Pub Date : 2025-07-09DOI: 10.1016/j.bpc.2025.107489
Michael Overduin , Gestél C. Kuyler , Mansoore Esmaili , Catharine A. Trieber , Claudia Acevedo-Morantes , Alexander P. Orazietti , Rustem Shaykhutdinov , Rakesh K. Bhat , Tomisin Omotoso , Sabiha Tajammul , Mohammad Rahim , Sophie Zinn-Justin , Russell E. Bishop , R. Scott Prosser , Holger Wille , Bert Klumperman
Copolymers formed by non-alternating distributions of styrene and maleic acid monomers directly solubilize intact membranes into ∼10 nm discs. However, these copolymers are inherently polydisperse in terms of polymer structure, difficult to detect, prone to precipitation with divalent cations, and have limited working pH ranges due to their charges. The exposed polar sidechain of nanodisc-forming amphipathic copolymers provides a handle for integrating critical chemical features for facile solubilization, purification, detection, and resolution of diverse membrane protein complexes, including 7-transmembrane G-Protein-Coupled Receptor (GPCR) and beta-barrel proteins directly from cellular material. Here, we report that when derivatized with amine oxide (AO) moieties, alternating and intrinsically fluorescent derivatives of poly(styrene-alt-maleic anhydride) (SMAnh) spontaneously convert biological membranes into nanodiscs with diameters of 15–30 nm that can be resolved by dynamic light scattering and electron microscopy. Compared to non-alternating poly(styrene-co-maleic acid) (SMA), their fluorescence signals allow monitoring under diverse solution conditions, whether free or lipid bilayer-bound. These copolymers are useful in a broad pH range, are tolerant of high levels of divalent cations (>200 mM CaCl2) and are designed to reduce undesirable nonspecific interactions. The resulting nanodiscs can accommodate the PagP palmitoyltransferase expressed in Escherichia coli outer membranes and the human adenosine A2A receptor expressed into Pichia pastoris membranes, resulting in readily purified proteins that are less likely to be perturbed by polymer charge or hydrophobicity.
苯乙烯和马来酸单体的非交替分布形成的共聚物直接将完整的膜溶解成约10 nm的圆盘。然而，就聚合物结构而言，这些共聚物本质上是多分散的，难以检测，容易与二价阳离子沉淀，并且由于它们的电荷而具有有限的工作pH范围。暴露的纳米盘状两亲共聚物的极性侧链为多种膜蛋白复合物（包括7-跨膜g蛋白偶联受体（GPCR）和直接来自细胞材料的β -桶蛋白）的快速溶解、纯化、检测和分离提供了关键的化学特性。在这里，我们报道了当与氧化胺（AO）部分衍生时，聚苯乙烯-马来酸酐（SMAnh）的交替和本质荧光衍生物自发地将生物膜转化为直径为15-30 nm的纳米片，可以通过动态光散射和电子显微镜分辨。与非交变聚苯乙烯-共马来酸（SMA）相比，它们的荧光信号可以在不同的溶液条件下进行监测，无论是游离的还是脂质双分子层结合的。这些共聚物适用于较宽的pH范围，可耐受高水平的二价阳离子（200 mM CaCl2），并可减少不良的非特异性相互作用。由此产生的纳米圆盘可以容纳大肠杆菌外膜中表达的PagP棕榈酰转移酶和毕赤酵母膜中表达的人腺苷A2A受体，从而产生易于纯化的蛋白质，这些蛋白质不太可能受到聚合物电荷或疏水性的干扰。
{"title":"Design of zwitterionic fluorescent polymers for membrane protein solubilization into native nanodiscs","authors":"Michael Overduin , Gestél C. Kuyler , Mansoore Esmaili , Catharine A. Trieber , Claudia Acevedo-Morantes , Alexander P. Orazietti , Rustem Shaykhutdinov , Rakesh K. Bhat , Tomisin Omotoso , Sabiha Tajammul , Mohammad Rahim , Sophie Zinn-Justin , Russell E. Bishop , R. Scott Prosser , Holger Wille , Bert Klumperman","doi":"10.1016/j.bpc.2025.107489","DOIUrl":"10.1016/j.bpc.2025.107489","url":null,"abstract":"<div><div>Copolymers formed by non-alternating distributions of styrene and maleic acid monomers directly solubilize intact membranes into ∼10 nm discs. However, these copolymers are inherently polydisperse in terms of polymer structure, difficult to detect, prone to precipitation with divalent cations, and have limited working pH ranges due to their charges. The exposed polar sidechain of nanodisc-forming amphipathic copolymers provides a handle for integrating critical chemical features for facile solubilization, purification, detection, and resolution of diverse membrane protein complexes, including 7-transmembrane G-Protein-Coupled Receptor (GPCR) and beta-barrel proteins directly from cellular material. Here, we report that when derivatized with amine oxide (AO) moieties, alternating and intrinsically fluorescent derivatives of poly(styrene-<em>alt</em>-maleic anhydride) (SMAnh) spontaneously convert biological membranes into nanodiscs with diameters of 15–30 nm that can be resolved by dynamic light scattering and electron microscopy. Compared to non-alternating poly(styrene-<em>co</em>-maleic acid) (SMA), their fluorescence signals allow monitoring under diverse solution conditions, whether free or lipid bilayer-bound. These copolymers are useful in a broad pH range, are tolerant of high levels of divalent cations (>200 mM CaCl<sub>2</sub>) and are designed to reduce undesirable nonspecific interactions. The resulting nanodiscs can accommodate the PagP palmitoyltransferase expressed in <em>Escherichia coli</em> outer membranes and the human adenosine A<sub>2A</sub> receptor expressed into <em>Pichia pastoris</em> membranes, resulting in readily purified proteins that are less likely to be perturbed by polymer charge or hydrophobicity.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107489"},"PeriodicalIF":3.3,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144606028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-07-09DOI: 10.1016/j.bpc.2025.107491
Swarnima Pandey , Afzal Azim , Neeraj Sinha
Despite the availability of advanced treatment, sepsis and septic shock have the highest mortality in the intensive care unit. Theories suggested that targeting hyper inflammation can aid treatment, but oxidative stress plays a major role in disease pathogenesis. The present study aimed to explore the nuclear magnetic resonance (NMR) – based serum biomarkers of sepsis and septic shock resultant of oxidative stress. The serum metabolic profile of n = 41 septic shock, n = 21 sepsis, and n = 16 disease control patients were collected and analyzed using a 1D 1H Carr Purcell Meiboom Gill (CPMG) pulse program. NMR spectroscopy-based quantitative assessment of metabolites was performed to compare the activity of lactate dehydrogenase and phenylalanine hydroxylase between sepsis, septic shock, and disease control in sepsis and septic shock by comparing pyruvate/lactate (Pyr/Lac) and phenylalanine/tyrosine (Phe/Tyr) ratios. These ratios were evaluated for their discriminatory potential, statistical and clinical significance. We found out that Pyr/Lac ratio was lowest in septic shock followed by sepsis and disease control, Phe/Tyr ratio was highest in septic shock, followed by sepsis and disease control. Pyr/Lac ratio and Phe/Tyr were negatively and positively correlated with APACHE II. Both the ratios illustrated high discriminatory potential in AUROC evaluation. The results presented in the study demonstrate that lactate dehydrogenase activity is elevated and phenylalanine hydroxylase declines in septic shock. This could be used as an effective tool for diagnosis, prognosis, evaluation of disease activity, and treatment response.
{"title":"Diagnostic biomarkers for Sepsis and septic shock: A NMR based serum metabolomics study","authors":"Swarnima Pandey , Afzal Azim , Neeraj Sinha","doi":"10.1016/j.bpc.2025.107491","DOIUrl":"10.1016/j.bpc.2025.107491","url":null,"abstract":"<div><div>Despite the availability of advanced treatment, sepsis and septic shock have the highest mortality in the intensive care unit. Theories suggested that targeting hyper inflammation can aid treatment, but oxidative stress plays a major role in disease pathogenesis. The present study aimed to explore the nuclear magnetic resonance (NMR) – based serum biomarkers of sepsis and septic shock resultant of oxidative stress. The serum metabolic profile of <em>n</em> = 41 septic shock, <em>n</em> = 21 sepsis, and <em>n</em> = 16 disease control patients were collected and analyzed using a 1D <sup>1</sup>H Carr Purcell Meiboom Gill (CPMG) pulse program. NMR spectroscopy-based quantitative assessment of metabolites was performed to compare the activity of lactate dehydrogenase and phenylalanine hydroxylase between sepsis, septic shock, and disease control in sepsis and septic shock by comparing pyruvate/lactate (Pyr/Lac) and phenylalanine/tyrosine (Phe/Tyr) ratios. These ratios were evaluated for their discriminatory potential, statistical and clinical significance. We found out that Pyr/Lac ratio was lowest in septic shock followed by sepsis and disease control, Phe/Tyr ratio was highest in septic shock, followed by sepsis and disease control. Pyr/Lac ratio and Phe/Tyr were negatively and positively correlated with APACHE II. Both the ratios illustrated high discriminatory potential in AUROC evaluation. The results presented in the study demonstrate that lactate dehydrogenase activity is elevated and phenylalanine hydroxylase declines in septic shock. This could be used as an effective tool for diagnosis, prognosis, evaluation of disease activity, and treatment response.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"326 ","pages":"Article 107491"},"PeriodicalIF":3.3,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144654621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fluorescein dyes are widely applied in fluorescence bioimaging to visualize a spatial distribution of substructures or to monitor a kinetics of certain processes in cells. However, optical properties of the dyes are sensitive to a number of physical and chemical parameters of the microenvironment and, when conjugated to a macromolecule, the dye can additionally serve as an indicator of these parameters in near-surface regions. The present study aims to reveal the relationships between the response of the fluorescein probe and the structure of the macromolecule to which it is attached. We conjugated fluorescein-5-isothiocyanate (FITC) to four proteins of different sizes and surface charges (hen egg-white lysozyme, bovine carbonic anhydrase II, bovine serum albumin, and luciferase from Photobacterium leiognathi) and analyzed the relationship of spectral, time-resolved, and polarization characteristics of the fluorescence probe with protein size and charge parameters. The study shows that ionic equilibrium of FITC and dielectric permittivity (ε) near the protein surface differ from those in the bulk phase at pH 6.50. For the first time, a strong negative correlation between local ε and the hydrophobic surface area of the protein and a strong positive correlation between net charge density of protein and the ratiometric fluorescence signal of FITC (I488/I435) were found. The combined effect of covalent and electrostatic binding of FITC to the protein was found to increase the rigidity of conjugation, allowing adequate estimation of protein size using the fluorescence depolarization technique.
{"title":"Local optical probing of proteins of various sizes and charges with FITC label","authors":"D.P. Surzhikova , E.V. Nemtseva , L.A. Sukovatyi , A.V. Borgoyakova , E.A. Slyusareva","doi":"10.1016/j.bpc.2025.107488","DOIUrl":"10.1016/j.bpc.2025.107488","url":null,"abstract":"<div><div>Fluorescein dyes are widely applied in fluorescence bioimaging to visualize a spatial distribution of substructures or to monitor a kinetics of certain processes in cells. However, optical properties of the dyes are sensitive to a number of physical and chemical parameters of the microenvironment and, when conjugated to a macromolecule, the dye can additionally serve as an indicator of these parameters in near-surface regions. The present study aims to reveal the relationships between the response of the fluorescein probe and the structure of the macromolecule to which it is attached. We conjugated fluorescein-5-isothiocyanate (FITC) to four proteins of different sizes and surface charges (hen egg-white lysozyme, bovine carbonic anhydrase II, bovine serum albumin, and luciferase from <em>Photobacterium leiognathi</em>) and analyzed the relationship of spectral, time-resolved, and polarization characteristics of the fluorescence probe with protein size and charge parameters. The study shows that ionic equilibrium of FITC and dielectric permittivity (ε) near the protein surface differ from those in the bulk phase at pH 6.50. For the first time, a strong negative correlation between local ε and the hydrophobic surface area of the protein and a strong positive correlation between net charge density of protein and the ratiometric fluorescence signal of FITC (I<sup>488</sup>/I<sup>435</sup>) were found. The combined effect of covalent and electrostatic binding of FITC to the protein was found to increase the rigidity of conjugation, allowing adequate estimation of protein size using the fluorescence depolarization technique.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107488"},"PeriodicalIF":3.3,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144572788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Characterization by various surface morphological and compositional analysis techniques showed that ZnO NPs have a cylindrical crystalline structure with a size of ≤50 nm. The analysis of ZnO NPs effects on UV–visible, CD, fluorescence, and 1H NMR spectra of horse myoglobin (h-MB) in aqueous and denaturant media at pH 7.4 revealed that ZnO NPs reinforce the urea impact by weakening the heme-globin interaction and protein structures in the denaturant medium. Analysis of ZnO NPs effects on urea- and heat-induced denaturation profiles of h-MB revealed that ZnO NPs reduce the local (heme-globin interaction) thermal stability of h-MB in an aqueous medium, but they decrease both local and structural thermodynamic stability in denaturant medium. Analysis of ZnO NPs effects on entropy-enthalpy plot, protein stability curve, and average fluorescence lifetime of h-MB revealed that the attractive enthalpic electrostatic interactions between the ZnO NPs and h-MB contribute to the decrease in thermodynamic stability of h-MB by ZnO NPs.
{"title":"Revealing the underlying mechanism of ZnO nanoparticles-induced modulation of structural features and thermodynamic stability of myoglobin","authors":"Beeta Kumari, Shabnam Yadav, Manisha Yadav, Rajesh Kumar","doi":"10.1016/j.bpc.2025.107487","DOIUrl":"10.1016/j.bpc.2025.107487","url":null,"abstract":"<div><div>Characterization by various surface morphological and compositional analysis techniques showed that ZnO NPs have a cylindrical crystalline structure with a size of ≤50 nm. The analysis of ZnO NPs effects on UV–visible, CD, fluorescence, and <sup>1</sup>H NMR spectra of horse myoglobin (h-MB) in aqueous and denaturant media at pH 7.4 revealed that ZnO NPs reinforce the urea impact by weakening the heme-globin interaction and protein structures in the denaturant medium. Analysis of ZnO NPs effects on urea- and heat-induced denaturation profiles of h-MB revealed that ZnO NPs reduce the local (heme-globin interaction) thermal stability of h-MB in an aqueous medium, but they decrease both local and structural thermodynamic stability in denaturant medium. Analysis of ZnO NPs effects on entropy-enthalpy plot, protein stability curve, and average fluorescence lifetime of h-MB revealed that the attractive enthalpic electrostatic interactions between the ZnO NPs and h-MB contribute to the decrease in thermodynamic stability of h-MB by ZnO NPs.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107487"},"PeriodicalIF":3.3,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144549550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alzheimer's disease is a paragon of neurodegenerative diseases with prominent vagueness of cognitive impairment due to dysregulation of cholinergic and monoaminergic systems. This research employed molecular mechanics and quantum Mechanics to evaluate the plausible role of designed phenothiazine-derivatives as dual MAO-B and Acetylcholinesterase inhibitors. Synthesis and Cytotoxicity studies were performed for the eloquent molecules. In-silico studies revealed that halogens may enhance the binding affinity of compounds towards the target. NJ3b-d exhibited moderate inhibition in the SH-SY5Y cell lines compared with memantine (IC5035.88 μg/ml). 150 ns MD studies revealed the stability of NJ3c (IC5048.06 μg/ml) in the catalytic pockets of enzymes. DFT, pKa, BDE, Fukui-function, Epik-state, and membrane-permeability studies were performed to analyze the chemical stability and permeability. The results of QM displayed the compound NJ3c as BBB-permeable and it has thermal and kinetic stability. Our findings suggested that NJ3c can be considered a potential candidate for dual targeting MAO-B and Acetylcholinesterase.
{"title":"Computational insights, synthesis and cytotoxicity evaluation of phenothiazine derivatives as a dual inhibitors targeting MAO-B and AChE","authors":"Neeru Dugar , Ashish Mohanrao Kanhed , Mohammed Afzal Azam , Srikanth Jupudi","doi":"10.1016/j.bpc.2025.107486","DOIUrl":"10.1016/j.bpc.2025.107486","url":null,"abstract":"<div><div>Alzheimer's disease is a paragon of neurodegenerative diseases with prominent vagueness of cognitive impairment due to dysregulation of cholinergic and monoaminergic systems. This research employed molecular mechanics and quantum Mechanics to evaluate the plausible role of designed phenothiazine-derivatives as dual MAO-B and Acetylcholinesterase inhibitors. Synthesis and Cytotoxicity studies were performed for the eloquent molecules. <em>In-silico</em> studies revealed that halogens may enhance the binding affinity of compounds towards the target. NJ3b-d exhibited moderate inhibition in the SH-SY5Y cell lines compared with memantine (IC<sub>50</sub>35.88 μg/ml). 150 ns MD studies revealed the stability of NJ3c (IC<sub>50</sub>48.06 μg/ml) in the catalytic pockets of enzymes. DFT, pKa, BDE, Fukui-function, Epik-state, and membrane-permeability studies were performed to analyze the chemical stability and permeability. The results of QM displayed the compound NJ3c as BBB-permeable and it has thermal and kinetic stability. Our findings suggested that NJ3c can be considered a potential candidate for dual targeting MAO-B and Acetylcholinesterase.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107486"},"PeriodicalIF":3.3,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144517652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-18DOI: 10.1016/j.bpc.2025.107485
A.I. Osetsky
The fluctuation microdeformations of biomolecules have been analyzed on the basis of Boltzmann principle taking into account their internal thermal dynamics. The “active biomolecule - passive medium” model, which is fundamentally different from the Brownian activation models, is considered. In the frame of that model, the exponential dependence of the reaction-rate constant of non-diffusion-controlled biochemical reactions on the dynamic viscosity of the medium has been obtained. The obtained dependencies are used to explain the experimentally observed deviations of the temperature behavior of the reaction-rate constant of enzymatic reactions from the Arrhenius equation and the influence of the medium viscosity on the conformational mobility of biomolecules.
{"title":"The Boltzmann principle in the theory of enzymatic catalysis and conformational mobility of biomolecules","authors":"A.I. Osetsky","doi":"10.1016/j.bpc.2025.107485","DOIUrl":"10.1016/j.bpc.2025.107485","url":null,"abstract":"<div><div>The fluctuation microdeformations of biomolecules have been analyzed on the basis of Boltzmann principle taking into account their internal thermal dynamics. The “active biomolecule - passive medium” model, which is fundamentally different from the Brownian activation models, is considered. In the frame of that model, the exponential dependence of the reaction-rate constant of non-diffusion-controlled biochemical reactions on the dynamic viscosity of the medium has been obtained. The obtained dependencies are used to explain the experimentally observed deviations of the temperature behavior of the reaction-rate constant of enzymatic reactions from the Arrhenius equation and the influence of the medium viscosity on the conformational mobility of biomolecules.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107485"},"PeriodicalIF":3.3,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144490236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-17DOI: 10.1016/j.bpc.2025.107484
Yuval Ben-Abu
Ion channels are essential membrane proteins that control ionic flow and cellular electrical activity. While traditional Markovian models have provided insights into channel gating, they fail to capture the memory-dependent dynamics of real ion channel behavior. This manuscript presents a novel semi non-Markovian framework for understanding ion channel gating processes. Using continuous time and discrete state space models for two and three-state systems, we derive Volterra convolution-type integral equations governing channel dynamics. Through Laplace transform analysis, we reveal asymptotic behaviors and previously hidden asymmetries between opening and closing rates. Our approach successfully predicts asymmetrical gating kinetics, characterizes infinite-state processes, and elucidates dynamic state creation—capabilities beyond conventional Markovian models. This breakthrough moves from phenomenological descriptions toward understanding the fundamental physics of ion channel gating, with significant implications for drug discovery and therapeutic development targeting ion channel dysfunction. This work establishes a new paradigm in ion channel research, providing the mathematical framework needed to unlock the full complexity of these critical cellular processes.
{"title":"From Markovian to Non-Markovian: Advancing ion channel rate process theory","authors":"Yuval Ben-Abu","doi":"10.1016/j.bpc.2025.107484","DOIUrl":"10.1016/j.bpc.2025.107484","url":null,"abstract":"<div><div>Ion channels are essential membrane proteins that control ionic flow and cellular electrical activity. While traditional Markovian models have provided insights into channel gating, they fail to capture the memory-dependent dynamics of real ion channel behavior. This manuscript presents a novel semi non-Markovian framework for understanding ion channel gating processes. Using continuous time and discrete state space models for two and three-state systems, we derive Volterra convolution-type integral equations governing channel dynamics. Through Laplace transform analysis, we reveal asymptotic behaviors and previously hidden asymmetries between opening and closing rates. Our approach successfully predicts asymmetrical gating kinetics, characterizes infinite-state processes, and elucidates dynamic state creation—capabilities beyond conventional Markovian models. This breakthrough moves from phenomenological descriptions toward understanding the fundamental physics of ion channel gating, with significant implications for drug discovery and therapeutic development targeting ion channel dysfunction. This work establishes a new paradigm in ion channel research, providing the mathematical framework needed to unlock the full complexity of these critical cellular processes.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107484"},"PeriodicalIF":3.3,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144366883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-12DOI: 10.1016/j.bpc.2025.107481
Metin Yildirim , Mehmet Cimentepe , Kemal Dogan , Adem Necip , Madina Amangeldinova
Multidrug-resistant (MDR) bacteria have become a significant global concern in recent years, necessitating the development of innovative strategies to combat these pathogens. Berberine, a bioactive alkaloid found in Berberis vulgaris, Berberis aquifolium, Coptis chinensis, Coptis japonica, and Hydrastis canadensis, exhibits a broad spectrum of biological activities, including antibacterial effects. However, its low aqueous solubility limits its bioavailability, restricting its therapeutic potential. Poly(2-hydroxyethyl methacrylate) (pHEMA)-based cryogel membranes, known for their biocompatibility and ease of synthesis, have been widely utilized in biomedical applications, particularly in wound healing. In this study, berberine was successfully incorporated into pHEMA cryogel membranes and characterized using FT-IR spectroscopy. Biocompatibility assessments were conducted using L929 fibroblast cells, and MTT assay results confirmed that cell viability remained above 88 %, indicating good biocompatibility. The antibacterial properties of the prepared membranes against MDR E. coli and MRSA were evaluated using the disk diffusion and time-kill methods. According to the time-kill assay, high-dose berberine-loaded cryogel membranes (BM2) exhibited inhibition rates of 87.2 % against MRSA and 96.8 % against MDR E. coli. The antibacterial and antibiofilm effects of the membranes were further validated by SEM imaging, which revealed that berberine effectively disrupted bacterial biofilms. To gain insight into the molecular mechanisms underlying antibacterial activity, molecular docking studies were performed on key bacterial proteins involved in essential physiological processes, including the OmpA transmembrane domain (PDB ID: 1BXW), E. coli DNA gyrase B (PDB IDs: 4WUB, 6KZX, 6KZV), E. coli hydrogenase (PDB ID: 5LMM), penicillin-binding protein 3 (PBP3; PDB ID: 3VSL), and PBP2a from MRSA (PDB IDs: 1MWT, 4CJN, 5M18, 6Q9N). The strongest interaction was observed between berberine and 6KZX, with a docking score of −7.898 kcal/mol, whereas the weakest interaction was noted with 4CJN, with a docking score of −3.743 kcal/mol. These findings highlight the potential of berberine-loaded pHEMA cryogel membranes as a promising antibacterial platform for combating MDR bacterial infections, particularly for wound healing applications.
{"title":"Next-generation antibacterial cryogels: Berberine-infused smart membranes with molecular docking-guided targeting of MRSA and MDR E. coli","authors":"Metin Yildirim , Mehmet Cimentepe , Kemal Dogan , Adem Necip , Madina Amangeldinova","doi":"10.1016/j.bpc.2025.107481","DOIUrl":"10.1016/j.bpc.2025.107481","url":null,"abstract":"<div><div>Multidrug-resistant (MDR) bacteria have become a significant global concern in recent years, necessitating the development of innovative strategies to combat these pathogens. Berberine, a bioactive alkaloid found in <em>Berberis vulgaris</em>, <em>Berberis aquifolium</em>, <em>Coptis chinensis</em>, <em>Coptis japonica</em>, and <em>Hydrastis canadensis</em>, exhibits a broad spectrum of biological activities, including antibacterial effects. However, its low aqueous solubility limits its bioavailability, restricting its therapeutic potential. Poly(2-hydroxyethyl methacrylate) (pHEMA)-based cryogel membranes, known for their biocompatibility and ease of synthesis, have been widely utilized in biomedical applications, particularly in wound healing. In this study, berberine was successfully incorporated into pHEMA cryogel membranes and characterized using FT-IR spectroscopy. Biocompatibility assessments were conducted using L929 fibroblast cells, and MTT assay results confirmed that cell viability remained above 88 %, indicating good biocompatibility. The antibacterial properties of the prepared membranes against MDR <em>E. coli</em> and MRSA were evaluated using the disk diffusion and time-kill methods. According to the time-kill assay, high-dose berberine-loaded cryogel membranes (BM2) exhibited inhibition rates of 87.2 % against MRSA and 96.8 % against MDR <em>E. coli</em>. The antibacterial and antibiofilm effects of the membranes were further validated by SEM imaging, which revealed that berberine effectively disrupted bacterial biofilms. To gain insight into the molecular mechanisms underlying antibacterial activity, molecular docking studies were performed on key bacterial proteins involved in essential physiological processes, including the OmpA transmembrane domain (PDB ID: <span><span>1BXW</span><svg><path></path></svg></span>), <em>E. coli</em> DNA gyrase B (PDB IDs: <span><span>4WUB</span><svg><path></path></svg></span>, <span><span>6KZX</span><svg><path></path></svg></span>, <span><span>6KZV</span><svg><path></path></svg></span>), <em>E. coli</em> hydrogenase (PDB ID: <span><span>5LMM</span><svg><path></path></svg></span>), penicillin-binding protein 3 (PBP3; PDB ID: <span><span>3VSL</span><svg><path></path></svg></span>), and PBP2a from MRSA (PDB IDs: <span><span>1MWT</span><svg><path></path></svg></span>, <span><span>4CJN</span><svg><path></path></svg></span>, <span><span>5M18</span><svg><path></path></svg></span>, <span><span>6Q9N</span><svg><path></path></svg></span>). The strongest interaction was observed between berberine and 6KZX, with a docking score of −7.898 kcal/mol, whereas the weakest interaction was noted with 4CJN, with a docking score of −3.743 kcal/mol. These findings highlight the potential of berberine-loaded pHEMA cryogel membranes as a promising antibacterial platform for combating MDR bacterial infections, particularly for wound healing applications.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107481"},"PeriodicalIF":3.3,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144306232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-06DOI: 10.1016/j.bpc.2025.107480
N.S. Mohd Nor Ihsan , S.F. Abdul Sani , L.M. Looi , Dharini Pathmanathan , P.L. Cheah , S.F. Chiew , D.A. Bradley
Amyloid fibrils, characterized by β-sheet-rich protein aggregates, are closely associated with various diseases. Understanding the structural and biochemical changes in amyloid formation requires detailed characterization of their Raman spectroscopic signatures. This study evaluated the application of Raman spectroscopy, utilizing a 532-nm laser excitation source, for differentiating amyloid from normal tissues. Raman spectroscopy effectively identifies protein secondary structures and distinguishes normal tissues from amyloid-containing tissues, offering potential for real-time diagnosis. A total of 13 amyloid tissue samples (heart, kidney, and thyroid) and 9 normal controls were analyzed. Key spectral differences were observed in the amide I (∼1660 cm−1) and amide III (∼1300 cm−1) regions, characteristic of β-sheet structures in amyloid fibrils. Spatially resolved Raman spectra revealed molecular heterogeneity between amide and lipid components in amyloid deposits. Ratiometric analysis further supported this, demonstrating significant differences in the amide-to-lipid ratio (with attributed significant peak intensities at 1660 cm−1 for amide I and 1440 cm−1 for lipids) between amyloid and control tissues. Statistical analysis (Mann-Whitney U test, p = 0.006) confirmed significant differences in amide group intensities between amyloid and control tissues. These findings highlight Raman spectroscopy as a promising tool for real-time identification and characterization of amyloid deposits, with potential clinical applications in diagnosing amyloid-related diseases.
{"title":"Raman spectroscopic signatures of amyloid fibrils: Insights into structural and biochemical changes in human tissues","authors":"N.S. Mohd Nor Ihsan , S.F. Abdul Sani , L.M. Looi , Dharini Pathmanathan , P.L. Cheah , S.F. Chiew , D.A. Bradley","doi":"10.1016/j.bpc.2025.107480","DOIUrl":"10.1016/j.bpc.2025.107480","url":null,"abstract":"<div><div>Amyloid fibrils, characterized by β-sheet-rich protein aggregates, are closely associated with various diseases. Understanding the structural and biochemical changes in amyloid formation requires detailed characterization of their Raman spectroscopic signatures. This study evaluated the application of Raman spectroscopy, utilizing a 532-nm laser excitation source, for differentiating amyloid from normal tissues. Raman spectroscopy effectively identifies protein secondary structures and distinguishes normal tissues from amyloid-containing tissues, offering potential for real-time diagnosis. A total of 13 amyloid tissue samples (heart, kidney, and thyroid) and 9 normal controls were analyzed. Key spectral differences were observed in the amide I (∼1660 cm<sup>−1</sup>) and amide III (∼1300 cm<sup>−1</sup>) regions, characteristic of β-sheet structures in amyloid fibrils. Spatially resolved Raman spectra revealed molecular heterogeneity between amide and lipid components in amyloid deposits. Ratiometric analysis further supported this, demonstrating significant differences in the amide-to-lipid ratio (with attributed significant peak intensities at 1660 cm<sup>−1</sup> for amide I and 1440 cm<sup>−1</sup> for lipids) between amyloid and control tissues. Statistical analysis (Mann-Whitney <em>U</em> test, <em>p</em> = 0.006) confirmed significant differences in amide group intensities between amyloid and control tissues. These findings highlight Raman spectroscopy as a promising tool for real-time identification and characterization of amyloid deposits, with potential clinical applications in diagnosing amyloid-related diseases.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107480"},"PeriodicalIF":3.3,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144254174","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-04DOI: 10.1016/j.bpc.2025.107473
Ji-Na Yoo , Ha-Neul Kim , Su-Yeon Choi , Yuxi Lin , Young-Ho Lee , Min-Duk Seo
Huntington's disease (HD) is a genetic neurodegenerative disorder caused by the abnormal expansion of the polyglutamine (polyQ) tract (> 35Q) in the first exon of the huntingtin (Htt), HttEx1. This N-terminal fragment tends to form fibrillar inclusions, which constitute a key pathological hallmark of HD. Although polyQ expansion is commonly understood to be a primary cause of HttEx1 pathology, the molecular mechanism of aggregations of non-pathogenic polyQ tract with the N-terminally flanking region of N17 in HttEx1 (HttEx1-17Q) remains largely unknown. In this study, we exclusively investigated the effect of the protein concentration on the structural transition of HttEx1-17Q and its relation to the amyloid fibril formation by employing biophysical techniques including nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), atomic force microscopy (AFM), and thioflavin T (ThT) fluorescence. Complementary analyses showed that monomeric HttEx1-17Q undergoes a multiple structural transition from largely unfolded structures to β structures via helical structures in a concentration-dependent manner in the early stages of aggregation. This structural rearrangement accelerates kinetically the formation of short amyloid fibrils of HttEx1-17Q by facilitating nucleation. Our findings provide new insights into the amyloid formation of HttEx1 by highlighting the critical role of a structural conversion into an amyloidogenic structure, of which mechanism is helpful to understand amyloidogenesis of other amyloid-forming molecules.
{"title":"Concentration-dependent structural transition of huntingtin protein in Huntington's disease","authors":"Ji-Na Yoo , Ha-Neul Kim , Su-Yeon Choi , Yuxi Lin , Young-Ho Lee , Min-Duk Seo","doi":"10.1016/j.bpc.2025.107473","DOIUrl":"10.1016/j.bpc.2025.107473","url":null,"abstract":"<div><div>Huntington's disease (HD) is a genetic neurodegenerative disorder caused by the abnormal expansion of the polyglutamine (polyQ) tract (> 35Q) in the first exon of the huntingtin (Htt), HttEx1. This N-terminal fragment tends to form fibrillar inclusions, which constitute a key pathological hallmark of HD. Although polyQ expansion is commonly understood to be a primary cause of HttEx1 pathology, the molecular mechanism of aggregations of non-pathogenic polyQ tract with the N-terminally flanking region of N17 in HttEx1 (HttEx1-17Q) remains largely unknown. In this study, we exclusively investigated the effect of the protein concentration on the structural transition of HttEx1-17Q and its relation to the amyloid fibril formation by employing biophysical techniques including nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy, transmission electron microscopy (TEM), atomic force microscopy (AFM), and thioflavin T (ThT) fluorescence. Complementary analyses showed that monomeric HttEx1-17Q undergoes a multiple structural transition from largely unfolded structures to β structures <em>via</em> helical structures in a concentration-dependent manner in the early stages of aggregation. This structural rearrangement accelerates kinetically the formation of short amyloid fibrils of HttEx1-17Q by facilitating nucleation. Our findings provide new insights into the amyloid formation of HttEx1 by highlighting the critical role of a structural conversion into an amyloidogenic structure, of which mechanism is helpful to understand amyloidogenesis of other amyloid-forming molecules.</div></div>","PeriodicalId":8979,"journal":{"name":"Biophysical chemistry","volume":"325 ","pages":"Article 107473"},"PeriodicalIF":3.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144230942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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