Coming in a variety of forms, melanin is one of the most abundant, stable, diverse, and evolutionarily ancient pigments found in living things in nature. These pigments often serve protective functions, typically well-adapted to their specific roles. One such protective function is metal chelation and cation exchange, which help regulate and buffer metal concentrations within cells. By binding to certain metals, melanin can acquire magnetic properties. Because of this, it may play a role in magnetic effects and possibly in the response of organisms to external magnetic fields and magnetic sensing. While there is melanin in plants, microbes, fungi, and invertebrates, certain types of melanin are specifically associated with the retina in vertebrates, including migrating bird and fish species. In this review, we examine studies focusing on the properties of melanin in these parts of the body and their possible association with magnetic sensing, and generally, magnetic sensing in the retina.
{"title":"Melanin in the Retinal Epithelium and Magnetic Sensing: A Review of Current Studies.","authors":"Lidia Zueva, Vassiliy Tsytsarev, Janaina Alves, Mikhail Inyushin","doi":"10.3390/biophysica4040030","DOIUrl":"10.3390/biophysica4040030","url":null,"abstract":"<p><p>Coming in a variety of forms, melanin is one of the most abundant, stable, diverse, and evolutionarily ancient pigments found in living things in nature. These pigments often serve protective functions, typically well-adapted to their specific roles. One such protective function is metal chelation and cation exchange, which help regulate and buffer metal concentrations within cells. By binding to certain metals, melanin can acquire magnetic properties. Because of this, it may play a role in magnetic effects and possibly in the response of organisms to external magnetic fields and magnetic sensing. While there is melanin in plants, microbes, fungi, and invertebrates, certain types of melanin are specifically associated with the retina in vertebrates, including migrating bird and fish species. In this review, we examine studies focusing on the properties of melanin in these parts of the body and their possible association with magnetic sensing, and generally, magnetic sensing in the retina.</p>","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"4 4","pages":"466-476"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11500728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142513973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-12DOI: 10.3390/biophysica4030025
Amber R. Titus, P. Madeira, V. Uversky, B. Zaslavsky
Aqueous two-phase systems (ATPSs) are formed when two nonionic polymers, or a single polymer and salt, are mixed in water above a specific concentration, resulting in the emergence of phase separation and the formation of two immiscible aqueous phases. The solvent properties of the aqueous media within the phases of ATPSs rely on the specific composition of the co-solutes and the arrangement of the hydrogen bond network within each phase. Here, we investigate the anion effect of various sodium salts on the enhancement or destabilization of polyethylene glycol (PEG)–salt ATPS formation. Relatively small changes in ATPS ionic composition were shown to result in significant changes in solute partitioning. Additionally, we previously established that the arrangement of hydrogen bonds within the coexisting phases of ATPSs is different, as evidenced by Attenuated Total Reflection—Fourier Transform Infrared (ATR-FTIR) spectroscopic analysis of OH-stretch bands. The hydrogen bond arrangement was shown to abruptly change at concentrations below the threshold of macroscopic phase separation in the ATPSs. Using dynamic light scattering (DLS), we observed a correlation between these abrupt changes in H-bond arrangement and the detection of agglomerate formation in both polymer–polymer and polymer–salt systems.
{"title":"Anion Effect on Phase Separation of Polyethylene Glycol-8000–Sodium Salt Two-Phase Systems","authors":"Amber R. Titus, P. Madeira, V. Uversky, B. Zaslavsky","doi":"10.3390/biophysica4030025","DOIUrl":"https://doi.org/10.3390/biophysica4030025","url":null,"abstract":"Aqueous two-phase systems (ATPSs) are formed when two nonionic polymers, or a single polymer and salt, are mixed in water above a specific concentration, resulting in the emergence of phase separation and the formation of two immiscible aqueous phases. The solvent properties of the aqueous media within the phases of ATPSs rely on the specific composition of the co-solutes and the arrangement of the hydrogen bond network within each phase. Here, we investigate the anion effect of various sodium salts on the enhancement or destabilization of polyethylene glycol (PEG)–salt ATPS formation. Relatively small changes in ATPS ionic composition were shown to result in significant changes in solute partitioning. Additionally, we previously established that the arrangement of hydrogen bonds within the coexisting phases of ATPSs is different, as evidenced by Attenuated Total Reflection—Fourier Transform Infrared (ATR-FTIR) spectroscopic analysis of OH-stretch bands. The hydrogen bond arrangement was shown to abruptly change at concentrations below the threshold of macroscopic phase separation in the ATPSs. Using dynamic light scattering (DLS), we observed a correlation between these abrupt changes in H-bond arrangement and the detection of agglomerate formation in both polymer–polymer and polymer–salt systems.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"43 23","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141654995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-01DOI: 10.3390/biophysica4030024
I. D. Zlotnikov, Alexander A. Ezhov, E. V. Kudryashova
Herein, we propose an analytical approach based on intermolecular fluorescent resonant energy transfer (FRET) pairs for the visualization of specific enzyme activity in model biomembranes and in living cells. Cell visualizations with fluorescent confocal laser microscopy usually rely on fluorescent probes, such as Fluorescein isothiocyanate (FITC), Alexa488, Tetramethylrhodamine isothiocyanate (TRITC) and many others. However, for more specific tasks, such as the detection of certain enzymatic activity inside the living cell, the toolbox is quite limited. In the case of enzyme-hydrolases for example, the choice is limited to organic molecules comprising a fluorescent dye (typically, 4-methylumbelliferone (MUmb) or 7-amino-4-methylcoumarin (AMC) derivatives) and a fluorescence quencher, bound via an enzyme-sensitive linker—so that when the linker is degraded, the fluorescent signal increases. Unfortunately, both MUmb and AMC are quenched and have a relatively low quantum yield in cells, and their excitation and emission ranges overlap with that of intracellular fluorophores, often producing a strong background noise. R6G, on the other hand, has excellent quantum yield apart from intracellular fluorophores, but there are no efficient quenchers that could be chemically linked to R6G. Herein, we show that R6G is able to form intermolecular FRET pairs with MUmb or AMC, with the latter serving as fluorescence donors. This yields a combination of R6G’s excellent fluorescence properties with a possibility to use an enzyme-sensitive linker in MUTMAC or AMC derivatives. This phenomenon was initially discovered in a model system, reversed micelles, where the donor, the acceptor, and the enzyme are forced to be in close proximity to each other, so that proximity could serve as an explanation for the intermolecular FRET effect. Surprisingly enough, the phenomenon has been reproduced in living cells. Moreover, we were able to create working intermolecular donor–acceptor FRET pairs for several different enzymes, including chymotrypsin, phosphatase, and asparaginase. This appears counterintuitive, as besides the overlap of the emission spectra of the donor and the absorption spectra of the acceptor, there are other criteria for the FRET effect, including the convergence of two fluorophores at a distance of about 1–10 nm, and the orientation of their dipoles at a certain angle, which is difficult to imagine in a bulk system like a living cell. We hypothesize that FRET-enabling donor–acceptor interaction may be taking place at the inner surface of the lipid bilayer, to which both donor and acceptor molecules would likely have an affinity. This hypothesis would require a more detailed investigation. Therefore, we have shown that the method suggested has good potential in the visualization of enzyme functioning inside living cells, which is often a challenging task. Shifting of the fluorescence signal to the long-wavelength region would increase the signal selectivi
{"title":"Intermolecular FRET Pairs as An Approach to Visualize Specific Enzyme Activity in Model Biomembranes and Living Cells","authors":"I. D. Zlotnikov, Alexander A. Ezhov, E. V. Kudryashova","doi":"10.3390/biophysica4030024","DOIUrl":"https://doi.org/10.3390/biophysica4030024","url":null,"abstract":"Herein, we propose an analytical approach based on intermolecular fluorescent resonant energy transfer (FRET) pairs for the visualization of specific enzyme activity in model biomembranes and in living cells. Cell visualizations with fluorescent confocal laser microscopy usually rely on fluorescent probes, such as Fluorescein isothiocyanate (FITC), Alexa488, Tetramethylrhodamine isothiocyanate (TRITC) and many others. However, for more specific tasks, such as the detection of certain enzymatic activity inside the living cell, the toolbox is quite limited. In the case of enzyme-hydrolases for example, the choice is limited to organic molecules comprising a fluorescent dye (typically, 4-methylumbelliferone (MUmb) or 7-amino-4-methylcoumarin (AMC) derivatives) and a fluorescence quencher, bound via an enzyme-sensitive linker—so that when the linker is degraded, the fluorescent signal increases. Unfortunately, both MUmb and AMC are quenched and have a relatively low quantum yield in cells, and their excitation and emission ranges overlap with that of intracellular fluorophores, often producing a strong background noise. R6G, on the other hand, has excellent quantum yield apart from intracellular fluorophores, but there are no efficient quenchers that could be chemically linked to R6G. Herein, we show that R6G is able to form intermolecular FRET pairs with MUmb or AMC, with the latter serving as fluorescence donors. This yields a combination of R6G’s excellent fluorescence properties with a possibility to use an enzyme-sensitive linker in MUTMAC or AMC derivatives. This phenomenon was initially discovered in a model system, reversed micelles, where the donor, the acceptor, and the enzyme are forced to be in close proximity to each other, so that proximity could serve as an explanation for the intermolecular FRET effect. Surprisingly enough, the phenomenon has been reproduced in living cells. Moreover, we were able to create working intermolecular donor–acceptor FRET pairs for several different enzymes, including chymotrypsin, phosphatase, and asparaginase. This appears counterintuitive, as besides the overlap of the emission spectra of the donor and the absorption spectra of the acceptor, there are other criteria for the FRET effect, including the convergence of two fluorophores at a distance of about 1–10 nm, and the orientation of their dipoles at a certain angle, which is difficult to imagine in a bulk system like a living cell. We hypothesize that FRET-enabling donor–acceptor interaction may be taking place at the inner surface of the lipid bilayer, to which both donor and acceptor molecules would likely have an affinity. This hypothesis would require a more detailed investigation. Therefore, we have shown that the method suggested has good potential in the visualization of enzyme functioning inside living cells, which is often a challenging task. Shifting of the fluorescence signal to the long-wavelength region would increase the signal selectivi","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"12 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141704417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-15DOI: 10.3390/biophysica4020017
Amena Mrabet, Bahia Abdelfattah, F. El Mansouri, Ayoub Simou, Mohamed Khaddor
Laurus nobilis, sometimes referred to as laurel, has been used for medicinal and culinary purposes for a very long time. The main subjects of this study are the phytochemical composition, mineralogical profile, and potential antioxidant properties of Laurus nobilis in Tangier, Northern Morocco. For phytochemical analysis of methanolic extracts, high-performance liquid chromatography (HPLC-UV-MS) was used, and Fourier transformation infrared spectroscopy (FT-IR) was used to identify each individual component. Minerals were studied by inductively coupled plasma atomic emission spectroscopy (ICP-AES) and wavelength dispersive X-ray fluorescence (WD-XRF). Total tannin, flavonoid, and phenolic amounts were quantified using aqueous and methanolic extracts. The antioxidant properties were assessed using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis (3ethylbenzothiazoline-6-sulfonic acid) (ABTS), ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC) assays. Research has revealed a complex array of phytochemicals, including tannins, flavonoids, and phenolic acids. Mineral analysis has revealed the existence of vital components that are beneficial to health. Comparing the methanolic extract to the water extract, it demonstrated higher levels of phenols, flavonoids, and tannins as well as stronger antioxidant activity, indicating greater health benefits. This comprehensive study highlights the importance of Laurus nobilis from Northern Morocco as a reliable botanic resource with potential pharmaceutical, nutritional, and cosmetic uses.
月桂（Laurus nobilis）有时也被称为月桂，很早以前就被用于药用和烹饪。本研究的主要内容是摩洛哥北部丹吉尔月桂的植物化学成分、矿物学特征和潜在的抗氧化特性。在对甲醇提取物进行植物化学分析时，采用了高效液相色谱法（HPLC-UV-MS），并使用傅立叶变换红外光谱法（FT-IR）对每种成分进行鉴定。矿物质采用电感耦合等离子体原子发射光谱（ICP-AES）和波长色散 X 射线荧光（WD-XRF）进行研究。使用水提取物和甲醇提取物对单宁酸、类黄酮和酚类物质的总量进行了量化。使用 2,2-二苯基-1-苦基肼（DPPH）、2,2′-偶氮双（3-乙基苯并噻唑啉-6-磺酸）（ABTS）、铁还原抗氧化能力（FRAP）和氧自由基吸收能力（ORAC）测定法评估了植物的抗氧化特性。研究还发现了一系列复杂的植物化学物质，包括单宁酸、类黄酮和酚酸。矿物质分析显示了对健康有益的重要成分。甲醇提取物与水提取物相比，酚类、类黄酮和单宁的含量更高，抗氧化活性更强，表明对健康的益处更大。这项综合研究强调了摩洛哥北部的月桂属植物作为一种可靠的植物资源的重要性，它具有潜在的制药、营养和美容用途。
{"title":"Bay Laurel of Northern Morocco: A Comprehensive Analysis of Its Phytochemical Profile, Mineralogical Composition, and Antioxidant Potential","authors":"Amena Mrabet, Bahia Abdelfattah, F. El Mansouri, Ayoub Simou, Mohamed Khaddor","doi":"10.3390/biophysica4020017","DOIUrl":"https://doi.org/10.3390/biophysica4020017","url":null,"abstract":"Laurus nobilis, sometimes referred to as laurel, has been used for medicinal and culinary purposes for a very long time. The main subjects of this study are the phytochemical composition, mineralogical profile, and potential antioxidant properties of Laurus nobilis in Tangier, Northern Morocco. For phytochemical analysis of methanolic extracts, high-performance liquid chromatography (HPLC-UV-MS) was used, and Fourier transformation infrared spectroscopy (FT-IR) was used to identify each individual component. Minerals were studied by inductively coupled plasma atomic emission spectroscopy (ICP-AES) and wavelength dispersive X-ray fluorescence (WD-XRF). Total tannin, flavonoid, and phenolic amounts were quantified using aqueous and methanolic extracts. The antioxidant properties were assessed using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis (3ethylbenzothiazoline-6-sulfonic acid) (ABTS), ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC) assays. Research has revealed a complex array of phytochemicals, including tannins, flavonoids, and phenolic acids. Mineral analysis has revealed the existence of vital components that are beneficial to health. Comparing the methanolic extract to the water extract, it demonstrated higher levels of phenols, flavonoids, and tannins as well as stronger antioxidant activity, indicating greater health benefits. This comprehensive study highlights the importance of Laurus nobilis from Northern Morocco as a reliable botanic resource with potential pharmaceutical, nutritional, and cosmetic uses.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"54 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140973495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-13DOI: 10.3390/biophysica4020016
K. Yeritsyan, Artem Badasyan
Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. In order to connect the measured profile to the properties of a particular protein, a model is required to fit. We discuss here the application of an exact two-state formula with its approximation and process the DSC experimental data on protein folding in water. The approximate formula relies on the smallness of the transition interval, which is different for each protein. With an example of the set of 33 different proteins, we show the practical validity of the approximation and the equivalence of exact and approximate two-state formulas for processing DSC data.
{"title":"Differential Scanning Calorimetry of Proteins and the Two-State Model: Comparison of Two Formulas","authors":"K. Yeritsyan, Artem Badasyan","doi":"10.3390/biophysica4020016","DOIUrl":"https://doi.org/10.3390/biophysica4020016","url":null,"abstract":"Differential Scanning Calorimetry (DSC) is a regular and powerful tool to measure the specific heat profile of various materials. In order to connect the measured profile to the properties of a particular protein, a model is required to fit. We discuss here the application of an exact two-state formula with its approximation and process the DSC experimental data on protein folding in water. The approximate formula relies on the smallness of the transition interval, which is different for each protein. With an example of the set of 33 different proteins, we show the practical validity of the approximation and the equivalence of exact and approximate two-state formulas for processing DSC data.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"43 24","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140983840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-12DOI: 10.3390/biophysica4020014
James P. Chambers, Miranda Aldis, Julie A Thomas, Cara B. Gonzales, Richard Allen White, Philip Serwer
Past anti-bacterial use of bacteriophages (phage therapy) is already well reviewed as a potential therapeutic response to the emergence of multidrug-resistant, pathogenic bacteria. Phage therapy has been limited by the following. (1) The success rate is too low for routine use and Food and Drug Administration (FDA) approval. (2) Current strategies of routine phage characterization do not sufficiently improve the success rate of phage therapy. (3) The stability of many phages at ambient temperature is not high enough to routinely store and transport phages at ambient temperature. In the present communication, we present new and previous data that we interpret as introductory to biophysically and efficiently transforming phage therapy to the needed level of effectiveness. Included are (1) procedure and preliminary data for the use of native gel electrophoresis (a low-cost procedure) for projecting the therapy effectiveness of a newly isolated phage, (2) data that suggest a way to achieve stabilizing of dried, ambient-temperature phages via polymer embedding, and (3) data that suggest means to increase the blood persistence, and therefore the therapy effectiveness, of what would otherwise be a relatively low-persistence phage.
{"title":"Biophysical Breakthroughs Projected for the Phage Therapy of Bacterial Disease","authors":"James P. Chambers, Miranda Aldis, Julie A Thomas, Cara B. Gonzales, Richard Allen White, Philip Serwer","doi":"10.3390/biophysica4020014","DOIUrl":"https://doi.org/10.3390/biophysica4020014","url":null,"abstract":"Past anti-bacterial use of bacteriophages (phage therapy) is already well reviewed as a potential therapeutic response to the emergence of multidrug-resistant, pathogenic bacteria. Phage therapy has been limited by the following. (1) The success rate is too low for routine use and Food and Drug Administration (FDA) approval. (2) Current strategies of routine phage characterization do not sufficiently improve the success rate of phage therapy. (3) The stability of many phages at ambient temperature is not high enough to routinely store and transport phages at ambient temperature. In the present communication, we present new and previous data that we interpret as introductory to biophysically and efficiently transforming phage therapy to the needed level of effectiveness. Included are (1) procedure and preliminary data for the use of native gel electrophoresis (a low-cost procedure) for projecting the therapy effectiveness of a newly isolated phage, (2) data that suggest a way to achieve stabilizing of dried, ambient-temperature phages via polymer embedding, and (3) data that suggest means to increase the blood persistence, and therefore the therapy effectiveness, of what would otherwise be a relatively low-persistence phage.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"26 17","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140711292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-10DOI: 10.3390/biophysica4020013
Kevin Taype-Huanca, Manuel I. Osorio, Diego Inostroza, Luis Leyva-Parra, L. Ruiz, Ana Valderrama-Negrón, J. Alvarado-Huayhuaz, O. Yáñez, W. Tiznado
This study explored the inhibitory potential of gallium maltolate against severe acute respiratory syndrome coronavirus 2 and main and papain-like proteases. Computational methods, including density functional theory and molecular docking, were used to assess gallium maltolate reactivity and binding interactions. Density functional theory calculations revealed gallium maltolate’s high electron-capturing capacity, particularly around the gallium metal atom, which may contribute to their activity. Molecular docking demonstrated that gallium maltolate can form strong hydrogen bonds with key amino acid residues like glutamate-166 and cysteine-145, tightly binding to main and papain-like proteases. The binding energy and interactions of gallium maltolate were comparable to known SARS-CoV-2 inhibitors like N-[(5-methyl-1,2-oxazol-3-yl)carbonyl]-L-alanyl-L-valyl-N-{(2S,3E)-5-(benzyloxy)-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pent-3-en-2-yl}-L-leucinamide, indicating its potential as an antiviral agent. However, further experimental validation is required to confirm its effectiveness in inhibiting SARS-CoV-2 replication and treating COVID-19.
{"title":"Deciphering the Molecular Interaction Process of Gallium Maltolate on SARS-CoV-2 Main and Papain-Like Proteases: A Theoretical Study","authors":"Kevin Taype-Huanca, Manuel I. Osorio, Diego Inostroza, Luis Leyva-Parra, L. Ruiz, Ana Valderrama-Negrón, J. Alvarado-Huayhuaz, O. Yáñez, W. Tiznado","doi":"10.3390/biophysica4020013","DOIUrl":"https://doi.org/10.3390/biophysica4020013","url":null,"abstract":"This study explored the inhibitory potential of gallium maltolate against severe acute respiratory syndrome coronavirus 2 and main and papain-like proteases. Computational methods, including density functional theory and molecular docking, were used to assess gallium maltolate reactivity and binding interactions. Density functional theory calculations revealed gallium maltolate’s high electron-capturing capacity, particularly around the gallium metal atom, which may contribute to their activity. Molecular docking demonstrated that gallium maltolate can form strong hydrogen bonds with key amino acid residues like glutamate-166 and cysteine-145, tightly binding to main and papain-like proteases. The binding energy and interactions of gallium maltolate were comparable to known SARS-CoV-2 inhibitors like N-[(5-methyl-1,2-oxazol-3-yl)carbonyl]-L-alanyl-L-valyl-N-{(2S,3E)-5-(benzyloxy)-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pent-3-en-2-yl}-L-leucinamide, indicating its potential as an antiviral agent. However, further experimental validation is required to confirm its effectiveness in inhibiting SARS-CoV-2 replication and treating COVID-19.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"27 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140716408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-03-27DOI: 10.3390/biophysica4020009
Geng-Bai Lin, Chia-Lung Shih, R. Liutkeviciene, V. Rovite, E. So, Chaochao Wu, Sheng Nan Wu
As the need for effective antiviral treatment intensifies, such as with the coronavirus disease 19 (COVID-19) infection, it is crucial to understand that while the mechanisms of action of these drugs or compounds seem apparent, they might also interact with unexplored targets, such as cell membrane ion channels in diverse cell types. In this review paper, we demonstrate that many different drugs or compounds, in addition to their known interference with viral infections, may also directly influence various types of ionic currents on the surface membrane of the host cell. These agents include artemisinin, cannabidiol, memantine, mitoxantrone, molnupiravir, remdesivir, SM-102, and sorafenib. If achievable at low concentrations, these regulatory effects on ion channels are highly likely to synergize with the identified initial mechanisms of viral replication interference. Additionally, the immediate regulatory impact of these agents on the ion-channel function may potentially result in unintended adverse effects, including changes in cardiac electrical activity and the prolongation of the QTc interval. Therefore, it is essential for patients receiving these related agents to exercise additional caution to prevent unnecessary complications.
{"title":"Assessing the Impact of Agents with Antiviral Activities on Transmembrane Ionic Currents: Exploring Possible Unintended Actions","authors":"Geng-Bai Lin, Chia-Lung Shih, R. Liutkeviciene, V. Rovite, E. So, Chaochao Wu, Sheng Nan Wu","doi":"10.3390/biophysica4020009","DOIUrl":"https://doi.org/10.3390/biophysica4020009","url":null,"abstract":"As the need for effective antiviral treatment intensifies, such as with the coronavirus disease 19 (COVID-19) infection, it is crucial to understand that while the mechanisms of action of these drugs or compounds seem apparent, they might also interact with unexplored targets, such as cell membrane ion channels in diverse cell types. In this review paper, we demonstrate that many different drugs or compounds, in addition to their known interference with viral infections, may also directly influence various types of ionic currents on the surface membrane of the host cell. These agents include artemisinin, cannabidiol, memantine, mitoxantrone, molnupiravir, remdesivir, SM-102, and sorafenib. If achievable at low concentrations, these regulatory effects on ion channels are highly likely to synergize with the identified initial mechanisms of viral replication interference. Additionally, the immediate regulatory impact of these agents on the ion-channel function may potentially result in unintended adverse effects, including changes in cardiac electrical activity and the prolongation of the QTc interval. Therefore, it is essential for patients receiving these related agents to exercise additional caution to prevent unnecessary complications.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"2 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140374231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-28DOI: 10.3390/biophysica4010008
David Naranjo, Pablo M. Blanco, J. Garcés, S. Madurga, Francesc Mas
A coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The influence of electrostatic interactions computing methods, factors concerning the structure of the chain, different functional groups, and the ionic strength on polyelectrolytes were studied. Langevin dynamics with constant pH simulations were performed using the ESPResSO package and the Python-based Molecule Builder for ESPResSo (pyMBE) library. The coverage was fitted to a polyfunctional Frumkin isotherm, with a mean-field interaction between charged beads. The composition of the chain affects the charge while ionic strength affects both the charge and the radius of gyration. Additionally, the parameters intrinsic to the polyelectrolyte model were well reproduced by fitting the polyfunctional Frumkin isotherm. In contrast, the non-intrinsic parameters depended on the ionic strength. The method developed and applied to a polyfunctional polypeptide model, that resembles a humic acid, will be very useful for characterizing biopolymers with several acid-base functional groups, where their structure, the composition of the different functional groups, and the determination of the main intrinsic proton binding constants and their proportion are not exactly known.
{"title":"Constant-pH Simulations of a Coarse-Grained Model of Polyfunctional Weak Charged Biopolymers","authors":"David Naranjo, Pablo M. Blanco, J. Garcés, S. Madurga, Francesc Mas","doi":"10.3390/biophysica4010008","DOIUrl":"https://doi.org/10.3390/biophysica4010008","url":null,"abstract":"A coarse-grained model of linear polyfunctional weak charged biopolymers was implemented, formed of different proportions of acid-base groups resembling the composition of humic substances. These substances are mainly present in dissolved organic matter in natural water. The influence of electrostatic interactions computing methods, factors concerning the structure of the chain, different functional groups, and the ionic strength on polyelectrolytes were studied. Langevin dynamics with constant pH simulations were performed using the ESPResSO package and the Python-based Molecule Builder for ESPResSo (pyMBE) library. The coverage was fitted to a polyfunctional Frumkin isotherm, with a mean-field interaction between charged beads. The composition of the chain affects the charge while ionic strength affects both the charge and the radius of gyration. Additionally, the parameters intrinsic to the polyelectrolyte model were well reproduced by fitting the polyfunctional Frumkin isotherm. In contrast, the non-intrinsic parameters depended on the ionic strength. The method developed and applied to a polyfunctional polypeptide model, that resembles a humic acid, will be very useful for characterizing biopolymers with several acid-base functional groups, where their structure, the composition of the different functional groups, and the determination of the main intrinsic proton binding constants and their proportion are not exactly known.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"46 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140421917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-02-21DOI: 10.3390/biophysica4010007
Ana-Marija Pavlek, Barbara Pem, Danijela Bakarić
As the water molecules found at the interface of lipid bilayers exhibit distinct structural and reorientation dynamics compared to water molecules found in bulk, the fluctuations in their hydrogen bond (HB) network are expected to be different from those generated by the bulk water molecules. The research presented here aims to gain an insight into temperature-dependent fluctuations of a HB network of water molecules found in an interfacial layer of multilamellar liposomes (MLVs) composed of anionic 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (DMPS) lipids. Besides suspending DMPS lipids in phosphate buffer saline (PBS) of different pH values (6.0, 7.4, and 8.0), the changes in HB network fluctuations were altered by the incorporation of a non-polar flavonoid molecule myricetin (MCE) within the hydrocarbon chain region. By performing a multivariate analysis on the water combination band observed in temperature-dependent FTIR spectra, the results of which were further mathematically analyzed, the temperature-dependent fluctuations of interfacial water molecules were captured; the latter were the greatest for DMPS in PBS with a pH value of 7.4 and in general were greater for DMPS multibilayers in the absence of MCE. The presence of MCE made DMPS lipids more separated, allowing deeper penetration of water molecules towards the non-polar region and their restricted motion that resulted in decreased fluctuations. The experimentally observed results were supported by MD simulations of DMPS (+MCE) lipid bilayers.
{"title":"The Signature of Fluctuations of the Hydrogen Bond Network Formed by Water Molecules in the Interfacial Layer of Anionic Lipids","authors":"Ana-Marija Pavlek, Barbara Pem, Danijela Bakarić","doi":"10.3390/biophysica4010007","DOIUrl":"https://doi.org/10.3390/biophysica4010007","url":null,"abstract":"As the water molecules found at the interface of lipid bilayers exhibit distinct structural and reorientation dynamics compared to water molecules found in bulk, the fluctuations in their hydrogen bond (HB) network are expected to be different from those generated by the bulk water molecules. The research presented here aims to gain an insight into temperature-dependent fluctuations of a HB network of water molecules found in an interfacial layer of multilamellar liposomes (MLVs) composed of anionic 1,2-dimyristoyl-sn-glycero-3-phospho-L-serine (DMPS) lipids. Besides suspending DMPS lipids in phosphate buffer saline (PBS) of different pH values (6.0, 7.4, and 8.0), the changes in HB network fluctuations were altered by the incorporation of a non-polar flavonoid molecule myricetin (MCE) within the hydrocarbon chain region. By performing a multivariate analysis on the water combination band observed in temperature-dependent FTIR spectra, the results of which were further mathematically analyzed, the temperature-dependent fluctuations of interfacial water molecules were captured; the latter were the greatest for DMPS in PBS with a pH value of 7.4 and in general were greater for DMPS multibilayers in the absence of MCE. The presence of MCE made DMPS lipids more separated, allowing deeper penetration of water molecules towards the non-polar region and their restricted motion that resulted in decreased fluctuations. The experimentally observed results were supported by MD simulations of DMPS (+MCE) lipid bilayers.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":"12 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140442899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号