Pub Date : 2022-08-05DOI: 10.3390/biophysica2030026
E. Alfinito, M. Cesaria, M. Beccaria
We propose a model for bacterial Quorum Sensing based on an auxiliary electrostatic-like interaction originating from a fictitious electrical charge that represents bacteria activity. A cooperative mechanism for charge/activity exchange is introduced to implement chemotaxis and replication. The bacteria system is thus represented by means of a complex resistor network where link resistances take into account the allowed activity-flow among individuals. By explicit spatial stochastic simulations, we show that the model exhibits different quasi-realistic behaviors from colony formation to biofilm aggregation. The electrical signal associated with Quorum Sensing is analyzed in space and time and provides useful information about the colony dynamics. In particular, we analyze the transition between the planktonic and colony phases as the intensity of Quorum Sensing is varied.
{"title":"Did Maxwell Dream of Electrical Bacteria?","authors":"E. Alfinito, M. Cesaria, M. Beccaria","doi":"10.3390/biophysica2030026","DOIUrl":"https://doi.org/10.3390/biophysica2030026","url":null,"abstract":"We propose a model for bacterial Quorum Sensing based on an auxiliary electrostatic-like interaction originating from a fictitious electrical charge that represents bacteria activity. A cooperative mechanism for charge/activity exchange is introduced to implement chemotaxis and replication. The bacteria system is thus represented by means of a complex resistor network where link resistances take into account the allowed activity-flow among individuals. By explicit spatial stochastic simulations, we show that the model exhibits different quasi-realistic behaviors from colony formation to biofilm aggregation. The electrical signal associated with Quorum Sensing is analyzed in space and time and provides useful information about the colony dynamics. In particular, we analyze the transition between the planktonic and colony phases as the intensity of Quorum Sensing is varied.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43706457","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 : 2022-07-28DOI: 10.3390/biophysica2030018
L. Mortati, Barbara Pergolizzi, C. Panuzzo, E. Bracco
From yeast to mammalian cells, ubiquitination is one of the most conserved, and reversible, eukaryotic post-translational modifications (PTMs) responsible for controlling nearly all cellular processes. Potentially, every single eukaryotic cell can accomplish different ubiquitination processes at once, which in turn control the execution of specific cellular events in time and space with different biological significance (e.g., protein degradation or protein–protein interaction). Overall, all these signals are highly dynamic and need to be finely integrated to achieve a proper cellular response. Altogether, ubiquitination appears to be an extremely complex process, likely more than any other PTMs. Until a few years ago, the prevailing experimental approaches to investigate the different aspects of the ubiquitin system entailed genetic and biochemical analysis. However, recently, reagents and technologies have been developed enabling microscopy-based imaging of ubiquitination to enter the scene. In this paper, we discuss the progress made with conventional (confocal fluorescence microscopy) and non-conventional non-linear microscopy (Atomic Force Microscopy—AFM, Coherent Anti-Stokes Raman Scattering—CARS, Stimulated Raman Scattering—SRS) and we speculate on future developments.
{"title":"Present and Future Opportunities in Imaging the Ubiquitin System (Ub-System)","authors":"L. Mortati, Barbara Pergolizzi, C. Panuzzo, E. Bracco","doi":"10.3390/biophysica2030018","DOIUrl":"https://doi.org/10.3390/biophysica2030018","url":null,"abstract":"From yeast to mammalian cells, ubiquitination is one of the most conserved, and reversible, eukaryotic post-translational modifications (PTMs) responsible for controlling nearly all cellular processes. Potentially, every single eukaryotic cell can accomplish different ubiquitination processes at once, which in turn control the execution of specific cellular events in time and space with different biological significance (e.g., protein degradation or protein–protein interaction). Overall, all these signals are highly dynamic and need to be finely integrated to achieve a proper cellular response. Altogether, ubiquitination appears to be an extremely complex process, likely more than any other PTMs. Until a few years ago, the prevailing experimental approaches to investigate the different aspects of the ubiquitin system entailed genetic and biochemical analysis. However, recently, reagents and technologies have been developed enabling microscopy-based imaging of ubiquitination to enter the scene. In this paper, we discuss the progress made with conventional (confocal fluorescence microscopy) and non-conventional non-linear microscopy (Atomic Force Microscopy—AFM, Coherent Anti-Stokes Raman Scattering—CARS, Stimulated Raman Scattering—SRS) and we speculate on future developments.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"69560246","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 : 2022-07-07DOI: 10.3390/biophysica2030017
U. Jeffet, S. Livne, Shir Dviker, N. Sterer
Previous studies have shown that sub-lethal exposure of blue light caused increased bacterial cell membrane permeability. We hypothesized that combining blue light exposure with other antibacterial agents may increase their efficacy. The aim of the present study was to test the combined effect of blue light and sodium fluoride against dental caries pathogen Streptococcus mutans. Sm biofilms were exposed to blue light (400–500 nm) with or without sodium fluoride. Exposed and non-exposed samples were studied for acid production (lactate assay kit), acid tolerance (ATPase assay kit) and bacterial cell membrane damage (fluorescence microscopy). Results showed that the combined treatment significantly reduced the virulence of Sm concomitant with an increase in bacterial cell membrane permeability. Taken together, these results suggest that adjacent blue light exposure may increase fluoride caries preventive properties.
{"title":"Blue Light Enhances Fluoride Anticariogenic Activity against Streptococcus mutans","authors":"U. Jeffet, S. Livne, Shir Dviker, N. Sterer","doi":"10.3390/biophysica2030017","DOIUrl":"https://doi.org/10.3390/biophysica2030017","url":null,"abstract":"Previous studies have shown that sub-lethal exposure of blue light caused increased bacterial cell membrane permeability. We hypothesized that combining blue light exposure with other antibacterial agents may increase their efficacy. The aim of the present study was to test the combined effect of blue light and sodium fluoride against dental caries pathogen Streptococcus mutans. Sm biofilms were exposed to blue light (400–500 nm) with or without sodium fluoride. Exposed and non-exposed samples were studied for acid production (lactate assay kit), acid tolerance (ATPase assay kit) and bacterial cell membrane damage (fluorescence microscopy). Results showed that the combined treatment significantly reduced the virulence of Sm concomitant with an increase in bacterial cell membrane permeability. Taken together, these results suggest that adjacent blue light exposure may increase fluoride caries preventive properties.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47249632","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 : 2022-06-24DOI: 10.3390/biophysica2030016
R. I. Barbhuiya, S. Ramalingam, Harsimran Kalra, A. Elsayed, W. Routray, M. Annamalai, Ashutosh Kumar Singh
The synthesis of tailored and highly engineered multifunctional pharmaceutical nanocarriers is an emerging field of study in drug delivery applications. They have a high surface-area-to-volume ratio, aiding the targeted drug’s biodistribution and pharmacokinetic properties. Therefore, the characterization of nanocarriers is critical for understanding their physicochemical properties, which significantly impact their molecular and systemic functioning. To achieve specific goals, particle size, surface characteristics, and drug release properties of nanocarriers must be managed. This mini review provides an overview of the applications of non-destructive testing techniques (NDTT) to reveal the characteristics of nanocarriers, considering their surface charge, porosity, size, morphology, and crystalline organization. The compositional and microstructural characterization of nanocarriers through NDTT, such as dynamic light scattering, X-ray diffraction, confocal laser scanning microscopy, ultraviolet-visible spectroscopy, scanning electron microscopy, atomic force microscopy, and nuclear magnetic resonance spectroscopy, have been comprehensively reviewed. Furthermore, NDTT is only used to characterize physicochemical parameters related to the physiological performance of nanocarriers but does not account for nanocarrier toxicity. Hence, it is highly recommended that in the future, NDTT be developed to assess the toxicity of nanocarriers. In addition, by developing more advanced, effective, and precise techniques, such as machine vision techniques using artificial intelligence, the future of using NDTT for nanocarrier characterization will improve the evaluation of internal quality parameters.
{"title":"Application of Non-Destructive Testing Techniques (NDTT) to Characterize Nanocarriers Used for Drug Delivery: A Mini Review","authors":"R. I. Barbhuiya, S. Ramalingam, Harsimran Kalra, A. Elsayed, W. Routray, M. Annamalai, Ashutosh Kumar Singh","doi":"10.3390/biophysica2030016","DOIUrl":"https://doi.org/10.3390/biophysica2030016","url":null,"abstract":"The synthesis of tailored and highly engineered multifunctional pharmaceutical nanocarriers is an emerging field of study in drug delivery applications. They have a high surface-area-to-volume ratio, aiding the targeted drug’s biodistribution and pharmacokinetic properties. Therefore, the characterization of nanocarriers is critical for understanding their physicochemical properties, which significantly impact their molecular and systemic functioning. To achieve specific goals, particle size, surface characteristics, and drug release properties of nanocarriers must be managed. This mini review provides an overview of the applications of non-destructive testing techniques (NDTT) to reveal the characteristics of nanocarriers, considering their surface charge, porosity, size, morphology, and crystalline organization. The compositional and microstructural characterization of nanocarriers through NDTT, such as dynamic light scattering, X-ray diffraction, confocal laser scanning microscopy, ultraviolet-visible spectroscopy, scanning electron microscopy, atomic force microscopy, and nuclear magnetic resonance spectroscopy, have been comprehensively reviewed. Furthermore, NDTT is only used to characterize physicochemical parameters related to the physiological performance of nanocarriers but does not account for nanocarrier toxicity. Hence, it is highly recommended that in the future, NDTT be developed to assess the toxicity of nanocarriers. In addition, by developing more advanced, effective, and precise techniques, such as machine vision techniques using artificial intelligence, the future of using NDTT for nanocarrier characterization will improve the evaluation of internal quality parameters.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46656451","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 : 2022-06-06DOI: 10.3390/biophysica2020014
Mai T Huynh, B. Sengupta
Single-molecule Förster resonance energy transfer (smFRET) enables the deconvolution of various conformational substates of biomolecules. Over the past two decades, it has been widely used to understand the conformational dynamics of enzymes. Commonly, enzymes undergo reversible transitions between active and inactive states in solution. Using smFRET, the details of these transitions and the effect of ligands on these dynamics have been determined. In this mini-review, we discuss the various works focused on the investigation of enzyme conformational dynamics using smFRET.
{"title":"Analysis of Enzyme Conformation Dynamics Using Single-Molecule Förster Resonance Energy Transfer (smFRET)","authors":"Mai T Huynh, B. Sengupta","doi":"10.3390/biophysica2020014","DOIUrl":"https://doi.org/10.3390/biophysica2020014","url":null,"abstract":"Single-molecule Förster resonance energy transfer (smFRET) enables the deconvolution of various conformational substates of biomolecules. Over the past two decades, it has been widely used to understand the conformational dynamics of enzymes. Commonly, enzymes undergo reversible transitions between active and inactive states in solution. Using smFRET, the details of these transitions and the effect of ligands on these dynamics have been determined. In this mini-review, we discuss the various works focused on the investigation of enzyme conformational dynamics using smFRET.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48978010","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 : 2022-06-01DOI: 10.3390/biophysica2020013
H. Ng
In recent years, we have seen an explosion of technological progress related to drug discovery, including computing power, artificial intelligence, and electron microscopy [...]
近年来，我们看到了与药物发现相关的技术进步的爆炸式增长，包括计算能力、人工智能和电子显微镜[…]
{"title":"Recent Biophysical Advances in Drug Discovery","authors":"H. Ng","doi":"10.3390/biophysica2020013","DOIUrl":"https://doi.org/10.3390/biophysica2020013","url":null,"abstract":"In recent years, we have seen an explosion of technological progress related to drug discovery, including computing power, artificial intelligence, and electron microscopy [...]","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47307972","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 : 2022-05-23DOI: 10.3390/biophysica2020012
Ahmad R. Alhankawi, Jacob K Al-Husseini, Archie Spindler, Clark Baker, Tonderai T. Shoniwa, Mohammed Ahmed, P. Chiarelli, M. Johal
In this paper, the quartz crystal microbalance with dissipation monitoring (QCM-D) was used to investigate hydrophobicity and binding strength (KD) for 10 different drugs interacting with human serum albumin (HSA). Quantitative structure activity relationship (QSAR) analysis was used to determine the relationship between drug hydrophobicity (ClogP) and HSA binding strength log(1/KD). The results are compared to prior knowledge on bovine serum albumin (BSA) binding. We demonstrate a positive correlation between drug hydrophobicity and the strength of ligand-protein binding to HSA and show a statistically significant similarity with the trend reported in BSA. The findings presented in this work provide insight into the role that bound water plays in ligand-protein interactions. Further, the comparison between HSA and BSA provides quantitative justification for the use of these proteins interchangeably in the analysis of drug-based binding kinetics.
{"title":"The Relationship between Hydrophobicity and Drug-Protein Binding in Human Serum Albumin: A Quartz Crystal Microbalance Study","authors":"Ahmad R. Alhankawi, Jacob K Al-Husseini, Archie Spindler, Clark Baker, Tonderai T. Shoniwa, Mohammed Ahmed, P. Chiarelli, M. Johal","doi":"10.3390/biophysica2020012","DOIUrl":"https://doi.org/10.3390/biophysica2020012","url":null,"abstract":"In this paper, the quartz crystal microbalance with dissipation monitoring (QCM-D) was used to investigate hydrophobicity and binding strength (KD) for 10 different drugs interacting with human serum albumin (HSA). Quantitative structure activity relationship (QSAR) analysis was used to determine the relationship between drug hydrophobicity (ClogP) and HSA binding strength log(1/KD). The results are compared to prior knowledge on bovine serum albumin (BSA) binding. We demonstrate a positive correlation between drug hydrophobicity and the strength of ligand-protein binding to HSA and show a statistically significant similarity with the trend reported in BSA. The findings presented in this work provide insight into the role that bound water plays in ligand-protein interactions. Further, the comparison between HSA and BSA provides quantitative justification for the use of these proteins interchangeably in the analysis of drug-based binding kinetics.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42854810","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 : 2022-04-29DOI: 10.3390/biophysica2020011
J. Sancho
Yes, we are made of proteins, and yes, we can profit from them [...]
是的，我们是由蛋白质组成的，是的，可以从中获利[…]
{"title":"Protein Engineering: The Present and the Future","authors":"J. Sancho","doi":"10.3390/biophysica2020011","DOIUrl":"https://doi.org/10.3390/biophysica2020011","url":null,"abstract":"Yes, we are made of proteins, and yes, we can profit from them [...]","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45848884","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 : 2022-03-30DOI: 10.3390/biophysica2020009
Matthias Buck, V. Muñoz
“I can’t believe another year has passed already” is what most of us think when another birthday is upon us or when we see our children grow [...]
“我不敢相信又过了一年”是我们大多数人在另一个生日即将到来或看到孩子长大时的想法[…]
{"title":"First Year of Biophysica","authors":"Matthias Buck, V. Muñoz","doi":"10.3390/biophysica2020009","DOIUrl":"https://doi.org/10.3390/biophysica2020009","url":null,"abstract":"“I can’t believe another year has passed already” is what most of us think when another birthday is upon us or when we see our children grow [...]","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44589698","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 : 2022-02-16DOI: 10.3390/biophysica2010008
I. Le-Deygen, A. Safronova, P. Mamaeva, A. Skuredina, E. Kudryashova
In this work, we studied the effect of as on the interaction of membrane DPPC with the key antifibrotic drug pirfenidone. Liposomal forms of pirfenidone were obtained using passive loading. The addition of cholesterol reduces the loading efficiency of pirfenidone by 10%. The main binding site of pirfenidone in DPPC liposomes is the carbonyl group: the interaction with PF significantly increases the proportion of low-hydrated carbonyl groups as revealed by ATR-FTIR spectroscopy. The phosphate group acts as an additional binding site; however, due to shielding by the choline group, this interaction is weak. The hydrophobic part of the bilayer is not involved in PF binding at room temperature. Cholesterol changes the way of interaction between carbonyl groups and pirfenidone probably because of the formation of two subpopulations of DPPC and causes a dramatic redistribution of carbonyl groups onto the degrees of hydration. The proportion of moderately hydrated carbonyl groups increases, apparently due to the deepening of pirfenidone into the circumpolar region of the bilayer. For the first time, a change in the microenvironment of pirfenidone upon binding to liposomes was shown: aromatic moiety interacts with the bilayer.
{"title":"Cholesterol Significantly Affects the Interactions between Pirfenidone and DPPC Liposomes: Spectroscopic Studies","authors":"I. Le-Deygen, A. Safronova, P. Mamaeva, A. Skuredina, E. Kudryashova","doi":"10.3390/biophysica2010008","DOIUrl":"https://doi.org/10.3390/biophysica2010008","url":null,"abstract":"In this work, we studied the effect of as on the interaction of membrane DPPC with the key antifibrotic drug pirfenidone. Liposomal forms of pirfenidone were obtained using passive loading. The addition of cholesterol reduces the loading efficiency of pirfenidone by 10%. The main binding site of pirfenidone in DPPC liposomes is the carbonyl group: the interaction with PF significantly increases the proportion of low-hydrated carbonyl groups as revealed by ATR-FTIR spectroscopy. The phosphate group acts as an additional binding site; however, due to shielding by the choline group, this interaction is weak. The hydrophobic part of the bilayer is not involved in PF binding at room temperature. Cholesterol changes the way of interaction between carbonyl groups and pirfenidone probably because of the formation of two subpopulations of DPPC and causes a dramatic redistribution of carbonyl groups onto the degrees of hydration. The proportion of moderately hydrated carbonyl groups increases, apparently due to the deepening of pirfenidone into the circumpolar region of the bilayer. For the first time, a change in the microenvironment of pirfenidone upon binding to liposomes was shown: aromatic moiety interacts with the bilayer.","PeriodicalId":72401,"journal":{"name":"Biophysica","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43916297","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}
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