European Biophysics Journal最新文献

{"title":"Inhibitor design for TMPRSS2: insights from computational analysis of its backbone hydrogen bonds using a simple descriptor","authors":"Suraj Ugrani","doi":"10.1007/s00249-023-01695-4","DOIUrl":"10.1007/s00249-023-01695-4","url":null,"abstract":"<div><p>Transmembrane protease serine 2 (TMPRSS2) is an important drug target due to its role in the infection mechanism of coronaviruses including SARS-CoV-2. Current understanding regarding the molecular mechanisms of known inhibitors and insights required for inhibitor design are limited. This study investigates the effect of inhibitor binding on the intramolecular backbone hydrogen bonds (BHBs) of TMPRSS2 using the concept of hydrogen bond wrapping, which is the phenomenon of stabilization of a hydrogen bond in a solvent environment as a result of being surrounded by non-polar groups. A molecular descriptor which quantifies the extent of wrapping around BHBs is introduced for this. First, virtual screening for TMPRSS2 inhibitors is performed by molecular docking using the program DOCK 6 with a Generalized Born surface area (GBSA) scoring function. The docking results are then analyzed using this descriptor and its relationship to the solvent-accessible surface area term ΔG_sa of the GBSA score is demonstrated with machine learning regression and principal component analysis. The effect of binding of the inhibitors camostat, nafamostat, and 4-guanidinobenzoic acid (GBA) on the wrapping of important BHBs in TMPRSS2 is also studied using molecular dynamics. For BHBs with a large increase in wrapping groups due to these inhibitors, the radial distribution function of water revealed that certain residues involved in these BHBs, like Gln438, Asp440, and Ser441, undergo preferential desolvation. The findings offer valuable insights into the mechanisms of these inhibitors and may prove useful in the design of new inhibitors.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"27 - 46"},"PeriodicalIF":2.2,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01695-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139069281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction: Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects","authors":"Abigail García‑Morales,&nbsp;Nancy O. Pulido,&nbsp;Daniel Balleza","doi":"10.1007/s00249-023-01692-7","DOIUrl":"10.1007/s00249-023-01692-7","url":null,"abstract":"","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"93 - 93"},"PeriodicalIF":2.2,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138796023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Peptide-based pore formation and cell membrane deformation: European Biophysics Journal Prizes at EBSA 2023","authors":"Robert J. C. Gilbert","doi":"10.1007/s00249-023-01691-8","DOIUrl":"10.1007/s00249-023-01691-8","url":null,"abstract":"<div><p>The European Biophysics Journal Prizes awarded at the European Biophysical Societies Association (EBSA) Congress in Stockholm in the Summer of 2023 recognised papers published in 2020 and 2021 which made use of multiple complementing experimental, theoretical and computational approaches. One of the winning papers addressed the specific role of arginine residues within antimicrobial and cell-penetrating peptides, in promoting membrane defect stabilisation and pore formation. The other winning paper described the influence of atomic force microscopy probe geometry on the measurement of surface deformability, assessed for investigation of the differing viscoelastic properties of non-malignant and cancerous cells. These papers showcase biophysical science; the importance of combining different experimental, modelling and molecular dynamics methods; and how researchers need to understand the theoretical basis and the limitations of the techniques they use. EBSA warmly congratulates the authors on their work and its subsequent recognition. Publication of these papers also demonstrates the ongoing commitment of the European Biophysics Journal to molecular scale and to systems biophysics, and to support of the international biophysical community.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"619 - 623"},"PeriodicalIF":2.0,"publicationDate":"2023-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138294475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Drug–ionic surfactant interactions: density, sound speed, spectroscopic, and electrochemical studies","authors":"Muhammad Sohail,&nbsp;Hafiz Muhammad Abd Ur Rahman,&nbsp;Muhammad Nadeem Asghar","doi":"10.1007/s00249-023-01689-2","DOIUrl":"10.1007/s00249-023-01689-2","url":null,"abstract":"<div><p>The failure of antibiotics against infectious diseases has become a global health issue due to the incessant use of antibiotics in the community and a lack of entry of new antibacterial drugs onto the market. The limited knowledge of biophysical interactions of existing antibiotics with bio-membranes is one of the major hurdles to design and develop more effective antibiotics. Surfactant systems are the simplest biological membrane models that not only mimic the cell membrane functions but are also used to investigate the biophysical interactions between pharmaceutical drugs and bio-membranes at the molecular level. In this work, volumetric and acoustic studies were used to investigate the molecular interactions of moxifloxacin (MXF), a potential antibacterial drug, with ionic surfactants (dodecyl-tri-methyl-ammonium bromide (DTAB), a cationic surfactant and sodium dodecyl sulfate (SDS), an anionic surfactant) under physiological conditions (phosphate buffer, pH 7.4) at <i>T</i> = 298.15–313.15 K at an interval of 5 K. Various volumetric and acoustic parameters were computed from the density and sound speed data and interpreted in terms of MXF–ionic surfactant interaction using electrostriction effect and co-sphere overlap model. Absorption spectroscopy and cyclic voltammetry were further used to determine the binding, partitioning, and related free energies of MXF with ionic micelles.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"735 - 747"},"PeriodicalIF":2.0,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71520145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Annexin A5 stabilizes matrix vesicle-biomimetic lipid membranes: unravelling a new role of annexins in calcification","authors":"Claudio R. Ferreira,&nbsp;Marcos Antônio E. Cruz,&nbsp;Maytê Bolean,&nbsp;Luiz Henrique da S. Andrilli,&nbsp;José Luis Millan,&nbsp;Ana Paula Ramos,&nbsp;Massimo Bottini,&nbsp;Pietro Ciancaglini","doi":"10.1007/s00249-023-01687-4","DOIUrl":"10.1007/s00249-023-01687-4","url":null,"abstract":"<div><p>Matrix vesicles are a special class of extracellular vesicles thought to actively contribute to both physiologic and pathologic mineralization. Proteomic studies have shown that matrix vesicles possess high amounts of annexin A5, suggesting that the protein might have multiple roles at the sites of calcification. Currently, Annexin A5 is thought to promote the nucleation of apatitic minerals close to the inner leaflet of the matrix vesicles’ membrane enriched in phosphatidylserine and Ca²⁺. Herein, we aimed at unravelling a possible additional role of annexin A5 by investigating the ability of annexin A5 to adsorb on matrix-vesicle biomimetic liposomes and Langmuir monolayers made of dipalmitoylphosphatidylserine (DPPS) and dipalmitoylphosphatidylcholine (DPPC) in the absence and in the presence of Ca²⁺. Differential scanning calorimetry and dynamic light scattering measurements showed that Ca²⁺ at concentrations in the 0.5–2.0 mM range induced the aggregation of liposomes probably due to the formation of DPPS-enriched domains. However, annexin A5 avoided the aggregation of liposomes at Ca²⁺ concentrations lower than 1.0 mM. Surface pressure versus surface area isotherms showed that the adsorption of annexin A5 on the monolayers made of a mixture of DPPC and DPPS led to a reduction in the area of excess compared to the theoretical values, which confirmed that the protein favored attractive interactions among the membrane lipids. The stabilization of the lipid membranes by annexin A5 was also validated by recording the changes with time of the surface pressure. Finally, fluorescence microscopy images of lipid monolayers revealed the formation of spherical lipid-condensed domains that became unshaped and larger in the presence of annexin A5. Our data support the model that annexin A5 in matrix vesicles is recruited at the membrane sites enriched in phosphatidylserine and Ca²⁺ not only to contribute to the intraluminal mineral formation but also to stabilize the vesicles’ membrane and prevent its premature rupture.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"721 - 733"},"PeriodicalIF":2.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01687-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476752","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction to: Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects","authors":"Abigail García‑Morales,&nbsp;Nancy O. Pulido,&nbsp;Daniel Balleza","doi":"10.1007/s00249-023-01690-9","DOIUrl":"10.1007/s00249-023-01690-9","url":null,"abstract":"","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"91 - 91"},"PeriodicalIF":2.2,"publicationDate":"2023-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71476753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Special Issue: 18th Congress of the Polish Biophysical Society","authors":"Jan M. Antosiewicz,&nbsp;Robert Gilbert,&nbsp;Piotr E. Marszalek","doi":"10.1007/s00249-023-01688-3","DOIUrl":"10.1007/s00249-023-01688-3","url":null,"abstract":"<div><p>The 18th Congress of the Polish Biophysical Society took place at the Faculty of Physics of the University of Warsaw in Warsaw, Poland, in September 2022. In total, 111 attendees (Attendance Profile: 107 in-person, 4 remote; Italy 1, Lithuania 1, Poland 104, United Kingdom 1, United States 4) participated in the event. The authors of lectures and posters at the Congress were invited to prepare their presentations in the form of articles in this special issue of the European Biophysics Journal. The 11 articles published in this special issue present a limited sampling of the subjects of the conference presentations. Nevertheless, they showcase excellence in Polish biophysics across a wide range of topics, using both theoretical and experimental approaches: mechanisms of receptor-ligand interactions, medical applications of proteins and nucleic acids, non-linear dynamics/molecular dynamics of protein systems, hydrodynamics and biosensing. We hope to improve on the representation of the international Polish biophysical community after the next Congress in 2025.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 6-7","pages":"483 - 486"},"PeriodicalIF":2.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50160221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stability of multilamellar lipid tubules in excess water","authors":"Tripta Bhatia","doi":"10.1007/s00249-023-01686-5","DOIUrl":"10.1007/s00249-023-01686-5","url":null,"abstract":"<div><p>In the lyotropic phase of lipids with excess water, multilamellar tubules (MLTs) grow from defects. A phenomenological model for the stability of MLTs is developed that is universal and independent of the underlying growth mechanisms of MLTs. The stability of MLTs implies that they are in hydrostatic equilibrium and stable as elastic objects that have compression and bending elasticity. The results show that even with solvent pressure differences of 0.1 atm, the density profile is not significantly altered, so suggesting the stability is due to the trapped solvent. The results are of sufficient value in relation to lamellar stability models and may have implications beyond the described MLT models, especially in other models of membrane systems.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"749 - 756"},"PeriodicalIF":2.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50160222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the role of calcium diffusion and its rapid buffering in intraflagellar signaling","authors":"M. V. Satarić,&nbsp;T. Nemeš","doi":"10.1007/s00249-023-01685-6","DOIUrl":"10.1007/s00249-023-01685-6","url":null,"abstract":"<div><p>We have considered the realistic mechanism of rapid Ca²⁺ (calcium ion) buffering within the wave of calcium ions progressing along the flagellar axoneme. This buffering is an essential part of the Ca²⁺ signaling pathway aimed at controlling the bending dynamics of flagella. It is primarily achieved by the mobile region of calmodulin molecules and by stationary calaxin, as well as by the part of calmodulin bound to calcium/calmodulin-dependent kinase II and kinase C. We derived and elaborated a model of Ca²⁺ diffusion within a signaling wave in the presence of these molecules which rapidly buffer Ca²⁺. This approach has led to a single nonlinear transport equation for the Ca²⁺ wave that contains the effects brought about by both as necessary buffers for signaling. The presence of mobile buffer calmodulin gives rise to a transport equation that is not strictly diffusive but also exhibits a sink-like effect. We solved straightforwardly the final transport equation in an analytical framework and obtained the implied function of calcium concentration. The effective diffusion coefficient depends on local Ca²⁺ concentration. It is plausible that these buffers' presence can impact Ca²⁺ wave speed and shape, which are essential for decoding Ca²⁺ signaling in flagella. We present the solution of the transport equation for a few specified cases with physiologically reasonable sets of parameters involved.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"705 - 720"},"PeriodicalIF":2.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41231470","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversity of hydrodynamic radii of intrinsically disordered proteins","authors":"Michał K. Białobrzewski,&nbsp;Barbara P. Klepka,&nbsp;Agnieszka Michaś,&nbsp;Maja K. Cieplak-Rotowska,&nbsp;Zuzanna Staszałek,&nbsp;Anna Niedźwiecka","doi":"10.1007/s00249-023-01683-8","DOIUrl":"10.1007/s00249-023-01683-8","url":null,"abstract":"<div><p>Intrinsically disordered proteins (IDPs) form an important class of biomolecules regulating biological processes in higher organisms. The lack of a fixed spatial structure facilitates them to perform their regulatory functions and allows the efficiency of biochemical reactions to be controlled by temperature and the cellular environment. From the biophysical point of view, IDPs are biopolymers with a broad configuration state space and their actual conformation depends on non-covalent interactions of its amino acid side chain groups at given temperature and chemical conditions. Thus, the hydrodynamic radius (<i>R</i>_<i>h</i>) of an IDP of a given polymer length (N) is a sequence- and environment-dependent variable. We have reviewed the literature values of hydrodynamic radii of IDPs determined experimentally by SEC, AUC, PFG NMR, DLS, and FCS, and complement them with our FCS results obtained for a series of protein fragments involved in the regulation of human gene expression. The data collected herein show that the values of hydrodynamic radii of IDPs can span the full space between the folded globular and denatured proteins in the <i>R</i>_<i>h</i>(<i>N</i>) diagram.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 6-7","pages":"607 - 618"},"PeriodicalIF":2.0,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41187713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}