Abigail García‑Morales, Nancy O. Pulido, Daniel Balleza
{"title":"Correction to: Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects","authors":"Abigail García‑Morales, Nancy O. Pulido, 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}
Jan M. Antosiewicz, Robert Gilbert, Piotr E. Marszalek
{"title":"Special Issue: 18th Congress of the Polish Biophysical Society","authors":"Jan M. Antosiewicz, Robert Gilbert, 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, 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 Ca<sup>2+</sup> (calcium ion) buffering within the wave of calcium ions progressing along the flagellar axoneme. This buffering is an essential part of the Ca<sup>2+</sup> 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 Ca<sup>2+</sup> diffusion within a signaling wave in the presence of these molecules which rapidly buffer Ca<sup>2+</sup>. This approach has led to a single nonlinear transport equation for the Ca<sup>2+</sup> 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 Ca<sup>2+</sup> concentration. It is plausible that these buffers' presence can impact Ca<sup>2+</sup> wave speed and shape, which are essential for decoding Ca<sup>2+</sup> 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}
Michał K. Białobrzewski, Barbara P. Klepka, Agnieszka Michaś, Maja K. Cieplak-Rotowska, Zuzanna Staszałek, Anna Niedźwiecka
{"title":"Diversity of hydrodynamic radii of intrinsically disordered proteins","authors":"Michał K. Białobrzewski, Barbara P. Klepka, Agnieszka Michaś, Maja K. Cieplak-Rotowska, Zuzanna Staszałek, 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><sub><i>h</i></sub>) 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><sub><i>h</i></sub>(<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}
Joanna Zuberek, Marek Warzecha, Mateusz Dobrowolski, Anna Modrak-Wojcik
{"title":"An intramolecular disulphide bond in human 4E-T affects its binding to eIF4E1a protein","authors":"Joanna Zuberek, Marek Warzecha, Mateusz Dobrowolski, Anna Modrak-Wojcik","doi":"10.1007/s00249-023-01684-7","DOIUrl":"10.1007/s00249-023-01684-7","url":null,"abstract":"<div><p>The cap at the 5’terminus of mRNA is a key determinant of gene expression in eukaryotic cells, which among others is required for cap dependent translation and protects mRNA from degradation. These properties of cap are mediated by several proteins. One of them is 4E-Transporter (4E-T), which plays an important role in translational repression, mRNA decay and P-bodies formation. 4E-T is also one of several proteins that interact with eukaryotic initiation factor 4E (eIF4E), a cap binding protein which is a key component of the translation initiation machinery. The molecular mechanisms underlying the interactions of these two proteins are crucial for mRNA processing. Studying the interactions between human eIF4E1a and the N-terminal fragment of 4E-T that possesses unstructured 4E-binding motifs under non-reducing conditions, we observed that 4E-T preferentially forms an intramolecular disulphide bond. This “disulphide loop” reduces affinity of 4E-T for eIF4E1a by about 300-fold. Considering that only human 4E-T possesses two cysteines located between the 4E binding motifs, we proposed that the disulphide bond may act as a switch to regulate interactions between the two proteins.</p><h3>Graphical Abstract</h3>\u0000 <div><figure><div><div><picture><source><img></source></picture></div></div></figure></div>\u0000 </div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 6-7","pages":"497 - 510"},"PeriodicalIF":2.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41094847","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}
Abigail García‑Morales, Nancy O. Pulido, Daniel Balleza
{"title":"Relation between flexibility and intrinsically disorder regions in thermosensitive TRP channels reveal allosteric effects","authors":"Abigail García‑Morales, Nancy O. Pulido, Daniel Balleza","doi":"10.1007/s00249-023-01682-9","DOIUrl":"10.1007/s00249-023-01682-9","url":null,"abstract":"<div><p>How a protein propagates the conformational changes throughout its structure remains largely unknown. In thermosensitive TRP channels, this allosteric communication is triggered by ligand interaction or in response to temperature changes. Because dynamic allostery suggests a dynamic role of disordered regions, in this work we set out to thoroughly evaluate these regions in six thermosensitive TRP channels. Thus, by contrasting the intrinsic flexibility of the transmembrane region as a function of the degree of disorder in those proteins, we discovered several residues that do not show a direct correlation in both parameters. This kind of structural discrepancy revealed residues that are either reported to be dynamic, functionally relevant or are involved in signal propagation and probably part of allosteric networks. These discrepant, potentially dynamic regions are not exclusive of TRP channels, as this same correlation was found in the Kv Shaker channel.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 1-2","pages":"77 - 90"},"PeriodicalIF":2.2,"publicationDate":"2023-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41097867","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":"Physics of collective cell migration","authors":"Ivana Pajic-Lijakovic, Milan Milivojevic","doi":"10.1007/s00249-023-01681-w","DOIUrl":"10.1007/s00249-023-01681-w","url":null,"abstract":"<div><p>Movement of cell clusters along extracellular matrices (ECM) during tissue development, wound healing, and early stage of cancer invasion involve various inter-connected migration modes such as: (1) cell movement within clusters, (2) cluster extension (wetting) and compression (de-wetting), and (3) directional cluster movement. It has become increasingly evident that dilational and volumetric viscoelasticity of cell clusters and their surrounding substrate significantly influence these migration modes through physical parameters such as: tissue and matrix surface tensions, interfacial tension between cells and substrate, gradients of surface and interfacial tensions, as well as, the accumulation of cell and matrix residual stresses. Inhomogeneous distribution of tissue surface tension along the cell–matrix biointerface can appear as a consequence of different contractility of various cluster regions. While the directional cell migration caused by the matrix stiffness gradient (i.e., durotaxis) has been widely elaborated, the structural changes of matrix surface caused by cell tractions which lead to the generation of the matrix surface tension gradient has not been considered yet. The main goal of this theoretical consideration is to clarify the roles of various physical parameters in collective cell migration based on the formulation of a biophysical model. This complex phenomenon is discussed with the help of model systems such as the movement of cell clusters on a collagen I gel matrix, simultaneously reviewing various experimental data with and without cells.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"625 - 640"},"PeriodicalIF":2.0,"publicationDate":"2023-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10231056","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":"MIL-CELL: a tool for multi-scale simulation of yeast replication and prion transmission","authors":"Damien Hall","doi":"10.1007/s00249-023-01679-4","DOIUrl":"10.1007/s00249-023-01679-4","url":null,"abstract":"<div><p>The single-celled baker’s yeast, <i>Saccharomyces cerevisiae</i>, can sustain a number of amyloid-based prions, the three most prominent examples being [URE3], [PSI+], and [PIN+]. In the laboratory, haploid <i>S. cerevisiae</i> cells of a single mating type can acquire an amyloid prion in one of two ways (i) spontaneous nucleation of the prion within the yeast cell, and (ii) receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost due to (i) dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool (<i>M</i>onitoring <i>I</i>nduction and <i>L</i>oss of prions in <i>Cell</i>s; MIL-CELL) for modelling these four general processes using a multiscale approach describing both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. We describe the workings of the model, assumptions upon which it is based and some interesting simulation results pertaining to the wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL is provided as a stand-alone GUI executable program for free download with the paper. MIL-CELL is equipped with a relational database allowing all simulated properties to be searched, collated and graphed. Its ability to incorporate variation in heritable properties means MIL-CELL is also capable of simulating loss of the isogenic nature of a cell population over time. The capability to monitor both chronological and reproductive age also makes MIL-CELL potentially useful in studies of cell aging.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 8","pages":"673 - 704"},"PeriodicalIF":2.0,"publicationDate":"2023-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01679-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10515694","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}
Karol Kurpiejewski, Marzena Jankowska-Anyszka, Renata Grzela
{"title":"N2 modified cap analogues as translation inhibitors and substrates for preparation of therapeutic mRNA","authors":"Karol Kurpiejewski, Marzena Jankowska-Anyszka, Renata Grzela","doi":"10.1007/s00249-023-01676-7","DOIUrl":"10.1007/s00249-023-01676-7","url":null,"abstract":"<div><p>In recent years many scientists have begun to focus on the mRNA molecule’s emeregence as a new type of drug. Its fast-moving and successful career as a vaccine technology cannot be underestimated. mRNA provides new opportunities and allows for the rapid preparation of effective drugs at low cost. These extensive possibilities stem from a number of factors, but the small cap structure located at the 5′ end of the mRNA is one contributing factor. Cap protects mRNA and ensures efficient recruitment to the biosynthesis machinery. Furthermore, it allows for the easy introduction of various modifications that influence the activity of the entire mRNA. Among the many different cap analogues that have been reported, those modified at the N2 position of guanosine have been systematically developed. N2-modified caps in the form of nucleoside monophosphates or dinucleotides show favorable biological properties, as well as a high capacity to inhibit the translation process in the cell-free RRL system. Modified N2 dinucleotides are efficiently incorporated into the structure of the mRNA transcript, and in specific circumstances with the correct orientation, making them an interesting alternative for ARCA-type analogues. Moreover, mRNA transcripts containing cap structures modified within the exocyclic amino group show very high translational activity. Therefore, analogues modified at the N2 position may have future applications as therapeutics against various manifestations of cancer and as desirable tools in RNA engineering.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 6-7","pages":"511 - 519"},"PeriodicalIF":2.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10132609","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}