Biophysics and Physicobiology最新文献_第5页

Simple dynamics underlying the survival behaviors of ciliates. 纤毛虫生存行为背后的简单动力学。

Biophysics and Physicobiology Pub Date : 2022-08-09 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0026

Takuya Ohmura, Yukinori Nishigami, Masatoshi Ichikawa

{"title":"Simple dynamics underlying the survival behaviors of ciliates.","authors":"Takuya Ohmura, Yukinori Nishigami, Masatoshi Ichikawa","doi":"10.2142/biophysico.bppb-v19.0026","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v19.0026","url":null,"abstract":"Ciliates are swimming microorganisms in aquatic environments. Habitats where ciliates accumulate include nutrient-rich solid-liquid interfaces such as pond bottom walls and waterweed surfaces. The ciliates stay near the walls to survive. We investigated the dynamics of the near-wall behavior of ciliates. In experiments, the ciliates were made to slide on a flat wall of glass substrate. When encountering the wall, the wall-side cilia of the cells stop their motion and lose their propelling activity, which indicates that the ciliates have a mechano-sensing system for cilia beating. Based on the experimental results, we hypothesized that the ciliary thrust force that propels the cell body becomes asymmetric, and the asymmetry of the thrust force generates a head-down torque to keep the cell sliding on the wall. To prove this hypothesis, we performed numerical simulations by using a developed hydrodynamic model for swimming ciliates. The model revealed that the loss of cilia activity on the wall side physically induces a sliding motion, and the aspect ratio of the cell body and effective cilium area are critical functions for the sliding behavior on a wall. In addition, we investigated the stability of the sliding motion against an external flow. We found that ciliates slide upstream on a wall. Interestingly, the dynamics of this upstream sliding, called rheotaxis, were also explained by the identical physical conditions for no-flow sliding. Only two simple physical conditions are required to explain the dynamics of ciliate survival behavior. This review article is an extended version of the Japanese article, Fluid Dynamic Model Reveals a Mechano-sensing System Underlying the Behavior of Ciliates, published in SEIBUTSU BUTSURI Vol. 61, p. 16-19 (2021).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190026"},"PeriodicalIF":0.0,"publicationDate":"2022-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/07/96/19_e190026.PMC9465405.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33484499","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}

引用次数: 0

Computational study of the impact of nucleotide variations on highly conserved proteins: In the case of actin. 核苷酸变异对高度保守蛋白影响的计算研究:以肌动蛋白为例。

Biophysics and Physicobiology Pub Date : 2022-07-28 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0025

Ha T T Duong, Hirofumi Suzuki, Saki Katagiri, Mayu Shibata, Misae Arai, Kei Yura

{"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":"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.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190025"},"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}

引用次数: 0

Biophysical elucidation of neural network and chemical regeneration of neural tissue. 神经网络的生物物理解释和神经组织的化学再生。

Biophysics and Physicobiology Pub Date : 2022-07-27 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0024

Takahiro Muraoka, Tomohide Saio, Masaki Okumura

引用次数: 0

Current status and future perspectives of the evaluation of missense variants by using three-dimensional structures of proteins. 利用蛋白质三维结构评价错义变异的现状和未来展望。

Biophysics and Physicobiology Pub Date : 2022-07-14 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0023

Matsuyuki Shirota, Kengo Kinoshita

引用次数: 0

Structural overview of the translocase of the mitochondrial outer membrane complex. 线粒体外膜复合体转位酶的结构概述。

Biophysics and Physicobiology Pub Date : 2022-06-07 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0022

Yuhei Araiso, Toshiya Endo

{"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":"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).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190022"},"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}

引用次数: 1

Diverse reactions catalyzed by cytochrome P450 and biosynthesis of steroid hormone. 细胞色素P450催化的多种反应和类固醇激素的生物合成。

Biophysics and Physicobiology Pub Date : 2022-06-01 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0021

Keisuke Fujiyama, Tomoya Hino, Shingo Nagano

{"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":"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).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"e190021"},"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}

引用次数: 2

Exploring order in active turbulence: Geometric rule and pairing order transition in confined bacterial vortices. 探索主动湍流中的秩序:受限细菌涡旋中的几何规则和配对顺序转换。

Biophysics and Physicobiology Pub Date : 2022-05-12 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0020

Kazusa Beppu, Yusuke T Maeda

{"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":"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).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"1-9"},"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}

引用次数: 1

Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. 400 kDa V2血红蛋白的氧解离中间体结构提供了蛋白质变构的粗略快照。

Biophysics and Physicobiology Pub Date : 2022-05-12 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0019

Nobutaka Numoto, Seiko Onoda, Yoshiaki Kawano, Hideo Okumura, Seiki Baba, Yoshihiro Fukumori, Kunio Miki, Nobutoshi Ito

{"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":"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.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"1-10"},"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}

引用次数: 0

Multistep growth of amyloid intermediates and its inhibition toward exploring therapeutic way: A case study using insulin B chain and fibrinogen. 淀粉样蛋白中间体的多步生长及其抑制，探索治疗方法：使用胰岛素 B 链和纤维蛋白原的案例研究。

Biophysics and Physicobiology Pub Date : 2022-05-10 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0017

Naoki Yamamoto, Eri Chatani

{"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":"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).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"1-10"},"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}

引用次数: 0

Practical considerations for feature assignment in high-speed AFM of live cell membranes. 活细胞膜高速AFM特征分配的实际考虑。

Biophysics and Physicobiology Pub Date : 2022-04-15 eCollection Date: 2022-01-01 DOI: 10.2142/biophysico.bppb-v19.0016

Damien Hall, Adam S Foster

{"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":"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.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":" ","pages":"1-21"},"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}

引用次数: 5