Biophysics and Physicobiology最新文献

Optogenetics II, sponsored by JST: Report for the session 13. 光遗传学 II，由 JST 赞助：会议报告 13.

Biophysics and Physicobiology Pub Date : 2023-03-02 eCollection Date: 2023-03-21 DOI: 10.2142/biophysico.bppb-v20.s020

Hiroo Imai, Hideki Kandori

引用次数: 0

MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV-visible spectroscopy combined with size-exclusion chromatography. MOLASS:用于自动处理从小角度x射线散射和紫外可见光谱结合尺寸排除色谱获得的矩阵数据的软件。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0001

Kento Yonezawa, Masatsuyo Takahashi, Keiko Yatabe, Yasuko Nagatani, Nobutaka Shimizu

{"title":"MOLASS: Software for automatic processing of matrix data obtained from small-angle X-ray scattering and UV-visible spectroscopy combined with size-exclusion chromatography.","authors":"Kento Yonezawa, Masatsuyo Takahashi, Keiko Yatabe, Yasuko Nagatani, Nobutaka Shimizu","doi":"10.2142/biophysico.bppb-v20.0001","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0001","url":null,"abstract":"Recent small-angle X-ray scattering (SAXS) for biological macromolecules (BioSAXS) is generally combined with size-exclusion chromatography (SEC-SAXS) at synchrotron facilities worldwide. For SEC-SAXS analysis, the final scattering profile for the target molecule is calculated from a large volume of continuously collected data. It would be ideal to automate this process; however, several complex problems exist regarding data measurement and analysis that have prevented automation. Here, we developed the analytical software MOLASS (Matrix Optimization with Low-rank factorization for Automated analysis of SEC-SAXS) to automatically calculate the final scattering profiles for solution structure analysis of target molecules. In this paper, the strategies for automatic analysis of SEC-SAXS data are described, including correction of baseline-drift using a low percentile method, optimization of peak decompositions composed of multiple scattering components using modified Gaussian fitting against the chromatogram, and rank determination for extrapolation to infinite dilution. In order to easily calculate each scattering component, the Moore-Penrose pseudo-inverse matrix is adopted as a basic calculation. Furthermore, this analysis method, in combination with UV-visible spectroscopy, led to better results in terms of accuracy in peak decomposition. Therefore, MOLASS will be able to smoothly suggest to users an accurate scattering profile for the subsequent structural analysis.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200001"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/6c/80/20_e200001.PMC10203098.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9518816","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

Revisiting oxytocin generation in keratinocytes. 重新审视角化细胞中催产素的产生。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0003

Kanta Fujimoto, Kosuke Inada, Kotaro Oka, Etsuro Ito

{"title":"Revisiting oxytocin generation in keratinocytes.","authors":"Kanta Fujimoto, Kosuke Inada, Kotaro Oka, Etsuro Ito","doi":"10.2142/biophysico.bppb-v20.0003","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0003","url":null,"abstract":"Some evidence suggests that oxytocin, which is a neuropeptide conventionally thought to be synthesized in the hypothalamus and released by the posterior pituitary, is generated in peripheral keratinocytes, but the details are lacking and the mRNA analysis is further required. Oxytocin and neurophysin I are generated together as cleavage products after splitting the precursor molecule, preprooxyphysin. To confirm that oxytocin and neurophysin I are also generated in the peripheral keratinocytes, it must first be clarified that these molecules contained in peripheral keratinocytes did not originate in the posterior pituitary gland and then the expression of oxytocin and neurophysin I mRNAs must be established in keratinocytes. Therefore, we attempted to quantify preprooxyphysin mRNA in keratinocytes using various primers. Using real-time PCR, we observed that the mRNAs of both oxytocin and neurophysin I were located in keratinocytes. However, the mRNA amounts of oxytocin, neurophysin I, and preprooxyphysin were too small to confirm their co-existence in keratinocytes. Thus, we had to further determine whether the PCR-amplified sequence was identical to preprooxyphysin. The PCR products analyzed by DNA sequencing were identical to preprooxyphysin, finally determining the co-existence of both oxytocin and neurophysin I mRNAs in keratinocytes. In addition, the immunocytochemical experiments showed that oxytocin and neurophysin I proteins were located in keratinocytes. These results of the present study provided further support indicating that oxytocin and neurophysin I are generated in peripheral keratinocytes.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200003"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d3/c5/20_e200003.PMC10205573.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9531814","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 third Japan-U.S. symposium on motor proteins and associated single-molecule biophysics 第三是日美关系。运动蛋白和相关的单分子生物物理学研讨会

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0037

Tomohiro Shima, Kumiko Hayashi

引用次数: 0

Regulation of motor activity of ciliary outer-arm dynein by the light chain 1; Implications from the structure of the light chain bound to the microtubule-binding domain of the heavy chain. 轻链1对纤毛外臂动力蛋白运动活动的调控轻链结合到重链微管结合域的结构意义。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0008

Toshiki Yagi, Akiyuki Toda, Muneyoshi Ichikawa, Genji Kurisu

{"title":"Regulation of motor activity of ciliary outer-arm dynein by the light chain 1; Implications from the structure of the light chain bound to the microtubule-binding domain of the heavy chain.","authors":"Toshiki Yagi, Akiyuki Toda, Muneyoshi Ichikawa, Genji Kurisu","doi":"10.2142/biophysico.bppb-v20.0008","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0008","url":null,"abstract":"Ciliary bending movements are powered by motor protein axonemal dyneins. They are largely classified into two groups, inner-arm dynein and outer-arm dynein. Outer-arm dynein, which is important for the elevation of ciliary beat frequency, has three heavy chains (α, β, and γ), two intermediate chains, and more than 10 light chains in green algae, Chlamydomonas. Most of intermediate chains and light chains bind to the tail regions of heavy chains. In contrast, the light chain LC1 was found to bind to the ATP-dependent microtubule-binding domain of outer-arm dynein γ-heavy chain. Interestingly, LC1 was also found to interact with microtubules directly, but it reduces the affinity of the microtubule-binding domain of γ-heavy chain for microtubules, suggesting the possibility that LC1 may control ciliary movement by regulating the affinity of outer-arm dyneins for microtubules. This hypothesis is supported by the LC1 mutant studies in Chlamydomonas and Planaria showing that ciliary movements in LC1 mutants were disordered with low coordination of beating and low beat frequency. To understand the molecular mechanism of the regulation of outer-arm dynein motor activity by LC1, X-ray crystallography and cryo-electron microscopy have been used to determine the structure of the light chain bound to the microtubule-binding domain of γ-heavy chain. In this review article, we show the recent progress of structural studies of LC1, and suggest the regulatory role of LC1 in the motor activity of outer-arm dyneins. This review article is an extended version of the Japanese article, The Complex of Outer-arm Dynein Light Chain-1 and the Microtubule-binding Domain of the Heavy Chain Shows How Axonemal Dynein Tunes Ciliary Beating, published in SEIBUTSU BUTSURI Vol. 61, p. 20-22 (2021).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200008"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/94/e3/20_e200008.PMC10205576.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9526629","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

Rocking Out Biophysics in IUPAB2024 Kyoto! IUPAB2024京都震撼生物物理学!

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0039

Hiroyuki Noji

引用次数: 0

What is Aromaphilicity? 什么是亲香性?

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0002

Atsushi Hirano

{"title":"What is Aromaphilicity?","authors":"Atsushi Hirano","doi":"10.2142/biophysico.bppb-v20.0002","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0002","url":null,"abstract":"Proteins and peptides have the ability to interact with various substances such as biological molecules and artificial objects. In principle, these interactions are attributed to the interplays of amino acid residues and peptide bonds with target substances and are often described in physical terms, including electrostatic interaction, hydrogen bond, and van der Waals interaction. However, in some practical cases, conceptual scales and indices for describing the nature of amino acids, such as the hydrophilicity scale and the hydropathy index, are more useful for understanding the interactions. In recent years, I have investigated the affinity of proteins and peptides for aromatic carbon materials, such as carbon nanotubes (CNTs) and graphene, and realized that this affinity is barely described by conventional scales and indices. After speculating whether a more suitable index for describing the affinity of amino acids for aromatic carbon materials is available in such a situation, I recognized the need for a new concept that describes such an affinity. Upon establishing this concept, I named the affinity for aromatic carbon material surfaces “aromaphilicity,” meaning an aromatic-loving nature. In this Commentary and Perspective, I summarized my recent works with my collaborators regarding physical interactions between amino acids (or amino acid residues) and aromatic carbon material surfaces and introduced a new index— aromaphilicity index—of amino acids. The aromaphilicity index is unique and distinct from conventional indices for amino acids, offering prospective applications as a universal index for describing the properties of amino acids.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200002"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/f5/b9/20_e200002.PMC10205572.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9531813","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

Stable wide-field voltage imaging for observing neuronal plasticity at the neuronal network level. 稳定宽场电压成像在神经网络水平上观察神经元可塑性。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0015

Takashi Tominaga, Riichi Kajiwara, Yoko Tominaga

引用次数: 1

Dieter Oesterhelt (1940–2022): Life with light and color, pioneer of membrane protein research Dieter Oesterhelt(1940-2022):光与色的生命，膜蛋白研究的先驱

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.s010

Peter Hegemann, Hartmut Michel

引用次数: 1

Mechanisms of polyphosphate-induced amyloid fibril formation triggered by breakdown of supersaturation. 过饱和分解触发多磷酸盐诱导淀粉样蛋白纤维形成的机制。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0013

Keiichi Yamaguchi, Kichitaro Nakajima, Yuji Goto

{"title":"Mechanisms of polyphosphate-induced amyloid fibril formation triggered by breakdown of supersaturation.","authors":"Keiichi Yamaguchi, Kichitaro Nakajima, Yuji Goto","doi":"10.2142/biophysico.bppb-v20.0013","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0013","url":null,"abstract":"Much effort has been devoted to elucidate mechanisms of amyloid fibril formation using various kinds of additives, such as salts, metals, detergents, and biopolymers. Here, we review the effects of additives with a focus on polyphosphate (polyP) on amyloid fibril formation of β2-microglobulin (β2m) and α-synuclein (αSyn). PolyP, consisting of up to 1,000 phosphoanhydride bond-linked phosphate monomers, is one of the most ancient, enigmatic, and negatively charged molecules in biology. Amyloid fibril formation of both β2m and αSyn could be accelerated by counter anion-binding and preferential hydration at relatively lower and higher concentrations of polyP, respectively, depending on the chain length of polyP. These bimodal concentration-dependent effects were also observed in salt- and heparin-induced amyloid fibril formation, indicating the generality of bimodal effects. We also address the effects of detergents, alcohols, and isoelectric point precipitation on amyloid fibril formation, in comparison with the effects of salts. Because polyP is present all around us, from cellular components to food additives, clarifying its effects and consequent biological roles will be important to further advance our understanding of amyloid fibrils. This review article is an extended version of the Japanese article, Linking Protein Folding to Amyloid Formation, published in SEIBUTSU BUTSURI Vol. 61, p. 358-365 (2021).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200013"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d3/86/20_e200013.PMC10338051.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9819953","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