发布求助
文献互助 智能选刊 最新文献

Biophysics reviews最新文献

筛选
英文 中文
Structural visualization of inhibitor binding in prolyl oligopeptidase. 脯氨酰寡肽酶抑制剂结合的结构可视化。
IF 3.4
Biophysics reviews Pub Date : 2024-08-22 eCollection Date: 2024-09-01 DOI: 10.1063/5.0226428
Katarzyna Walczewska-Szewc, Jakub Rydzewski
{"title":"Structural visualization of inhibitor binding in prolyl oligopeptidase.","authors":"Katarzyna Walczewska-Szewc, Jakub Rydzewski","doi":"10.1063/5.0226428","DOIUrl":"10.1063/5.0226428","url":null,"abstract":"<p><p>The association and dissociation of proteins and ligands are crucial in biophysics for potential drug development [Baron and McCammon, Annu. Rev. Phys. Chem. <b>64</b>, 151-175 (2013)]. However, identifying and characterizing the reaction pathways for these rare events has been a long-standing challenge. Molecular dynamics (MD) simulations are limited in exploring biophysical processes on experimental timescales, so ligand transport processes through complex transient tunnels formed by proteins during dynamics are often simulated using enhanced sampling MD [Rydzewski and Nowak, Phys. Life Rev. <b>22-23</b>, 58-74 (2017)]. Erroneously identified ligand binding pathways can affect thermodynamic and kinetic characteristics calculated from MD trajectories. A system that has the potential to be a therapeutic target for neurodegenerative diseases is prolyl oligopeptidase (PREP). This is due to its involvement in promoting protein aggregation and disrupting cellular function through affecting protein-protein interactions (PPI). The recent discovery of a new type of PREP inhibitor that targets PPI raises important questions about the diversity of ligand binding pathways in PREP and their impact on protein dynamics [Pätsi <i>et al.</i>, J. Med. Chem. <b>67</b>, 5421-5436 (2024); Kilpeläinen <i>et al.</i>, J. Med. Chem. <b>66</b>, 7475-7496 (2023); and Walczewska-Szewc <i>et al.</i>, Phys. Chem. Chem. Phys. <b>24</b>, 4366-4373 (2022)]. In this article, using results from enhanced sampling MD, we visually present how the binding process in PREP depends on subtle changes in inhibitors, which could be crucial in treating neurodegenerative disorders.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 3","pages":"032105"},"PeriodicalIF":3.4,"publicationDate":"2024-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11343612/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142057446","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}
引用次数: 0
Capturing the illusive ring-shaped intermediates in Aβ42 amyloid formation. 捕捉 Aβ42 淀粉样蛋白形成过程中虚幻的环形中间体
IF 3.4
Biophysics reviews Pub Date : 2024-08-13 eCollection Date: 2024-09-01 DOI: 10.1063/5.0222349
Yu Yuan, Xiaozhe Dong, Huan Wang, Feng Gai
{"title":"Capturing the illusive ring-shaped intermediates in A<b>β</b>42 amyloid formation.","authors":"Yu Yuan, Xiaozhe Dong, Huan Wang, Feng Gai","doi":"10.1063/5.0222349","DOIUrl":"10.1063/5.0222349","url":null,"abstract":"<p><p>Protein/peptide amyloid fibril formation is associated with various neurodegenerative diseases and, hence, has been the subject of extensive studies. From a structure-evolution point of view, we now know a great deal about the initial and final states of this process; however, we know very little about its intermediate states. Herein, we employ liquid-phase transmission electron microscopy to directly visualize the formation of one of the intermediates formed during the aggregation process of an amyloid-forming peptide. As shown in figure, we find that Aβ42, the amyloid formation of which has been linked to the development of Alzheimer's disease, can populate a ring-shaped intermediate structure with a diameter of tens of nanometers; additionally, the air-liquid interface can \"catalyze\" the formation of amyloid fibrils.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 3","pages":"032104"},"PeriodicalIF":3.4,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11444734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142367674","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}
引用次数: 0
Structural interspecies variability of mammals' hairs. 哺乳动物毛发的种间结构变异。
IF 3.4
Biophysics reviews Pub Date : 2024-08-08 eCollection Date: 2024-09-01 DOI: 10.1063/5.0225513
Gabriele Greco, Anna Rising
{"title":"Structural interspecies variability of mammals' hairs.","authors":"Gabriele Greco, Anna Rising","doi":"10.1063/5.0225513","DOIUrl":"10.1063/5.0225513","url":null,"abstract":"<p><p>Hairs are fundamental structures for mammals, serving crucial functions such as thermal insulation and hydrophobicity. In domestic animals, hair is also a valuable source of high-performance fibers for the textile industry, which has led to intensive study. However, there is limited comparative knowledge about the physical properties of hair across different wild mammalian species. In our lab, we are investigating the physical properties of hairs from a diverse range of wild mammalian species, laying the groundwork for an in-depth comparative study. These physical properties can be linked to the internal structures of the hairs. Using polarized light microscopy, we can visualize the internal structure of hairs, which are composed of a hollow channel (medulla) surrounded by a cortex and a keratin cuticle(<i>1</i>). By examining the brown hairs of three distinct mammals-the Patagonian mara, the brown bear, and the Amur tiger-we observe striking differences in their internal structures. We speculate that these structural differences correspond to varying physical properties, which we are currently investigating.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 3","pages":"032103"},"PeriodicalIF":3.4,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11315580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918228","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}
引用次数: 0
Decoding physical principles of cell migration under controlled environment using microfluidics. 利用微流体技术解码细胞在受控环境下迁移的物理原理。
IF 3.4
Biophysics reviews Pub Date : 2024-07-29 eCollection Date: 2024-09-01 DOI: 10.1063/5.0199161
Young Joon Suh, Alan T Li, Mrinal Pandey, Cassidy S Nordmann, Yu Ling Huang, Mingming Wu
{"title":"Decoding physical principles of cell migration under controlled environment using microfluidics.","authors":"Young Joon Suh, Alan T Li, Mrinal Pandey, Cassidy S Nordmann, Yu Ling Huang, Mingming Wu","doi":"10.1063/5.0199161","DOIUrl":"10.1063/5.0199161","url":null,"abstract":"<p><p>Living cells can perform incredible tasks that man-made micro/nano-sized robots have not yet been able to accomplish. One example is that white blood cells can sense and move to the site of pathogen attack within minutes. The robustness and precision of cellular functions have been perfected through billions of years of evolution. In this context, we ask the question whether cells follow a set of physical principles to sense, adapt, and migrate. Microfluidics has emerged as an enabling technology for recreating well-defined cellular environment for cell migration studies, and its ability to follow single cell dynamics allows for the results to be amenable for theoretical modeling. In this review, we focus on the development of microfluidic platforms for recreating cellular biophysical (e.g., mechanical stress) and biochemical (e.g., nutrients and cytokines) environments for cell migration studies in 3D. We summarize the basic principles that cells (including bacteria, algal, and mammalian cells) use to respond to chemical gradients learned from microfluidic systems. We also discuss about novel biological insights gained from studies of cell migration under biophysical cues and the need for further quantitative studies of cell function under well-controlled biophysical environments in the future.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 3","pages":"031302"},"PeriodicalIF":3.4,"publicationDate":"2024-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11290890/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141876856","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}
引用次数: 0
Recent advances and applications of artificial intelligence in 3D bioprinting. 人工智能在 3D 生物打印中的最新进展和应用。
IF 2.9
Biophysics reviews Pub Date : 2024-07-19 eCollection Date: 2024-09-01 DOI: 10.1063/5.0190208
Hongyi Chen, Bin Zhang, Jie Huang
{"title":"Recent advances and applications of artificial intelligence in 3D bioprinting.","authors":"Hongyi Chen, Bin Zhang, Jie Huang","doi":"10.1063/5.0190208","DOIUrl":"10.1063/5.0190208","url":null,"abstract":"<p><p>3D bioprinting techniques enable the precise deposition of living cells, biomaterials, and biomolecules, emerging as a promising approach for engineering functional tissues and organs. Meanwhile, recent advances in 3D bioprinting enable researchers to build <i>in vitro</i> models with finely controlled and complex micro-architecture for drug screening and disease modeling. Recently, artificial intelligence (AI) has been applied to different stages of 3D bioprinting, including medical image reconstruction, bioink selection, and printing process, with both classical AI and machine learning approaches. The ability of AI to handle complex datasets, make complex computations, learn from past experiences, and optimize processes dynamically makes it an invaluable tool in advancing 3D bioprinting. The review highlights the current integration of AI in 3D bioprinting and discusses future approaches to harness the synergistic capabilities of 3D bioprinting and AI for developing personalized tissues and organs.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 3","pages":"031301"},"PeriodicalIF":2.9,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11260195/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735840","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}
引用次数: 0
Visualizing the degradation of fibrin fibers. 纤维蛋白纤维降解的可视化。
IF 2.9
Biophysics reviews Pub Date : 2024-07-01 eCollection Date: 2024-09-01 DOI: 10.1063/5.0220356
Rebecca A Risman, Valerie Tutwiler
{"title":"Visualizing the degradation of fibrin fibers.","authors":"Rebecca A Risman, Valerie Tutwiler","doi":"10.1063/5.0220356","DOIUrl":"10.1063/5.0220356","url":null,"abstract":"<p><p>Polymeric fibrin provides the structural and mechanical stability of a blood clot. Fibrin fibers are rod-like and create a network mesh that holds blood cells. When a clot has performed its physiological function in wound healing and preventing excessive blood loss, it must be resolved by the enzymatic degradation of fibrin, otherwise known as fibrinolysis. If a blood clot forms when or where it is not needed, as occurs in ischemic strokes and myocardial infarctions, the blood clot (thrombus) can obstruct blood flow to downstream organs. Obstructive thrombi must be degraded or removed to prevent further complications. If a clot is not degraded on its own, lytic agents (i.e., tissue plasminogen activator, tPA) are given exogenously to induce fibrinolysis. Here, we fluorescently labeled both fibrin and tPA to visualize degradation at the edge of the clot. The fibers with bound tPA were looped or coiled while the fibers farther into the clot remain straight and stable displaying the diffusion of tPA and depth of lysis. This image provides (1) a new method to monitor fibrinolysis with a commercially available chamber with convenient inlets and (2) the visualization of tPA-bound fibrin and the behavior of fibers during degradation. Future work could utilize this technique to study tPA molecule and fibrin interactions, lysis front degradation, and fibrin fiber linearity to understand the mechanisms of intermolecular dynamics dependent on network structure. An enhanced insight into this process can aid in the development of optimized therapeutics to target stubborn clots.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 3","pages":"032101"},"PeriodicalIF":2.9,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11219076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141499799","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}
引用次数: 0
Engineered heart tissue: Design considerations and the state of the art. 工程心脏组织：设计考虑因素和最新技术。
IF 2.9
Biophysics reviews Pub Date : 2024-06-20 eCollection Date: 2024-06-01 DOI: 10.1063/5.0202724
Ilhan Gokhan, Thomas S Blum, Stuart G Campbell
{"title":"Engineered heart tissue: Design considerations and the state of the art.","authors":"Ilhan Gokhan, Thomas S Blum, Stuart G Campbell","doi":"10.1063/5.0202724","DOIUrl":"10.1063/5.0202724","url":null,"abstract":"<p><p>Originally developed more than 20 years ago, engineered heart tissue (EHT) has become an important tool in cardiovascular research for applications such as disease modeling and drug screening. Innovations in biomaterials, stem cell biology, and bioengineering, among other fields, have enabled EHT technologies to recapitulate many aspects of cardiac physiology and pathophysiology. While initial EHT designs were inspired by the isolated-trabecula culture system, current designs encompass a variety of formats, each of which have unique strengths and limitations. In this review, we describe the most common EHT formats, and then systematically evaluate each aspect of their design, emphasizing the rational selection of components for each application.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 2","pages":"021308"},"PeriodicalIF":2.9,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11192576/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141444070","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}
引用次数: 0
Macrophages on the wrinkle: Exploring microscale interactions with substrate topography. 皱纹上的巨噬细胞：探索微观尺度上与基底形貌的相互作用。
Biophysics reviews Pub Date : 2024-06-11 eCollection Date: 2024-06-01 DOI: 10.1063/5.0215563
Francesca Cecilia Lauta, Luca Pellegrino, Roberto Rusconi
{"title":"Macrophages on the wrinkle: Exploring microscale interactions with substrate topography.","authors":"Francesca Cecilia Lauta, Luca Pellegrino, Roberto Rusconi","doi":"10.1063/5.0215563","DOIUrl":"10.1063/5.0215563","url":null,"abstract":"<p><p>Macrophages play pivotal roles in the immune response, participating in both inflammatory and pro-healing processes. Like other cells, macrophages continually survey their microenvironment through mechanosensing, adapting their intracellular organization in response to mechanical signals. In this study, we elucidate how macrophages perceive the topographical cues of wrinkled surfaces through actin-based structures, which align with the main pattern direction, thus modulating cell cytoskeletal dynamics. Given that such alterations may regulate mechanosensitive gene expression programs, exploring cellular responses to biomaterial design becomes crucial for developing biomaterials that mitigate adverse reactions.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 2","pages":"022001"},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11168750/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141312378","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}
引用次数: 0
How cytoskeletal crosstalk makes cells move: Bridging cell-free and cell studies. 细胞骨架串联如何使细胞运动：无细胞研究与细胞研究的桥梁
Biophysics reviews Pub Date : 2024-06-03 eCollection Date: 2024-06-01 DOI: 10.1063/5.0198119
James P Conboy, Irene Istúriz Petitjean, Anouk van der Net, Gijsje H Koenderink
{"title":"How cytoskeletal crosstalk makes cells move: Bridging cell-free and cell studies.","authors":"James P Conboy, Irene Istúriz Petitjean, Anouk van der Net, Gijsje H Koenderink","doi":"10.1063/5.0198119","DOIUrl":"10.1063/5.0198119","url":null,"abstract":"<p><p>Cell migration is a fundamental process for life and is highly dependent on the dynamical and mechanical properties of the cytoskeleton. Intensive physical and biochemical crosstalk among actin, microtubules, and intermediate filaments ensures their coordination to facilitate and enable migration. In this review, we discuss the different mechanical aspects that govern cell migration and provide, for each mechanical aspect, a novel perspective by juxtaposing two complementary approaches to the biophysical study of cytoskeletal crosstalk: live-cell studies (often referred to as top-down studies) and cell-free studies (often referred to as bottom-up studies). We summarize the main findings from both experimental approaches, and we provide our perspective on bridging the two perspectives to address the open questions of how cytoskeletal crosstalk governs cell migration and makes cells move.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 2","pages":"021307"},"PeriodicalIF":0.0,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11151447/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141263438","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}
引用次数: 0
The magnetocardiogram. 磁心动图
IF 2.9
Biophysics reviews Pub Date : 2024-05-29 eCollection Date: 2024-06-01 DOI: 10.1063/5.0201950
Bradley J Roth
{"title":"The magnetocardiogram.","authors":"Bradley J Roth","doi":"10.1063/5.0201950","DOIUrl":"10.1063/5.0201950","url":null,"abstract":"<p><p>The magnetic field produced by the heart's electrical activity is called the magnetocardiogram (MCG). The first 20 years of MCG research established most of the concepts, instrumentation, and computational algorithms in the field. Additional insights into fundamental mechanisms of biomagnetism were gained by studying isolated hearts or even isolated pieces of cardiac tissue. Much effort has gone into calculating the MCG using computer models, including solving the inverse problem of deducing the bioelectric sources from biomagnetic measurements. Recently, most magnetocardiographic research has focused on clinical applications, driven in part by new technologies to measure weak biomagnetic fields.</p>","PeriodicalId":72405,"journal":{"name":"Biophysics reviews","volume":"5 2","pages":"021305"},"PeriodicalIF":2.9,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11139488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141201436","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}
引用次数: 0
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：604180095
Book学术官方微信