on the conformational properties of all-alpha proteins. Molecular dynamics simulations were used to analyze the structural characteristics of the protein samples. The results showed that higher frequencies of the electric field influenced the rapid response to secondary structural transitions, but had a diminished effect on conformational changes measured by RMSD. The dipole moment analysis revealed a direct relationship between the magnitude and frequency of the dipole moment and the strength and frequency of the external electric field. The type of electric field also played a role, with pulsed electric fields leading to larger average values of RMSD and RMSF for the whole protein. Additionally, the secondary structure analysis showed simultaneous transitions of alpha-helix segments to turns or random coils in a pulsed electric field, while different characteristic times were observed in an oscillating electric field. The study also demonstrated that proteins with fewer charged residues or more residues forming alpha-helical structures exhibited higher conformational stability. These findings have important theoretical implications for understanding the effect of frequency and expression form of external electric fields on conformational changes in all-alpha proteins with charged residues and provide guidance for potential applications.
Article
Biochemistry & Molecular Biology
Neha V. Kalmankar, Bhuvaneshwari Rajendrakumar Gehi, Ramanathan Sowdhamini
Summary: Cyclotides extracted from Clitoria ternatea can inhibit the aggregation of beta-amyloid peptides, reduce oxidative stress, and weaken inter-strand hydrogen bonds of A beta peptides, thereby opening up their beta-sheet conformation. This study provides novel structural insights on the interaction between cyclotides and A beta fibrils and describes their potential in anti-amyloid aggregation.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Yonatan Kurniawan, Cody L. Petrie, Kinamo J. J. Williams, Mark K. Transtrum, Ellad B. Tadmor, Ryan S. Elliott, Daniel S. Karls, Mingjian Wen
Summary: This paper investigates the quantification of parametric uncertainty in classical empirical interatomic potentials using Bayesian and frequentist methods. It reveals that these potentials are typically insensitive and parameters are unidentifiable. Information geometry is used to explain the underlying cause and suggest new parameterizations and simplified models.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Applied
Tong Lou, Xiuqin Bai, Xiaoyan He, Ying Yang, Chengqing Yuan
Summary: Biofouling is a serious issue in marine environments that can be addressed by modifying contact surfaces with antimicrobial peptides. This study utilized molecular dynamics simulations to analyze peptide attachment behaviors on different Al-based surfaces, finding that surface atom distribution and water molecules play key roles. Surface modification with active groups like amino, hydroxyl, and carboxyl was shown to effectively capture peptides, offering insights for developing new peptides for ship antifouling applications.
PROGRESS IN ORGANIC COATINGS
(2021)
Article
Physics, Multidisciplinary
Jose Luis Alonso, Carlos Bouthelier-Madre, Jesus Clemente-Gallardo, David Martinez-Crespo, Javier Pomar
Summary: The paper discusses the nonlinear relationship of the Ehrenfest dynamics on systems defined by a probability density and the obstruction to define a consistent dynamics for the first quantum moment of the distribution. It argues that only a finite number of higher order quantum moments are physically measurable. An effective solution for the hybrid dynamics problem is proposed based on approximating the distribution by these moments and representing the states by them.
EUROPEAN PHYSICAL JOURNAL PLUS
(2023)
Article
Chemistry, Physical
N. Yu. Kruchinin, M. G. Kucherenko
Summary: The study utilizing molecular dynamics shows that the conformational structure of polyampholytic polypeptides adsorbed on the surface of gold nanowires and on transversely polarized nanowires can be rearranged by electrically induced changes. The thickness and structure of the polyampholytic fringe vary depending on the surface properties.
SURFACES AND INTERFACES
(2021)
Article
Chemistry, Applied
Ming Lei, Weian Huang, Zhehui Jin, Jinsheng Sun, Mingshan Zhang, Shuangliang Zhao
Summary: This study investigates the aggregation behavior of carboxymethyl chitosan (CMCS) in water using molecular dynamics simulations. The effects of degrees of deacetylation (DD) and substitution (DS) and ionization states on CMCS aggregation are also examined. The results show that CMCS prefers to aggregate in neutral condition, forming multimeric forms with interlaced stacking of molecular chains. The presence of specific intra- and intermolecular interactions stabilizes the aggregation structures.
CARBOHYDRATE POLYMERS
(2022)
Article
Biochemistry & Molecular Biology
David L. Cheung
Summary: Solid surfaces have a significant impact on the aggregation and assembly of biomolecular systems, with protein fibrillation being an important example. The molecular and oligomer structures adopted by proteins on surfaces play a crucial role in the rate of fibrillation. Molecular dynamics simulation is used in this study to investigate the aggregation of a model amyloidogenic peptide on a gold surface. The simulations reveal that the peptide adopts different conformations on the surface compared to bulk solution, resulting in significant differences in the formed oligomer structures. The adsorption of oligomers on the surface can also lead to restructuring, offering an explanation for the inhibition of fibrillation observed experimentally.
Article
Engineering, Electrical & Electronic
Jae-Kyeong Kim, Kyeon Hur
Summary: This paper investigates the relationship between the accuracy of finite difference-based trajectory sensitivity (FDTS) analysis and the perturbation size in non-smooth systems. The study reveals that the approximation accuracy is significantly influenced by the perturbation size, and linear approximation is the most suitable method for practical applications.
INTERNATIONAL JOURNAL OF ELECTRICAL POWER & ENERGY SYSTEMS
(2024)
Article
Biochemistry & Molecular Biology
Puspita Halder, Pralay Mitra
Summary: Human familial prion diseases are associated with different single-point mutants of the gene coding for prion protein, with 12 identified pathogenic mutants of human prion protein. These mutants exhibit unfolding of the helical structures, extension and generation of the b-sheet structures, and highly exposed hydrophobic surfaces, possibly leading to the production of aggregate/fibril structures of the prion protein.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Food Science & Technology
Yijing Liao, Xing Hu, Junhui Pan, Guowen Zhang
Summary: In this study, baicalein, a bioactive flavonoid, was found to competitively inhibit acetylcholinesterase (AChE) through a static process. The binding of baicalein to AChE was mainly driven by hydrogen bonding and hydrophobic interaction, resulting in structural changes of AChE. Molecular docking and dynamics simulations confirmed the inhibitory effect of baicalein on AChE. This study provides insights into the molecular-level understanding of the interaction between baicalein and AChE, which may contribute to the development of anti-Alzheimer's disease functional foods and drugs.
Article
Biochemistry & Molecular Biology
Hina Qaiser, Maria Saeed, Dmitry Nerukh, Zaheer Ul-Haq
Summary: In this study, three potential small molecule inhibitors targeting TNF-α were identified using in silico approaches, and their stability and mechanism of action were confirmed through molecular dynamics studies. ADME analysis indicated good pharmacokinetic properties of these compounds with low toxicity risks, except for one compound.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Article
Chemistry, Physical
Vladimir V. Sharoyko, Nailia R. Iamalova, Sergei Ageev, Anatolii A. Meshcheriakov, Gleb O. Iurev, Andrey Petrov, Dmitry A. Nerukh, Vladimir S. Farafonov, Lubov V. Vasina, Anastasia Penkova, Konstantin N. Semenov
Summary: Fullerenol C-60(OH)(24) shows good biocompatibility, making it a promising candidate for potential use in biomedicine.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Abdelsattar O. E. Abdelhalim, Konstantin N. Semenov, Dmitry A. Nerukh, Igor V. Murin, Dmitrii N. Maistrenko, Oleg E. Molchanov, Vladimir V. Sharoyko
Summary: This review summarizes the origins and methods of functionalization of graphene-based nanomaterials (GBN), and introduces their applications in various fields such as material development, drug delivery, and biosensing. It will be very useful for professionals in the fields of material science and nanobiomedicine.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Abdelsattar O. E. Abdelhalim, Vladimir V. Sharoyko, Sergei Ageev, Vladimir S. Farafonov, Dmitry A. Nerukh, Viktor N. Postnov, Andrey Petrov, Konstantin N. Semenov
Summary: The study introduces a new modification of graphene oxide with high oxygen-containing functional groups and a faster synthesis method that allows control of particle size in solution. Characterization by various methods and modeling reveals a unique multilayered sheet structure of the synthesized compound.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Chemistry, Physical
Olga Mikolaichuk, Elena A. Popova, Alexandra Protas, Ilnaz T. Rakipov, Dmitry A. Nerukh, Andrey Petrov, Nikolay A. Charykov, Sergei Ageev, Grigorii Tochilnikov, Iulia G. Zmitrichenko, Aleksandr N. Stukov, Konstantin N. Semenov, Vladimir V. Sharoyko
Summary: This study presents a comprehensive investigation of a water-soluble substance from the class of triazine derivatives alkylating agents, including physicochemical properties, biological activity, and computational modeling.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Natalya Vodolazkaya, Marina Nikolskaya, Anna Laguta, Vladimir Farafonov, Zita Balklava, Michael Stich, Nikolay Mchedlov-Petrossyan, Dmitry Nerukh
Summary: The surface properties of the MS2 phage were investigated using dynamic light scattering and laser Doppler electrophoresis. It was found that the surface of the virus is hydrophilic and the charge distribution is mosaic-like, which contradicts the commonly accepted hypothesis and provides more information about the virus surface.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Biophysics
Vasiliy T. Lebedev, Nikolay A. Charykov, Olga S. Shemchuk, Igor V. Murin, Dmitry A. Nerukh, Andrey V. Petrov, Dmitriy N. Maystrenko, Oleg E. Molchanov, Vladimir V. Sharoyko, Konstantin N. Semenov
Summary: This article reviews all aspects of endometallofullerenes (EMF) synthesis, properties, and applications over the past 20 years. EMF is a new class of nanosized objects with specific physicochemical properties determined by the encapsulation of individual atoms and small molecules, showing significant potential in practical applications in biology and medicine. One application is an EMF-based anticancer drug that can activate antitumor immune response, inhibit tumor development, angiogenesis, and metastasis. Another separate application direction is the use of EMF as contrast agents.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Article
Chemistry, Physical
Vladimir S. Farafonov, Alexander Lebed, Dmitry A. Nerukh, Nikolay O. Mchedlov-Petrossyan
Summary: Exploiting acid-base indicators as molecular probes is a popular method for determining the surface electrostatic potential in hydrophilic colloids. However, there is a problem of dissimilarity in the psi values obtained with different indicators. This study used molecular dynamics simulations to examine the factors affecting this dissimilarity and found that hydration of the indicator in the nonionic surfactant solution contributes to approximately half of the dissimilarity range. It is proposed to supplement psi measurement experiments with molecular dynamics simulations to improve the efficacy of the indicator method.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Vladimir S. Farafonov, Alexander V. Lebed, Dmitry A. Nerukh, Nikolay O. Mchedlov-Petrossyan
Summary: Using acid-base indicators as molecular probes is a popular method for determining the surface electrostatic potential in hydrophilic colloids. However, there is a problem of obtaining different potential values with different indicators. In this study, molecular dynamics simulations were used to examine the factors affecting the dissimilarity, including the choice of nonionic surfactant, probe's localization, and micellar pseudophase hydration. The most accurate indicators were identified, and it is proposed to supplement experiments with simulations to improve the efficacy of the indicator method.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Sergey A. Karabasov, Mihail A. Zaitsev, Dmitry A. Nerukh
Summary: This study models the "nut-and-bolt" mechanism of bacteriophage-bacteria flagellum translocation motion by numerically integrating the 3D Stokes equations using a Finite-Element Method (FEM). By comparing the Stokes solution with the Resistive Force Theory (RFT) solutions and asymptotic theory, the researchers investigate how the phage translocation speed depends on the phage tail length. Using complete hydrodynamics solutions, the study aims to understand the divergence between two mechanical models of the same biological system.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Physical
Vladimir S. Farafonov, Michael Stich, Dmitry A. Nerukh
Summary: For the first time, a complete all-atom molecular dynamics (MD) model of virus MS2, including its protein outer shell, genomic RNA, and surrounding explicit aqueous solution, was built and tested. The model can be used for reconstructing other large biomolecular structures and studying the biology and dynamics of the MS2 virus and its interaction with host bacteria.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Natalya Vodolazkaya, Anna Laguta, Vladimir Farafonov, Marina Nikolskaya, Zita Balklava, Reza Khayat, Michael Stich, Nikolay Mchedlov-Petrossyan, Dmitry Nerukh
Summary: The colloidal nanostructure and properties of the MS2 bacteriophage were investigated by studying the effect of electrolytes and colloidal surfactants on its water solution. The addition of electrolytes reduced the charge and size of the virus particles. Both ionic and non-ionic colloidal surfactants destabilized the MS2 particles. The surface properties of another virus, PCV2, were also studied and found to have a mosaic charge distribution similar to MS2.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Vladimir S. Farafonov, Michael Stich, Dmitry Nerukh
Summary: It is very difficult to computationally reconstruct a large biomolecular complex from experimental data. We successfully reconstructed a complete MS2 virus at atomistic resolution for the first time from published cryo-EM density, and validated it with molecular dynamics simulation.
FARADAY DISCUSSIONS
(2022)
Article
Chemistry, Physical
Elvira Tarasova, Noriaki Okimoto, Shanshan Feng, Dmitry Nerukh, Reza Khayat, Makoto Taiji
Summary: The study found that pure PCV2 capsid proteins require acidic conditions to assemble into empty capsids in vitro in the absence of nucleic acids. Molecular dynamics simulation revealed that an appropriate protonation configuration is necessary for driving capsid assembly, with assembly being prohibited at neutral pH due to electrostatic repulsion.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Natalya Vodolazkaya, Marina Nikolskaya, Anna Laguta, Vladimir Farafonov, Zita Balklava, Michael Stich, Nikolay Mchedlov-Petrossyan, Dmitry Nerukh
Summary: The study on the surface properties of MS2 bacteriophage revealed that its surface is hydrophilic instead of hydrophobic, and lacks hydrophobic interactions. By measuring the hydrodynamic diameter and ζ potential values, as well as using acid-base indicator dyes of different charge types, the sensitivity of the microenvironment on the virus surface was uncovered.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)