Protein functions associated with biological activity are precisely regulated by both tertiary structure and dynamic behavior. Thus, elucidating the high-resolution structures and quantitative information on in-solution dynamics is essential for understanding the molecular mechanisms. The main experimental approaches for determining tertiary structures include nuclear magnetic resonance (NMR), X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Among these procedures, recent remarkable advances in the hardware and analytical techniques of cryo-EM have increasingly determined novel atomic structures of macromolecules, especially those with large molecular weights and complex assemblies. In addition to these experimental approaches, deep learning techniques, such as AlphaFold 2, accurately predict structures from amino acid sequences, accelerating structural biology research. Meanwhile, the quantitative analyses of the protein dynamics are conducted using experimental approaches, such as NMR and hydrogen-deuterium mass spectrometry, and computational approaches, such as molecular dynamics (MD) simulations. Although these procedures can quantitatively explore dynamic behavior at high resolution, the fundamental difficulties, such as signal crowding and high computational cost, greatly hinder their application to large and complex biological macromolecules. In recent years, machine learning techniques, especially deep learning techniques, have been actively applied to structural data to identify features that are difficult for humans to recognize from big data. Here, we review our approach to accurately estimate dynamic properties associated with local fluctuations from three-dimensional cryo-EM density data using a deep learning technique combined with MD simulations.
{"title":"Quantitative analysis of protein dynamics using a deep learning technique combined with experimental cryo-EM density data and MD simulations.","authors":"Shigeyuki Matsumoto, Shoichi Ishida, Kei Terayama, Yasuhshi Okuno","doi":"10.2142/biophysico.bppb-v20.0022","DOIUrl":"10.2142/biophysico.bppb-v20.0022","url":null,"abstract":"<p><p>Protein functions associated with biological activity are precisely regulated by both tertiary structure and dynamic behavior. Thus, elucidating the high-resolution structures and quantitative information on in-solution dynamics is essential for understanding the molecular mechanisms. The main experimental approaches for determining tertiary structures include nuclear magnetic resonance (NMR), X-ray crystallography, and cryogenic electron microscopy (cryo-EM). Among these procedures, recent remarkable advances in the hardware and analytical techniques of cryo-EM have increasingly determined novel atomic structures of macromolecules, especially those with large molecular weights and complex assemblies. In addition to these experimental approaches, deep learning techniques, such as AlphaFold 2, accurately predict structures from amino acid sequences, accelerating structural biology research. Meanwhile, the quantitative analyses of the protein dynamics are conducted using experimental approaches, such as NMR and hydrogen-deuterium mass spectrometry, and computational approaches, such as molecular dynamics (MD) simulations. Although these procedures can quantitatively explore dynamic behavior at high resolution, the fundamental difficulties, such as signal crowding and high computational cost, greatly hinder their application to large and complex biological macromolecules. In recent years, machine learning techniques, especially deep learning techniques, have been actively applied to structural data to identify features that are difficult for humans to recognize from big data. Here, we review our approach to accurately estimate dynamic properties associated with local fluctuations from three-dimensional cryo-EM density data using a deep learning technique combined with MD simulations.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76574180","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 : 2023-05-10eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0021
Hiroshi Imamura
Small-angle scattering (SAS) is a powerful tool for the detailed structural analysis of objects at the nanometer scale. In contrast to techniques such as electron microscopy, SAS data are presented as reciprocal space information, which hinders the intuitive interpretation of SAS data. This study presents a workflow: (1) creating objects, (2) 3D scanning, (3) the representation of the object as point clouds on a laptop, (4) computation of a distance distribution function, and (5) computation of SAS, executed via the computer program Phone2SAS. This enables us to realize SAS and perform the interactive modeling of SAS of the object of interest. Because 3D scanning is easily accessible through smartphones, this workflow driven by Phone2SAS contributes to the widespread use of SAS. The application of Phone2SAS for the structural assignment of SAS to Y-shaped antibodies is reported in this study.
小角散射(SAS)是对纳米尺度物体进行详细结构分析的有力工具。与电子显微镜等技术相比,SAS 数据是以倒易空间信息的形式呈现的,这妨碍了对 SAS 数据的直观解读。本研究介绍了一个工作流程:(1) 创建对象;(2) 三维扫描;(3) 在笔记本电脑上将对象表示为点云;(4) 计算距离分布函数;(5) 通过计算机程序 Phone2SAS 计算 SAS。这样,我们就能实现 SAS 并对感兴趣的物体进行 SAS 互动建模。由于三维扫描很容易通过智能手机实现,由 Phone2SAS 驱动的这一工作流程有助于 SAS 的广泛应用。本研究报告了应用 Phone2SAS 对 Y 型抗体进行 SAS 结构赋值的情况。
{"title":"Phone2SAS: 3D scanning by smartphone aids the realization of small-angle scattering.","authors":"Hiroshi Imamura","doi":"10.2142/biophysico.bppb-v20.0021","DOIUrl":"10.2142/biophysico.bppb-v20.0021","url":null,"abstract":"<p><p>Small-angle scattering (SAS) is a powerful tool for the detailed structural analysis of objects at the nanometer scale. In contrast to techniques such as electron microscopy, SAS data are presented as reciprocal space information, which hinders the intuitive interpretation of SAS data. This study presents a workflow: (1) creating objects, (2) 3D scanning, (3) the representation of the object as point clouds on a laptop, (4) computation of a distance distribution function, and (5) computation of SAS, executed via the computer program Phone2SAS. This enables us to realize SAS and perform the interactive modeling of SAS of the object of interest. Because 3D scanning is easily accessible through smartphones, this workflow driven by Phone2SAS contributes to the widespread use of SAS. The application of Phone2SAS for the structural assignment of SAS to Y-shaped antibodies is reported in this study.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941956/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81270883","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 : 2023-04-27eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0020
Shingo Wakao, Noriko Saitoh, Akinori Awazu
Nuclear speckles are nuclear bodies consisting of populations of small and irregularly shaped droplet-like molecular condensates that contain various splicing factors. Recent experiments have revealed the following structural features of nuclear speckles: (I) Each molecular condensate contains SON and SRRM2 proteins, and MALAT1 non-coding RNA surrounds these condensates; (II) During normal interphase of the cell cycle in multicellular organisms, these condensates are broadly distributed throughout the nucleus. In contrast, when cell transcription is suppressed, the condensates fuse and form strongly condensed spherical droplets; (III) SON is dispersed spatially in MALAT1 knocked-down cells and MALAT1 is dispersed in SON knocked-down cells because of the collapse of the nuclear speckles. However, the detailed interactions among the molecules that are mechanistically responsible for the structural variation remain unknown. In this study, a coarse-grained molecular dynamics model of the nuclear speckle was developed by considering the dynamics of SON, SRRM2, MALAT1, and pre-mRNA as representative components of the condensates. The simulations reproduced the structural changes, which were used to predict the interaction network among the representative components of the condensates.
核斑点是由形状不规则的小液滴状分子凝聚体组成的核体,其中含有各种剪接因子。最近的实验揭示了核斑点的以下结构特征:(I)每个分子凝聚体都含有 SON 和 SRRM2 蛋白,MALAT1 非编码 RNA 环绕在这些凝聚体周围;(II)在多细胞生物细胞周期的正常间期,这些凝聚体广泛分布在整个细胞核中。相反,当细胞转录受到抑制时,凝聚体融合并形成强烈凝聚的球形液滴;(III) 在 MALAT1 基因敲除的细胞中,SON 在空间上是分散的,而在 SON 基因敲除的细胞中,MALAT1 是分散的,因为核斑点塌陷了。然而,从机理上导致结构变化的分子间相互作用的细节仍然未知。在本研究中,通过考虑 SON、SRRM2、MALAT1 和 pre-mRNA 作为凝集物代表性成分的动力学,建立了核斑点的粗粒度分子动力学模型。模拟再现了结构的变化,并以此预测凝集物代表性成分之间的相互作用网络。
{"title":"Mathematical model of structural changes in nuclear speckle.","authors":"Shingo Wakao, Noriko Saitoh, Akinori Awazu","doi":"10.2142/biophysico.bppb-v20.0020","DOIUrl":"10.2142/biophysico.bppb-v20.0020","url":null,"abstract":"<p><p>Nuclear speckles are nuclear bodies consisting of populations of small and irregularly shaped droplet-like molecular condensates that contain various splicing factors. Recent experiments have revealed the following structural features of nuclear speckles: (I) Each molecular condensate contains SON and SRRM2 proteins, and <i>MALAT</i>1 non-coding RNA surrounds these condensates; (II) During normal interphase of the cell cycle in multicellular organisms, these condensates are broadly distributed throughout the nucleus. In contrast, when cell transcription is suppressed, the condensates fuse and form strongly condensed spherical droplets; (III) SON is dispersed spatially in <i>MALAT1</i> knocked-down cells and <i>MALAT1</i> is dispersed in SON knocked-down cells because of the collapse of the nuclear speckles. However, the detailed interactions among the molecules that are mechanistically responsible for the structural variation remain unknown. In this study, a coarse-grained molecular dynamics model of the nuclear speckle was developed by considering the dynamics of SON, SRRM2, <i>MALAT1</i>, and pre-mRNA as representative components of the condensates. The simulations reproduced the structural changes, which were used to predict the interaction network among the representative components of the condensates.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76513698","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 : 2023-04-21eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0019
Atsushi Mochizuki
Progress of molecular biology resulted in the accumulation of information on biomolecular interactions, which are complex enough to be termed as networks. Dynamical behavior generated by complex network systems is considered to be the origin of the biological functions. One of the largest missions in modern life science is to obtain logical understanding for the dynamics of complex systems based on experimentally identified networks. However, a network does not provide sufficient information to specify dynamics explicitly, i.e. it lacks information of mathematical formulae of functions or parameter values. One has to develop mathematical models under assumptions of functions and parameter values to know the detail of dynamics of network systems. In this review, on the other hand, we introduce our own mathematical theory to understand the behavior of biological systems from the information of regulatory networks alone. Using the theory, important aspects of dynamical properties can be extracted from networks. Namely, key factors for observing/controlling the whole dynamical system are determined from network structure alone. We also show an application of the theory to a real biological system, a gene regulatory network for cell-fate specification in ascidian. We demonstrate that the system was completely controllable by experimental manipulations of the key factors identified by the theory from the information of network alone. This review article is an extended version of the Japanese article, Controlling Cell-Fate Specification System Based on a Mathematical Theory of Network Dynamics, published in SEIBUTSU BUTSURI Vol. 60, p. 349-351 (2020).
分子生物学的发展积累了大量有关生物分子相互作用的信息,这些相互作用非常复杂,可以被称为网络。复杂网络系统产生的动态行为被认为是生物功能的起源。现代生命科学的最大使命之一就是根据实验确定的网络,获得对复杂系统动态的逻辑理解。然而,网络并不能提供足够的信息来明确说明动力学,即缺乏函数或参数值的数学公式信息。人们必须在函数和参数值的假设条件下建立数学模型,才能了解网络系统动力学的细节。而在这篇综述中,我们提出了自己的数学理论,仅从调控网络的信息来理解生物系统的行为。利用该理论,可以从网络中提取动态特性的重要方面。也就是说,仅从网络结构就能确定观察/控制整个动态系统的关键因素。我们还展示了该理论在一个真实生物系统中的应用,该系统是腹水动物细胞命运规范的基因调控网络。我们证明,仅从网络信息出发,通过实验操作该理论确定的关键因素,就能完全控制该系统。这篇综述文章是日文文章《基于网络动力学数学理论的细胞命运规格系统控制》(Controlling Cell-Fate Specification System Based on a Mathematical Theory of Network Dynamics)的扩展版,发表于《科学文摘》(SEIBUTSU BUTSURI)第 60 卷第 349-351 页(2020 年)。
{"title":"Controlling complex dynamical systems based on the structure of the networks.","authors":"Atsushi Mochizuki","doi":"10.2142/biophysico.bppb-v20.0019","DOIUrl":"10.2142/biophysico.bppb-v20.0019","url":null,"abstract":"<p><p>Progress of molecular biology resulted in the accumulation of information on biomolecular interactions, which are complex enough to be termed as networks. Dynamical behavior generated by complex network systems is considered to be the origin of the biological functions. One of the largest missions in modern life science is to obtain logical understanding for the dynamics of complex systems based on experimentally identified networks. However, a network does not provide sufficient information to specify dynamics explicitly, i.e. it lacks information of mathematical formulae of functions or parameter values. One has to develop mathematical models under assumptions of functions and parameter values to know the detail of dynamics of network systems. In this review, on the other hand, we introduce our own mathematical theory to understand the behavior of biological systems from the information of regulatory networks alone. Using the theory, important aspects of dynamical properties can be extracted from networks. Namely, key factors for observing/controlling the whole dynamical system are determined from network structure alone. We also show an application of the theory to a real biological system, a gene regulatory network for cell-fate specification in ascidian. We demonstrate that the system was completely controllable by experimental manipulations of the key factors identified by the theory from the information of network alone. This review article is an extended version of the Japanese article, Controlling Cell-Fate Specification System Based on a Mathematical Theory of Network Dynamics, published in SEIBUTSU BUTSURI Vol. 60, p. 349-351 (2020).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83572043","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}
Mesenchymal stem cells (MSCs) have the potential for self-renewal and multipotency to differentiate into various lineages. Thus, they are of great interest in regenerative medicine as a cell source for tissue engineering. Substrate stiffness is one of the most extensively studied exogenous physical factors; however, consistent results have not always been reported for controlling MSCs. Conventionally used stiff culture substrates, such as tissue-culture polystyrene and glass, enhance nuclear localization of a mechanotransducer YAP and a pre-osteogenic transcription factor RUNX2, and bias MSCs towards the osteogenic lineage, even without osteogenic-inducing soluble factors. The mechanosensitive nature and intrinsic heterogeneity present challenges for obtaining reproducible results. This review summarizes the heterogeneity in human MSC response, specifically, nuclear/cytoplasmic localization changes in the mechanotransducer yes-associated protein (YAP) and the osteogenic transcription factor RUNX2, in response to substrate stiffness. In addition, a perspective on the intracellular factors attributed to response heterogeneity is discussed. The optimal range of stiffness parameters, Young's modulus, for MSC expansion culture to suppress osteogenic differentiation bias through the suppression of YAP and RUNX2 nuclear localization, and cell cycle progression is likely to be surprisingly narrow for a cell population from an identical donor and vary among cell populations from different donors. We believe that characterization of the heterogeneity of MSCs and understanding their biological meaning is an exciting research direction to establish guidelines for the design of culture substrates for the sophisticated control of MSC properties.
{"title":"Guideline for design of substrate stiffness for mesenchymal stem cell culture based on heterogeneity of YAP and RUNX2 responses.","authors":"Hiromi Miyoshi, Masashi Yamazaki, Hiromichi Fujie, Satoru Kidoaki","doi":"10.2142/biophysico.bppb-v20.0018","DOIUrl":"10.2142/biophysico.bppb-v20.0018","url":null,"abstract":"<p><p>Mesenchymal stem cells (MSCs) have the potential for self-renewal and multipotency to differentiate into various lineages. Thus, they are of great interest in regenerative medicine as a cell source for tissue engineering. Substrate stiffness is one of the most extensively studied exogenous physical factors; however, consistent results have not always been reported for controlling MSCs. Conventionally used stiff culture substrates, such as tissue-culture polystyrene and glass, enhance nuclear localization of a mechanotransducer YAP and a pre-osteogenic transcription factor RUNX2, and bias MSCs towards the osteogenic lineage, even without osteogenic-inducing soluble factors. The mechanosensitive nature and intrinsic heterogeneity present challenges for obtaining reproducible results. This review summarizes the heterogeneity in human MSC response, specifically, nuclear/cytoplasmic localization changes in the mechanotransducer yes-associated protein (YAP) and the osteogenic transcription factor RUNX2, in response to substrate stiffness. In addition, a perspective on the intracellular factors attributed to response heterogeneity is discussed. The optimal range of stiffness parameters, Young's modulus, for MSC expansion culture to suppress osteogenic differentiation bias through the suppression of YAP and RUNX2 nuclear localization, and cell cycle progression is likely to be surprisingly narrow for a cell population from an identical donor and vary among cell populations from different donors. We believe that characterization of the heterogeneity of MSCs and understanding their biological meaning is an exciting research direction to establish guidelines for the design of culture substrates for the sophisticated control of MSC properties.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941962/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82322641","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}
Cooking with fire produces foods containing carbohydrates that are not naturally occurring, such as α-d-fructofuranoside found in caramel. Each of the hundreds of compounds produced by caramelization reactions is considered to possess its own characteristics. Various studies from the viewpoints of biology and biochemistry have been conducted to elucidate some of the scientific characteristics. Here, we review the composition of caramelized sugars and then describe the enzymatic studies that have been conducted and the physiological functions of the caramelized sugar components that have been elucidated. In particular, we recently identified a glycoside hydrolase (GH), GH172 difructose dianhydride I synthase/hydrolase (αFFase1), from oral and intestinal bacteria, which is implicated in the degradation of oligosaccharides in caramel. The structural basis of αFFase1 and its ligands provided many insights. This discovery opened the door to several research fields, including the structural and phylogenetic relationship between the GH172 family enzymes and viral capsid proteins and the degradation of cell membrane glycans of acid-fast bacteria by some αFFase1 homologs. This review article is an extended version of the Japanese article, Identification and Structural Basis of an Enzyme Degrading Oligosaccharides in Caramel, published in SEIBUTSU BUTSURI Vol. 62, p. 184-186 (2022).
用火烹饪会产生含有非天然碳水化合物的食物,例如焦糖中的α-d-呋喃果糖苷。焦糖化反应产生的数百种化合物被认为各具特色。为了阐明其中的一些科学特征,人们从生物学和生物化学的角度进行了各种研究。在此,我们回顾了焦糖的组成,然后介绍了已开展的酶学研究和已阐明的焦糖成分的生理功能。特别是,我们最近从口腔和肠道细菌中发现了一种糖苷水解酶(GH),即 GH172 二果糖二酐 I 合成酶/水解酶(αFFase1),它与焦糖中低聚糖的降解有关。αFFase1及其配体的结构基础提供了许多见解。这一发现为多个研究领域打开了大门,包括 GH172 家族酶与病毒帽蛋白之间的结构和系统发育关系,以及一些 αFFase1 同源物对酸性无菌细菌细胞膜糖的降解作用。本综述文章是日文文章《Identification and Structural Basis of an Enzyme Degrading Oligosaccharides in Caramel》(焦糖低聚糖降解酶的鉴定与结构基础)的扩展版,发表于《科学文摘》(SEIBUTSU BUTSURI)第 62 卷第 184-186 页(2022 年)。
{"title":"Identification and structural basis of an enzyme that degrades oligosaccharides in caramel.","authors":"Toma Kashima, Akihiro Ishiwata, Kiyotaka Fujita, Shinya Fushinobu","doi":"10.2142/biophysico.bppb-v20.0017","DOIUrl":"10.2142/biophysico.bppb-v20.0017","url":null,"abstract":"<p><p>Cooking with fire produces foods containing carbohydrates that are not naturally occurring, such as α-d-fructofuranoside found in caramel. Each of the hundreds of compounds produced by caramelization reactions is considered to possess its own characteristics. Various studies from the viewpoints of biology and biochemistry have been conducted to elucidate some of the scientific characteristics. Here, we review the composition of caramelized sugars and then describe the enzymatic studies that have been conducted and the physiological functions of the caramelized sugar components that have been elucidated. In particular, we recently identified a glycoside hydrolase (GH), GH172 difructose dianhydride I synthase/hydrolase (αFFase1), from oral and intestinal bacteria, which is implicated in the degradation of oligosaccharides in caramel. The structural basis of αFFase1 and its ligands provided many insights. This discovery opened the door to several research fields, including the structural and phylogenetic relationship between the GH172 family enzymes and viral capsid proteins and the degradation of cell membrane glycans of acid-fast bacteria by some αFFase1 homologs. This review article is an extended version of the Japanese article, Identification and Structural Basis of an Enzyme Degrading Oligosaccharides in Caramel, published in SEIBUTSU BUTSURI Vol. 62, p. 184-186 (2022).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76796845","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 : 2023-03-25eCollection Date: 2023-01-01DOI: 10.2142/biophysico.bppb-v20.0016
Tatsuki Negami, Tohru Terada
The evaluation of the inhibitory activities of drugs on multiple cardiac ion channels is required for the accurate assessment of proarrhythmic risks. Moreover, the in silico prediction of such inhibitory activities of drugs on cardiac channels can improve the efficiency of the drug-development process. Here, we performed molecular docking simulations to predict the complex structures of 25 reference drugs that were proposed by the Comprehensive in vitro Proarrhythmia Assay consortium using two cardiac ion channels, the human ether-a-go-go-related gene (hERG) potassium channel and human NaV1.5 (hNaV1.5) sodium channel, with experimentally available structures. The absolute binding free energy (ΔGbind) values of the predicted structures were calculated by a molecular dynamics-based method and compared with the experimental half-maximal inhibitory concentration (IC50) data. Furthermore, the regression analysis between the calculated values and negative of the common logarithm of the experimental IC50 values (pIC50) revealed that the calculated values of four and ten drugs deviated significantly from the regression lines of the hERG and hNaV1.5 channels, respectively. We reconsidered the docking poses and protonation states of the drugs based on the experimental data and recalculated their ΔGbind values. Finally, the calculated ΔGbind values of 24 and 19 drugs correlated with their experimental pIC50 values (coefficients of determination=0.791 and 0.613 for the hERG and hNaV1.5 channels, respectively). Thus, the regression analysis between the calculated ΔGbind and experimental IC50 data ensured the realization of an increased number of reliable complex structures.
{"title":"Calculations of the binding free energies of the Comprehensive <i>in vitro</i> Proarrhythmia Assay (CiPA) reference drugs to cardiac ion channels.","authors":"Tatsuki Negami, Tohru Terada","doi":"10.2142/biophysico.bppb-v20.0016","DOIUrl":"10.2142/biophysico.bppb-v20.0016","url":null,"abstract":"<p><p>The evaluation of the inhibitory activities of drugs on multiple cardiac ion channels is required for the accurate assessment of proarrhythmic risks. Moreover, the <i>in silico</i> prediction of such inhibitory activities of drugs on cardiac channels can improve the efficiency of the drug-development process. Here, we performed molecular docking simulations to predict the complex structures of 25 reference drugs that were proposed by the Comprehensive <i>in vitro</i> Proarrhythmia Assay consortium using two cardiac ion channels, the human ether-a-go-go-related gene (hERG) potassium channel and human Na<sub>V</sub>1.5 (hNa<sub>V</sub>1.5) sodium channel, with experimentally available structures. The absolute binding free energy (Δ<i>G</i><sub>bind</sub>) values of the predicted structures were calculated by a molecular dynamics-based method and compared with the experimental half-maximal inhibitory concentration (IC<sub>50</sub>) data. Furthermore, the regression analysis between the calculated values and negative of the common logarithm of the experimental IC<sub>50</sub> values (pIC<sub>50</sub>) revealed that the calculated values of four and ten drugs deviated significantly from the regression lines of the hERG and hNa<sub>V</sub>1.5 channels, respectively. We reconsidered the docking poses and protonation states of the drugs based on the experimental data and recalculated their Δ<i>G</i><sub>bind</sub> values. Finally, the calculated Δ<i>G</i><sub>bind</sub> values of 24 and 19 drugs correlated with their experimental pIC<sub>50</sub> values (coefficients of determination=0.791 and 0.613 for the hERG and hNa<sub>V</sub>1.5 channels, respectively). Thus, the regression analysis between the calculated Δ<i>G</i><sub>bind</sub> and experimental IC<sub>50</sub> data ensured the realization of an increased number of reliable complex structures.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941965/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83917689","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 : 2023-03-08eCollection Date: 2023-03-21DOI: 10.2142/biophysico.bppb-v20.s023
María Del Carmen Marín, Alexander L Jaffe, Patrick T West, Masae Konno, Jillian F Banfield, Keiichi Inoue
Microbial rhodopsins are photoreceptive transmembrane proteins that transport ions or regulate other intracellular biological processes. Recent genomic and metagenomic analyses found many microbial rhodopsins with unique sequences distinct from known ones. Functional characterization of these new types of microbial rhodopsins is expected to expand our understanding of their physiological roles. Here, we found microbial rhodopsins having a DSE motif in the third transmembrane helix from members of the Actinobacteria. Although the expressed proteins exhibited blue-green light absorption, either no or extremely small outward H+ pump activity was observed. The turnover rate of the photocycle reaction of the purified proteins was extremely slow compared to typical H+ pumps, suggesting these rhodopsins would work as photosensors or H+ pumps whose activities are enhanced by an unknown regulatory system in the hosts. The discovery of this rhodopsin group with the unique motif and functionality expands our understanding of the biological role of microbial rhodopsins.
{"title":"Biophysical characterization of microbial rhodopsins with DSE motif.","authors":"María Del Carmen Marín, Alexander L Jaffe, Patrick T West, Masae Konno, Jillian F Banfield, Keiichi Inoue","doi":"10.2142/biophysico.bppb-v20.s023","DOIUrl":"10.2142/biophysico.bppb-v20.s023","url":null,"abstract":"<p><p>Microbial rhodopsins are photoreceptive transmembrane proteins that transport ions or regulate other intracellular biological processes. Recent genomic and metagenomic analyses found many microbial rhodopsins with unique sequences distinct from known ones. Functional characterization of these new types of microbial rhodopsins is expected to expand our understanding of their physiological roles. Here, we found microbial rhodopsins having a DSE motif in the third transmembrane helix from members of the Actinobacteria. Although the expressed proteins exhibited blue-green light absorption, either no or extremely small outward H<sup>+</sup> pump activity was observed. The turnover rate of the photocycle reaction of the purified proteins was extremely slow compared to typical H<sup>+</sup> pumps, suggesting these rhodopsins would work as photosensors or H<sup>+</sup> pumps whose activities are enhanced by an unknown regulatory system in the hosts. The discovery of this rhodopsin group with the unique motif and functionality expands our understanding of the biological role of microbial rhodopsins.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10865882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82939535","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 : 2023-03-07eCollection Date: 2023-03-21DOI: 10.2142/biophysico.bppb-v20.s022
Takayuki Uchihashi, Hideki Kandori
{"title":"Introduction of Session 2, \"Advanced methods for retinal proteins\".","authors":"Takayuki Uchihashi, Hideki Kandori","doi":"10.2142/biophysico.bppb-v20.s022","DOIUrl":"10.2142/biophysico.bppb-v20.s022","url":null,"abstract":"","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10865833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84443683","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 : 2023-03-04eCollection Date: 2023-03-21DOI: 10.2142/biophysico.bppb-v20.s021
Yuki Sudo
{"title":"Introduction of Session 1, \"Photochemistry of retinal proteins\".","authors":"Yuki Sudo","doi":"10.2142/biophysico.bppb-v20.s021","DOIUrl":"10.2142/biophysico.bppb-v20.s021","url":null,"abstract":"","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10865872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88559469","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}