Biophysics and physicobiology最新文献

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

Product release and substrate entry of aldehyde deformylating oxygenase revealed by molecular dynamics simulations. 分子动力学模拟揭示了醛脱甲酰基加氧酶的产物释放和底物进入。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-01-09 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0003

Masataka Yoshimura, Munehito Arai

{"title":"Product release and substrate entry of aldehyde deformylating oxygenase revealed by molecular dynamics simulations.","authors":"Masataka Yoshimura, Munehito Arai","doi":"10.2142/biophysico.bppb-v22.0003","DOIUrl":"10.2142/biophysico.bppb-v22.0003","url":null,"abstract":"Cyanobacteria can produce alkanes equivalent to diesel fuels through a two-step enzymatic process involving acyl-(acyl carrier protein) reductase (AAR) and aldehyde deformylating oxygenase (ADO), providing a potential renewable biofuel source. AAR binds to ADO for efficient delivery of an aldehyde substrate and they have been proposed to dissociate when the alkane product is released from the same site as the substrate entrance of ADO. However, the dynamics of the substrate and product in ADO during substrate entry and product release are poorly understood. Here, we performed molecular dynamics (MD) simulations of ADO in the presence of substrate or product. We found that while the aldehyde substrate remains close to the active center of ADO before catalysis, the alkane product can dynamically rotate within the hydrophobic tunnel inside ADO toward the product exit after catalysis. Furthermore, the parallel cascade selection (PaCS)-MD simulations of ADO and the AAR/ADO complex identified the locations of the substrate entrance and the multiple exits for product release on ADO. Strikingly, the PaCS-MD simulations revealed that the alkane product can be released from the exit different from the substrate entrance without dissociation of AAR. Based on these results, we propose a reaction model for efficient alkane production by the AAR/ADO complex in which aldehydes and alkanes are synthesized simultaneously while AAR and ADO remain bound, and the aldehyde substrate can be delivered to ADO immediately after alkane release. Our study will be useful in improving the efficiency of bioalkane production using AAR and ADO.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 1","pages":"e220003"},"PeriodicalIF":1.6,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876802/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569173","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

Measurement of protoplasmic streaming over the entire body of Physarum plasmodium, and estimation of the transport and mixing of protoplasma through the intricate vein network. 绒泡菌整个体的原生质流的测量，以及原生质通过复杂的静脉网络的运输和混合的估计。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-01-09 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0002

Yo Sato, Charles Fosseprez, Yukinori Nishigami, Katsuhiko Sato, Hiroshi Orihara, Toshiyuki Nakagaki

引用次数: 0

Near-infrared spectroscopic study of blood flow changes in the dorsolateral prefrontal cortex during pain relief by odor stimulation. 气味刺激缓解疼痛时背外侧前额叶皮层血流变化的近红外光谱研究。

IF 1.6

Biophysics and physicobiology Pub Date : 2024-12-26 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.0001

Yuki Okamura, Shogo Takayama, Kengo Namiki, Fusako Koshikawa, Etsuro Ito

{"title":"Near-infrared spectroscopic study of blood flow changes in the dorsolateral prefrontal cortex during pain relief by odor stimulation.","authors":"Yuki Okamura, Shogo Takayama, Kengo Namiki, Fusako Koshikawa, Etsuro Ito","doi":"10.2142/biophysico.bppb-v22.0001","DOIUrl":"10.2142/biophysico.bppb-v22.0001","url":null,"abstract":"Chronic pain is an unpleasant experience caused by sensory and emotional instability, sometimes independent of actual tissue damage. Pain relief can greatly impact psychologic, social, and economic well-being. Aromatherapy has long been used to alleviate pain and previous studies demonstrated that odors alter cerebral blood flow. In the present study, we used near-infrared spectroscopy to test our hypothesis that olfactory stimulation contributes to pain relief by altering cerebral blood flow in brain regions associated with pain. Pain was induced by transcutaneous electrical stimulation and assessed using a visual analog scale. Peppermint and lavender olfactory stimuli were used. Based on previous results, we focused on the prefrontal cortex. A placebo experiment in which only air stimulation was presented revealed minimal changes in blood flow in the ventromedial prefrontal cortex when comparing pain stimulation alone and a combination of placebo and pain stimulation. We then examined changes in blood flow following the presentation of peppermint or lavender scents. Significant differences in blood flow were observed in the dorsolateral prefrontal cortex (DLPFC) between pain stimulation alone and pain stimulation combined with odor stimulation. These findings supported our previous finding that the DLPFC is involved in pain relief by patch-adhered stimulation, but odor stimulation activated the right DLPFC whereas patch-adhered stimulation suppressed the left DLPFC. One interpretation of the discrepancy is that the contrast of activation between the right and left DLPFC is important in pain relief. Our research will help to elucidate the neurologic mechanisms underlying pain relief.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"22 1","pages":"e220001"},"PeriodicalIF":1.6,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876804/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143569162","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