Physical biology最新文献

Active Gaussian network model: a non-equilibrium description of protein fluctuations and allosteric behavior. 主动高斯网络模型：蛋白质波动和变构行为的非平衡描述。

IF 1.6 4区生物学

Physical biology Pub Date : 2025-09-10 DOI: 10.1088/1478-3975/ae0081

Giulio Costantini, Lorenzo Caprini, Umberto Marini Bettolo Marconi, Fabio Cecconi

{"title":"Active Gaussian network model: a non-equilibrium description of protein fluctuations and allosteric behavior.","authors":"Giulio Costantini, Lorenzo Caprini, Umberto Marini Bettolo Marconi, Fabio Cecconi","doi":"10.1088/1478-3975/ae0081","DOIUrl":"10.1088/1478-3975/ae0081","url":null,"abstract":"Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery-where the binding of a molecule at one site affects the activity of a distant site-emerges as a further manifestation of the intricate interplay between structure, function, and intrinsic dynamics. This study explores how allosteric regulation is modified when intrinsic protein dynamics operates under out-of-equilibrium conditions. To this purpose, we introduce a simple non-equilibrium model of protein dynamics, inspired by active matter systems, by generalizing the widely employed Gaussian network model to incorporate non-thermal effects. Our approach underscores the advantage of framing allostery as a causal process by using, as a benchmark system, the second PDZ domain of the human phosphatase human Protein Tyrosine Phosphatase 1E that mediates protein-protein interactions. We employ causal indicators, such as response functions and transfer entropy, to identify the network of PDZ2 residues through which the allosteric signal propagates across the protein structure. These indicators reveal specific regions that align well with experimental observations. Furthermore, our results suggest that deviations from purely thermal fluctuations can significantly influence allosteric communication by introducing distinct timescales and memory effects. This influence is particularly relevant when the allosteric response unfolds on timescales incompatible with relaxation to equilibrium. Accordingly, non-thermal fluctuations may become essential for accurately describing protein responses to ligand binding and developing a comprehensive understanding of allosteric regulation.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144965984","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}

引用次数: 0

Regulation and functional roles revealed by clustering of microarray expression data ofEscherichia coligenes. 大肠杆菌基因微阵列表达数据聚类揭示的调控及其功能作用。

IF 1.6 4区生物学

Physical biology Pub Date : 2025-08-14 DOI: 10.1088/1478-3975/adf61a

Mishael Sánchez-Pérez, Humberto Peralta, M Cecilia Ishida-Guitierrez, Alberto Santos-Zavaleta, Irma Martínez-Flores, Faviola Tavares-Carreon, Cesaré Ovando-Vázquez

{"title":"Regulation and functional roles revealed by clustering of microarray expression data ofEscherichia coligenes.","authors":"Mishael Sánchez-Pérez, Humberto Peralta, M Cecilia Ishida-Guitierrez, Alberto Santos-Zavaleta, Irma Martínez-Flores, Faviola Tavares-Carreon, Cesaré Ovando-Vázquez","doi":"10.1088/1478-3975/adf61a","DOIUrl":"10.1088/1478-3975/adf61a","url":null,"abstract":"An enormous amount of gene expression data is currently available online in repositories for several organisms. Microarray data can be used to identify co-expressed genes that may be involved in the same biological process. Therefore, the analysis and interpretation of this information could help organize and understand the knowledge it contains, representing a major challenge in the post-genomic era. Here, we grouped genes ofEscherichia coliK-12 using expression data to infer meaningful transcriptional regulatory information. Our method assumes that co-expressed genes reflect functional units, as evidenced by their genetic structure, including gene arrangement, regulation, and participation in defined biological processes. These functionally linked clusters were validated with curated transcriptional regulatory information from RegulonDB. From 907 growth conditions, 420 clusters were formed involving 1674 genes. Clusters contained from 2 to 64 genes. We found that co-expressed genes participate in related metabolic pathways and share similar types of regulation (through transcription factors,σ-factors, allosteric regulation, or micro-RNA regulation). This study is helpful for identifying novel transcriptional regulatory interactions.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":1.6,"publicationDate":"2025-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144754097","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}

引用次数: 0

Investigating substrate binding mechanism in prolyl oligopeptidase through molecular dynamics. 从分子动力学角度研究脯氨寡肽酶的底物结合机制。

IF 1.6 4区生物学

Physical biology Pub Date : 2025-08-05 DOI: 10.1088/1478-3975/adf429

Sylwia Czach, Katarzyna Walczewska-Szewc

引用次数: 0

Biofilm vertical growth dynamics are captured by an active fluid framework. 生物膜垂直生长动态是由一个活跃的流体框架捕获的。

IF 2 4区生物学

Physical biology Pub Date : 2025-07-11 DOI: 10.1088/1478-3975/ade928

Raymond Copeland, Peter J Yunker

{"title":"Biofilm vertical growth dynamics are captured by an active fluid framework.","authors":"Raymond Copeland, Peter J Yunker","doi":"10.1088/1478-3975/ade928","DOIUrl":"10.1088/1478-3975/ade928","url":null,"abstract":"Bacterial biofilms, surface-attached microbial communities, grow horizontally across surfaces and vertically above them. Although a simple heuristic model for vertical growth was experimentally shown to accurately describe the behavior of diverse microbial species, the biophysical implications and theoretical basis for this empirical model were unclear. Here, we demonstrate that this heuristic model emerges naturally from fundamental principles of active fluid dynamics. By analytically deriving solutions for an active fluid model of vertical biofilm growth, we show that the governing equations reduce to the same form as the empirical model in both early- and late-stage growth regimes. Our analysis reveals that cell death and decay rates likely play key roles in determining the characteristic parameters of vertical growth. The active fluid model produces a single, simple equation governing growth at all heights that is surprisingly simpler than the heuristic model. With this theoretical basis, we explain why the vertical growth rate reaches a maximum at a height greater than the previously identified characteristic length scale. These results provide a theoretical foundation for a simple mathematical model of vertical growth, enabling deeper understanding of how biological and biophysical factors interact during biofilm development.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12247187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512435","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}

引用次数: 0

Resource allocation to cell envelopes and the scaling of bacterial growth rate. 资源分配到细胞包膜和细菌生长速率的缩放。

IF 2 4区生物学

Physical biology Pub Date : 2025-07-08 DOI: 10.1088/1478-3975/adea04

Bogi Trickovic, Michael Lynch

引用次数: 0

Why swarming insects have perplexing spatial statistics. 为什么成群的昆虫有令人困惑的空间统计。

IF 2 4区生物学

Physical biology Pub Date : 2025-06-12 DOI: 10.1088/1478-3975/addf08

Andy Reynolds

引用次数: 0

Methods in quantitative biology-from analysis of single-cell microscopy images to inference of predictive models for stochastic gene expression. 定量生物学的方法-从单细胞显微镜图像的分析到随机基因表达预测模型的推断。

IF 2 4区生物学

Physical biology Pub Date : 2025-06-10 DOI: 10.1088/1478-3975/adda85

Luis U Aguilera, Lisa M Weber, Eric Ron, Connor R King, Kaan Öcal, Alex Popinga, Joshua Cook, Michael P May, William S Raymond, Zachary R Fox, Linda S Forero-Quintero, Jack R Forman, Alexandre David, Brian Munsky

{"title":"Methods in quantitative biology-from analysis of single-cell microscopy images to inference of predictive models for stochastic gene expression.","authors":"Luis U Aguilera, Lisa M Weber, Eric Ron, Connor R King, Kaan Öcal, Alex Popinga, Joshua Cook, Michael P May, William S Raymond, Zachary R Fox, Linda S Forero-Quintero, Jack R Forman, Alexandre David, Brian Munsky","doi":"10.1088/1478-3975/adda85","DOIUrl":"10.1088/1478-3975/adda85","url":null,"abstract":"The field of quantitative biology (q-bio) seeks to provide precise and testable explanations for observed biological phenomena by applying mathematical and computational methods. The central goals of q-bio are to (1) systematically propose quantitative hypotheses in the form of mathematical models, (2) demonstrate that these models faithfully capture a specific essence of a biological process, and (3) correctly forecast the dynamics of the process in new, and previously untested circumstances. Achieving these goals depends on accurate analysis and incorporating informative experimental data to constrain the set of potential mathematical representations. In this introductory tutorial, we provide an overview of the state of the field and introduce some of the computational methods most commonly used in q-bio. In particular, we examine experimental techniques in single-cell imaging, computational tools to process images and extract quantitative data, various mechanistic modeling approaches used to reproduce these quantitative data, and techniques for data-driven model inference and model-driven experiment design. All topics are presented in the context of additional online resources, including open-source Python notebooks and open-ended practice problems that comprise the technical content of the annual Undergraduate Quantitative Biology Summer School (UQ-Bio).","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":" ","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12150428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144102425","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}

引用次数: 0

Comparing regression-based approaches for identifying microbial functional groups. 比较基于回归的微生物功能群鉴定方法。

IF 2 4区生物学

Physical biology Pub Date : 2025-05-30 DOI: 10.1088/1478-3975/addc2a

Fang Yu, Mikhail Tikhonov

引用次数: 0

Effect of membrane tension on pore formation induced by antimicrobial peptides and other membrane-active peptides. 膜张力对抗菌肽和其他膜活性肽诱导的孔形成的影响。

IF 2 4区生物学

Physical biology Pub Date : 2025-05-06 DOI: 10.1088/1478-3975/add071

Marzuk Ahmed, Md Masum Billah, Masahito Yamazaki

{"title":"Effect of membrane tension on pore formation induced by antimicrobial peptides and other membrane-active peptides.","authors":"Marzuk Ahmed, Md Masum Billah, Masahito Yamazaki","doi":"10.1088/1478-3975/add071","DOIUrl":"https://doi.org/10.1088/1478-3975/add071","url":null,"abstract":"Membrane tension plays an important role in various aspects of the dynamics and functions of cells. Here, we review recent studies of the effect of membrane tension on pore formation in lipid bilayers and pore formation induced by membrane-active peptides (MAPs) including antimicrobial peptides (AMPs). For this purpose, the micropipette aspiration method using a patch of cell membrane/lipid bilayers and a giant unilamellar vesicle (GUV)/a total cell, and the application of osmotic pressure (Π) to suspensions of large unilamellar vesicles (LUVs) have been used. However, these conventional methods have some drawbacks for the investigation of the effect of membrane tension on the actions of MAPs such as AMPs. Recently, to overcome these drawbacks, a new Π method using GUVs has been developed. Here, we focus on this Π method as a new technique for revealing the effect of membrane tension on the MAPs-induced pore formation. Firstly, we review studies of the effect of membrane tension on pore formation in lipid bilayers as determined by conventional methods. Secondly, after a brief review of studies of the effect of Π on LUVs, we describe the estimation of membrane tension in GUVs induced by Π and the Π-induced pore formation. Thirdly, after a review of the effect of membrane tension on the MAPs-induced pore formation as obtained by the conventional methods, we describe an application of the Π method to studies of the effect of membrane tension on AMP-induced pore formation. Finally, we discuss the advantages of the Π method over conventional methods and consider future perspectives.","PeriodicalId":20207,"journal":{"name":"Physical biology","volume":"22 3","pages":""},"PeriodicalIF":2.0,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040789","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}

引用次数: 0

Quantum features of the transport through ion channels in the soft knock-on model. 软撞击模型中离子通道输运的量子特征。

IF 2 4区生物学

Physical biology Pub Date : 2024-12-27 DOI: 10.1088/1478-3975/ad9cde

Mateusz Polakowski, Miłosz Panfil

引用次数: 0