Biophysics and physicobiology最新文献_第3页

Constructing virtual DNA-nanomachines. 构建虚拟dna纳米机器。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-10-22 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2011

Nathan Nunes Evangelista, Masahiro Takinoue

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Using interactive deep learning to track cells: A report on a 3-day hands-on training program at IUPAB 2024. 使用交互式深度学习来跟踪细胞：关于IUPAB 2024为期3天的实践培训计划的报告。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-10-19 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2010

Lissy M Hartmann, Samara Bridge

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GENESIS and CHARMM-GUI: Advances and applications from Hands-on training program C at RIKEN. GENESIS和CHARMM-GUI: RIKEN动手培训项目C的进展和应用。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-10-17 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2008

Nor Akmalyati Sulong, Vannajan Sanghiran Lee

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DNA nanomachine tutorial. DNA纳米机器教程。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-10-17 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2009

Huong T Vu

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Artificial cell system as a tool for investigating pattern formation mechanisms of intracellular reaction-diffusion waves. 人工细胞系统作为研究细胞内反应扩散波模式形成机制的工具。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-10-10 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0022

Sakura Takada, Kei Fujiwara

{"title":"Artificial cell system as a tool for investigating pattern formation mechanisms of intracellular reaction-diffusion waves.","authors":"Sakura Takada, Kei Fujiwara","doi":"10.2142/biophysico.bppb-v21.0022","DOIUrl":"10.2142/biophysico.bppb-v21.0022","url":null,"abstract":"Intracellular positional information is crucial for the precise control of biological phenomena, including cell division, polarity, and motility. Intracellular reaction-diffusion (iRD) waves are responsible for regulating positional information within cells as morphogens in multicellular tissues. However, iRD waves are explained by the coupling of biochemical reactions and molecular diffusion which indicates nonlinear systems under far from equilibrium conditions. Because of this complexity, experiments using defined elements rather than living cells containing endogenous factors are necessary to elucidate their pattern formation mechanisms. In this review, we summarize the effectiveness of artificial cell systems for investigating iRD waves derived from their high controllability and ability to emulate cell-size space effects. We describe how artificial cell systems reveal the characteristics of iRD waves, including the mechanisms of wave generation, mode selection, and period regulation. Furthermore, we introduce remaining open questions and discuss future challenges even in Min waves and in applying artificial cell systems to various iRD waves.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 4","pages":"e210022"},"PeriodicalIF":1.6,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11830476/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143442950","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

Editorial: Hands-on Training Program. 社论：实践培训计划。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-10-10 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2007

Kumiko Hayashi

引用次数: 0

Data-driven score tuning for ChooseLD: A structure-based drug design algorithm with empirical scoring and evaluation of ligand-protein docking predictability. ChooseLD的数据驱动评分调整：一种基于结构的药物设计算法，具有配体-蛋白质对接可预测性的经验评分和评估。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-09-21 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0021

Akihiro Masuda, Daichi Sadato, Mitsuo Iwadate

{"title":"Data-driven score tuning for ChooseLD: A structure-based drug design algorithm with empirical scoring and evaluation of ligand-protein docking predictability.","authors":"Akihiro Masuda, Daichi Sadato, Mitsuo Iwadate","doi":"10.2142/biophysico.bppb-v21.0021","DOIUrl":"10.2142/biophysico.bppb-v21.0021","url":null,"abstract":"Computerized molecular docking methodologies are pivotal in in-silico screening, a crucial facet of modern drug design. ChooseLD, a docking simulation software, combines structure- and ligand-based drug design methods with empirical scoring. Despite advancements in computerized molecular docking methodologies, there remains a gap in optimizing the predictive capabilities of docking simulation software. Accordingly, using the docking scores output by ChooseLD, we evaluated its performance in predicting the bioactivity of G-protein coupled receptor (GPCR) and kinase bioactivity, specifically focusing on Ki and IC50 values. We evaluated the accuracy of our algorithm through a comparative analysis using force-field-based predictions from AutoDock Vina. Our findings suggested that the modified ChooseLD could accurately predict the bioactivity, especially in scenarios with a substantial number of known ligands. These findings highlight the importance of selecting algorithms based on the characteristics of the prediction targets. Furthermore, addressing partial model fitting with database knowledge was demonstrated to be effective in overcoming this challenge. Overall, these findings contribute to the refinement and optimization of methodologies in computer-aided drug design, ultimately advancing the efficiency and reliability of in-silico screening processes.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 3","pages":"e210021"},"PeriodicalIF":1.6,"publicationDate":"2024-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11718169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142974184","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

IUPAB and BSJ meeting Kyoto: Reflections on hands on workshop "Real-time single-molecule experiments with optical tweezers and correlated fluorescence microscopy" with LUMICKS C-trap, emphasizing the importance of practicing international and interdisciplinary science. IUPAB和BSJ会议京都：在LUMICKS C-trap研讨会上“使用光镊和相关荧光显微镜进行实时单分子实验”的实践反思，强调实践国际和跨学科科学的重要性。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-09-21 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2005

Karina New

引用次数: 0

Experience report of Hands-on Training Program E: Exploring multi-cellular mechanics. 实践训练项目E：探索多细胞力学经验报告。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-09-21 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2006

Asuka Takeda-Sakazume

引用次数: 0

Four-color single-molecule imaging system for tracking GPCR dynamics with fluorescent HiBiT peptide. 利用荧光HiBiT肽跟踪GPCR动力学的四色单分子成像系统。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-09-20 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0020

Toshiki Yoda, Yasushi Sako, Asuka Inoue, Masataka Yanagawa

{"title":"Four-color single-molecule imaging system for tracking GPCR dynamics with fluorescent HiBiT peptide.","authors":"Toshiki Yoda, Yasushi Sako, Asuka Inoue, Masataka Yanagawa","doi":"10.2142/biophysico.bppb-v21.0020","DOIUrl":"10.2142/biophysico.bppb-v21.0020","url":null,"abstract":"Single-molecule imaging provides information on diffusion dynamics, oligomerization, and protein-protein interactions in living cells. To simultaneously monitor different types of proteins at the single-molecule level, orthogonal fluorescent labeling methods with different photostable dyes are required. G-protein-coupled receptors (GPCRs), a major class of drug targets, are prototypical membrane receptors that have been studied using single-molecule imaging techniques. Here we developed a method for labeling cell-surface GPCRs inspired by the HiBiT system, which utilizes the high affinity complementation between LgBiT and HiBiT fragments of the NanoLuc luciferase. We synthesized four fluorescence-labeled HiBiT peptides (F-FiBiTs) with a different color dye (Setau-488, TMR, SaraFluor 650 and SaraFluor 720). We constructed a multicolor total internal reflection fluorescence microscopy system that allows us to track four color dyes simultaneously. As a proof-of-concept experiment, we labeled an N-terminally LgBiT-fused GPCR (Lg-GPCR) with a mixture of the four F-FiBiTs and successfully tracked each dye within a cell at the single-molecule level. The F-FiBiT-labeled Lg-GPCRs showed agonist-dependent changes in the diffusion dynamics and accumulation into the clathrin-coated pits as observed with a conventional method using a C-terminally HaloTag-fused GPCR. Taking advantage of luciferase complementation by the F-FiBiT and Lg-GPCRs, the F-FiBiT was also applicable to bioluminescence plate-reader-based assays. By combining existing labeling methods such as HaloTag, SNAP-tag, and fluorescent proteins, the F-FiBiT method will be useful for multicolor single-molecule imaging and will enhance our understanding of GPCR signaling at the single-molecule level.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 3","pages":"e210020"},"PeriodicalIF":1.6,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11718171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142974224","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