Pub Date : 2022-07-28eCollection Date: 2022-01-01DOI: 10.2142/biophysico.bppb-v19.0025
Ha T T Duong, Hirofumi Suzuki, Saki Katagiri, Mayu Shibata, Misae Arai, Kei Yura
Sequencing of individual human genomes enables studying relationship among nucleotide variations, amino acid substitutions, effect on protein structures and diseases. Many studies have found general tendencies, for instance, that pathogenic variations tend to be found in the buried regions of the protein structures, that benign variations tend to be found on the surface of the proteins, and that variations on evolutionary conserved residues tend to be pathogenic. These tendencies were deduced from globular proteins with standard evolutionary changes in amino acid sequences. In this study, we investigated the variation distribution on actin, one of the highly conserved proteins. Many nucleotide variations and three-dimensional structures of actin have been registered in databases. By combining those data, we found that variations buried inside the protein were rather benign and variations on the surface of the protein were pathogenic. This idiosyncratic distribution of the variation impact is likely ascribed to the extensive use of the surface of the protein for protein-protein interactions in actin.
{"title":"Computational study of the impact of nucleotide variations on highly conserved proteins: In the case of actin.","authors":"Ha T T Duong, Hirofumi Suzuki, Saki Katagiri, Mayu Shibata, Misae Arai, Kei Yura","doi":"10.2142/biophysico.bppb-v19.0025","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0025","url":null,"abstract":"<p><p>Sequencing of individual human genomes enables studying relationship among nucleotide variations, amino acid substitutions, effect on protein structures and diseases. Many studies have found general tendencies, for instance, that pathogenic variations tend to be found in the buried regions of the protein structures, that benign variations tend to be found on the surface of the proteins, and that variations on evolutionary conserved residues tend to be pathogenic. These tendencies were deduced from globular proteins with standard evolutionary changes in amino acid sequences. In this study, we investigated the variation distribution on actin, one of the highly conserved proteins. Many nucleotide variations and three-dimensional structures of actin have been registered in databases. By combining those data, we found that variations buried inside the protein were rather benign and variations on the surface of the protein were pathogenic. This idiosyncratic distribution of the variation impact is likely ascribed to the extensive use of the surface of the protein for protein-protein interactions in actin.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/3a/ef/19_e190025.PMC9465404.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33484500","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 : 2022-07-27eCollection Date: 2022-01-01DOI: 10.2142/biophysico.bppb-v19.0024
Takahiro Muraoka, Tomohide Saio, Masaki Okumura
Brain science has made remarkable progress over the past decade. Unveiling the development of neural tissue, understanding neural circuits, and elucidation of signal transduction processes at the molecular level have been carried out. Not only neuroscience but also mechanistic biochemical and biophysical studies on neural diseases are progressing. Neurodegenerative diseases are one representative example, and the structure and dynamics of the causative proteins are being investigated at the molecular level. Integrating discussions between biophysical neuroscience and biochemical research of the brain should address important unexplored issues such as the molecular- and cellular-scale elucidation
{"title":"Biophysical elucidation of neural network and chemical regeneration of neural tissue.","authors":"Takahiro Muraoka, Tomohide Saio, Masaki Okumura","doi":"10.2142/biophysico.bppb-v19.0024","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0024","url":null,"abstract":"Brain science has made remarkable progress over the past decade. Unveiling the development of neural tissue, understanding neural circuits, and elucidation of signal transduction processes at the molecular level have been carried out. Not only neuroscience but also mechanistic biochemical and biophysical studies on neural diseases are progressing. Neurodegenerative diseases are one representative example, and the structure and dynamics of the causative proteins are being investigated at the molecular level. Integrating discussions between biophysical neuroscience and biochemical research of the brain should address important unexplored issues such as the molecular- and cellular-scale elucidation","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/52/ee/19_e190024.PMC9402262.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33447897","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 : 2022-07-14eCollection Date: 2022-01-01DOI: 10.2142/biophysico.bppb-v19.0023
Matsuyuki Shirota, Kengo Kinoshita
Changes in the amino acid sequences of proteins may cause changes in molecular function, resulting in phenotypic variations among species and individuals. Such amino acid changes occur naturally due to mutations in the genome sequence of an organism and can be inherited. Recent advances in genome sequencing technologies have enabled us to sequence the genomes of millions of humans, as performed by various large-scale projects such as the Genome Aggregation Database (gnomAD) [1], Trans-Omics for Precision Medicine (TOPMed) [2], and UK Biobank [3]. Further, it has enabled us to accumulate known pathogenic variants in databases such as ClinVar [4], Human Genome Mutation Database (HGMD) [5] and Catalogue of Somatic Mutations in Cancer (COSMIC) [6]. These studies
{"title":"Current status and future perspectives of the evaluation of missense variants by using three-dimensional structures of proteins.","authors":"Matsuyuki Shirota, Kengo Kinoshita","doi":"10.2142/biophysico.bppb-v19.0023","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0023","url":null,"abstract":"Changes in the amino acid sequences of proteins may cause changes in molecular function, resulting in phenotypic variations among species and individuals. Such amino acid changes occur naturally due to mutations in the genome sequence of an organism and can be inherited. Recent advances in genome sequencing technologies have enabled us to sequence the genomes of millions of humans, as performed by various large-scale projects such as the Genome Aggregation Database (gnomAD) [1], Trans-Omics for Precision Medicine (TOPMed) [2], and UK Biobank [3]. Further, it has enabled us to accumulate known pathogenic variants in databases such as ClinVar [4], Human Genome Mutation Database (HGMD) [5] and Catalogue of Somatic Mutations in Cancer (COSMIC) [6]. These studies","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/38/5f/19_e190023.PMC9402263.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33447896","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 : 2022-06-07eCollection Date: 2022-01-01DOI: 10.2142/biophysico.bppb-v19.0022
Yuhei Araiso, Toshiya Endo
Most mitochondrial proteins are synthesized as precursor proteins (preproteins) in the cytosol and imported into mitochondria. The translocator of the outer membrane (TOM) complex functions as a main entry gate for the import of mitochondrial proteins. The TOM complex is a multi-subunit membrane protein complex composed of a β-barrel channel Tom40 and six single-pass membrane proteins. Recent cryo-EM studies have revealed high-resolution structures of the yeast and human TOM complexes, which enabled us to discuss the mechanism of protein import at an amino-acid residue level. The cryo-EM structures show that two Tom40 β-barrels are surrounded by two sets of small Tom subunits to form a dimeric structure. The intermembrane space (IMS) domains of Tom40, Tom22, and Tom7 form a binding site for presequence-containing preproteins in the middle of the dimer to achieve their efficient transfer of to the downstream translocase, the TIM23 complex. The N-terminal segment of Tom40 spans the channel from the cytosol to the IMS to interact with Tom5 at the periphery of the dimer, where downstream components of presequence-lacking preproteins are recruited. Structure-based biochemical analyses together with crosslinking experiments revealed that each Tom40 channel possesses two distinct paths and exit sites for protein translocation of different sets of mitochondrial preproteins. Here we summarize the current knowledge on the structural features, protein translocation mechanisms, and remaining questions for the TOM complexes, with particular emphasis on their determined cryo-EM structures. This article is an extended version of the Japanese article, Structural basis for protein translocation by the translocase of the outer mitochondrial membrane, published in SEIBUTSU BUTSURI Vol. 60, p. 280-283 (2020).
大多数线粒体蛋白在细胞质中作为前体蛋白(preprotein)合成并导入线粒体。外膜转运子(TOM)复合物是线粒体蛋白输入的主要入口。TOM复合物是一种多亚基膜蛋白复合物,由一个β桶通道Tom40和6个单通膜蛋白组成。最近的冷冻电镜研究揭示了酵母和人类TOM复合物的高分辨率结构,这使我们能够在氨基酸残留水平上讨论蛋白质进口的机制。低温电镜结构表明,两个Tom40 β-桶被两组小的Tom亚基包围,形成二聚体结构。Tom40、Tom22和Tom7的膜间空间(IMS)结构域在二聚体中间形成含有序列的前蛋白的结合位点,以实现它们向下游转位酶TIM23复合物的有效转移。Tom40的n端片段跨越从细胞质到IMS的通道,在二聚体的外围与Tom5相互作用,在那里招募了缺乏序列的前蛋白的下游组分。基于结构的生化分析和交联实验表明,每个Tom40通道具有不同线粒体前蛋白组蛋白质易位的两个不同路径和出口位点。在这里,我们总结了目前对TOM复合物的结构特征、蛋白质易位机制和遗留问题的了解,特别强调了它们确定的低温电镜结构。本文是日本文章《the translocase for protein translocation by the outer mitochondrial membrane的结构基础》的扩展版,发表于SEIBUTSU BUTSURI Vol. 60, p. 280-283(2020)。
{"title":"Structural overview of the translocase of the mitochondrial outer membrane complex.","authors":"Yuhei Araiso, Toshiya Endo","doi":"10.2142/biophysico.bppb-v19.0022","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0022","url":null,"abstract":"<p><p>Most mitochondrial proteins are synthesized as precursor proteins (preproteins) in the cytosol and imported into mitochondria. The translocator of the outer membrane (TOM) complex functions as a main entry gate for the import of mitochondrial proteins. The TOM complex is a multi-subunit membrane protein complex composed of a β-barrel channel Tom40 and six single-pass membrane proteins. Recent cryo-EM studies have revealed high-resolution structures of the yeast and human TOM complexes, which enabled us to discuss the mechanism of protein import at an amino-acid residue level. The cryo-EM structures show that two Tom40 β-barrels are surrounded by two sets of small Tom subunits to form a dimeric structure. The intermembrane space (IMS) domains of Tom40, Tom22, and Tom7 form a binding site for presequence-containing preproteins in the middle of the dimer to achieve their efficient transfer of to the downstream translocase, the TIM23 complex. The N-terminal segment of Tom40 spans the channel from the cytosol to the IMS to interact with Tom5 at the periphery of the dimer, where downstream components of presequence-lacking preproteins are recruited. Structure-based biochemical analyses together with crosslinking experiments revealed that each Tom40 channel possesses two distinct paths and exit sites for protein translocation of different sets of mitochondrial preproteins. Here we summarize the current knowledge on the structural features, protein translocation mechanisms, and remaining questions for the TOM complexes, with particular emphasis on their determined cryo-EM structures. This article is an extended version of the Japanese article, Structural basis for protein translocation by the translocase of the outer mitochondrial membrane, published in SEIBUTSU BUTSURI Vol. 60, p. 280-283 (2020).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/be/b1/19_e190022.PMC9260164.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40621546","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 : 2022-06-01eCollection Date: 2022-01-01DOI: 10.2142/biophysico.bppb-v19.0021
Keisuke Fujiyama, Tomoya Hino, Shingo Nagano
Steroid hormones modulate numerous physiological processes in various higher organisms. Research on the physiology, biosynthesis, and metabolic degradation of steroid hormones is crucial for developing drugs, agrochemicals, and anthelmintics. Most steroid hormone biosynthetic pathways, excluding those in insects, have been elucidated, and the roles of several cytochrome P450s (CYPs, P450s), heme (iron protoporphyrin IX)-containing monooxygenases, have been identified. Specifically, P450s of the animal steroid hormone biosynthetic pathways and their three dimensional structures and reaction mechanisms have been extensively studied; however, the mechanisms of several uncommon P450 reactions involved in animal steroid hormone biosynthesis and structures and reaction mechanisms of various P450s involved in plant and insect steroid hormone biosynthesis remain unclear. Recently, we determined the crystal structure of P450 responsible for the first and rate-determining step in brassinosteroids biosynthesis and clarified the regio- and stereo-selectivity in the hydroxylation reaction mechanism. In this review, we have outlined the general catalytic cycle, reaction mechanism, and structure of P450s. Additionally, we have described the recent advances in research on the reaction mechanisms of steroid hormone biosynthesis-related P450s, some of which catalyze unusual P450 reactions including C-C bond cleavage reactions by utilizing either a heme-peroxo anion species or compound I as an active oxidizing species. This review article is an extended version of the Japanese article, Structure and mechanism of cytochrome P450s involved in steroid hormone biosynthesis, published in SEIBUTSU BUTSURI Vol. 61, p. 189-191 (2021).
类固醇激素在各种高等生物中调节许多生理过程。研究类固醇激素的生理、生物合成和代谢降解对开发药物、农用化学品和驱虫药至关重要。除昆虫外,大多数类固醇激素的生物合成途径已经被阐明,并且已经确定了几种细胞色素p450 (CYPs, p450),含血红素(铁原卟啉IX)的单加氧酶的作用。其中,动物类固醇激素生物合成途径的p450及其三维结构和反应机制得到了广泛的研究;然而,动物类固醇激素生物合成中几种不常见的P450反应的机制以及植物和昆虫类固醇激素生物合成中各种P450的结构和反应机制尚不清楚。最近,我们确定了油菜素内酯生物合成第一步和速率决定步骤P450的晶体结构,并阐明了羟基化反应机制中的区域选择性和立体选择性。本文综述了p450的催化循环、反应机理和结构。此外,我们还介绍了近年来类固醇激素生物合成相关的P450反应机制的研究进展,其中一些P450通过利用血红素-过氧阴离子或化合物I作为活性氧化物质来催化罕见的P450反应,包括C-C键裂解反应。这篇综述文章是日本文章《细胞色素p450参与类固醇激素生物合成的结构和机制》的扩展版,发表于SEIBUTSU BUTSURI Vol. 61, p. 189-191(2021)。
{"title":"Diverse reactions catalyzed by cytochrome P450 and biosynthesis of steroid hormone.","authors":"Keisuke Fujiyama, Tomoya Hino, Shingo Nagano","doi":"10.2142/biophysico.bppb-v19.0021","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0021","url":null,"abstract":"<p><p>Steroid hormones modulate numerous physiological processes in various higher organisms. Research on the physiology, biosynthesis, and metabolic degradation of steroid hormones is crucial for developing drugs, agrochemicals, and anthelmintics. Most steroid hormone biosynthetic pathways, excluding those in insects, have been elucidated, and the roles of several cytochrome P450s (CYPs, P450s), heme (iron protoporphyrin IX)-containing monooxygenases, have been identified. Specifically, P450s of the animal steroid hormone biosynthetic pathways and their three dimensional structures and reaction mechanisms have been extensively studied; however, the mechanisms of several uncommon P450 reactions involved in animal steroid hormone biosynthesis and structures and reaction mechanisms of various P450s involved in plant and insect steroid hormone biosynthesis remain unclear. Recently, we determined the crystal structure of P450 responsible for the first and rate-determining step in brassinosteroids biosynthesis and clarified the regio- and stereo-selectivity in the hydroxylation reaction mechanism. In this review, we have outlined the general catalytic cycle, reaction mechanism, and structure of P450s. Additionally, we have described the recent advances in research on the reaction mechanisms of steroid hormone biosynthesis-related P450s, some of which catalyze unusual P450 reactions including C-C bond cleavage reactions by utilizing either a heme-peroxo anion species or compound I as an active oxidizing species. This review article is an extended version of the Japanese article, Structure and mechanism of cytochrome P450s involved in steroid hormone biosynthesis, published in SEIBUTSU BUTSURI Vol. 61, p. 189-191 (2021).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/9f/23/19_e190021.PMC9260165.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40621547","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 : 2022-05-12eCollection Date: 2022-01-01DOI: 10.2142/biophysico.bppb-v19.0020
Kazusa Beppu, Yusuke T Maeda
Ordered collective motion emerges in a group of autonomously motile elements (known as active matter) as their density increases. Microswimmers, such as swimming bacteria, have been extensively studied in physics and biology. A dense suspension of bacteria forms seemingly chaotic turbulence in viscous fluids. Interestingly, this active turbulence driven by bacteria can form a hidden ensemble of many vortices. Understanding the active turbulence in a bacterial suspension can provide physical principles for pattern formation and insight into the instability underlying biological phenomena. This review presents recent findings regarding ordered structures causing active turbulence and discusses a physical approach for controlling active turbulence via geometric confinement. When the active matter is confined in a compartment with a size comparable to the correlation length of the collective motion, vortex-like rotation appears, and the vortex pairing order is indicated by the patterns of interacting vortices. Additionally, we outline the design principle for controlling collective motions via the geometric rule of the vortex pairing, which may advance engineering microdevices driven by a group of active matter. This article is an extended version of the Japanese article, Ordered Structure and Geometric Control of Active Matter in Dense Bacterial Suspensions, published in SEIBUTSU BUTSURI Vol. 60, p. 13-18 (2020).
有序的集体运动出现在一组自主运动的元素(被称为活性物质),因为它们的密度增加。微游泳者,如游泳细菌,已经在物理学和生物学上得到了广泛的研究。稠密的细菌悬浮液在粘性流体中形成看似混乱的湍流。有趣的是,这种由细菌驱动的活跃湍流可以形成许多旋涡的隐藏集合。了解细菌悬浮液中的活跃湍流可以为模式形成提供物理原理,并深入了解生物现象背后的不稳定性。本文综述了引起主动湍流的有序结构的最新发现,并讨论了通过几何约束控制主动湍流的物理方法。当活性物质被限制在一个与集体运动相关长度相当的空间中时,就会出现涡状旋转,并通过相互作用的涡的模式来指示涡的配对顺序。此外,我们还概述了通过涡旋配对的几何规则控制集体运动的设计原理,这可能会推动由一组活性物质驱动的工程微器件。本文是日语文章《密集细菌悬浊液中活性物质的有序结构和几何控制》的扩展版,发表于SEIBUTSU BUTSURI Vol. 60, p. 13-18(2020)。
{"title":"Exploring order in active turbulence: Geometric rule and pairing order transition in confined bacterial vortices.","authors":"Kazusa Beppu, Yusuke T Maeda","doi":"10.2142/biophysico.bppb-v19.0020","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0020","url":null,"abstract":"<p><p>Ordered collective motion emerges in a group of autonomously motile elements (known as active matter) as their density increases. Microswimmers, such as swimming bacteria, have been extensively studied in physics and biology. A dense suspension of bacteria forms seemingly chaotic turbulence in viscous fluids. Interestingly, this active turbulence driven by bacteria can form a hidden ensemble of many vortices. Understanding the active turbulence in a bacterial suspension can provide physical principles for pattern formation and insight into the instability underlying biological phenomena. This review presents recent findings regarding ordered structures causing active turbulence and discusses a physical approach for controlling active turbulence via geometric confinement. When the active matter is confined in a compartment with a size comparable to the correlation length of the collective motion, vortex-like rotation appears, and the vortex pairing order is indicated by the patterns of interacting vortices. Additionally, we outline the design principle for controlling collective motions via the geometric rule of the vortex pairing, which may advance engineering microdevices driven by a group of active matter. This article is an extended version of the Japanese article, Ordered Structure and Geometric Control of Active Matter in Dense Bacterial Suspensions, published in SEIBUTSU BUTSURI Vol. 60, p. 13-18 (2020).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ab/59/19_e190020.PMC9173862.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40478162","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}
Ever since the historic discovery of the cooperative oxygenation of its multiple subunits, hemoglobin (Hb) has been among the most exhaustively studied allosteric proteins. However, the lack of structural information on the intermediates between oxygenated and deoxygenated forms prevents our detailed understanding of the molecular mechanism of its allostery. It has been difficult to prepare crystals of intact oxy-deoxy intermediates and to individually identify the oxygen saturation for each subunit. However, our recent crystallographic studies have demonstrated that giant Hbs from annelids are suitable for overcoming these problems and can provide abundant information on oxy-deoxy intermediate structures. Here, we report the crystal structures of oxy-deoxy intermediates of a 400 kDa Hb (V2Hb) from the annelid Lamellibrachia satsuma, following up on a series of previous studies of similar giant Hbs. Four intermediate structures had average oxygen saturations of 78%, 69%, 55%, and 26%, as determined by the occupancy refinement of the bound oxygen based on ambient temperature factors. The structures demonstrate that the cooperative oxygen dissociation is weaker, large ternary and quaternary changes are induced at a later stage of the oxygen dissociation process, and the ternary and quaternary changes are smaller with local perturbations. Nonetheless, the overall structural transition seemed to proceed in the manner of the MWC two-state model. Our crystallographic snapshots of the allosteric transition of V2Hb provide important experimental evidence for a more detailed understanding of the allostery of Hbs by extension of the Monod-Wyman-Changeux (MWC) model.
{"title":"Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.","authors":"Nobutaka Numoto, Seiko Onoda, Yoshiaki Kawano, Hideo Okumura, Seiki Baba, Yoshihiro Fukumori, Kunio Miki, Nobutoshi Ito","doi":"10.2142/biophysico.bppb-v19.0019","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0019","url":null,"abstract":"<p><p>Ever since the historic discovery of the cooperative oxygenation of its multiple subunits, hemoglobin (Hb) has been among the most exhaustively studied allosteric proteins. However, the lack of structural information on the intermediates between oxygenated and deoxygenated forms prevents our detailed understanding of the molecular mechanism of its allostery. It has been difficult to prepare crystals of intact oxy-deoxy intermediates and to individually identify the oxygen saturation for each subunit. However, our recent crystallographic studies have demonstrated that giant Hbs from annelids are suitable for overcoming these problems and can provide abundant information on oxy-deoxy intermediate structures. Here, we report the crystal structures of oxy-deoxy intermediates of a 400 kDa Hb (V2Hb) from the annelid <i>Lamellibrachia satsuma</i>, following up on a series of previous studies of similar giant Hbs. Four intermediate structures had average oxygen saturations of 78%, 69%, 55%, and 26%, as determined by the occupancy refinement of the bound oxygen based on ambient temperature factors. The structures demonstrate that the cooperative oxygen dissociation is weaker, large ternary and quaternary changes are induced at a later stage of the oxygen dissociation process, and the ternary and quaternary changes are smaller with local perturbations. Nonetheless, the overall structural transition seemed to proceed in the manner of the MWC two-state model. Our crystallographic snapshots of the allosteric transition of V2Hb provide important experimental evidence for a more detailed understanding of the allostery of Hbs by extension of the Monod-Wyman-Changeux (MWC) model.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/7e/c0/19_e190019.PMC9173864.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40478160","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 : 2022-05-10eCollection Date: 2022-01-01DOI: 10.2142/biophysico.bppb-v19.0017
Naoki Yamamoto, Eri Chatani
It is crucial to understand the mechanism of amyloid fibril formation for the development of the therapeutic ways against amyloidoses and neurodegenerative diseases. Prefibrillar intermediates, which emerge prior to the fibril formation, seem to play a key role to the occurrence of nuclei of amyloid fibrils. We have focused on an insulin-derived peptide, B chain, to precisely clarify the mechanism of the fibril formation via prefibrillar intermediates. Various kinds of methods such as circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering, and atomic force microscopy were employed to track the structural changes in prefibrillar intermediates. The prefibrillar intermediates possessing rod-shaped structures elongated as a function of time, which led to fibril formation. We have also found that a blood clotting protein, fibrinogen, inhibits the amyloid fibril formation of B chain. This was caused by the stabilization of prefibrillar intermediates and thus the suppression of their elongation by fibrinogen. These findings have not only shed light on detailed mechanisms about how prefibrillar intermediates convert to the amyloid fibril, but also demonstrated that inhibiting the structural development of prefibrillar intermediates is an effective strategy to develop therapeutic ways against amyloid-related diseases. This review article is an extended version of the Japanese article, Observing Development of Amyloid Prefibrillar Intermediates and their Interaction with Chaperones for Inhibiting the Fibril Formation, published in SEIBUTSU BUTSURI Vol. 61, p. 236-239 (2021).
了解淀粉样蛋白纤维的形成机制对于开发治疗淀粉样蛋白病和神经退行性疾病的方法至关重要。在纤维形成之前出现的前纤维中间体似乎对淀粉样纤维核的出现起着关键作用。我们以胰岛素衍生肽 B 链为研究对象,旨在精确阐明淀粉样蛋白纤维通过前纤维中间体形成的机制。我们采用了圆二色性光谱、动态光散射、小角 X 射线散射和原子力显微镜等多种方法来追踪前纤维素中间体的结构变化。具有杆状结构的前纤维中间体随着时间的推移而伸长,从而形成纤维。我们还发现,凝血蛋白纤维蛋白原能抑制 B 链淀粉样纤维的形成。这是因为纤维蛋白原稳定了纤维前中间体,从而抑制了它们的伸长。这些发现不仅揭示了前纤维中间产物如何转化为淀粉样纤维的详细机制,还证明了抑制前纤维中间产物的结构发展是开发淀粉样相关疾病治疗方法的有效策略。本综述文章是日文文章《观察淀粉样蛋白纤前中间体的发展及其与伴侣蛋白的相互作用以抑制纤维的形成》(Observing Development of Amyloid Prefibrillar Intermediates and their Interaction with Chaperones for Inhibiting the Fibril Formation)的扩展版,发表于《科学文摘》(SEIBUTSU BUTSURI)第61卷第236-239页(2021年)。
{"title":"Multistep growth of amyloid intermediates and its inhibition toward exploring therapeutic way: A case study using insulin B chain and fibrinogen.","authors":"Naoki Yamamoto, Eri Chatani","doi":"10.2142/biophysico.bppb-v19.0017","DOIUrl":"10.2142/biophysico.bppb-v19.0017","url":null,"abstract":"<p><p>It is crucial to understand the mechanism of amyloid fibril formation for the development of the therapeutic ways against amyloidoses and neurodegenerative diseases. Prefibrillar intermediates, which emerge prior to the fibril formation, seem to play a key role to the occurrence of nuclei of amyloid fibrils. We have focused on an insulin-derived peptide, B chain, to precisely clarify the mechanism of the fibril formation via prefibrillar intermediates. Various kinds of methods such as circular dichroism spectroscopy, dynamic light scattering, small-angle X-ray scattering, and atomic force microscopy were employed to track the structural changes in prefibrillar intermediates. The prefibrillar intermediates possessing rod-shaped structures elongated as a function of time, which led to fibril formation. We have also found that a blood clotting protein, fibrinogen, inhibits the amyloid fibril formation of B chain. This was caused by the stabilization of prefibrillar intermediates and thus the suppression of their elongation by fibrinogen. These findings have not only shed light on detailed mechanisms about how prefibrillar intermediates convert to the amyloid fibril, but also demonstrated that inhibiting the structural development of prefibrillar intermediates is an effective strategy to develop therapeutic ways against amyloid-related diseases. This review article is an extended version of the Japanese article, Observing Development of Amyloid Prefibrillar Intermediates and their Interaction with Chaperones for Inhibiting the Fibril Formation, published in SEIBUTSU BUTSURI Vol. 61, p. 236-239 (2021).</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/4e/5b/19_e190017.PMC9173859.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40478159","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 : 2022-04-15eCollection Date: 2022-01-01DOI: 10.2142/biophysico.bppb-v19.0016
Damien Hall, Adam S Foster
High speed atomic force microscopy (HS-AFM) is, in principle, capable of yielding nanometer level detail about the surface of static structures. However, for highly dynamic samples HS-AFM may struggle with the correct feature assignment both within and between frames. Feature assignment in HS-AFM is dependent on (i) the intrinsic sampling rate, and (ii) the rate of internal redistribution of the sample. Whilst the first quantity (the sampling rate) is defined by the device parameters, the second quantity is frequently unknown, and is often the desired target of the measurement. This work examines how, even in the absence of gross cell morphological change, the rapid dynamics of living cell membranes, may impose an upper spatial limit to the frame-to-frame assignment of cell micro-topography and other related properties (such as local elasticity) whose motion may be described stochastically. Such a practical maximum may prove useful in the setup of HS-AFM experiments involving dynamic surfaces thereby facilitating selection of the most parsimonious relationship between observation size, image pixilation and sampling rates. To assist with performing the described calculations a graphical user interface-based software package called HS-AFM UGOKU is made freely available.
{"title":"Practical considerations for feature assignment in high-speed AFM of live cell membranes.","authors":"Damien Hall, Adam S Foster","doi":"10.2142/biophysico.bppb-v19.0016","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0016","url":null,"abstract":"<p><p>High speed atomic force microscopy (HS-AFM) is, in principle, capable of yielding nanometer level detail about the surface of static structures. However, for highly dynamic samples HS-AFM may struggle with the correct feature assignment both within and between frames. Feature assignment in HS-AFM is dependent on (i) the intrinsic sampling rate, and (ii) the rate of internal redistribution of the sample. Whilst the first quantity (the sampling rate) is defined by the device parameters, the second quantity is frequently unknown, and is often the desired target of the measurement. This work examines how, even in the absence of gross cell morphological change, the rapid dynamics of living cell membranes, may impose an upper spatial limit to the frame-to-frame assignment of cell micro-topography and other related properties (such as local elasticity) whose motion may be described stochastically. Such a practical maximum may prove useful in the setup of HS-AFM experiments involving dynamic surfaces thereby facilitating selection of the most parsimonious relationship between observation size, image pixilation and sampling rates. To assist with performing the described calculations a graphical user interface-based software package called HS-AFM UGOKU is made freely available.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1f/99/19_e190016.PMC9173863.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40478161","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 : 2022-04-14eCollection Date: 2022-01-01DOI: 10.2142/biophysico.bppb-v19.0015
Keisuke Inoue, Shoji Takada, Tsuyoshi Terakawa
DNA mismatches are frequently generated by various intrinsic and extrinsic factors including DNA replication errors, oxygen species, ultraviolet, and ionizing radiation. These mismatches should be corrected by the mismatches repair (MMR) pathway to maintain genome integrity. In the Escherichia coli (E. coli) MMR pathway, MutS searches and recognizes a base-pair mismatch from millions of base-pairs. Once recognized, ADP bound to MutS is exchanged with ATP, which induces a conformational change in MutS. Previous single-molecule fluorescence microscopy studies have suggested that ADP-bound MutS temporarily slides along double-stranded DNA in a rotation-coupled manner to search a base-pair mismatch and so does ATP-bound MutS in a rotation-uncoupled manner. However, the detailed structural dynamics of the sliding remains unclear. In this study, we performed coarse-grained molecular dynamics simulations of the E. coli MutS bound on DNA in three different conformations: ADP-bound (MutSADP), ATP-bound open clamp ( ), and ATP-bound closed clamp ( ) conformations. In the simulations, we observed conformation-dependent diffusion of MutS along DNA. MutSADP and diffused along DNA in a rotation-coupled manner with rare and frequent groove-crossing events, respectively. In the groove-crossing events, MutS overcame an edge of a groove and temporarily diffused in a rotation-uncoupled manner. It was also indicated that mismatch searches by is inefficient in terms of mismatch checking even though it diffuses along DNA and reaches unchecked regions more rapidly than MutSADP.
DNA错配经常由各种内在和外在因素引起,包括DNA复制错误、氧气种类、紫外线和电离辐射。这些错配应该通过错配修复(MMR)途径来纠正,以维持基因组的完整性。在大肠杆菌(E. coli) MMR通路中,MutS从数百万个碱基对中搜索并识别碱基对不匹配。一旦被识别,结合在MutS上的ADP与ATP交换,引起MutS的构象变化。先前的单分子荧光显微镜研究表明,adp结合的MutS以旋转偶联的方式暂时沿着双链DNA滑动以搜索碱基对不匹配,atp结合的MutS也以旋转不偶联的方式滑动。然而,滑动的详细结构动力学仍然不清楚。在这项研究中,我们以三种不同的构象进行了大肠杆菌MutS结合DNA的粗颗粒分子动力学模拟:adp结合(MutSADP), atp结合的开放钳形(Mu到S O p和A t p)和atp结合的封闭钳形(Mu到S C l和A t p)。在模拟中,我们观察到MutS沿DNA的构象依赖扩散。MutSADP和M - t - S - C分别以旋转耦合的方式沿DNA扩散,具有罕见和频繁的凹槽交叉事件。在槽交叉事件中,MutS克服了槽的边缘,并以旋转不耦合的方式暂时扩散。研究还表明,尽管M - t - S - O - p - A - t - p沿着DNA扩散并比MutSADP更快地到达未检查区域,但在错配检查方面,M - t - S - O - p的错配搜索效率较低。
{"title":"Coarse-grained molecular dynamics simulations of base-pair mismatch recognition protein MutS sliding along DNA.","authors":"Keisuke Inoue, Shoji Takada, Tsuyoshi Terakawa","doi":"10.2142/biophysico.bppb-v19.0015","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0015","url":null,"abstract":"<p><p>DNA mismatches are frequently generated by various intrinsic and extrinsic factors including DNA replication errors, oxygen species, ultraviolet, and ionizing radiation. These mismatches should be corrected by the mismatches repair (MMR) pathway to maintain genome integrity. In the <i>Escherichia coli</i> (<i>E. coli</i>) MMR pathway, MutS searches and recognizes a base-pair mismatch from millions of base-pairs. Once recognized, ADP bound to MutS is exchanged with ATP, which induces a conformational change in MutS. Previous single-molecule fluorescence microscopy studies have suggested that ADP-bound MutS temporarily slides along double-stranded DNA in a rotation-coupled manner to search a base-pair mismatch and so does ATP-bound MutS in a rotation-uncoupled manner. However, the detailed structural dynamics of the sliding remains unclear. In this study, we performed coarse-grained molecular dynamics simulations of the <i>E. coli</i> MutS bound on DNA in three different conformations: ADP-bound (MutS<sup>ADP</sup>), ATP-bound open clamp ( <math> <msubsup><mrow><mi>M</mi> <mi>u</mi> <mi>t</mi> <mi>S</mi></mrow> <mrow><mi>O</mi> <mi>p</mi> <mi>e</mi> <mi>n</mi></mrow> <mrow><mi>A</mi> <mi>T</mi> <mi>P</mi></mrow> </msubsup> </math> ), and ATP-bound closed clamp ( <math> <msubsup><mrow><mi>M</mi> <mi>u</mi> <mi>t</mi> <mi>S</mi></mrow> <mrow><mi>C</mi> <mi>l</mi> <mi>o</mi> <mi>s</mi> <mi>e</mi> <mi>d</mi></mrow> <mrow><mi>A</mi> <mi>T</mi> <mi>P</mi></mrow> </msubsup> </math> ) conformations. In the simulations, we observed conformation-dependent diffusion of MutS along DNA. MutS<sup>ADP</sup> and <math> <msubsup><mrow><mi>M</mi> <mi>u</mi> <mi>t</mi> <mi>S</mi></mrow> <mrow><mi>C</mi> <mi>l</mi> <mi>o</mi> <mi>s</mi> <mi>e</mi> <mi>d</mi></mrow> <mrow><mi>A</mi> <mi>T</mi> <mi>P</mi></mrow> </msubsup> </math> diffused along DNA in a rotation-coupled manner with rare and frequent groove-crossing events, respectively. In the groove-crossing events, MutS overcame an edge of a groove and temporarily diffused in a rotation-uncoupled manner. It was also indicated that mismatch searches by <math> <msubsup><mrow><mi>M</mi> <mi>u</mi> <mi>t</mi> <mi>S</mi></mrow> <mrow><mi>O</mi> <mi>p</mi> <mi>e</mi> <mi>n</mi></mrow> <mrow><mi>A</mi> <mi>T</mi> <mi>P</mi></mrow> </msubsup> </math> is inefficient in terms of mismatch checking even though it diffuses along DNA and reaches unchecked regions more rapidly than MutS<sup>ADP</sup>.</p>","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/52/d6/19_e190015.PMC9173861.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40478164","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}