Biophysics and Physicobiology最新文献_第2页

Bottom-up creation of cell-free molecular systems: Basic research toward social implementation 无细胞分子系统自下而上的创造:面向社会实施的基础研究

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0042

Izuru Kawamura, Ryuji Kawano, Tomoaki Matsuura

引用次数: 0

Recent progress in primitive polyester synthesis and membraneless microdroplet assembly. 原始聚酯合成及无膜微滴组装研究进展。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0012

Tony Z Jia, Kuhan Chandru

{"title":"Recent progress in primitive polyester synthesis and membraneless microdroplet assembly.","authors":"Tony Z Jia, Kuhan Chandru","doi":"10.2142/biophysico.bppb-v20.0012","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0012","url":null,"abstract":"While it is often believed that the origins of life required participation of early biomolecules, it has been recently proposed that \"non-biomolecules\", which would have been just as, if not more, abundant on early Earth, could have played a part. In particular, recent research has highlighted the various ways by which polyesters, which do not participate in modern biology, could have played a major role during the origins of life. Polyesters could have been synthesized readily on early Earth through simple dehydration reactions at mild temperatures involving abundant \"non-biological\" alpha hydroxy acid (AHA) monomers. This dehydration synthesis process results in a polyester gel, which upon further rehydration, can assemble into membraneless droplets proposed to be protocell models. These proposed protocells can provide functions to a primitive chemical system, such as analyte segregation or protection, which could have further led to chemical evolution from prebiotic chemistry to nascent biochemistry. Here, to further shed light into the importance of \"non-biomolecular\" polyesters at the origins of life and to highlight future directions of study, we review recent studies which focus on primitive synthesis of polyesters from AHAs and assembly of these polyesters into membraneless droplets. Specifically, most of the recent progress in this field in the last five years has been led by laboratories in Japan, and these will be especially highlighted. This article is based on an invited presentation at the 60th Annual Meeting of the Biophysical Society of Japan held in September, 2022 as an 18th Early Career Awardee.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200012"},"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/eb/b6/20_e200012.PMC10205575.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9526627","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

Updating view of membrane transport proteins by simulation studies 通过模拟研究更新膜转运蛋白的观点

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0041

Takashi Sumikama, Ben Corry, Junichi Ono, Chigusa Kobayashi, Kei-ichi Okazaki

引用次数: 0

Near-field optical microscopy toward its applications for biological studies. 近场光学显微镜在生物学研究中的应用。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0011

Takayuki Umakoshi

{"title":"Near-field optical microscopy toward its applications for biological studies.","authors":"Takayuki Umakoshi","doi":"10.2142/biophysico.bppb-v20.0011","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0011","url":null,"abstract":"Near-field scanning optical microscopy (NSOM) is a super-resolution optical microscopy based on nanometrically small near-field light at a metallic tip. It can be combined with various types of optical measurement techniques, including Raman spectroscopy, infrared absorption spectroscopy, and photoluminescence measurements, which provides unique analytical capabilities to a variety of scientific fields. In particular, to understand nanoscale details of advance materials and physical phenomena, NSOM has been often adopted in the fields of material science and physical chemistry. However, owing to the recent critical developments showing the great potential for biological studies, NSOM has also recently gained much attention in the biological field. In this article, we introduce recent developments made in NSOM, aiming at biological applications. The drastic improvement in the imaging speed has shown a promising application of NSOM for super-resolution optical observation of biological dynamics. Furthermore, stable imaging and broadband imaging were made possible owing to the advanced technologies, which provide a unique imaging method to the biological field. As NSOM has not been well exploited in biological studies to date, several rooms need to be explored to determine its distinct advantages. We discuss the possibility and perspective of NSOM for biological applications. This review article is an extended version of the Japanese article, Development of Near-field Scanning Optical Microscopy toward Its Application for Biological Studies, published in SEIBUTSU BUTSURI Vol. 62, p. 128-130 (2022).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200011"},"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/2a/88/20_e200011.PMC10205578.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9526624","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

Regulatory mechanisms of mitochondrial calcium uptake by the calcium uniporter complex. 单输钙复合物对线粒体钙摄取的调节机制。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0004

Akiko Yamada, Akira Watanabe, Takenori Yamamoto

引用次数: 0

E. coli production of a multi-disulfide bonded SARS-CoV-2 Omicron BA.5 RBD exhibiting native-like biochemical and biophysical properties & lt; i> E。coli产生多二硫键合SARS-CoV-2 Omicron BA.5 RBD，具有类似天然生物化学和生物物理特性

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0036

Rawiwan Wongnak, Subbaian Brindha, Takahiro Yoshizue, Sawaros Onchaiya, Kenji Mizutani, Yutaka Kuroda

{"title":"E. coli production of a multi-disulfide bonded SARS-CoV-2 Omicron BA.5 RBD exhibiting native-like biochemical and biophysical properties","authors":"Rawiwan Wongnak, Subbaian Brindha, Takahiro Yoshizue, Sawaros Onchaiya, Kenji Mizutani, Yutaka Kuroda","doi":"10.2142/biophysico.bppb-v20.0036","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0036","url":null,"abstract":"Low-cost bacterial production of the receptor binding domain (RBD) of the SARS-CoV-2 Omicron spike protein holds significant potential in expediting the development of therapeutics against COVID-19. However, RBD contains eight cysteines forming four disulfide bonds, and expression in E. coli produces insoluble RBD forming non-native disulfide bonds. Here, we expressed RBD in E. coli T7 SHuffle with high aeration, which enhanced disulfide formation in the cytoplasm and reshuffling of non-native disulfide bonds, and at a low temperature of 16°C, which stabilized the native conformation and thus the formation of the native disulfide bonds. The yield of RBD was as high as 3mg per 200 mL culture. We analyzed the conformational and biophysical properties of our E. coli-expressed RBD. First, the RP-HPLC elution profile indicated a single peak suggesting that RBD was folded with a single disulfide bond pairing pattern. Next, circular dichroism analysis indicated a secondary structure content very close to that computed from the crystal structure. RBD’s thermal denaturation monitored by CD was cooperative, strongly indicating a well-folded protein structure. Moreover, limited proteolysis showed that RBD was nearly as stable as RNase A, and the formation of native disulfide bonds was confirmed by LC-MS analysis. Furthermore, BLI analysis indicated a strong binding of RBD with the hACE2 with a dissociation constant of 0.83 nM, confirming the folded nature of RBD. Altogether, these results demonstrate that our E. coli-expression system can provide a large amount of highly purified RBD with correct disulfide bonds and native-like biochemical and biophysical properties.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"26 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135596303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hybrid Biophysics: Interdisciplinary approaches for trans-scale analysis of organism-environment interactions 混合生物物理学:跨尺度分析生物-环境相互作用的跨学科方法

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0043

Madoka Suzuki, Kotaro Oyama, Toshiko Yamazawa

引用次数: 0

Removing the parachuting artifact using two-way scanning data in high-speed atomic force microscopy. 利用高速原子力显微镜的双向扫描数据去除跳伞伪影。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0006

Shintaroh Kubo, Kenichi Umeda, Noriyuki Kodera, Shoji Takada

{"title":"Removing the parachuting artifact using two-way scanning data in high-speed atomic force microscopy.","authors":"Shintaroh Kubo, Kenichi Umeda, Noriyuki Kodera, Shoji Takada","doi":"10.2142/biophysico.bppb-v20.0006","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0006","url":null,"abstract":"The high-speed atomic force microscopy (HS-AFM) is a unique and prominent method to observe structural dynamics of biomolecules at single molecule level at near-physiological condition. To achieve high temporal resolution, the probe tip scans the stage at high speed which can cause the so-called parachuting artifact in the HS-AFM images. Here, we develop a computational method to detect and remove the parachuting artifact in HS-AFM images using the two-way scanning data. To merge the two-way scanning images, we employed a method to infer the piezo hysteresis effect and to align the forward- and backward-scanning images. We then tested our method for HS-AFM videos of actin filaments, molecular chaperone, and duplex DNA. Together, our method can remove the parachuting artifact from the raw HS-AFM video containing two-way scanning data and make the processed video free from the parachuting artifact. The method is general and fast so that it can easily be applied to any HS-AFM videos with two-way scanning data.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200006"},"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/31/3e/20_e200006.PMC10205583.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9526628","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

Changes in protein phosphorylation by insulin administration in the central nervous system of the gastropod mollusk Lymnaea stagnalis 胰岛素对腹足类软体动物中枢神经系统蛋白磷酸化的影响

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0038

Junko Nakai, Kengo Namiki, Yuki Totani, Shigeki Yasumasu, Teruki Yoshimura, Takashi Aoki, Etsuro Ito

{"title":"Changes in protein phosphorylation by insulin administration in the central nervous system of the gastropod mollusk Lymnaea stagnalis","authors":"Junko Nakai, Kengo Namiki, Yuki Totani, Shigeki Yasumasu, Teruki Yoshimura, Takashi Aoki, Etsuro Ito","doi":"10.2142/biophysico.bppb-v20.0038","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0038","url":null,"abstract":"In the gastropod mollusk Lymnaea stagnalis, insulin-like peptides in the central nervous system (CNS) control behavioral changes associated with associative learning. Insulin administration to the Lymnaea CNS enhances the synaptic plasticity involved in this type of learning, but it has remained unclear which molecules in the insulin response cascade are involved. Here, to advance a comprehensive analysis, we used two-dimensional electrophoresis and comparative quantitative mass spectrometry to perform a protein analysis investigating the CNS molecules that respond to insulin administration. Our results revealed increased phosphorylation of AKT and RICTOR in the PI3K/AKT/mTOR signaling cascade and cytoskeleton-related proteins. Although it was expected that the molecules in the PI3K/AKT/mTOR signaling cascade were phosphorylated by insulin administration, our findings confirmed the correlation between insulin-induced phosphorylation of cytoskeleton-related proteins strongly involved in the synaptic changes and learning and memory mechanisms. These results contribute to elucidate the relationship between the insulin response and learning and memory mechanisms not only in Lymnaea but also in various invertebrates and vertebrates.","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136256802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Molecular mechanisms of amyloid-β peptide fibril and oligomer formation: NMR-based challenges. 淀粉样蛋白-β肽原纤维和寡聚物形成的分子机制:基于核磁共振的挑战。

Biophysics and Physicobiology Pub Date : 2023-01-01 DOI: 10.2142/biophysico.bppb-v20.0007

Hidekazu Hiroaki

{"title":"Molecular mechanisms of amyloid-β peptide fibril and oligomer formation: NMR-based challenges.","authors":"Hidekazu Hiroaki","doi":"10.2142/biophysico.bppb-v20.0007","DOIUrl":"https://doi.org/10.2142/biophysico.bppb-v20.0007","url":null,"abstract":"To completely treat and ultimately prevent dementia, it is essential to elucidate its pathogenic mechanisms in detail. There are two major hypotheses for the pathogenesis of Alzheimer's dementia: the β-amyloid (Aβ) hypothesis and the tau hypothesis. The modified amyloid hypothesis, which proposes that toxic oligomers rather than amyloid fibrils are the essential cause, has recently emerged. Aβ peptides [Aβ(1-40) and Aβ(1-42)] form highly insoluble aggregates in vivo and in vitro. These Aβ aggregates contain many polymorphisms, whereas Aβ peptides are intrinsically disordered in physiological aqueous solutions without any compact conformers. Over the last three decades, solid-state nuclear magnetic resonance (NMR) has greatly contributed to elucidating the structure of each polymorph, while solution NMR has revealed the dynamic nature of the transient conformations of the monomer. Moreover, several methods to investigate the aggregation process based on the observation of magnetization saturation transfer have also been developed. The complementary use of NMR methods with cryo-electron microscopy, which has rapidly matured, is expected to clarify the relationship between the amyloid and molecular pathology of Alzheimer's dementia in the near future. This review article is an extended version of the Japanese article, Insights into the Mechanisms of Oligomerization/Fibrilization of Amyloid β Peptide from Nuclear Magnetic Resonance, published in SEIBUTSU BUTSURI Vol. 62, p. 39-42 (2022).","PeriodicalId":8976,"journal":{"name":"Biophysics and Physicobiology","volume":"20 1","pages":"e200007"},"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/c2/bf/20_e200007.PMC10205579.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9520297","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