Biophysics and physicobiology最新文献

NMR evidence for residue-based LFER relationship in two-state folding-unfolding equilibrium of the spectrin SH3 domain in acidic solutions. 酸性溶液中SH3谱域两态折叠-展开平衡中残基LFER关系的核磁共振证据。

IF 1.6

Biophysics and physicobiology Pub Date : 2026-03-05 eCollection Date: 2026-01-01 DOI: 10.2142/biophysico.bppb-v23.0011

Seiichiro Hayashi, Daisuke Fujinami, Daisuke Kohda

{"title":"NMR evidence for residue-based LFER relationship in two-state folding-unfolding equilibrium of the spectrin SH3 domain in acidic solutions.","authors":"Seiichiro Hayashi, Daisuke Fujinami, Daisuke Kohda","doi":"10.2142/biophysico.bppb-v23.0011","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v23.0011","url":null,"abstract":"The conformational change of a protein molecule is described by the single equilibrium constant K and the single rate constants, k (forward) and k' (reverse). The underlying assumption is that all amino acid residues undergo state changes with perfect cooperativity. However, residue-specific measurements such as NMR often show residue-to-residue variations in these constants, indicating that proteins are not fully cooperative. Theoretical considerations based on \"the consistency principle of protein folding\" demonstrated that the linear free energy relationship (LFER) observed in residue-specific log k vs. log K plots is the physicochemical basis for smooth conformational changes of protein molecules. The residue-based LFER was found in many protein-related phenomena, but the structural changes have been limited to relatively small ones, such as fluctuations in the folded state and the coupled binding and folding of intrinsically disordered proteins. Here, we applied NMR to the two-state exchange equilibrium of the spectrin SH3 domain in acidic solutions and determined residue-specific equilibrium and rate constants. The data points obtained from the wild-type and its two single amino acid mutants were aligned on a single line in the log k vs. log K plot, indicating that residue-based LFER applies to large structural changes between the unfolded and folded states of the SH3 domain. The mutation-induced shifts in the distribution ranges of residue-specific equilibrium and rate constants are useful for establishing residue-based LFERs for all kinds of protein structural changes, including the refolding from a fully unfolded state, caused by the removal of a denaturant.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"23 1","pages":"e230011"},"PeriodicalIF":1.6,"publicationDate":"2026-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694671","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

Liquid-liquid phase separation and its regulation of the BACH2 intrinsically disordered region. 液液相分离及其对BACH2本质无序区的调控。

IF 1.6

Biophysics and physicobiology Pub Date : 2026-02-25 eCollection Date: 2026-01-01 DOI: 10.2142/biophysico.bppb-v23.0010

Hironori Hayashi, Miyuki Kato-Murayama, Takeshi Kurasawa, Eiichi N Kodama, Mikako Shirouzu, Kazuhiko Igarashi, Kazutaka Murayama

{"title":"Liquid-liquid phase separation and its regulation of the BACH2 intrinsically disordered region.","authors":"Hironori Hayashi, Miyuki Kato-Murayama, Takeshi Kurasawa, Eiichi N Kodama, Mikako Shirouzu, Kazuhiko Igarashi, Kazutaka Murayama","doi":"10.2142/biophysico.bppb-v23.0010","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v23.0010","url":null,"abstract":"Intrinsically disordered regions (IDRs) are vital for several cellular processes. They play a significant role in liquid-liquid phase separation (LLPS). LLPS enhances reaction efficiency by locally concentrating proteins and nucleic acids. The BACH2 transcription factor contains such IDRs. Early observations hinted at the phase separation capabilities of BACH2. However, how BACH2-IDR directly participates in LLPS is not fully understood. Its precise modulation by heme binding and phosphorylation also requires further elucidation. This study experimentally demonstrated the intrinsic capability of BACH2-IDR (residues 331-520) to undergo LLPS in vitro. Microscopic observations revealed that TANK-binding kinase 1(TBK1)-mediated phosphorylation suppressed LLPS of BACH2-IDR. Conversely, the coexistence of heme enhanced LLPS, initiating LLPS at lower polyethylene glycol concentrations. Bioinformatic analyses supported these experimental observations. Tools such as FuzDrop and CIDER were used to predict LLPS propensity from sequences. Specifically, the calculations for the sequence of phosphorylation-mimic mutations showed changes in LLPS-promoting regions. Heme binding influenced TBK1-mediated phosphorylation sites. Some of these sites overlap with predicted LLPS-driving regions. Heme binding also induced substantial conformational alterations within BACH2-IDR. Consequently, we propose LLPS as a fundamental regulatory mechanism for BACH2 protein function. This process complements its known regulation through heme binding and phosphorylation.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"23 1","pages":"e230010"},"PeriodicalIF":1.6,"publicationDate":"2026-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694636","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 Norway-Japan bilateral symposium: Dialogue in biophysics beginning in Nara. 挪威-日本双边研讨会：生物物理学对话在奈良开始。

IF 1.6

Biophysics and physicobiology Pub Date : 2026-02-20 eCollection Date: 2026-01-01 DOI: 10.2142/biophysico.bppb-v23.0009

Yoshihiko Furuike, Oliver Vanderpoorten

引用次数: 0

Mirror life at the crossroads: Report on the symposia in Japan for discussion toward mirror life synthesis. 十字路口的镜像生命：在日本讨论镜像生命合成的专题讨论会报告。

IF 1.6

Biophysics and physicobiology Pub Date : 2026-02-20 eCollection Date: 2026-01-01 DOI: 10.2142/biophysico.bppb-v23.0008

Kei Fujiwara, Wataru Aoki, Chikara Furusawa, Ai Hasegawa, Gosuke Hayashi, Daisuke Kiga, Koichi Mikami, Sakura Takada, Yoshihiro Shimizu

{"title":"Mirror life at the crossroads: Report on the symposia in Japan for discussion toward mirror life synthesis.","authors":"Kei Fujiwara, Wataru Aoki, Chikara Furusawa, Ai Hasegawa, Gosuke Hayashi, Daisuke Kiga, Koichi Mikami, Sakura Takada, Yoshihiro Shimizu","doi":"10.2142/biophysico.bppb-v23.0008","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v23.0008","url":null,"abstract":"The synthesis of mirror life, an organism composed entirely of the mirror-image counterparts of naturally occurring biomolecules, may be a topic for science fiction today but is suggested to be a reality in the future. Scientists called for strict preemptive regulation for the synthesis of mirror life due to concerns regarding biosecurity risks, such as the potential threat of mirror life to humans and non-human ecosystems. This perspective reports on the discussions held at two recent symposia in Japan, at the Japanese Society for Cell Synthesis Research (JSCSR) meeting and at the Biophysical Society of Japan (BSJ) annual meeting. Participants, including synthetic biologists, social scientists and artists, discussed the feasibility of the synthesis of mirror-image artificial self-replicating cells and the balance between the risks and benefits of this emerging technology. The discussions indicate that, while safety management is essential, a rational, evidence-based framework developed through open dialogue with society is crucial for the responsible advancement of mirror life research.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"23 1","pages":"e230008"},"PeriodicalIF":1.6,"publicationDate":"2026-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694701","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

Modeling of viscous frictional force in multicellular morphogenesis. 多细胞形态发生过程中粘性摩擦力的建模。

IF 1.6

Biophysics and physicobiology Pub Date : 2026-02-19 eCollection Date: 2026-01-01 DOI: 10.2142/biophysico.bppb-v23.0007

Hiroshi Koyama, Yasuhiro Inoue

{"title":"Modeling of viscous frictional force in multicellular morphogenesis.","authors":"Hiroshi Koyama, Yasuhiro Inoue","doi":"10.2142/biophysico.bppb-v23.0007","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v23.0007","url":null,"abstract":"In morphogenesis, mechanical forces are the fundamental drivers of tissue deformation. To elucidate the principles governing this process, a thorough understanding of these forces is indispensable, and mathematical models are invaluable tools for this purpose. Various models have been developed, including vertex models suitable for representing epithelial cell mechanics, cell particle models for simulating the dynamics of large cell populations, and deformable cell models for describing complicated cell shapes. In these models, the motion of the objects is usually assumed to be overdamped by viscous friction. The viscous frictional forces are likely provided by liquid medium or body fluid, and they are also exerted in cell-cell and cell-extracellular matrix contacts. Furthermore, if these components, including the ECM, are in motion, the viscous frictional forces are affected by their motions. Because there seems to be little consensus on how to model the viscous frictional forces, we organize and review them in this article where we exemplified the vertex model and the particle model.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"23 1","pages":"e230007"},"PeriodicalIF":1.6,"publicationDate":"2026-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694623","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

Comparative evaluation of electrode configuration for optimizing positive dielectrophoresis trapping of CCRF-CEM cells. 优化CCRF-CEM细胞正电介质电泳捕获的电极配置比较评价。

IF 1.6

Biophysics and physicobiology Pub Date : 2026-02-17 eCollection Date: 2026-01-01 DOI: 10.2142/biophysico.bppb-v23.0006

Miftakhul Firdhaus, Ulya Farahdina, Nasori Nasori, Endarko Endarko, Agus Rubiyanto

{"title":"Comparative evaluation of electrode configuration for optimizing positive dielectrophoresis trapping of CCRF-CEM cells.","authors":"Miftakhul Firdhaus, Ulya Farahdina, Nasori Nasori, Endarko Endarko, Agus Rubiyanto","doi":"10.2142/biophysico.bppb-v23.0006","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v23.0006","url":null,"abstract":"Dielectrophoresis (DEP) is a promising label-free technique for bioparticle manipulation, offering significant potential for diagnostic application such as isolation and trapping of cancerous CCRF-CEM cells. The efficacy of DEP trapping is critically dependent on the interaction between the cell's dielectric properties and the spatial gradient of the squared electric field (∇|E2|), which is governed by electrode geometry. This study conducts a comparative evaluation, via finite element method (FEM) analysis, to quantify the positive dielectrophoresis (pDEP) force exerted on CCRF-CEM cells. Four distinct electrode configurations were analyzed: parallel (rectangular, triangular, cylindrical) and interdigitated. Based on a single-shell model for CCRF-CEM cells within a low-conductivity buffer, the Clausius-Mossotti factor was determined at 4.6 MHz, confirming a strong pDEP response that attracts cells to high-field regions. Results demonstrate that the pDEP force scales quadratically with applied voltage and is significantly enhanced by reducing the electrode gap. At a standardized 25 Vpp and 100 μm gap, the interdigitated configuration generated the highest maximum pDEP force, substantially exceeding the parallel rectangular, triangular, and cylindrical designs. Furthermore, the interdigitated geometry produced the most extensive and uniform high-force zones along the electrode edges, creating a superior trapping area. This comparative evaluation provides quantitative guidelines for optimizing electrode design, identifying the interdigitated configuration as the most effective for developing high-efficiency microdevices for CCRF-CEM cell trapping.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"23 1","pages":"e230006"},"PeriodicalIF":1.6,"publicationDate":"2026-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694641","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

Mechanistic insights into a cold-adapted glucokinase with high thermal stability were revealed by site-directed spin labeling ESR. 通过位点定向自旋标记ESR揭示了具有高热稳定性的冷适应葡萄糖激酶的机制。

IF 1.6

Biophysics and physicobiology Pub Date : 2026-02-17 eCollection Date: 2026-01-01 DOI: 10.2142/biophysico.bppb-v23.0005

Akane Yato, Masaki Horitani

{"title":"Mechanistic insights into a cold-adapted glucokinase with high thermal stability were revealed by site-directed spin labeling ESR.","authors":"Akane Yato, Masaki Horitani","doi":"10.2142/biophysico.bppb-v23.0005","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v23.0005","url":null,"abstract":"The structural flexibility of enzymes plays an essential role in determining their catalytic efficiency and thermal stability. Cold-adapted enzymes are typically highly flexible, resulting in high catalytic activity but low stability. Glucokinase (GK) consists of the large substrates binding domain, small catalytic domain, and hinge region that undergoes conformational changes upon substrates binding. We recently reported that the psychrophilic GK from Pseudoalteromonas sp. AS-131 (PsGK) exhibits both high catalytic efficiency and remarkable thermal stability compared to the mesophilic GK from Escherichia coli (EcGK). We also found that a disulfide bond connecting the N- and C-termini in PsGK contributes to its unusual thermal stability. However, cold adaptation mechanism of cold-adapted PsGK has remained unclear. To clarify how PsGK acquires high activity, we utilized site-directed spin labeling electron spin resonance (SDSL-ESR) spectroscopy for PsGK and EcGK in the absence and presence of substrates in the wide range of temperatures. PsGK without substrates was more flexible than EcGK. Particularly, the small domain and hinge region of PsGK were highly flexible while its large domain was relatively rigid. In contrast, EcGK showed lower entire flexibility and did not exhibit domain dependent differences. When the substrates were bound, both enzymes became more rigid, but the small domain and hinge region of PsGK was still flexible whereas its large domain was considerably rigid. These results suggest that enhancing catalytic activity requires increasing flexibility only in proper sites rather than in the entire enzyme. These findings provide insight into how cold-adapted enzymes balance activity and stability.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"23 1","pages":"e230005"},"PeriodicalIF":1.6,"publicationDate":"2026-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13077128/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147694667","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

Resurrecting lost ancient myoglobin proteins to elucidate mechanisms of diving adaptation in mammals. 复活消失的古代肌红蛋白以阐明哺乳动物潜水适应的机制。

IF 1.6

Biophysics and physicobiology Pub Date : 2026-01-16 eCollection Date: 2026-01-01 DOI: 10.2142/biophysico.bppb-v23.0004

Hiroshi Imamura, Yasuhiro Isogai, Tsuyoshi Shirai

引用次数: 0

Development of electromagnetic tweezers for single-molecule energetics of kinesin. 单分子动力学电磁镊子的研制。

IF 1.6

Biophysics and physicobiology Pub Date : 2026-01-07 eCollection Date: 2026-01-01 DOI: 10.2142/biophysico.bppb-v23.0003

Haruyuki Fukuzawa, Yuga Ihara, Masato Sawa, Hidekazu Shirai, Sawako Enoki, Keigo Ikezaki, Taketoshi Kambara, Yasushi Okada

{"title":"Development of electromagnetic tweezers for single-molecule energetics of kinesin.","authors":"Haruyuki Fukuzawa, Yuga Ihara, Masato Sawa, Hidekazu Shirai, Sawako Enoki, Keigo Ikezaki, Taketoshi Kambara, Yasushi Okada","doi":"10.2142/biophysico.bppb-v23.0003","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v23.0003","url":null,"abstract":"Optical tweezers have enabled single-molecule measurements of kinesin mechanics and energetics but face challenges for in vivo applications due to photothermal effects and refractive-index-dependent force calibration. Here, we developed electromagnetic tweezers featuring horizontal magnetic field geometry that enables force application along the microtubule axis for translational motor measurements. We validated the platform by reproducing established kinesin mechanics: stall force of ~6 pN and, using the Harada-Sasa equality to quantify nonequilibrium dissipation, an estimated energy conversion efficiency of ~20%, both consistent with optical tweezers results. We further demonstrated that FDT violations increase with ATP concentration following Michaelis-Menten kinetics, consistent with kinesin's enzymatic turnover. These results establish electromagnetic tweezers as a complementary tool offering advantages in high-throughput measurements and environment-independent force calibration, providing a foundation for future applications where these capabilities are essential.","PeriodicalId":101323,"journal":{"name":"Biophysics and physicobiology","volume":"23 1","pages":"e230003"},"PeriodicalIF":1.6,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12972615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147439060","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

Towards the International Conference on Biophysics and Biomedical Sciences: ICBBS 2026. 迈向生物物理学和生物医学科学国际会议：ICBBS 2026。

IF 1.6

Biophysics and physicobiology Pub Date : 2025-12-26 eCollection Date: 2025-01-01 DOI: 10.2142/biophysico.bppb-v22.s001

Sam-Yong Park, Haruki Nakamura

引用次数: 0