Biophysics and physicobiology最新文献

A method for isolating and cryopreserving intact mitochondria with improved integrity and functionality. 一种分离和低温保存完整线粒体的方法，具有更好的完整性和功能。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-05-16 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0012

Arima Okutani, Jannatul Naima, Asaka Ogihara, Taihei Motoichi, Ikuroh Ohsawa, Yoshihiro Ohta

{"title":"A method for isolating and cryopreserving intact mitochondria with improved integrity and functionality.","authors":"Arima Okutani, Jannatul Naima, Asaka Ogihara, Taihei Motoichi, Ikuroh Ohsawa, Yoshihiro Ohta","doi":"10.2142/biophysico.bppb-v22.0012","DOIUrl":"10.2142/biophysico.bppb-v22.0012","url":null,"abstract":"Mitochondria isolated from cells are essential tools in biological research. However, many mitochondria are often damaged during the isolation process. Although cryopreservation can greatly improve the usability of isolated mitochondria, it typically leads to significant loss of activity following freezing and thawing. In this study, we present our own techniques for mitochondrial isolation and cryopreservation to overcome these challenges. Our isolation method begins by selectively weakening the plasma membrane through the incorporation of digitonin, under conditions that do not increase membrane permeability. The plasma membrane is then selectively ruptured to release mitochondria. Notably, mitochondria contract within the cell before the plasma membrane ruptures, a process that facilitates their extraction. The isolated mitochondria showed polarized inner membranes in approximately 90% of the population. Compared to mitochondria isolated by homogenization, they retained more intermembrane space proteins and exhibited greater outer membrane integrity. For cryopreservation, rapid thawing was critical to maintaining mitochondrial activity after freeze-thaw cycles. When thawing was completed in under 1.5 minutes, the proportion of polarized mitochondria decreased by only about 10%. These findings suggest that our isolation and cryopreservation protocols are promising for applications requiring intact, functional mitochondria.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 2","pages":"e220012"},"PeriodicalIF":1.6,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12226260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144577474","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

A low-cost electric micromanipulator and its application to single-cell electroporation. 一种低成本的电动微机械臂及其在单细胞电穿孔中的应用。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-04-26 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0010

Kazuma Shimizu, Norihiko Nishimura, Manato Oku, Chika Okimura, Yoshiaki Iwadate

{"title":"A low-cost electric micromanipulator and its application to single-cell electroporation.","authors":"Kazuma Shimizu, Norihiko Nishimura, Manato Oku, Chika Okimura, Yoshiaki Iwadate","doi":"10.2142/biophysico.bppb-v22.0010","DOIUrl":"10.2142/biophysico.bppb-v22.0010","url":null,"abstract":"Micromanipulation techniques are essential in studies of cell function, both for single cells and for cell collectives. Various types of micromanipulators are now commercially available. Hydraulic micromanipulators have the advantage of analogue operation, allowing the user to move the glass microneedle in direct response to their own hand movements. However, they require regular maintenance to maintain their performance. On the other hand, some electric micromanipulators can operate in minute steps of several hundred nanometers, but they are expensive. This paper describes our assembly of a low-cost electric micromanipulator. The device consists of three commercially available stages, three linear DC motors to drive them, and a lab-made control circuit. Using this device, we were able to direct a glass microneedle to cut an MDCK cell sheet. We also manipulated an aspiration pipette to aspirate a portion of a Dictyostelium cell. In addition, we were able to gently touch the tip of an electroporation pipette to the surface of a single target cell in a sheet of fish epidermal keratocytes and load FITC into the cell. Our device can be assembled at one-fourth the cost of commercially available hydraulic micromanipulators. This could make it easier, both economically and technically, to add micromanipulators to all of a laboratory's microscopes.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 2","pages":"e220010"},"PeriodicalIF":1.6,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12151732/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277284","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

A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape. 一个虚拟系统耦合的分子动力学模拟，不需要结合位点的实验知识：应用于rna -配体结合的自由能景观。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-04-26 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0011

Junichi Higo, Kota Kasahara, Shun Sakuraba, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Takuya Takahashi, Yoshifumi Fukunishi

{"title":"A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.","authors":"Junichi Higo, Kota Kasahara, Shun Sakuraba, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Takuya Takahashi, Yoshifumi Fukunishi","doi":"10.2142/biophysico.bppb-v22.0011","DOIUrl":"10.2142/biophysico.bppb-v22.0011","url":null,"abstract":"Ligand-receptor docking simulation is difficult when the biomolecules have high intrinsic flexibility. If some knowledge on the ligand-receptor complex structure or inter-molecular contact sites are presented in advance, the difficulty of docking problem considerably decreases. This paper proposes a generalized-ensemble method \"cartesian-space division mD-VcMD\" (or CSD-mD-VcMD), which calculates stable complex structures without assist of experimental knowledge on the complex structure. This method is an extension of our previous method that requires the knowledge on the ligand-receptor complex structure in advance. Both the present and previous methods enhance the conformational sampling, and finally produce a binding free-energy landscape starting from a completely dissociated conformation, and provide a free-energy landscape. We applied the present method to same system studied by the previous method: A ligand (ribocil A or ribocil B) binding to an RNA (the aptamer domain of the FMN riboswitch). The two methods produced similar results, which explained experimental data. For instance, ribocil B bound to the aptamer's deep binding pocket more strongly than ribocil A did. However, this does not mean that two methods have a similar performance. Note that the present method did not use the experimental knowledge of binding sites although the previous method was supported by the knowledge. The RNA-ligand binding site could be a cryptic site because RNA and ligand are highly flexible in general. The current study showed that CSD-mD-VcMD is actually useful to obtain a binding free-energy landscape of a flexible system, i.e., the RNA-ligand interacting system.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 2","pages":"e220011"},"PeriodicalIF":1.6,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12151736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144277285","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-activity relationship of PET-degrading cutinase regulated by weak Ca²⁺ binding and temperature. 弱Ca2+结合和温度调控pet降解角质酶的构效关系。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-04-24 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0009

Fumiya Kondo, Narutoshi Kamiya, Gert-Jan Bekker, Satoshi Nagao, Nobutaka Numoto, Hiroshi Sekiguchi, Nobutoshi Ito, Masayuki Oda

{"title":"Structure-activity relationship of PET-degrading cutinase regulated by weak Ca2+ binding and temperature.","authors":"Fumiya Kondo, Narutoshi Kamiya, Gert-Jan Bekker, Satoshi Nagao, Nobutaka Numoto, Hiroshi Sekiguchi, Nobutoshi Ito, Masayuki Oda","doi":"10.2142/biophysico.bppb-v22.0009","DOIUrl":"10.2142/biophysico.bppb-v22.0009","url":null,"abstract":"Enzyme function is often regulated by weak metal-ion binding, which results from conformational changes while maintaining conformational fluctuations. We analyzed the structure and function of cutinase-like enzyme, Cut190, using biophysical methods such as X-ray crystallography and molecular dynamics (MD) simulations, showing that its structure and function are finely regulated by weak Ca2+ binding and release. We succeeded to stabilize the enzyme by introducing a disulfide-bond which can degrade polyethylene terephthalate (PET) to PET monomers at the glass transition temperature of PET, ≈70°C. In this study, using the stabilized Cut190 mutants, Cut190**SS and Cut190**SS_F77L, we evaluated the requirement of Ca2+ for catalytic activity at 70°C, showing that the enzyme expressed the activity even in the absence of Ca2+, in contrast to that at 37°C. These results were supported by multicanonical MD analysis, which showed that the respective forms of the enzyme, such as closed, open, and engaged forms, were exchangeable, possibly because the potential energy barriers between the respective forms were lowered. Taken together, the conformational equilibrium to express the catalytic activity was regulated by weak Ca2+ binding at 37°C, and was also regulated by increasing temperature. The respective conformational states of Cut190**SS and Cut190**SS_F77L correlated well with their different catalytic activities for PET.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 2","pages":"e220009"},"PeriodicalIF":1.6,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12105869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144153118","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

Genetically-encoded temperature indicators for thermal biology. 用于热生物学的基因编码温度指示器。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-04-08 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0008

Tetsuichi Wazawa, Ryohei Ozaki-Noma, Lu Kai, Shun-Ichi Fukushima, Tomoki Matsuda, Takeharu Nagai

{"title":"Genetically-encoded temperature indicators for thermal biology.","authors":"Tetsuichi Wazawa, Ryohei Ozaki-Noma, Lu Kai, Shun-Ichi Fukushima, Tomoki Matsuda, Takeharu Nagai","doi":"10.2142/biophysico.bppb-v22.0008","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v22.0008","url":null,"abstract":"Temperature crucially affects molecular processes in living organisms and thus it is one of the vital physical parameters for life. To investigate how temperature is biologically maintained and regulated and its biological impact on organisms, it is essential to measure the spatial distribution and/or temporal changes of temperature across different biological scales, from whole organism to subcellular structures. Fluorescent nanothermometers have been developed as probes for temperature measurement by fluorescence microscopy for applications in microscopic scales where macroscopic temperature sensors are inaccessible, such as embryos, tissues, cells, and organelles. Although fluorescent nanothermometers have been developed from various materials, fluorescent protein-based ones are especially of interest because they can be introduced into cells as the transgenes for expression with or without specific localization, making them suitable for less-invasive temperature observation in living biological samples. In this article, we review protein-based fluorescent nanothermometers also known as genetically-encoded temperature indicators (GETIs), covering most published GETIs, for developers, users, and researchers in thermal biology as well as interested readers. We provide overviews of the temperature sensing mechanisms and measurement methods of these protein-based fluorescent nanothermometers. We then outline key information for GETI development, focusing on unique protein engineering techniques and building blocks distinct to GETIs, unlike other fluorescent nanothermometers. Furthermore, we propose several standards for the characterization of GETIs. Additionally, we explore various issues and offer perspectives in the field of thermal biology.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 2","pages":"e220008"},"PeriodicalIF":1.6,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12040488/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144061305","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

Time-resolved small-angle X-ray scattering system development for the biological macromolecules at SACLA: A pilot study. SACLA生物大分子的时间分辨小角x射线散射系统的开发：一个试点研究。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-03-27 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0007

Nobutaka Shimizu, Fangjia Luo, Tomoyuki Tanaka, Kensuke Tono, Keiko Yatabe, So Iwata, Eriko Nango

引用次数: 0

Gliding direction of Mycoplasma mobile correlates with the curved configuration of its cell shape. 移动支原体的滑动方向与其细胞形状的弯曲结构有关。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-02-26 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0006

Kana Suzuki, Daisuke Nakane, Masaki Mizutani, Takayuki Nishizaka

{"title":"Gliding direction of Mycoplasma mobile correlates with the curved configuration of its cell shape.","authors":"Kana Suzuki, Daisuke Nakane, Masaki Mizutani, Takayuki Nishizaka","doi":"10.2142/biophysico.bppb-v22.0006","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v22.0006","url":null,"abstract":"The gliding motility of bacteria is not linear but somehow exhibits a curved trajectory. This general observation is explained by the helical structure of protein tracks (Nakane et al., 2013) or the asymmetric array of gliding machineries (Morio et al., 2016), but these interpretations have not been directly examined. Here, we introduced a simple assumption: the gliding trajectory of M. mobile is guided by the cell shape. To test this idea, the intensity profile of a bacterium, Mycoplasma mobile, was analyzed and reconstructed at the single-cell level from images captured under a highly stable dark-field microscope, which minimized the mechanical drift and noise during sequential image recording. The raw image with the size of ~1 μm, which is about four times larger than the diffraction limit of visible light, was successfully fitted by double Gaussians to quantitatively determine the curved configuration of its shape. By comparing the shape and curvature of a gliding motility, we found that the protruded portion of M. mobile correlated with, or possibly guided, its gliding direction. Considering the balance between decomposed gliding force and torque as a drag, a simple and general model that explains the curved trajectory of biomolecules under a low Reynolds number is proposed.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 1","pages":"e220006"},"PeriodicalIF":1.6,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018303/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056771","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

Exploring hydrophilic sequence space to search for uncharted foldable proteins by AlphaFold2. 利用AlphaFold2探索亲水序列空间，寻找未知的可折叠蛋白。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-02-01 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0005

Naoki Tomita, Hiroki Onoda, Leonard M G Chavas, George Chikenji

{"title":"Exploring hydrophilic sequence space to search for uncharted foldable proteins by AlphaFold2.","authors":"Naoki Tomita, Hiroki Onoda, Leonard M G Chavas, George Chikenji","doi":"10.2142/biophysico.bppb-v22.0005","DOIUrl":"10.2142/biophysico.bppb-v22.0005","url":null,"abstract":"Proteins typically fold into unique three-dimensional structures largely driven by interactions between hydrophobic amino acids. This understanding has helped improve our knowledge of protein folding. However, recent research has shown an exception to this idea, demonstrating that specific threonine-rich peptides have a strong tendency to form β-hairpin structures, even in the highly hydrophilic amino acid sequences. This finding suggests that the hydrophilic amino acid sequence space still leaves room for exploring foldable amino acid sequences. In this study, we conducted a systematic exploration of the repetitive amino acid sequence space by AlphaFold2 (AF2), with a focus on sequences composed exclusively of hydrophilic residues, to investigate their potential for adopting unique structures. As a result, the sequence space exploration suggested that several repetitive threonine-rich sequences adopt distinctive conformations and these conformational shapes can be influenced by the length of the sequence unit. Moreover, the analysis of structural dataset suggested that threonine contributes to the structural stabilization by forming non-polar atom packing that tolerates unsatisfied hydrogen bonds, and while also supporting other residues in forming hydrogen bonds. Our findings will broaden the horizons for the discovery of foldable amino acid sequences consisting solely of hydrophilic residues and help us clarify the unknown mechanisms of protein structural stabilization.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 1","pages":"e220005"},"PeriodicalIF":1.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936462/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712492","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

Improvement in positional accuracy of neural-network predicted hydration sites of proteins by incorporating atomic details of water-protein interactions and site-searching algorithm. 通过结合水-蛋白相互作用的原子细节和位点搜索算法，提高了神经网络预测蛋白质水化位点的定位精度。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-01-30 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0004

Kochi Sato, Masayoshi Nakasako

{"title":"Improvement in positional accuracy of neural-network predicted hydration sites of proteins by incorporating atomic details of water-protein interactions and site-searching algorithm.","authors":"Kochi Sato, Masayoshi Nakasako","doi":"10.2142/biophysico.bppb-v22.0004","DOIUrl":"10.2142/biophysico.bppb-v22.0004","url":null,"abstract":"Visualization of hydration structures over the entire protein surface is necessary to understand why the aqueous environment is essential for protein folding and functions. However, it is still difficult for experiments. Recently, we developed a convolutional neural network (CNN) to predict the probability distribution of hydration water molecules over protein surfaces and in protein cavities. The deep network was optimized using solely the distribution patterns of protein atoms surrounding each hydration water molecule in high-resolution X-ray crystal structures and successfully provided probability distributions of hydration water molecules. Despite the effectiveness of the probability distribution, the positional differences of the predicted positions obtained from the local maxima as predicted sites remained inadequate in reproducing the hydration sites in the crystal structure models. In this work, we modified the deep network by subdividing atomic classes based on the electronic properties of atoms composing amino acids. In addition, the exclusion volumes of each protein atom and hydration water molecule were taken to predict the hydration sites from the probability distribution. These information on chemical properties of atoms leads to an improvement in positional prediction accuracy. We selected the best CNN from 47 CNNs constructed by systematically varying the number of channels and layers of neural networks. Here, we report the improvements in prediction accuracy by the reorganized CNN together with the details in the architecture, training data, and peak search algorithm.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 1","pages":"e220004"},"PeriodicalIF":1.6,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569133","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

A round table at IUPAB Congress in Kyoto 2024: Dreaming the next 50 years in our biophysics. 2024年京都IUPAB大会圆桌会议：生物物理学未来50年的梦想。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-01-25 eCollection Date: 2024-01-01 DOI: 10.2142/biophysico.bppb-v21.e2012

Kumiko Hayashi, Gerhard Hummer, Jerelle A Joseph, Rong Li, Takeharu Nagai, Shuichi Onami, Feng Zhang

引用次数: 0