Biophysics reviews最新文献

{"title":"General principles of secondary active transporter function.","authors":"Oliver Beckstein, Fiona Naughton","doi":"10.1063/5.0047967","DOIUrl":"10.1063/5.0047967","url":null,"abstract":"<p><p>Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondary active transporters couple the spontaneous influx of a \"driving\" ion such as Na⁺ or H⁺ to the flux of the substrate. The thermodynamics of such cyclical non-equilibrium systems are well understood, and recent work has focused on the molecular mechanism of secondary active transport. The fact that these transporters change their conformation between an inward-facing and outward-facing conformation in a cyclical fashion, called the alternating access model, is broadly recognized as the molecular framework in which to describe transporter function. However, only with the advent of high resolution crystal structures and detailed computer simulations, it has become possible to recognize common molecular-level principles between disparate transporter families. Inverted repeat symmetry in secondary active transporters has shed light onto how protein structures can encode a bi-stable two-state system. Based on structural data, three broad classes of alternating access transitions have been described as rocker-switch, rocking-bundle, and elevator mechanisms. More detailed analysis indicates that transporters can be understood as gated pores with at least two coupled gates. These gates are not just a convenient cartoon element to illustrate a putative mechanism but map to distinct parts of the transporter protein. Enumerating all distinct gate states naturally includes occluded states in the alternating access picture and also suggests what kind of protein conformations might be observable. By connecting the possible conformational states and ion/substrate bound states in a kinetic model, a unified picture emerges in which the symporter, antiporter, and uniporter functions are extremes in a continuum of functionality. As usual with biological systems, few principles and rules are absolute and exceptions are discussed as well as how biological complexity may be integrated in quantitative kinetic models that may provide a bridge from the structure to function.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"3 1","pages":"011307"},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8984959/pdf/BRIEIM-000003-011307_1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9253621","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cataloguing the proteome: Current developments in single-molecule protein sequencing.","authors":"Morgan M Brady, Anne S Meyer","doi":"10.1063/5.0065509","DOIUrl":"https://doi.org/10.1063/5.0065509","url":null,"abstract":"<p><p>The cellular proteome is complex and dynamic, with proteins playing a critical role in cell-level biological processes that contribute to homeostasis, stimuli response, and disease pathology, among others. As such, protein analysis and characterization are of extreme importance in both research and clinical settings. In the last few decades, most proteomics analysis has relied on mass spectrometry, affinity reagents, or some combination thereof. However, these techniques are limited by their requirements for large sample amounts, low resolution, and insufficient dynamic range, making them largely insufficient for the characterization of proteins in low-abundance or single-cell proteomic analysis. Despite unique technical challenges, several single-molecule protein sequencing (SMPS) technologies have been proposed in recent years to address these issues. In this review, we outline several approaches to SMPS technologies and discuss their advantages, limitations, and potential contributions toward an accurate, sensitive, and high-throughput platform.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"3 1","pages":"011304"},"PeriodicalIF":0.0,"publicationDate":"2022-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10903494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140177975","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Graphene nanostructures for input-output bioelectronics.","authors":"Raghav Garg,&nbsp;Daniel San Roman,&nbsp;Yingqiao Wang,&nbsp;Devora Cohen-Karni,&nbsp;Tzahi Cohen-Karni","doi":"10.1063/5.0073870","DOIUrl":"https://doi.org/10.1063/5.0073870","url":null,"abstract":"<p><p>The ability to manipulate the electrophysiology of electrically active cells and tissues has enabled a deeper understanding of healthy and diseased tissue states. This has primarily been achieved via input/output (I/O) bioelectronics that interface engineered materials with biological entities. Stable long-term application of conventional I/O bioelectronics advances as materials and processing techniques develop. Recent advancements have facilitated the development of graphene-based I/O bioelectronics with a wide variety of functional characteristics. Engineering the structural, physical, and chemical properties of graphene nanostructures and integration with modern microelectronics have enabled breakthrough high-density electrophysiological investigations. Here, we review recent advancements in 2D and 3D graphene-based I/O bioelectronics and highlight electrophysiological studies facilitated by these emerging platforms. Challenges and present potential breakthroughs that can be addressed via graphene bioelectronics are discussed. We emphasize the need for a multidisciplinary approach across materials science, micro-fabrication, and bioengineering to develop the next generation of I/O bioelectronics.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"2 4","pages":"041304"},"PeriodicalIF":0.0,"publicationDate":"2021-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8717360/pdf/BRIEIM-000002-041304_1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10820587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High-throughput assays show the timescale for phagocytic success depends on the target toughness.","authors":"Layla A Bakhtiari,&nbsp;Marilyn J Wells,&nbsp;Vernita D Gordon","doi":"10.1063/5.0057071","DOIUrl":"10.1063/5.0057071","url":null,"abstract":"<p><p>Phagocytic immune cells can clear pathogens from the body by engulfing them. Bacterial biofilms are communities of bacteria that are bound together in a matrix that gives biofilms viscoelastic mechanical properties that do not exist for free-swimming bacteria. Since a neutrophil is too small to engulf an entire biofilm, it must be able to detach and engulf a few bacteria at a time if it is to use phagocytosis to clear the infection. We recently found a negative correlation between the target elasticity and phagocytic success. That earlier work used time-consuming, manual analysis of micrographs of neutrophils and fluorescent beads. Here, we introduce and validate flow cytometry as a fast and high-throughput technique that increases the number of neutrophils analyzed per experiment by two orders of magnitude, while also reducing the time required to do so from hours to minutes. We also introduce the use of polyacrylamide gels in our assay for engulfment success. The tunability of polyacrylamide gels expands the mechanical parameter space we can study, and we find that high toughness and yield strain, even with low elasticity, also impact the phagocytic success as well as the timescale thereof. For stiff gels with low-yield strain, and consequent low toughness, phagocytic success is nearly four times greater when neutrophils are incubated with gels for 6 h than after only 1 h of incubation. In contrast, for soft gels with high-yield strain and consequent high toughness, successful engulfment is much less time-sensitive, increasing by less than a factor of two from 1 to 6 h incubation.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"2 3","pages":"031402"},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8485781/pdf/BRIEIM-000002-031402_1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39506847","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Coupling between cardiac cells-An important determinant of electrical impulse propagation and arrhythmogenesis.","authors":"André G Kléber,&nbsp;Qianru Jin","doi":"10.1063/5.0050192","DOIUrl":"https://doi.org/10.1063/5.0050192","url":null,"abstract":"<p><p>Cardiac arrhythmias are an important cause of sudden cardiac death-a devastating manifestation of many underlying causes, such as heart failure and ischemic heart disease leading to ventricular tachyarrhythmias and ventricular fibrillation, and atrial fibrillation causing cerebral embolism. Cardiac electrical propagation is a main factor in the initiation and maintenance of cardiac arrhythmias. In the heart, gap junctions are the basic unit at the cellular level that host intercellular low-resistance channels for the diffusion of ions and small regulatory molecules. The dual voltage clamp technique enabled the direct measurement of electrical conductance between cells and recording of single gap junction channel openings. The rapid turnover of gap junction channels at the intercalated disk implicates a highly dynamic process of trafficking and internalization of gap junction connexons. Recently, non-canonical roles of gap junction proteins have been discovered in mitochondria function, cytoskeletal organization, trafficking, and cardiac rescue. At the tissue level, we explain the concepts of linear propagation and safety factor based on the model of linear cellular structure. Working myocardium is adequately represented as a discontinuous cellular network characterized by cellular anisotropy and connective tissue heterogeneity. Electrical propagation in discontinuous cellular networks reflects an interplay of three main factors: cell-to-cell electrical coupling, flow of electrical charge through the ion channels, and the microscopic tissue structure. This review provides a state-of-the-art update of the cardiac gap junction channels and their role in cardiac electrical impulse propagation and highlights a combined approach of genetics, cell biology, and physics in modern cardiac electrophysiology.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"2 3","pages":"031301"},"PeriodicalIF":0.0,"publicationDate":"2021-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8281002/pdf/BRIEIM-000002-031301_1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39211245","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Forgotten but not gone: Particulate matter as contaminations of mucosal systems.","authors":"Matthias Marczynski, Oliver Lieleg","doi":"10.1063/5.0054075","DOIUrl":"https://doi.org/10.1063/5.0054075","url":null,"abstract":"<p><p>A decade ago, environmental issues, such as air pollution and the contamination of the oceans with microplastic, were prominently communicated in the media. However, these days, political topics, as well as the ongoing COVID-19 pandemic, have clearly taken over. In spite of this shift in focus regarding media representation, researchers have made progress in evaluating the possible health risks associated with particulate contaminations present in water and air. In this review article, we summarize recent efforts that establish a clear link between the increasing occurrence of certain pathological conditions and the exposure of humans (or animals) to airborne or waterborne particulate matter. First, we give an overview of the physiological functions mucus has to fulfill in humans and animals, and we discuss different sources of particulate matter. We then highlight parameters that govern particle toxicity and summarize our current knowledge of how an exposure to particulate matter can be related to dysfunctions of mucosal systems. Last, we outline how biophysical tools and methods can help researchers to obtain a better understanding of how particulate matter may affect human health. As we discuss here, recent research has made it quite clear that the structure and functions of those mucosal systems are sensitive toward particulate contaminations. Yet, our mechanistic understanding of how (and which) nano- and microparticles can compromise human health via interacting with mucosal barriers is far from complete.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"2 3","pages":"031302"},"PeriodicalIF":0.0,"publicationDate":"2021-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10903497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140177978","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bringing the interaction of silver nanoparticles with bacteria to light.","authors":"Simone Normani, Nicholas Dalla Vedova, Guglielmo Lanzani, Francesco Scotognella, Giuseppe Maria Paternò","doi":"10.1063/5.0048725","DOIUrl":"https://doi.org/10.1063/5.0048725","url":null,"abstract":"<p><p>In past decades, the exploitation of silver nanoparticles in novel antibacterial and detection devices has risen to prominence, owing to the well-known specific interaction of silver with bacteria. The vast majority of the investigations focus on the investigation over the mechanism of action underpinning bacterial eradication, while few efforts have been devoted to the study of the modification of silver optical properties upon interaction with bacteria. Specifically, given the characteristic localized surface plasmon resonance of silver nanostructures, which is sensitive to changes in the charge carrier density or in the dielectric environment, these systems can offer a handle in the detection of bacteria pathogens. In this review, we present the state of art of the research activity on the interaction of silver nanoparticles with bacteria, with strong emphasis on the modification of their optical properties. This may indeed lead to easy color reading of bacterial tests and pave the way to the development of nanotechnologic silver-based bacterial detection systems and drug-screening platforms.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"2 2","pages":"021304"},"PeriodicalIF":0.0,"publicationDate":"2021-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10903507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140177977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Polyphasic linkage and the impact of ligand binding on the regulation of biomolecular condensates.","authors":"Kiersten M Ruff, Furqan Dar, Rohit V Pappu","doi":"10.1063/5.0050059","DOIUrl":"10.1063/5.0050059","url":null,"abstract":"<p><p>Cellular matter can be spatially and temporally organized into membraneless biomolecular condensates. The current thinking is that these condensates form and dissolve via phase transitions driven by one or more condensate-specific multivalent macromolecules known as scaffolds. Cells likely regulate condensate formation and dissolution by exerting control over the concentrations of regulatory molecules, which we refer to as ligands. Wyman and Gill introduced the framework of <i>polyphasic linkage</i> to explain how ligands can exert thermodynamic control over phase transitions. This review focuses on describing the concepts of polyphasic linkage and the relevance of such a mechanism for controlling condensate formation and dissolution. We describe how ligand-mediated control over scaffold phase behavior can be quantified experimentally. Further, we build on recent studies to highlight features of ligands that make them suppressors vs drivers of phase separation. Finally, we highlight areas where advances are needed to further understand ligand-mediated control of condensates in complex cellular environments. These advances include understanding the effects of networks of ligands on condensate behavior and how ligands modulate phase transitions controlled by different combinations of homotypic and heterotypic interactions among scaffold macromolecules. Insights gained from the application of polyphasic linkage concepts should be useful for designing novel pharmaceutical ligands to regulate condensates.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"2 2","pages":"021302"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8211317/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39134767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Addressing cervical cancer screening disparities through advances in artificial intelligence and nanotechnologies for cellular profiling.","authors":"Zhenzhong Yang, Jack Francisco, Alexandra S Reese, David R Spriggs, Hyungsoon Im, Cesar M Castro","doi":"10.1063/5.0043089","DOIUrl":"10.1063/5.0043089","url":null,"abstract":"<p><p>Almost all cases of cervical cancer are caused by the human papilloma virus (HPV). Detection of pre-cancerous cervical changes provides a window of opportunity for cure of an otherwise lethal disease when metastatic. With a greater understanding of the biology and natural course of high-risk HPV infections, screening methods have shifted beyond subjective Pap smears toward more sophisticated and objective tactics. This has led to a substantial growth in the breadth and depth of HPV-based cervical cancer screening tests, especially in developed countries without constrained resources. Many low- and middle-income countries (LMICs) have less access to advanced laboratories and healthcare resources, so new point-of-care (POC) technologies have been developed to provide test results in real time, improve the efficiency of techniques, and increase screening adoption. In this Review, we will discuss how novel decentralized screening technologies and computational strategies improve upon traditional methods and how their realized promise could further democratize cervical cancer screening and promote greater disease prevention.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"2 1","pages":"011303"},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8015256/pdf/BRIEIM-000002-011303_1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25583191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanisms of ligand binding.","authors":"Enrico Di Cera","doi":"10.1063/5.0020997","DOIUrl":"10.1063/5.0020997","url":null,"abstract":"<p><p>Many processes in chemistry and biology involve interactions of a ligand with its molecular target. Interest in the mechanism governing such interactions has dominated theoretical and experimental analysis for over a century. The interpretation of molecular recognition has evolved from a simple rigid body association of the ligand with its target to appreciation of the key role played by conformational transitions. Two conceptually distinct descriptions have had a profound impact on our understanding of mechanisms of ligand binding. The first description, referred to as induced fit, assumes that conformational changes follow the initial binding step to optimize the complex between the ligand and its target. The second description, referred to as conformational selection, assumes that the free target exists in multiple conformations in equilibrium and that the ligand selects the optimal one for binding. Both descriptions can be merged into more complex reaction schemes that better describe the functional repertoire of macromolecular systems. This review deals with basic mechanisms of ligand binding, with special emphasis on induced fit, conformational selection, and their mathematical foundations to provide rigorous context for the analysis and interpretation of experimental data. We show that conformational selection is a surprisingly versatile mechanism that includes induced fit as a mathematical special case and even captures kinetic properties of more complex reaction schemes. These features make conformational selection a dominant mechanism of molecular recognition in biology, consistent with the rich conformational landscape accessible to biological macromolecules being unraveled by structural biology.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"1 1","pages":"011303"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7714259/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38707519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}