Biophysics and Physicobiology最新文献

{"title":"Protein large-scale motions revealed by quantum beams: A new era in understanding protein dynamics.","authors":"Naoki Yamamoto, Rintaro Inoue, Ikuo Kurisaki, Tatsuhito Matsuo, Yuki Hishikawa, Wenyang Zhao, Hiroshi Sekiguchi","doi":"10.2142/biophysico.bppb-v19.0035","DOIUrl":"10.2142/biophysico.bppb-v19.0035","url":null,"abstract":"","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190035"},"PeriodicalIF":0.0,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/00/48/19_e190035.PMC9592564.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452697","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":"Quantum nanodiamonds for sensing of biological quantities: Angle, temperature, and thermal conductivity.","authors":"Shingo Sotoma,&nbsp;Hirotaka Okita,&nbsp;Shunsuke Chuma,&nbsp;Yoshie Harada","doi":"10.2142/biophysico.bppb-v19.0034","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0034","url":null,"abstract":"<p><p>Measuring physical quantities in the nanometric region inside single cells is of great importance for understanding cellular activity. Thus, the development of biocompatible, sensitive, and reliable nanobiosensors is essential for progress in biological research. Diamond nanoparticles containing nitrogen-vacancy centers (NVCs), referred to as fluorescent nanodiamonds (FNDs), have recently emerged as the sensors that show great promise for ultrasensitive nanosensing of physical quantities. FNDs emit stable fluorescence without photobleaching. Additionally, their distinctive magneto-optical properties enable an optical readout of the quantum states of the electron spin in NVC under ambient conditions. These properties enable the quantitative sensing of physical parameters (temperature, magnetic field, electric field, pH, etc.) in the vicinity of an FND; hence, FNDs are often described as \"quantum sensors\". In this review, recent advancements in biosensing applications of FNDs are summarized. First, the principles of orientation and temperature sensing using FND quantum sensors are explained. Next, we introduce surface coating techniques indispensable for controlling the physicochemical properties of FNDs. The achievements of practical biological sensing using surface-coated FNDs, including orientation, temperature, and thermal conductivity, are then highlighted. Finally, the advantages, challenges, and perspectives of the quantum sensing of FND are discussed. This review article is an extended version of the Japanese article, In Situ Measurement of Intracellular Thermal Conductivity Using Diamond Nanoparticle, published in SEIBUTSU BUTSURI Vol. 62, p. 122-124 (2022).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190034"},"PeriodicalIF":0.0,"publicationDate":"2022-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9c/b4/19_e190034.PMC9592573.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452694","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":"Participation in 44th Indian Biophysical Society Meeting.","authors":"Kayo Hibino","doi":"10.2142/biophysico.bppb-v19.0033","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0033","url":null,"abstract":"The Biophysical Societies of Japan and the Indian Biophysical Society regularly organize India-Japan joint symposiums and other exchange opportunities for further development of the biophysics field and international exchange of scientists. Here I report on the 44th Indian Biophysical Society Meeting [1] held in Mumbai, India as a hybrid of the online meeting, on March 30-31 and April 1, 2022. The conference theme was \"Conceptual Advances in Biophysics and its Applications\", and over 300 scientists and students from all over the world participated. The conference hosted five lectures, including the GN Ramachandran Lecture, and 24 invited talks in seven sessions on: 1) Protein-Protein Interactions, 2) Protein Folding, 3) Aggregation & Related Diseases, 4) Molecular & Cellular Biophysics, 5) Structural Biology & its applications, 6) Protein Conformational Dynamics, and 7) Biophysical Techniques & Disease Intervention. It also had","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190033"},"PeriodicalIF":0.0,"publicationDate":"2022-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ac/92/19_e190033.PMC9592566.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452695","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":"Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies.","authors":"Ryo Iizuka,&nbsp;Hirohito Yamazaki,&nbsp;Sotaro Uemura","doi":"10.2142/biophysico.bppb-v19.0032","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0032","url":null,"abstract":"<p><p>Single-molecule technologies can provide detailed information regarding molecular mechanisms and interactions that cannot easily be studied on the bulk scale; generally, individual molecular behaviors cannot be distinguished, and only average characteristics can be measured. Nevertheless, the development of the single-molecule sequencer had a significant impact on conventional <i>in vitro</i> single-molecule research, featuring automated equipment, high-throughput chips, and automated analysis systems. However, the utilization of sequencing technology in <i>in vitro</i> single-molecule research is not yet globally prevalent, owing to the large gap between highly organized single-molecule sequencing and manual-based <i>in vitro</i> single-molecule research. Here, we describe the principles of zero-mode waveguides (ZMWs) and nanopore methods used as single-molecule DNA sequencing techniques, and provide examples of functional biological measurements beyond DNA sequencing that contribute to a global understanding of the current applications of these sequencing technologies. Furthermore, through a comparison of these two technologies, we discuss future applications of DNA sequencing technologies in <i>in vitro</i> single-molecule research.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190032"},"PeriodicalIF":0.0,"publicationDate":"2022-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/61/cb/19_e190032.PMC9592571.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452699","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":"A five-course meal symposium on \"The Future of Muscle is Now\".","authors":"Madoka Suzuki,&nbsp;Kotaro Oyama","doi":"10.2142/biophysico.bppb-v19.0029","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0029","url":null,"abstract":"Muscles are the source of mechanical force. Muscles enable us to move our arms and legs, speak, pump blood, and digest food. Muscle mechanics has been an important subject in biophysics. Accordingly, it is now possible to explain how mechanical force is produced and assembled at all levels of the hierarchy of the muscle contractile system, that is, from a single protein molecule at the smallest scale, to an assembly of the molecules (sarcomere; a highly ordered bipolar structure mainly composed of actin filaments that are protein polymers of actin monomers, and their counterpart myosin filaments that are of myosin motor proteins), to a myofibril (assembly of sarcomeres connected in series) and muscle cell, and finally, to a tissue. Then, are there no intriguing questions that can be asked regarding biophysics? We have organized a symposium titled “The Future of Muscle is Now” at the 60th Annual Meeting of the Biophysical Society of Japan, held in September 2022 (Figure 1). In the symposium, we intend to demonstrate that the previously mentioned tragic perspective may be incorrect.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190029"},"PeriodicalIF":0.0,"publicationDate":"2022-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/45/43/19_e190029.PMC9592567.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40462102","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":"Uncovering the design principles of supramolecular assemblies through manipulation of the structures, dynamics, and functions.","authors":"Makito Miyazaki, Takahiro Kosugi","doi":"10.2142/biophysico.bppb-v19.0031","DOIUrl":"10.2142/biophysico.bppb-v19.0031","url":null,"abstract":"","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190031"},"PeriodicalIF":0.0,"publicationDate":"2022-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7c/5d/19_e190031.PMC9592565.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452700","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":"Japan-US symposium on motor proteins and associated single-molecule biophysics.","authors":"Kumiko Hayashi, Jakia Jannat Keya","doi":"10.2142/biophysico.bppb-v19.0030","DOIUrl":"10.2142/biophysico.bppb-v19.0030","url":null,"abstract":"","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190030"},"PeriodicalIF":0.0,"publicationDate":"2022-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b2/0e/19_e190030.PMC9592572.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452698","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":"Phase separation by biopolymers: Basics and applications.","authors":"Ryo Kitahara,&nbsp;Tomoshi Kameda","doi":"10.2142/biophysico.bppb-v19.0028","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0028","url":null,"abstract":"In recent years, various intracellular components, such as P-bodies, nucleoli, and stress granules, have been shown to be aggregates of proteins and RNA via liquid–liquid phase separation (LLPS) [1]. Since such protein granules can reversibly form, disappear, and play their respective roles in the cell, they are called membraneless organelles. To date, many proteins, especially nuclear proteins, and artificial peptides have been reported to form protein granules, namely condensed liquid droplets, via LLPS (Figure 1) [2,3]. Interestingly, amyloid fibril formation is gradually accelerated in droplets [4]. By elucidating the formation mechanism of irreversible aggregates from the homogeneous phase state (1-phase) of proteins via liquid droplets in vitro and in vivo, effective drugs can be developed for neurodegenerative diseases. To discuss the cutting-edge research on the LLPS of biopolymers [5-9], the “Phase Separation by Biopolymers: Basics and Applications” symposium will be held at the 60th Annual Meeting of the Biophysical Society of Japan in September, 2022. The invited speakers at the symposium will be Ryo Kitahara, Akira Nomoto, Shinji Kajimoto, Kiyoto Kamagata, and Tomoshi Kameda. Kitahara et al. will introduce a pressure-temperature phase diagram of LLPS for fused in sarcoma (FUS) and the application of a pressure-jump spectroscopic technique to study the formation and vanishing dynamics of FUS-LLPS [6,7]. Nomoto et al. will discuss the solubility parameters of amino acids during LLPS and the aggregation of proteins, based on the solubility of aromatic amino acids in a solution containing 20 different amino acids [5]. Kajimoto et al. will explain Raman and Brillouin microscopy as a tool for quantitative analysis of LLPS. This method is a powerful technique to determine the chemical nature of LLPS and its relationship with protein aggregation [9]. Kamagara et al. will introduce rational peptide design for regulating LLPS on the basis of residue-residue contact energy. The effects of designed peptides on p53 LLPS analysis will be discussed [8]. Kameda et al. will introduce theoretical approaches combined with molecular dynamics simulations and machine learning. The aggregation nature of tetra-peptides will be discussed.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190028"},"PeriodicalIF":0.0,"publicationDate":"2022-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1b/8e/19_e190028.PMC9592568.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40462101","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":"Chapter 3: Changing the Rules.","authors":"","doi":"10.2142/biophysico.bppb-v18.s005","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.s005","url":null,"abstract":"In the previous chapter, the rule was that if a person with 0 gaming chips was hit, the number of trials were incremented without debt. An interesting variation of this rule involves elimination of the player via inclusion of the concept of bankruptcy from society, i.e., a person with 0 gaming chips is eliminated from the game (Fig. 3.1)3.1. In this case, since the total number of gaming chips will be the same, however, the number of players will decrease, therefore the average number of gaming chips per person will increase. Nevertheless, the number of bankruptcies (persons with 0 gaming chips) will continue to increase, as such persons appear every moment (Fig. 3.1; Bar at the left end of the figure on the right). If we keep it going, only a small number of rich people will survive.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"S025-S034"},"PeriodicalIF":0.0,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/de/65/18_S025.PMC9465403.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33484764","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":"Molecular dynamics analysis of biomolecular systems including nucleic acids.","authors":"Takeru Kameda,&nbsp;Akinori Awazu,&nbsp;Yuichi Togashi","doi":"10.2142/biophysico.bppb-v19.0027","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0027","url":null,"abstract":"<p><p>With the recent progress in structural biology and genome biology, structural dynamics of molecular systems that include nucleic acids has attracted attention in the context of gene regulation. The structure-function relationship is an important topic that highlights the importance of the physicochemical properties of nucleotides, as well as that of amino acids in proteins. Simulations are a useful tool for the detailed analysis of molecular dynamics that complement experiments in molecular biology; however, molecular simulation of nucleic acids is less well developed than that of proteins partly due to the physical nature of nucleic acids. In this review, we briefly describe the current status and future directions of the field as a guide to promote collaboration between experimentalists and computational biologists.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190027"},"PeriodicalIF":0.0,"publicationDate":"2022-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/17/65/19_e190027.PMC9592887.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40452692","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}