Biophysics and physicobiology最新文献_第4页

Resonance frequency measurement to identify stiffness variations based on photoacoustic imaging. 基于光声成像的共振频率测量，用于识别硬度变化。

Biophysics and physicobiology Pub Date : 2024-01-20 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0008

Ananta Kusuma Yoga Pratama, Andreas Setiawan, Rini Widyaningrum, Mitrayana

引用次数: 0

Analysis of the singularity cells controlling the pattern formation in multi-cellular systems. 控制多细胞系统模式形成的奇异细胞分析。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-01-19 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.s001

Kazuki Horikawa, Tatsuya Takemoto

引用次数: 0

Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol ol- factory receptor. 小鼠丁香酚 O- 工厂受体中气味氢键诱导的结构动态交叉相关性的分子动力学模拟分析。

Biophysics and physicobiology Pub Date : 2024-01-18 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0007

Chisato Okamoto, Koji Ando

{"title":"Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol ol- factory receptor.","authors":"Chisato Okamoto, Koji Ando","doi":"10.2142/biophysico.bppb-v21.0007","DOIUrl":"10.2142/biophysico.bppb-v21.0007","url":null,"abstract":"Structural fluctuations and dynamic cross-correlations in the mouse eugenol olfactory receptor (Olfr73) were studied by molecular dynamics (MD) simulation to characterize the dynamic response of the protein upon ligand binding. The initial structure was generated by the artificial intelligence tool AlphaFold2 due to the current lack of experimental data. We focused on the hydrogen (H) bond of the odorant eugenol to Ser113, Asn207, and Tyr260 of the receptor protein, the importance of which has been suggested by previous experimental studies. The H-bond was not observed in docking simulations, but in subsequent MD simulations the H-bond to Ser113 was formed in 2-4 ns. The lifetime of the H-bond was in the range of 1-20 ns. On the trajectory with the most stable (20 ns) H-bond, the structural fluctuation of the α-carbon atoms of the receptor main chain was studied by calculating the root mean square fluctuations, the dynamic cross-correlation map, and the time-dependent dynamic cross-correlation. The analysis suggested a correlation transfer pathway Ser113 → Phe182 → (Leu259 or Tyr260) → Tyr291 induced by the ligand binding with a time scale of 4-6 ns.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210007"},"PeriodicalIF":0.0,"publicationDate":"2024-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159367","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

Observation of sarcomere chaos induced by changes in calcium concentration in cardiomyocytes. 观察心肌细胞中钙浓度变化引起的肌节混乱。

Biophysics and physicobiology Pub Date : 2024-01-12 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0006

Seine A Shintani

{"title":"Observation of sarcomere chaos induced by changes in calcium concentration in cardiomyocytes.","authors":"Seine A Shintani","doi":"10.2142/biophysico.bppb-v21.0006","DOIUrl":"10.2142/biophysico.bppb-v21.0006","url":null,"abstract":"Heating cardiomyocytes to 38-42°C induces hyperthermal sarcomeric oscillations (HSOs), which combine chaotic instability and homeostatic stability. These properties are likely important for achieving periodic and rapid ventricular expansion during the diastole phase of the heartbeat. Compared with spontaneous oscillatory contractions in cardiomyocytes, which are sarcomeric oscillations induced in the presence of a constant calcium concentration, we found that calcium concentration fluctuations cause chaotic instability during HSOs. We believe that the experimental fact that sarcomeres, autonomously oscillating, exhibit such instability due to the action of calcium concentration changes is important for understanding the physiological function of sarcomeres. Therefore, we have named this chaotic sarcomere instability that appears under conditions involving changes in calcium concentration as Sarcomere Chaos with Changes in Calcium Concentration (S4C). Interestingly, sarcomere instability that could be considered S4C has also been observed in the relaxation dynamics of EC coupling. Unlike ADP-SPOCs and Cell-SPOCs under constant calcium concentration conditions, fluctuations in oscillation amplitude indistinguishable from HSOs were observed. Additionally, like HSO, a positive Lyapunov exponent was measured. S4C is likely a crucial sarcomeric property supporting the rapid and flexible ventricular diastole with each heartbeat of the heart.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210006"},"PeriodicalIF":0.0,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128306/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159256","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

Physicochemical mechanisms of aggregation and fibril formation of α-synuclein and apolipoprotein A-I. α-突触核蛋白和脂蛋白 A-I 的聚集和纤维形成的物理化学机制。

Biophysics and physicobiology Pub Date : 2023-12-29 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0005

Takashi Ohgita, Hiroki Kono, Norihiro Namba, Hiroyuki Saito

{"title":"Physicochemical mechanisms of aggregation and fibril formation of α-synuclein and apolipoprotein A-I.","authors":"Takashi Ohgita, Hiroki Kono, Norihiro Namba, Hiroyuki Saito","doi":"10.2142/biophysico.bppb-v21.0005","DOIUrl":"10.2142/biophysico.bppb-v21.0005","url":null,"abstract":"Deposition and accumulation of amyloid fibrils is a hallmark of a group of diseases called amyloidosis and neurodegenerative disorders. Although polypeptides potentially have a fibril-forming propensity, native proteins have evolved into proper functional conformations to avoid aggregation and fibril formation. Understanding the mechanism for regulation of fibril formation of native proteins provides clues for the rational design of molecules for inhibiting fibril formation. Although fibril formation is a complex multistep reaction, experimentally obtained fibril formation curves can be fitted with the Finke-Watzky (F-W) two-step model for homogeneous nucleation followed by autocatalytic fibril growth. The resultant F-W rate constants for nucleation and fibril formation provide information on the chemical kinetics of fibril formation. Using the F-W two-step model analysis, we investigated the physicochemical mechanisms of fibril formation of a Parkinson's disease protein α-synuclein (αS) and a systemic amyloidosis protein apolipoprotein A-I (apoA-I). The results indicate that the C-terminal region of αS enthalpically and entropically suppresses nucleation through the intramolecular interaction with the N-terminal region and the intermolecular interaction with existing fibrils. In contrast, the nucleation of the N-terminal fragment of apoA-I is entropically driven likely due to dehydration of large hydrophobic segments in the molecule. Based on our recent findings, we discuss the similarity and difference of the fibril formation mechanisms of αS and the N-terminal fragment of apoA-I from the physicochemical viewpoints.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210005"},"PeriodicalIF":0.0,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159208","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

Shape of scaffold controlling the direction of cell migration. 控制细胞迁移方向的支架形状。

Biophysics and physicobiology Pub Date : 2023-12-29 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0004

Hiroshi Sunami, Yusuke Shimizu, Hidehiro Kishimoto

{"title":"Shape of scaffold controlling the direction of cell migration.","authors":"Hiroshi Sunami, Yusuke Shimizu, Hidehiro Kishimoto","doi":"10.2142/biophysico.bppb-v21.0004","DOIUrl":"10.2142/biophysico.bppb-v21.0004","url":null,"abstract":"Cell migration plays an important role in the development and maintenance of multicellular organisms. Factors that induce cell migration and mechanisms controlling their expression are important for determining the mechanisms of factor-induced cell migration. Despite progress in the study of factor-induced cytotaxis, including chemotaxis and haptotaxis, precise control of the direction of cell migration over a wide area has not yet been achieved. Success in this area would update the cell migration assays, superior cell separation technologies, and artificial organs with high biocompatibility. The present study therefore sought to control the direction of cell migration over a wide area by adjusting the three-dimensional shape of the cell scaffold. The direction of cell migration was influenced by the shape of the cell scaffold, thereby optimizing cell adhesion and protrusion. Anisotropic arrangement of these three-dimensional shapes into a periodic structure induced unidirectional cell migration. Three factors were required for unidirectional cell migration: 1) the sizes of the anisotropic periodic structures had to be equal to or lower than the size of the spreading cells, 2) cell migration was restricted to a runway approximately the width of the cell, and 3) cells had to be prone to extension of long protrusions in one direction. Because the first two factors had been identified previously in studies of cell migration in one direction using two-dimensional shaped patterns, these three factors are likely important for the mechanism by which cell scaffold shapes regulate cell migration.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210004"},"PeriodicalIF":0.0,"publicationDate":"2023-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128307/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159222","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

The potential of nanopore technologies toward empowering biophysical research: Brief history, basic principle and applications. 纳米孔技术在加强生物物理研究方面的潜力：简史、基本原理和应用。

Biophysics and physicobiology Pub Date : 2023-12-26 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0003

Hirohito Yamazaki, Zugui Peng, Ryuji Kawano, Kan Shoji

引用次数: 0

Concepts of a synthetic minimal cell: Information molecules, metabolic pathways, and vesicle reproduction. 合成最小细胞的概念：信息分子、代谢途径和囊泡繁殖。

Biophysics and physicobiology Pub Date : 2023-12-19 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0002

Minoru Kurisu, Masayuki Imai

{"title":"Concepts of a synthetic minimal cell: Information molecules, metabolic pathways, and vesicle reproduction.","authors":"Minoru Kurisu, Masayuki Imai","doi":"10.2142/biophysico.bppb-v21.0002","DOIUrl":"10.2142/biophysico.bppb-v21.0002","url":null,"abstract":"How do the living systems emerge from non-living molecular assemblies? What physical and chemical principles supported the process? To address these questions, a promising strategy is to artificially reconstruct living cells in a bottom-up way. Recently, the authors developed the \"synthetic minimal cell\" system showing recursive growth and division cycles, where the concepts of information molecules, metabolic pathways, and cell reproduction were artificially and concisely redesigned with the vesicle-based system. We intentionally avoided using the sophisticated molecular machinery of the biological cells and tried to redesign the cells in the simplest forms. This review focuses on the similarities and differences between the biological cells and our synthetic minimal cell concerning each concept of cells. Such comparisons between natural and artificial cells will provide insights on how the molecules should be assembled to create living systems to the wide readers in the field of synthetic biology, artificial cells, and protocells research. This review article is an extended version of the Japanese article \"Growth and division of vesicles coupled with information molecules,\" published in SEIBUTSU-BUTSURI vol. 61, p. 378-381 (2021).","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210002"},"PeriodicalIF":0.0,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159252","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

Structure-function relationship of KaiC around dawn. 黎明前后 KaiC 的结构-功能关系。

Biophysics and physicobiology Pub Date : 2023-12-16 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.0001

Yoshihiko Furuike, Eiki Yamashita, Shuji Akiyama

{"title":"Structure-function relationship of KaiC around dawn.","authors":"Yoshihiko Furuike, Eiki Yamashita, Shuji Akiyama","doi":"10.2142/biophysico.bppb-v21.0001","DOIUrl":"10.2142/biophysico.bppb-v21.0001","url":null,"abstract":"KaiC is a multifunctional enzyme functioning as the core of the circadian clock system in cyanobacteria: its N-terminal domain has adenosine triphosphatase (ATPase) activity, and its C-terminal domain has autokinase and autophosphatase activities targeting own S431 and T432. The coordination of these multiple biochemical activities is the molecular basis for robust circadian rhythmicity. Therefore, much effort has been devoted to elucidating the cooperative relationship between the two domains. However, structural and functional relationships between the two domains remain unclear especially with respect to the dawn phase, at which KaiC relieves its nocturnal history through autodephosphorylation. In this study, we attempted to design a double mutation of S431 and T432 that can capture KaiC as a fully dephosphorylated form with minimal impacts on its structure and function, and investigated the cooperative relationship between the two domains in the night to morning phases from many perspectives. The results revealed that both domains cooperate at the dawn phase through salt bridges formed between the domains, thereby non-locally co-activating two events, ATPase de-inhibition and S431 dephosphorylation. Our further analysis using existing crystal structures of KaiC suggests that the states of both domains are not always in one-to-one correspondence at every phase of the circadian cycle, and their coupling is affected by the interactions with KaiA or adjacent subunits within a KaiC hexamer.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"21 1","pages":"e210001"},"PeriodicalIF":0.0,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11128299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141159238","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

Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics. 小分子粘合剂和非粘合剂与 FMN 核糖开关的结合自由能图谱：全原子分子动力学

Biophysics and physicobiology Pub Date : 2023-12-13 eCollection Date: 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0047

Junichi Higo, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Yoshifumi Fukunishi

{"title":"Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics.","authors":"Junichi Higo, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Yoshifumi Fukunishi","doi":"10.2142/biophysico.bppb-v20.0047","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0047","url":null,"abstract":"A small and flexible molecule, ribocil A (non-binder) or B (binder), binds to the deep pocket of the aptamer domain of the FMN riboswitch, which is an RNA molecule. This binding was studied by mD-VcMD, which is a generalized-ensemble simulation method. Ribocil A and B are structurally similar because they are optical isomers to each other. In the initial conformation of simulation, the ligands and the aptamer were completely dissociated in explicit solvent. The aptamer-ribocil B binding was stronger than the aptamer-ribocil A binding, which agrees with experiments. The computed free-energy landscape for the aptamer-ribocil B binding was funnel-like, whereas that for the aptamer-ribocil A binding was rugged. When passing through the gate (named \"front gate\") of the binding pocket, each ligand interacted with bases of the riboswitch by non-native π-π stackings, and the stackings restrained the ligand's orientation to be advantageous to reach the binding site smoothly. When the ligands reached the binding site in the pocket, the non-native stackings were replaced by the native stackings. The ligand's orientation restriction is discussed referring to a selection mechanism reported in an earlier work on a drug-GPCR interaction. The present simulation showed another pathway leading the ligands to the binding site. The gate (\"rear gate\") for this pathway was located completely opposite to the front gate on the aptamer's surface. However, the approach from the rear gate required overcoming a free-energy barrier regarding ligand's rotation before reaching the binding site.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"20 4","pages":"e200047"},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10853809/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725620","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