Article
Biochemistry & Molecular Biology
Raghvendra Agrawal, H. B. Punarva, Gagan O. Heda, Y. M. Vishesh, Prashantha Karunakar
Summary: Developments in computational structural biology and increasing computing speeds have led to the study of large compound libraries in virtual screening. However, handling the interaction details of a large number of protein-ligand complexes can be laborious, highlighting the need for automation tools.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Gyorgy G. Ferenczy, Miklos Kellermayer
Summary: The contributions of hydrophobic and hydrogen bonds to protein mechanical stability were found to be different, with hydrogen bonds playing a more important role in mechanical resistance while hydrophobic interactions are relatively more important for providing thermodynamic stability. The contribution of hydrogen bonds to force peaks becomes increasingly important for mechanically resistant protein domains.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biochemical Research Methods
Justyna D. Krys, Dominik Gront
Summary: Understanding protein structure and dynamics is crucial for investigating biological processes. We propose a novel hydrogen bond energy function for coarse-grained simulations, which accurately recognizes hydrogen bonds and identifies β-sheet structures in amyloid peptide simulations.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2023)
Review
Chemistry, Multidisciplinary
Cherumuttathu H. Suresh, Sebastian Anila
Summary: Molecular electrostatic potential (MESP) topology is a powerful tool for studying intermolecular noncovalent interactions. MESP mapping is achieved by computing backward difference V(r) data and Hessian matrix elements at the critical point V(r) = 0. MESP minimum (V(min)) and MESP at a reaction center (V(n)) have been used as electronic parameters to interpret reactivity variations and other molecular interactions.
ACCOUNTS OF CHEMICAL RESEARCH
(2023)
Article
Chemistry, Physical
Kyoko Fujita, Kazune Kobayashi, Anna Ito, Shun Yanagisawa, Kimiyoshi Ichida, Kouta Takeda, Nobuhumi Nakamura, Hiroyuki Ohno
Summary: This study evaluates the use of hydrated ionic liquids (ILs) to directly dissolve aggregated recombinant proteins and induce refolding. The selection of suitable ion pairs and water content significantly improves the dissolution and refolding of the proteins. The column method shows potential in removing ILs and purifying the proteins.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Multidisciplinary
Sergey Shityakov, Aleksandr S. Aglikov, Ekaterina V. Skorb, Michael Nosonovsky
Summary: This study investigates the correlation between the Voronoi entropy (VE) of ligand molecules and their affinity to receptors. The findings suggest a strong correlation between ligand complexity and affinity, indicating the importance of atomic spatial arrangement for molecular mobility and binding.
Article
Chemistry, Applied
Alena Kolarikova, Eva Kutalkova, Vaclav Bus, Roman Witasek, Josef Hrncirik, Marek Ingr
Summary: This study investigates the stability and dynamics of temporary duplex structures formed by hyaluronic acid (HA) at different NaCl concentrations using molecular dynamics simulations. The tendency for duplex formation increases with NaCl concentration, reaching its maximum at 0.6 M. This is influenced by the counteracting effects of electrostatic repulsion screening and disruption of hydrogen bond formation.
CARBOHYDRATE POLYMERS
(2022)
Article
Chemistry, Physical
Artashes A. Khachatrian, Timur A. Mukhametzyanov, Dmitry G. Yakhvarov, Oleg G. Sinyashin, Bulat F. Garifullin, Ilnaz T. Rakipov, Diana A. Mironova, Vladimir A. Burilov, Boris N. Solomonov
Summary: The intermolecular interactions between ionic liquids and hen egg-white lysozyme (HEWL) were studied using spectral, thermodynamic, and computational methods. The results showed that the stability of HEWL is influenced by the proton acceptor ability of the ionic liquids. Furthermore, fluorescence and molecular docking data indicated a lack of strong binding between the studied ionic liquids and HEWL.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Miyu Hirose, Hajime Torii
Summary: An electrostatic interaction model is developed for the vibrational frequency changes in the C=N stretching mode of benzonitrile. The model considers both hydrogen-bonding solvent and uniform electric field interactions, and correlates the frequency changes to intermolecular structural properties. The results suggest that electrostatic interactions modulate the frequency through these structural properties.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Chemistry, Physical
Shashi Kumar, N. N. Subrahmanyeswara Rao, K. S. S. V. Prasad Reddy, Manjusha C. C. Padole, Parag A. A. Deshpande
Summary: This study used a QM/MM framework to study OPRT derived from Saccharomyces cerevisiae and obtained insights into the competitive binding of OA and OA-mimetic inhibitors by quantifying their interactions with OPRT. 4-Hydroxy-6-methylpyridin-2(1H) one showed the best inhibiting activity among the structurally similar OA-mimetic inhibitors and was found to interact with a strong network of hydrogen bonds, hydrophobic contacts, and bridging water molecules in the binding site.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Fareeha K. Malik, Jun-tao Guo
Summary: Hydrogen bonds were compared among three non-redundant datasets of protein-protein, protein-peptide, and protein-DNA complexes. Interfacial hydrogen bonds were found to be more prevalent and displayed a unique energy distribution in protein-DNA complexes, while most interfacial hydrogen bonds in protein-protein and protein-peptide complexes had high strength with low energy. The energy distribution of minor groove hydrogen bonds also differed significantly between protein-DNA complexes with different binding specificity.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2022)
Article
Food Science & Technology
Daqiao Yang, Chunsheng Li, Laihao Li, Yueqi Wang, Shengjun Chen, Yongqiang Zhao, Xiao Hu, Hui Rong
Summary: DPP-IV inhibitory peptides from fermented foods like Chouguiyu have the potential to alleviate type 2 diabetes mellitus. This study identified 125 DPP-IV inhibitory peptides in Chouguiyu and selected four novel peptides with the lowest docking energy. These peptides possess structures that easily connect with DPP-IV enzyme through hydrogen bond, salt bridge, and alkyl interactions, and show potential for remission of T2DM.
CURRENT RESEARCH IN FOOD SCIENCE
(2022)
Article
Engineering, Environmental
Shih-Hao Yu, Chun-Chao Chang, Fu-Der Mai, Chih-Ping Yang, Yu-Chuan Liu
Summary: Liquid water is widely used in physical processes and chemical reactions as an environmentally friendly polar solvent. Plasmon-activated water (PAW) created in 2014, utilizing hot electron transfer from gold nanoparticles, shows enhanced stability and solubility when combined with alcohols and hydrophobic solutes. The innovative PAW demonstrates increased solubilities and densities in various solutions compared to traditional deionized water systems, making it a promising green solvent for both hydrophilic and hydrophobic solutions.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Biochemical Research Methods
Dinesh Kumar Sriramulu, Sun-Gu Lee
Summary: This study investigated the effects of ligand torsion number, ligand hydrophobicity, and binding-site hydrophobicity on the prediction accuracy of Autodock. Combinatorial analysis showed that the best prediction accuracy came from the combination of low ligand torsion number-hydrophilic ligand-hydrophobic binding site, while the worst prediction accuracy came from high ligand torsion number hydrophilic ligand-hydrophobic binding pocket combination.
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
(2021)
Article
Biochemistry & Molecular Biology
Michele Pieroni, Francesco Madeddu, Jessica Di Martino, Manuel Arcieri, Valerio Parisi, Paolo Bottoni, Tiziana Castrignano
Summary: Molecular dynamics simulation is a computational technique used to study the dynamic behavior of molecular systems. MDLR software is presented in this study to explore the interactions between ligands and receptors over time. It goes beyond static analysis, uncovering long-lasting molecular interactions and predicting drug activity. The optimized pipeline allows for efficient processing of large molecular dynamics trajectories.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Camille Albrecht, Aline Appert-Collin, Dominique Bagnard, Sebastien Blaise, Beatrice Romier-Crouzet, Roman G. Efremov, Herve Sartelet, Laurent Duca, Pascal Maurice, Amar Bennasroune
FRONTIERS IN ONCOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Andrey Sosorev, Dmitry Dominskiy, Ivan Chernyshov, Roman Efremov
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Pharmacology & Pharmacy
Andrei M. Gigolaev, Alexey Kuzmenkov, Steve Peigneur, Valentin M. Tabakmakher, Ernesto L. Pinheiro-Junior, Anton O. Chugunov, Roman G. Efremov, Jan Tytgat, Alexander A. Vassilevski
FRONTIERS IN PHARMACOLOGY
(2020)
Article
Chemistry, Medicinal
Olga A. Belozerova, Dmitry Osmakov, Andrey Vladimirov, Sergey G. Koshelev, Anton O. Chugunov, Yaroslav A. Andreev, Victor A. Palikov, Yulia A. Palikova, Elvira R. Shaykhutdinova, Artem N. Gvozd, Igor A. Dyachenko, Roman G. Efremov, Vadim S. Kublitski, Sergey A. Kozlov
Article
Biochemistry & Molecular Biology
Kseniya Lubova, Anton O. Chugunov, Pavel E. Volynsky, Yuri A. Trofimov, Yuliya Korolkova, Irina Mosharova, Sergey A. Kozlov, Yaroslav A. Andreev, Roman G. Efremov
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2020)
Article
Cell Biology
Camille Albrecht, Andrey S. Kuznetsov, Aline Appert-Collin, Zineb Dhaideh, Maite Callewaert, Yaroslav Bershatsky, Anatoly S. Urban, Eduard Bocharov, Dominique Bagnard, Stephanie Baud, Sebastien Blaise, Beatrice Romier-Crouzet, Roman G. Efremov, Manuel Dauchez, Laurent Duca, Marc Gueroult, Pascal Maurice, Amar Bennasroune
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Elena T. Aliper, Nikolay A. Krylov, Dmitry E. Nolde, Anton A. Polyansky, Roman G. Efremov
Summary: This study proposes a comprehensive computational framework to model the spike transmembrane domain (TMD) of SARS-CoV-2 spike protein based on its primary structure. The stability of the model was tested through molecular dynamics simulations and was found to conform to basic principles of TM helix packing. The framework shows promise and can potentially be applied to construct 3D models of transmembrane trimers for other membrane proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Irina S. Panina, Nikolay A. Krylov, Anton O. Chugunov, Roman G. Efremov, Larisa V. Kordyukova
Summary: S-acylation is an important post-translational modification that links long chain fatty acids to cysteines. This process is catalyzed by a family of 23 membrane DHHC-acyltransferases in human cells. In this study, the researchers used molecular dynamics simulations to investigate the structure of membrane-bound hDHHC20 before acylation by different chain length acyl-CoA substrates. The results showed that regardless of the chain length, the terminal methyl group of the substrate always reaches the ceiling of the enzyme's cavity. Only C16 showed optimal reactivity for autoacylation. These findings provide insights into the specific recognition of acyl-CoA substrates by DHHC-acyltransferases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Yaroslav V. V. Bershatsky, Andrey S. S. Kuznetsov, Aisha R. R. Idiatullina, Olga V. V. Bocharova, Sofya M. M. Dolotova, Alina A. A. Gavrilenkova, Oxana V. V. Serova, Igor E. E. Deyev, Tatiana V. V. Rakitina, Olga T. T. Zangieva, Konstantin V. V. Pavlov, Oleg V. V. Batishchev, Vladimir V. V. Britikov, Sergey A. A. Usanov, Alexander S. S. Arseniev, Roman G. G. Efremov, Eduard V. V. Bocharov
Summary: The InsR, IGF1R, and IRR receptor tyrosine kinases (RTK) of the insulin receptor subfamily play a crucial role in various physiological processes and are associated with several diseases, including neurodegenerative diseases. This study examines the structural and dynamic characteristics of these receptors and highlights the significant differences in their transmembrane domains and lipid interactions. The membrane-mediated control of receptor signaling offers promising opportunities for the development of targeted therapies for diseases related to insulin subfamily receptors dysfunction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ekaterina Goryacheva, Roman Efremov, Nikolai Krylov, Igor Artemyev, Alexey Bogdanov, Anastasia Mamontova, Sergei Pletnev, Nadya Pletneva, Vladimir Pletnev
Summary: The rapid development of new microscopy techniques has highlighted the need for genetically encoded fluorescent tags with special properties. One such tag, the BrUSLEE protein, has an extremely short fluorescence lifetime and exceptional brightness, making it useful for fluorescent lifetime image microscopy (FLIM). By comparing its structure to the precursor EGFP protein, insights have been gained into the molecular details that contribute to the differences in their photophysical properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Elena T. Aliper, Roman G. Efremov
Summary: Transmembrane domains (TMDs) in proteins have attracted significant attention from the scientific community in the past few decades. These domains not only act as anchors for protein localization, but also play an active role in protein function. However, due to their complex molecular organization and experimental challenges, structural data on TMDs are still incomplete. This review aims to integrate the currently available data on the structure and dynamics of TMDs to better understand the molecular mechanisms of virus-mediated fusion and provide a basis for the development of effective treatments for infectious diseases caused by SARS-CoV-2 and related viruses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Igor E. Mikhnovets, Jiri Holoubek, Irina S. Panina, Jan Kotoucek, Daniil A. Gvozdev, Stepan P. Chumakov, Maxim S. Krasilnikov, Mikhail Y. Zhitlov, Evgeny L. Gulyak, Alexey A. Chistov, Timofei D. Nikitin, Vladimir A. Korshun, Roman G. Efremov, Vera A. Alferova, Daniel Ruzek, Ludek Eyer, Alexey V. Ustinov
Summary: Amphipathic perylene derivatives are effective antiviral compounds that target the viral envelope and act as fusion inhibitors. They damage the viral envelope using lipophilic perylene and singlet oxygen generated by light. Short alkyl chains contribute to strong antiviral activity, while longer alkyl chains reduce activity due to increased lipophilicity and aggregation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Andrey S. Kuznetsov, Miftakh F. Zamaletdinov, Yaroslav Bershatsky, Anatoly S. Urban, Olga Bocharova, Amar Bennasroune, Pascal Maurice, Eduard Bocharov, Roman G. Efremov
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2020)
Meeting Abstract
Biophysics
Yuri A. Trofimov, Nikolay A. Krylov, Roman G. Efremov
BIOPHYSICAL JOURNAL
(2020)
Meeting Abstract
Biophysics
Eduard V. Bocharov, Dmitry M. Lesovoy, Olga V. Bocharova, Anatoly S. Urban, Yaroslav V. Bershacky, Pavel E. Volynsky, Roman G. Efremov, Alexander S. Arseniev
BIOPHYSICAL JOURNAL
(2020)