Pub Date : 2023-09-06eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0035
Yuya Hanazono, Yu Hirano, Taro Tamada, Kunio Miki
Neutron crystallography is a highly effective method for visualizing hydrogen atoms in proteins. In our recent study, we successfully determined the high-resolution (1.2 Å) neutron structure of high-potential iron-sulfur protein, refining the coordinates of some amide protons without any geometric restraints. Interestingly, we observed that amide protons are deviated from the peptide plane due to electrostatic interactions. Moreover, the difference in the position of the amide proton of Cys75 between reduced and oxidized states is possibly attributed to the electron storage capacity of the iron-sulfur cluster. Additionally, we have discussed about the rigidity of the iron-sulfur cluster based on the results of the hydrogen-deuterium exchange. Our research underscores the significance of neutron crystallography in protein structure elucidation, enriching our understanding of protein functions at an atomic resolution.
{"title":"Description of peptide bond planarity from high-resolution neutron crystallography.","authors":"Yuya Hanazono, Yu Hirano, Taro Tamada, Kunio Miki","doi":"10.2142/biophysico.bppb-v20.0035","DOIUrl":"10.2142/biophysico.bppb-v20.0035","url":null,"abstract":"<p><p>Neutron crystallography is a highly effective method for visualizing hydrogen atoms in proteins. In our recent study, we successfully determined the high-resolution (1.2 Å) neutron structure of high-potential iron-sulfur protein, refining the coordinates of some amide protons without any geometric restraints. Interestingly, we observed that amide protons are deviated from the peptide plane due to electrostatic interactions. Moreover, the difference in the position of the amide proton of Cys75 between reduced and oxidized states is possibly attributed to the electron storage capacity of the iron-sulfur cluster. Additionally, we have discussed about the rigidity of the iron-sulfur cluster based on the results of the hydrogen-deuterium exchange. Our research underscores the significance of neutron crystallography in protein structure elucidation, enriching our understanding of protein functions at an atomic resolution.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84491148","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}
Pub Date : 2023-09-02eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0034
So Nakashima, Tetsuya J Kobayashi
Adaptability to changing environments is one of the universal characteristics of living organisms. Because individual modes of adaptation are diverse, a unified understanding of these diverse modes is essential to comprehend adaptation. Adaptations can be categorized from at least two perspectives with respect to information. One is the passivity and activity of adaptation and the other is the type of information transmission. In Darwinian natural selection, organisms are selected among randomly generated traits under which individual organisms are passive in the sense that they do not process any environmental information. On the other hand, organisms can also adapt by sensing their environment and changing their traits. This is an active adaptation in that it makes use of environmental information. In terms of information transfer, adaptation through phenotypic heterogeneity, such as bacterial bet-hedging, is intragenerational in which traits are not passed on to the next generation. In contrast, adaptation through genetic diversity is intergenerational. The theory of population dynamics enables us to unify these various modes of adaptations and their properties can be analyzed qualitatively and quantitatively using techniques from quantitative genetics and information thermodynamics. In addition, such methods can be applied to situations where organisms can learn from past experiences and pass them on from generation to generation. In this work, we introduce the unified theory of biological adaptation based on population dynamics and show its potential applications to evaluate the fitness value of information and to analyze experimental lineage tree data. Finally, we discuss future perspectives for its development. This review article is an extended version of the Japanese article in SEIBUTSU BUTSURI Vol. 57, p. 287-290 (2017).
{"title":"Population dynamics models for various forms of adaptation.","authors":"So Nakashima, Tetsuya J Kobayashi","doi":"10.2142/biophysico.bppb-v20.0034","DOIUrl":"10.2142/biophysico.bppb-v20.0034","url":null,"abstract":"<p><p>Adaptability to changing environments is one of the universal characteristics of living organisms. Because individual modes of adaptation are diverse, a unified understanding of these diverse modes is essential to comprehend adaptation. Adaptations can be categorized from at least two perspectives with respect to information. One is the passivity and activity of adaptation and the other is the type of information transmission. In Darwinian natural selection, organisms are selected among randomly generated traits under which individual organisms are passive in the sense that they do not process any environmental information. On the other hand, organisms can also adapt by sensing their environment and changing their traits. This is an active adaptation in that it makes use of environmental information. In terms of information transfer, adaptation through phenotypic heterogeneity, such as bacterial bet-hedging, is intragenerational in which traits are not passed on to the next generation. In contrast, adaptation through genetic diversity is intergenerational. The theory of population dynamics enables us to unify these various modes of adaptations and their properties can be analyzed qualitatively and quantitatively using techniques from quantitative genetics and information thermodynamics. In addition, such methods can be applied to situations where organisms can learn from past experiences and pass them on from generation to generation. In this work, we introduce the unified theory of biological adaptation based on population dynamics and show its potential applications to evaluate the fitness value of information and to analyze experimental lineage tree data. Finally, we discuss future perspectives for its development. This review article is an extended version of the Japanese article in SEIBUTSU BUTSURI Vol. 57, p. 287-290 (2017).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79827191","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}
Pub Date : 2023-08-31eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0033
Tohru Minamino, Daisuke Nakane, Shuichi Nakamura, Hana Kiyama, Yusuke V Morimoto, Makoto Miyata
{"title":"Frontiers of microbial movement research.","authors":"Tohru Minamino, Daisuke Nakane, Shuichi Nakamura, Hana Kiyama, Yusuke V Morimoto, Makoto Miyata","doi":"10.2142/biophysico.bppb-v20.0033","DOIUrl":"10.2142/biophysico.bppb-v20.0033","url":null,"abstract":"","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88065540","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}
Pub Date : 2023-08-19eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0032
Ryota Sakamoto, Yusuke T Maeda
Single-cell behaviors cover many biological functions, such as cell division during morphogenesis and tissue metastasis, and cell migration during cancer cell invasion and immune cell responses. Symmetry breaking of the positioning of organelles and the cell shape are often associated with these biological functions. One of the main players in symmetry breaking at the cellular scale is the actin cytoskeleton, comprising actin filaments and myosin motors that generate contractile forces. However, because the self-organization of the actomyosin network is regulated by the biochemical signaling in cells, how the mechanical contraction of the actin cytoskeleton induces diverse self-organized behaviors and drives the cell-scale symmetry breaking remains unclear. In recent times, to understand the physical underpinnings of the symmetry breaking exhibited in the actin cytoskeleton, artificial cell models encapsulating the cytoplasmic actomyosin networks covered with lipid monolayers have been developed. By decoupling the actomyosin mechanics from the complex biochemical signaling within living cells, this system allows one to study the self-organization of actomyosin networks confined in cell-sized spaces. We review the recent developments in the physics of confined actomyosin networks and provide future perspectives on the artificial cell-based approach. This review article is an extended version of the Japanese article, The Physical Principle of Cell Migration Under Confinement: Artificial Cell-based Bottom-up Approach, published in SEIBUTSU BUTSURI Vol. 63, p. 163-164 (2023).
{"title":"Unveiling the physics underlying symmetry breaking of the actin cytoskeleton: An artificial cell-based approach.","authors":"Ryota Sakamoto, Yusuke T Maeda","doi":"10.2142/biophysico.bppb-v20.0032","DOIUrl":"10.2142/biophysico.bppb-v20.0032","url":null,"abstract":"<p><p>Single-cell behaviors cover many biological functions, such as cell division during morphogenesis and tissue metastasis, and cell migration during cancer cell invasion and immune cell responses. Symmetry breaking of the positioning of organelles and the cell shape are often associated with these biological functions. One of the main players in symmetry breaking at the cellular scale is the actin cytoskeleton, comprising actin filaments and myosin motors that generate contractile forces. However, because the self-organization of the actomyosin network is regulated by the biochemical signaling in cells, how the mechanical contraction of the actin cytoskeleton induces diverse self-organized behaviors and drives the cell-scale symmetry breaking remains unclear. In recent times, to understand the physical underpinnings of the symmetry breaking exhibited in the actin cytoskeleton, artificial cell models encapsulating the cytoplasmic actomyosin networks covered with lipid monolayers have been developed. By decoupling the actomyosin mechanics from the complex biochemical signaling within living cells, this system allows one to study the self-organization of actomyosin networks confined in cell-sized spaces. We review the recent developments in the physics of confined actomyosin networks and provide future perspectives on the artificial cell-based approach. This review article is an extended version of the Japanese article, The Physical Principle of Cell Migration Under Confinement: Artificial Cell-based Bottom-up Approach, published in SEIBUTSU BUTSURI Vol. 63, p. 163-164 (2023).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728624/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80408913","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}
Pub Date : 2023-07-12eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0031
Tatsuya Iida, Hajime Shinoda, Rikiya Watanabe
With the recent global outbreak of COVID-19, there is an urgent need to establish a versatile diagnostic method for viral infections. Gene amplification test or antigen test are widely used to diagnose viral infections; however, these methods generally have technical drawbacks either in terms of sensitivity, accuracy, or throughput. To address this issue, we recently developed an amplification-free digital RNA detection method (SATORI), which can identify and detect viral genes at the single-molecule level in approximately 9 min, satisfying almost all detection performance requirements for the diagnosis of viral infections. In addition, we also developed practical platforms for SATORI, such as an automated platform (opn-SATORI) and a low-cost compact fluorescence imaging system (COWFISH), with the aim of application in clinical settings. Our latest technologies can be inherently applied to diagnose a variety of RNA viral infections, such as COVID-19 and Influenza A/B, and therefore, we expect that SATORI will be established as a versatile platform for point-of-care testing of a wide range of infectious diseases, thus contributing to the prevention of future epidemics. This article is an extended version of the Japanese article published in the SEIBUTSU BUTSURI Vol. 63, p. 115-118 (2023).
{"title":"SATORI: Amplification-free digital RNA detection method for the diagnosis of viral infections.","authors":"Tatsuya Iida, Hajime Shinoda, Rikiya Watanabe","doi":"10.2142/biophysico.bppb-v20.0031","DOIUrl":"10.2142/biophysico.bppb-v20.0031","url":null,"abstract":"<p><p>With the recent global outbreak of COVID-19, there is an urgent need to establish a versatile diagnostic method for viral infections. Gene amplification test or antigen test are widely used to diagnose viral infections; however, these methods generally have technical drawbacks either in terms of sensitivity, accuracy, or throughput. To address this issue, we recently developed an amplification-free digital RNA detection method (SATORI), which can identify and detect viral genes at the single-molecule level in approximately 9 min, satisfying almost all detection performance requirements for the diagnosis of viral infections. In addition, we also developed practical platforms for SATORI, such as an automated platform (opn-SATORI) and a low-cost compact fluorescence imaging system (COWFISH), with the aim of application in clinical settings. Our latest technologies can be inherently applied to diagnose a variety of RNA viral infections, such as COVID-19 and Influenza A/B, and therefore, we expect that SATORI will be established as a versatile platform for point-of-care testing of a wide range of infectious diseases, thus contributing to the prevention of future epidemics. This article is an extended version of the Japanese article published in the SEIBUTSU BUTSURI Vol. 63, p. 115-118 (2023).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89113319","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}
Pub Date : 2023-06-28eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0030
Tetsuichi Wazawa, Takeharu Nagai
Ion currents associated with channel proteins in the presence of membrane potential are ubiquitous in cellular and organelle membranes. When an ion current occurs through a channel protein, Joule heating should occur. However, this Joule heating seems to have been largely overlooked in biology. Here we show theoretical investigation of Joule heating involving channel proteins in biological processes. We used electrochemical potential to derive the Joule's law for an ion current through an ion transport protein in the presence of membrane potential, and we suggest that heat production and absorption can occur. Simulation of temperature distribution around a single channel protein with the Joule heating revealed that the temperature increase was as small as <10-3 K, although an ensemble of channel proteins was suggested to exhibit a noticeable temperature increase. Thereby, we theoretically investigated the Joule heating of systems containing ensembles of channel proteins. Nerve is known to undergo rapid heat production followed by heat absorption during the action potential, and our simulation of Joule heating for a squid giant axon combined with the Hodgkin-Huxley model successfully reproduced the feature of the heat. Furthermore, we extended the theory of Joule heating to uncoupling protein 1 (UCP1), a solute carrier family transporter, which is important to the non-shivering thermogenesis in brown adipose tissue mitochondria (BATM). Our calculations showed that the Joule heat involving UCP1 was comparable to the literature calorimetry data of BATM. Joule heating of ion transport proteins is likely to be one of important mechanisms of cellular thermogenesis.
{"title":"Joule heating involving ion currents through channel proteins.","authors":"Tetsuichi Wazawa, Takeharu Nagai","doi":"10.2142/biophysico.bppb-v20.0030","DOIUrl":"10.2142/biophysico.bppb-v20.0030","url":null,"abstract":"<p><p>Ion currents associated with channel proteins in the presence of membrane potential are ubiquitous in cellular and organelle membranes. When an ion current occurs through a channel protein, Joule heating should occur. However, this Joule heating seems to have been largely overlooked in biology. Here we show theoretical investigation of Joule heating involving channel proteins in biological processes. We used electrochemical potential to derive the Joule's law for an ion current through an ion transport protein in the presence of membrane potential, and we suggest that heat production and absorption can occur. Simulation of temperature distribution around a single channel protein with the Joule heating revealed that the temperature increase was as small as <10<sup>-3</sup> K, although an ensemble of channel proteins was suggested to exhibit a noticeable temperature increase. Thereby, we theoretically investigated the Joule heating of systems containing ensembles of channel proteins. Nerve is known to undergo rapid heat production followed by heat absorption during the action potential, and our simulation of Joule heating for a squid giant axon combined with the Hodgkin-Huxley model successfully reproduced the feature of the heat. Furthermore, we extended the theory of Joule heating to uncoupling protein 1 (UCP1), a solute carrier family transporter, which is important to the non-shivering thermogenesis in brown adipose tissue mitochondria (BATM). Our calculations showed that the Joule heat involving UCP1 was comparable to the literature calorimetry data of BATM. Joule heating of ion transport proteins is likely to be one of important mechanisms of cellular thermogenesis.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10728626/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75616610","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}
Pub Date : 2023-06-09eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0029
Hiroki Yasuga
Herein, I review our recent work toward developing methods for generating three-dimensional (3D) droplet arrays driven by capillarity. Microdroplet array-based systems are useful for bioassays and bioengineering because they require only small amounts of samples and reagents and provide the high throughput. Various methods have been developed for preparing droplet arrays, among which methods based on capillarity have attracted considerable attention owing to their simplicity. I and collaborators have developed such methods based on capillary flow, including a method for preparing droplet arrays via oil-water replacement. We recently proposed our own concept of "fluid-fluid interfacial energy driven 3D structure emergence in a micropillar scaffold (FLUID3EAMS)" and its application. FLUID3EAMS allows a 3D droplet (or hydrogel bead) array to be generated in a micropillar scaffold by passing a fluid-fluid interface through the scaffold. This approach is useful for applications requiring ordered or arrayed microdroplets in biosensors, biophysics, biology, and tissue engineering. This review is an extended version of the article "FLUID3EAMS: Fluid-Fluid Interfacial Energy Driven 3D Structure Emergence in a Micropillar Scaffold and Development in Bioengineering" published in Seibutsu Butsuri (vol. 62, p. 110-113, 2022).
在此,我将回顾我们最近在开发由毛细管驱动的三维液滴阵列方法方面所做的工作。基于微液滴阵列的系统对生物测定和生物工程非常有用,因为它们只需要少量样品和试剂,而且通量高。目前已开发出多种制备液滴阵列的方法,其中基于毛细管的方法因其简便性而备受关注。我和合作者已经开发了基于毛细管流动的此类方法,包括通过油水置换制备液滴阵列的方法。最近,我们提出了自己的 "微柱支架中流体-流体界面能驱动的三维结构出现(FLUID3EAMS)"概念及其应用。FLUID3EAMS 允许通过流体-流体界面穿过微柱支架,从而在微柱支架中生成三维液滴(或水凝胶珠)阵列。这种方法适用于生物传感器、生物物理学、生物学和组织工程学中需要有序或阵列微滴的应用。本综述是文章 "FLUID3EAMS:Seibutsu Butsuri》(第 62 卷,第 110-113 页,2022 年)上发表的 "Fluid-Fluid Interfacial Energy Driven 3D Structure Emergence in a Micropillar Scaffold and Development in Bioengineering "一文的扩展版。
{"title":"Methods to spontaneously generate three dimensionally arrayed microdroplets triggered by capillarity for bioassays and bioengineering.","authors":"Hiroki Yasuga","doi":"10.2142/biophysico.bppb-v20.0029","DOIUrl":"10.2142/biophysico.bppb-v20.0029","url":null,"abstract":"<p><p>Herein, I review our recent work toward developing methods for generating three-dimensional (3D) droplet arrays driven by capillarity. Microdroplet array-based systems are useful for bioassays and bioengineering because they require only small amounts of samples and reagents and provide the high throughput. Various methods have been developed for preparing droplet arrays, among which methods based on capillarity have attracted considerable attention owing to their simplicity. I and collaborators have developed such methods based on capillary flow, including a method for preparing droplet arrays via oil-water replacement. We recently proposed our own concept of \"fluid-fluid interfacial energy driven 3D structure emergence in a micropillar scaffold (FLUID3EAMS)\" and its application. FLUID3EAMS allows a 3D droplet (or hydrogel bead) array to be generated in a micropillar scaffold by passing a fluid-fluid interface through the scaffold. This approach is useful for applications requiring ordered or arrayed microdroplets in biosensors, biophysics, biology, and tissue engineering. This review is an extended version of the article \"FLUID3EAMS: Fluid-Fluid Interfacial Energy Driven 3D Structure Emergence in a Micropillar Scaffold and Development in Bioengineering\" published in Seibutsu Butsuri (vol. 62, p. 110-113, 2022).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81168039","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}
Pub Date : 2023-06-06eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0027
Yutaro Nagasawa, Hiromi H Ueda, Haruka Kawabata, Hideji Murakoshi
Optogenetic techniques offer a high spatiotemporal resolution to manipulate cellular activity. For instance, Channelrhodopsin-2 with global light illumination is the most widely used to control neuronal activity at the cellular level. However, the cellular scale is much larger than the diffraction limit of light (<1 μm) and does not fully exploit the features of the "high spatial resolution" of optogenetics. For instance, until recently, there were no optogenetic methods to induce synaptic plasticity at the level of single synapses. To address this, we developed an optogenetic tool named photoactivatable CaMKII (paCaMKII) by fusing a light-sensitive domain (LOV2) to CaMKIIα, which is a protein abundantly expressed in neurons of the cerebrum and hippocampus and essential for synaptic plasticity. Combining photoactivatable CaMKII with two-photon excitation, we successfully activated it in single spines, inducing synaptic plasticity (long-term potentiation) in hippocampal neurons. We refer to this method as "Local Optogenetics", which involves the local activation of molecules and measurement of cellular responses. In this review, we will discuss the characteristics of LOV2, the recent development of its derivatives, and the development and application of paCaMKII.
{"title":"LOV2-based photoactivatable CaMKII and its application to single synapses: Local Optogenetics.","authors":"Yutaro Nagasawa, Hiromi H Ueda, Haruka Kawabata, Hideji Murakoshi","doi":"10.2142/biophysico.bppb-v20.0027","DOIUrl":"10.2142/biophysico.bppb-v20.0027","url":null,"abstract":"<p><p>Optogenetic techniques offer a high spatiotemporal resolution to manipulate cellular activity. For instance, Channelrhodopsin-2 with global light illumination is the most widely used to control neuronal activity at the cellular level. However, the cellular scale is much larger than the diffraction limit of light (<1 μm) and does not fully exploit the features of the \"high spatial resolution\" of optogenetics. For instance, until recently, there were no optogenetic methods to induce synaptic plasticity at the level of single synapses. To address this, we developed an optogenetic tool named photoactivatable CaMKII (paCaMKII) by fusing a light-sensitive domain (LOV2) to CaMKIIα, which is a protein abundantly expressed in neurons of the cerebrum and hippocampus and essential for synaptic plasticity. Combining photoactivatable CaMKII with two-photon excitation, we successfully activated it in single spines, inducing synaptic plasticity (long-term potentiation) in hippocampal neurons. We refer to this method as \"Local Optogenetics\", which involves the local activation of molecules and measurement of cellular responses. In this review, we will discuss the characteristics of LOV2, the recent development of its derivatives, and the development and application of paCaMKII.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89954682","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}
Pub Date : 2023-06-02eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0026
Shunsuke Tagami
Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).
{"title":"Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life.","authors":"Shunsuke Tagami","doi":"10.2142/biophysico.bppb-v20.0026","DOIUrl":"10.2142/biophysico.bppb-v20.0026","url":null,"abstract":"<p><p>Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77411299","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}
Pub Date : 2023-05-24eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0023
Kenta Odagiri, Hiroshi Fujisaki, Hiroya Takada, Rei Ogawa
To computationally investigate the recent experimental finding such that extracellular ATP release caused by exogeneous mechanical forces promote wound closure, we introduce a mathematical model, the Cellular Potts Model (CPM), which is a popular discretized model on a lattice, where the movement of a "cell" is determined by a Monte Carlo procedure. In the experiment, it was observed that there is mechanosensitive ATP release from the leading cells facing the wound gap and the subsequent extracellular Ca2+ influx. To model these phenomena, the Reaction-Diffusion equations for extracellular ATP and intracellular Ca2+ concentrations are adopted and combined with CPM, where we also add a polarity term because the cell migration is enhanced in the case of ATP release. From the numerical simulations using this hybrid model, we discuss effects of the collective cell migration due to the ATP release and the Ca2+ influx caused by the mechanical forces and the consequent promotion of wound closure.
为了通过计算研究最近的实验发现,即外来机械力引起的细胞外 ATP 释放可促进伤口闭合,我们引入了一个数学模型--细胞波茨模型(CPM),它是一种流行的晶格离散化模型,"细胞 "的运动由蒙特卡洛程序决定。在实验中观察到,面向伤口间隙的前导细胞会释放机械敏感的 ATP,随后细胞外 Ca2+ 流入。为了模拟这些现象,我们采用了细胞外 ATP 和细胞内 Ca2+ 浓度的反应-扩散方程,并将其与 CPM 相结合,其中还加入了极性项,因为在 ATP 释放的情况下,细胞迁移会增强。通过使用该混合模型进行数值模拟,我们讨论了 ATP 释放导致的细胞集体迁移和机械力引起的 Ca2+ 流入的影响,以及由此产生的促进伤口闭合的作用。
{"title":"Mathematical model for promotion of wound closure with ATP release.","authors":"Kenta Odagiri, Hiroshi Fujisaki, Hiroya Takada, Rei Ogawa","doi":"10.2142/biophysico.bppb-v20.0023","DOIUrl":"10.2142/biophysico.bppb-v20.0023","url":null,"abstract":"<p><p>To computationally investigate the recent experimental finding such that extracellular ATP release caused by exogeneous mechanical forces promote wound closure, we introduce a mathematical model, the Cellular Potts Model (CPM), which is a popular discretized model on a lattice, where the movement of a \"cell\" is determined by a Monte Carlo procedure. In the experiment, it was observed that there is mechanosensitive ATP release from the leading cells facing the wound gap and the subsequent extracellular Ca<sup>2+</sup> influx. To model these phenomena, the Reaction-Diffusion equations for extracellular ATP and intracellular Ca<sup>2+</sup> concentrations are adopted and combined with CPM, where we also add a polarity term because the cell migration is enhanced in the case of ATP release. From the numerical simulations using this hybrid model, we discuss effects of the collective cell migration due to the ATP release and the Ca<sup>2+</sup> influx caused by the mechanical forces and the consequent promotion of wound closure.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941958/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91505270","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}