Biophysics and Physicobiology最新文献

{"title":"Protein hydration and its freezing phenomena: Toward the application for cell freezing and frozen food storage.","authors":"Naoki Yamamoto, Masahiro Nakanishi, Robin Rajan, Hiroshi Nakagawa","doi":"10.2142/biophysico.bppb-v18.034","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.034","url":null,"abstract":"Needless to say, water is an indispensable solvent for living things. ~60 % of our body is composed of water, the lack of which causes lots of fatal problems. It has also been known that protein function is performed only when it accompanies water molecules around the surface, i.e. hydration water molecules [1]. Therefore, it is essential to understand how water and biological component interact with each other in the view point of structure and dynamics. Freezing is a fundamental and simple phenomenon of water, and thus can be used as a “probe” for the purpose. Furthermore, preservation of cells and proteins under low temperature is crucial for numerous applications, which in turn triggers a myriad of undesirable consequences because of the freezing [2]. For these issues, we have a symposium at the 59th Annual Meeting of the Biophysical Society of Japan held in November 2021 inviting four speakers. At the symposium, the speakers review recent progresses on the understanding of the freezing phenomenon of water around cells (by Nakanishi), proteins (by Yamamoto), and model compound (by Nakagawa), which is linked to scrutinizing mode of action of biomaterials working for protecting biological specimens against freezing (by Rajan).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"284-288"},"PeriodicalIF":0.0,"publicationDate":"2021-11-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/27/be/18_284.PMC8677416.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39662411","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":"The insights into calcium ion selectivity provided by ancestral prokaryotic ion channels.","authors":"Katsumasa Irie","doi":"10.2142/biophysico.bppb-v18.033","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.033","url":null,"abstract":"<p><p>Prokaryotic channels play an important role in the structural biology of ion channels. At the end of the 20^th century, the first structure of a prokaryotic ion channel was revealed. Subsequently, the reporting of structures of various prokaryotic ion channels have provided fundamental insights into the structure of ion channels of higher organisms. Voltage-dependent Ca²⁺ channels (Cavs) are indispensable for coupling action potentials with Ca²⁺ signaling. Similar to other proteins, Cavs were predicted to have a prokaryotic counterpart; however, it has taken more than 20 years for one to be identified. The homotetrameric channel obtained from <i>Meiothermus ruber</i> generates the calcium ion specific current, so it is named as CavMr. Its selectivity filter contains a smaller number of negatively charged residues than mutant Cavs generated from other prokaryotic channels. CavMr belonged to a different cluster of phylogenetic trees than canonical prokaryotic cation channels. The glycine residue of the CavMr selectivity filter is a determinant for calcium selectivity. This glycine residue is conserved among eukaryotic Cavs, suggesting that there is a universal mechanism for calcium selectivity. A family of homotetrameric channels has also been identified from eukaryotic unicellular algae, and the investigation of these channels can help to understand the mechanism for ion selection that is conserved from prokaryotes to eukaryotes.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"274-283"},"PeriodicalIF":0.0,"publicationDate":"2021-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/2c/6e/18_274.PMC8677417.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39662410","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":"Increasing complexity of primitive compartments.","authors":"Tony Z Jia,&nbsp;Yutetsu Kuruma","doi":"10.2142/biophysico.bppb-v18.032","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.032","url":null,"abstract":"Corresponding authors: Tony Z. Jia, Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan. Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, Washington 98154, USA. ORCID iD: https://orcid.org/0000-0001-5175-4599, e-mail: tzjia@elsi.jp; Yutetsu Kuruma, Extra-cutting-edge Science and Technology Avant-garde Research Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushimacho, Yokosuka, Kanagawa 237-0061, Japan. Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan. ORCID iD: https://orcid.org/0000-0001-8147-5646, email: ykuruma@jamstec.go.jp Biophysics and Physicobiology","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"269-273"},"PeriodicalIF":0.0,"publicationDate":"2021-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/44/47/18_269.PMC8639197.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39815913","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":"Technical development and sharing of high-resolution cryo-electron microscopes.","authors":"Haruki Nakamura,&nbsp;Masahide Kikkawa,&nbsp;Takeshi Murata","doi":"10.2142/biophysico.bppb-v18.030","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.030","url":null,"abstract":"The BINDS program, Basis for Supporting Innovative Drug Discovery and Life Science Research (https://www.binds.jp/en/), has been running since 2017 for five years to promote drug discovery in academia at preclinical phase and basic life science research by the AMED, Japan Agency for Medical Research and Development. Total 59 research groups were selected in diverse fields, such as Pharmaceutics, Medicine, Chemistry, Genomics, Structural Biology, Informatics, and Computer Science, from all over Japan with a total basic budget of about 3 billion yen every year. The BINDS program has a characteristic feature to support researchers even outside of the program for drug discovery and general life science. So far, about 3,000 research projects have been supported. In particular, the BINDS program strongly promotes technical development and sharing cryo-electron microscopes (cryo-EMs) to solve high-resolution structures of proteins and their complexes. Since 2017, high-end cryo-EMs have been installed with equipment grants by the BINDS project. In addition, eight more cryo-EMs are being installed in 2021 at several laboratories in Japan. To promote cryo-EM usage among many researchers, the BINDS program created the cryoEM network (https://www.cryoemnet.org/), so that most of the cryo-EM machines in Japan are shared by users with the well-organized schedule as much as possible. These new shared cryo-EM facilities enable higher-resolution and higherthroughput structural analysis, together with the recent technological progress, including the development of new grids and methods for online remote cryo-EM operation. At the 59th Annual Meeting of the Biophysical Society of Japan in November 2021, six speakers are invited to share the recent results of single particle analysis, tomography, and micro-ED by cryo-EMs, and to discuss the issues to be overcome by technical development. This symposium is cosponsored by the AMED-BINDS. Dr. Masahide Kikkawa from the University of Tokyo reviews the studies by cryo-EMs at the University of Tokyo for structural analysis to researchers and companies throughout Japan. At present, nearly 50 projects are being supported by them, and six companies are also using the facility. In their facility, they use three cryo-EM methods to perform crossscale observation ranging from atoms to cellular structures. Single particle analysis is used to observe biological molecules, microED is for atomic resolution structures of tiny crystals [1, 2], and cryo-electron tomography is used for cellular structures. In the symposium, he shows the recent results using the three methods and discusses what is necessary to utilize the cryo-EM shared facility further. Dr. Keiichi Namba group from Osaka Univ. and RIKEN developed a cryo-TEM named “CRYO ARM” with JEOL over the last decade. The groups determined the structure of apoferritin at 1.53Å from about 900 images collected in one day in 2019 [3]. Since then, they developed a new TEM control software","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"265-266"},"PeriodicalIF":0.0,"publicationDate":"2021-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/dc/6d/18_265.PMC8639199.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39727512","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":"Beyond multi-disciplinary and cross-scale analyses of the cyanobacterial circadian clock system.","authors":"Shuji Akiyama, Hironari Kamikubo","doi":"10.2142/biophysico.bppb-v18.031","DOIUrl":"10.2142/biophysico.bppb-v18.031","url":null,"abstract":"","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"267-268"},"PeriodicalIF":0.0,"publicationDate":"2021-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/80/22/18_267.PMC8639195.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39815912","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":"Information biophysics of gradient sensing in organisms.","authors":"Akihiko Ishijima,&nbsp;Yasushi Okada","doi":"10.2142/biophysico.bppb-v18.029","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.029","url":null,"abstract":"Corresponding author: Yasushi Okada, Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research (BDR), 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan. ORCID iD: https://orcid.org/0000-0003-2601-3689, email: y.okada@riken.jp; Department of Cell Biology, Department of Physics Universal Biology Institute (UBI), and International Research Center for Neurointelligence (WPI-IRCN), the University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. Biophysics and Physicobiology","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"263-264"},"PeriodicalIF":0.0,"publicationDate":"2021-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e8/53/18_263.PMC8639196.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39727511","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":"Collective pattern formations of animals in active matter physics.","authors":"Takuma Sugi,&nbsp;Hiroshi Ito,&nbsp;Ken H Nagai","doi":"10.2142/biophysico.bppb-v18.028","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.028","url":null,"abstract":"<p><p>Active matter refers to systems composed of elements that are self-propelled by the dissipation of energy, in which dynamical patterns emerge, as is the case of flocks of birds and schools of fish. Some researchers in active matter physics seek to identify unified descriptions of such collective motions through interdisciplinary approaches by biologists and physicists. Through such collaborations, experimental studies pertaining to active matter physics have been developing recently, which allow us to verify the proposed mathematical models. Here, we review collective pattern formations and behaviors of animals from the perspective of active matter physics.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"254-262"},"PeriodicalIF":0.0,"publicationDate":"2021-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f6/15/18_254.PMC8639198.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39727510","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":"Application of quantitative cell imaging using label-free optical diffraction tomography.","authors":"Chan-Gi Pack","doi":"10.2142/biophysico.bppb-v18.027","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v18.027","url":null,"abstract":"<p><p>The cell is three-dimensionally and dynamically organized into cellular compartments, including the endoplasmic reticulum, mitochondria, vesicles, and nucleus, which have high relative molecular density. The structure and functions of these compartments and organelles may be deduced from the diffusion and interaction of related biomolecules. Among these cellular components, various protein molecules can freely access the nucleolus or mitotic chromosome through Brownian diffusion, even though they have a densely packed structure. However, physicochemical properties of the nucleolus and chromosomes, such as molecular density and volume, are not yet fully understood under changing cellular conditions. Many studies have been conducted based on high-resolution imaging and analysis techniques using fluorescence. However, there are limitations in imaging only fluorescently labeled molecules, and cytotoxicity occurs during three-dimensional imaging. Alternatively, the recently developed label-free three-dimensional optical diffraction tomography (ODT) imaging technique can divide various organelles in cells into volumes and analyze them by refractive index, although specific molecules cannot be observed. A previous study established an analytical method that provides comprehensive insights into the physical properties of the nucleolus and mitotic chromosome by utilizing the advantages of ODT and fluorescence techniques, such as fluorescence correlation spectroscopy and confocal laser scanning microscopy. This review article summarizes a recent study and discusses the future aspects of the ODT for cellular compartments.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"244-253"},"PeriodicalIF":0.0,"publicationDate":"2021-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/99/0b/18_244.PMC8550874.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39598291","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 cytoskeletal motor proteins and their associated proteins.","authors":"Kumiko Hayashi, Shinsuke Niwa","doi":"10.2142/biophysico.bppb-v18.026","DOIUrl":"10.2142/biophysico.bppb-v18.026","url":null,"abstract":"","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"241-243"},"PeriodicalIF":0.0,"publicationDate":"2021-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ef/6c/18_241.PMC8550873.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39598289","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":"Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins.","authors":"Atsushi Hijikata, Clara Shionyu, Setsu Nakae, Masafumi Shionyu, Motonori Ota, Shigehiko Kanaya, Tsuyoshi Shirai","doi":"10.2142/biophysico.bppb-v18.025","DOIUrl":"10.2142/biophysico.bppb-v18.025","url":null,"abstract":"<p><p>More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of <i>in silico</i> and <i>in vitro</i> screenings for drug repurposing, there is only a limited number of drugs had been successfully authorized by drug regulation organizations. Although many approved drugs and natural compounds, which exhibited antiviral activity <i>in vitro</i>, were considered potential drugs against COVID-19, a further multidisciplinary investigation is required for understanding the mechanisms underlying the antiviral effects of the drugs.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"226-240"},"PeriodicalIF":0.0,"publicationDate":"2021-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/cd/3c/18_226.PMC8550875.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39598290","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}