生物物理学报:英文版最新文献_第2页

Identifying intact N-glycopeptides from tandem mass spectrometry data using StrucGP. 使用StrucGP从串联质谱数据中鉴定完整的n -糖肽。

生物物理学报:英文版 Pub Date : 2022-12-31 DOI: 10.52601/bpr.2022.220010

Jiechen Shen, Zexuan Chen, Shisheng Sun

引用次数: 0

A protocol of using PTMiner for quality control and localization of protein modifications identified by open or closed search of tandem mass spectra. 一种使用PTMiner进行质量控制和定位的方案，通过开放或封闭的串联质谱搜索来鉴定蛋白质修饰。

生物物理学报:英文版 Pub Date : 2022-12-31 DOI: 10.52601/bpr.2022.220024

Zhiyuan Cheng, Ge Song, Yan Fu

引用次数: 0

DIA-MS2pep: a library-free framework for comprehensive peptide identification from data-independent acquisition data. DIA-MS2pep:从数据无关的采集数据中进行全面肽鉴定的无库框架。

生物物理学报:英文版 Pub Date : 2022-12-31 DOI: 10.52601/bpr.2022.220011

Junjie Hou, Jifeng Wang, Fuquan Yang, Tao Xu

{"title":"DIA-MS2pep: a library-free framework for comprehensive peptide identification from data-independent acquisition data.","authors":"Junjie Hou, Jifeng Wang, Fuquan Yang, Tao Xu","doi":"10.52601/bpr.2022.220011","DOIUrl":"https://doi.org/10.52601/bpr.2022.220011","url":null,"abstract":"Identifying peptides directly from data-independent acquisition (DIA) data remains challenging due to the highly multiplexed MS/MS spectra. Spectral library-based peptide detection is sensitive, but it is limited to the depth of the library and mutes the discovery potential of DIA data. We present here, DIA-MS2pep, a library-free framework for comprehensive peptide identification from DIA data. DIA-MS2pep uses a data-driven algorithm for MS/MS spectrum demultiplexing using the fragments data without the need of a precursor. With a large precursor mass tolerance database search, DIA-MS2pep can identify the peptides and their modified forms. We demonstrate the performance of DIA-MS2pep by comparing it to conventional library-free tools in accuracy and sensitivity of peptide identifications using publicly available DIA datasets of varying samples, including HeLa cell lysates, phosphopeptides, plasma, etc. Compared with data-dependent acquisition-based spectral libraries, spectral libraries built directly from DIA data with DIA-MS2pep improve the accuracy and reproducibility of the quantitative proteome.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":"8 5-6","pages":"253-268"},"PeriodicalIF":0.0,"publicationDate":"2022-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10166510/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9955043","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

Fast cross-linking by DOPA2 promotes the capturing of a stereospecific protein complex over nonspecific encounter complexes. DOPA2的快速交联促进了立体特异性蛋白复合物在非特异性相遇复合物上的捕获。

生物物理学报:英文版 Pub Date : 2022-12-31 DOI: 10.52601/bpr.2022.220014

Jian-Hua Wang, Zhou Gong, Xu Dong, Shu-Qun Liu, Yu-Liang Tang, Xiaoguang Lei, Chun Tang, Meng-Qiu Dong

{"title":"Fast cross-linking by DOPA2 promotes the capturing of a stereospecific protein complex over nonspecific encounter complexes.","authors":"Jian-Hua Wang, Zhou Gong, Xu Dong, Shu-Qun Liu, Yu-Liang Tang, Xiaoguang Lei, Chun Tang, Meng-Qiu Dong","doi":"10.52601/bpr.2022.220014","DOIUrl":"https://doi.org/10.52601/bpr.2022.220014","url":null,"abstract":"Transient and weak protein-protein interactions are essential to many biochemical reactions, yet are technically challenging to study. Chemical cross-linking of proteins coupled with mass spectrometry analysis (CXMS) provides a powerful tool in the analysis of such interactions. Central to this technology are chemical cross-linkers. Here, using two transient heterodimeric complexes EIN/HPr and EIIAGlc/EIIBGlc as our model systems, we evaluated the effects of two amine-specific homo-bifunctional cross-linkers with different reactivities. We showed previously that DOPA2 (di-ortho-phthalaldehyde with a di-ethylene glycol spacer arm) cross-links proteins 60-120 times faster than DSS (disuccinimidyl suberate). We found that though most of the intermolecular cross-links of either cross-linker are consistent with the encounter complexes (ECs), an ensemble of short-lived binding intermediates, more DOPA2 intermolecular cross-links could be assigned to the stereospecific complex (SC), the final lowest-energy conformational state for the two interacting proteins. Our finding suggests that faster cross-linking captures the SC more effectively and cross-linkers of different reactivities potentially probe protein-protein interaction dynamics across multiple timescales.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":"8 5-6","pages":"239-252"},"PeriodicalIF":0.0,"publicationDate":"2022-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10166511/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9955041","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: 1

Cell membrane sample preparation method of combined AFM and dSTORM analysis. 结合原子力显微镜和 dSTORM 分析的细胞膜样品制备方法。

生物物理学报:英文版 Pub Date : 2022-08-31 DOI: 10.52601/bpr.2022.220004

Mingjun Cai, Huili Wang, Guanfang Zhao, Hongru Li, Jing Gao, Hongda Wang

{"title":"Cell membrane sample preparation method of combined AFM and dSTORM analysis.","authors":"Mingjun Cai, Huili Wang, Guanfang Zhao, Hongru Li, Jing Gao, Hongda Wang","doi":"10.52601/bpr.2022.220004","DOIUrl":"10.52601/bpr.2022.220004","url":null,"abstract":"A major role of cell membranes is to provide an ideal environment for the constituent proteins to perform their biological functions. A deep understanding of the membrane proteins assembly process under physiological conditions is quite important to elucidate both the structure and the function of the cell membranes. Along these lines, in this work, a complete workflow of the cell membrane sample preparation and the correlated AFM and dSTORM imaging analysis methods are presented. A specially designed, angle-controlled sample preparation device was used to prepare the cell membrane samples. The correlated distributions of the specific membrane proteins with the topography of the cytoplasmic side of the cell membranes can be obtained by performing correlative AFM and dSTORM measurements. These methods are ideal for systematically studying the structure of the cell membranes. The proposed method of the sample characterization was not only limited to the measurement of the cell membrane but also can be applied for both biological tissue section analysis and detection.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":"8 4","pages":"183-192"},"PeriodicalIF":0.0,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10185485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9597302","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

DNA-binding proteins studied by mechanical manipulation and AFM imaging of single DNA molecules. 通过机械操作和单DNA分子的AFM成像研究DNA结合蛋白。

生物物理学报:英文版 Pub Date : 2022-08-31 DOI: 10.52601/bpr.2022.220015

Xiaodan Zhao, Xuyao Priscilla Liu, Jie Yan

引用次数: 1

Two-state model explaining thermodynamic regulation of thermo-gating channels. 解释热控通道热力学调节的双态模型。

生物物理学报:英文版 Pub Date : 2022-08-31 DOI: 10.52601/bpr.2022.220012

Xuejun C Zhang, Zhuoya Yu

{"title":"Two-state model explaining thermodynamic regulation of thermo-gating channels.","authors":"Xuejun C Zhang, Zhuoya Yu","doi":"10.52601/bpr.2022.220012","DOIUrl":"https://doi.org/10.52601/bpr.2022.220012","url":null,"abstract":"Temperature-sensitive ion channels, such as those from the TRP family (thermo-TRPs) present in all animal cells, serve to perceive heat and cold sensations. A considerable number of protein structures have been reported for these ion channels, providing a solid basis for revealing their structure-function relationship. Previous functional studies suggest that the thermosensing ability of TRP channels is primarily determined by the properties of their cytosolic domain. Despite their importance in sensing and wide interests in the development of suitable therapeutics, the precise mechanisms underlying acute and steep temperature-mediated channel gating remain enigmatic. Here, we propose a model in which the thermo-TRP channels directly sense external temperature through the formation and dissociation of metastable cytoplasmic domains. An open-close bistable system is described in the framework of equilibrium thermodynamics, and the middle-point temperature T½ similar to the V½ parameter for a voltage-gating channel is defined. Based on the relationship between channel opening probability and temperature, we estimate the change in entropy and enthalpy during the conformational change for a typical thermosensitive channel. Our model is able to accurately reproduce the steep activation phase in experimentally determined thermal-channel opening curves, and thus should greatly facilitate future experimental verification.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":"8 4","pages":"205-211"},"PeriodicalIF":0.0,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10185483/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9597312","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

Molecular mechanism of anionic stabilizer for telomere G-quadruplex. 端粒g -四重体阴离子稳定剂的分子机制。

生物物理学报:英文版 Pub Date : 2022-08-31 DOI: 10.52601/bpr.2022.220039

Zhiguo Wang, Jianfeng Li, Jun Liu, Lihui Wang, Yanhua Lu, Jun-Ping Liu

{"title":"Molecular mechanism of anionic stabilizer for telomere G-quadruplex.","authors":"Zhiguo Wang, Jianfeng Li, Jun Liu, Lihui Wang, Yanhua Lu, Jun-Ping Liu","doi":"10.52601/bpr.2022.220039","DOIUrl":"https://doi.org/10.52601/bpr.2022.220039","url":null,"abstract":"Telomere DNA assumes a high-order G-quadruplex (G4) structure, stabilization of which prevents telomere lengthening by telomerase in cancer. Through applying combined molecular simulation methods, an investigation on the selective binding mechanism of anionic phthalocyanine 3,4',4'',4'''-tetrasulfonic acid (APC) and human hybrid (3 + 1) G4s was firstly performed at the atomic level. Compared to the groove binding mode of APC and the hybrid type I (hybrid-I) telomere G4, APC preferred to bind to the hybrid type II (hybrid-II) telomere G4 via end-stacking interactions, which showed much more favorable binding free energies. Analyses of the non-covalent interaction and binding free energy decomposition revealed a decisive role of van der Waals interaction in the binding of APC and telomere hybrid G4s. And the binding of APC and hybrid-II G4 that showed the highest binding affinity adopted the end-stacking binding mode to form the most extensive van der Waals interactions. These findings add new knowledge to the design of selective stabilizers targeting telomere G4 in cancer.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":"8 4","pages":"225-238"},"PeriodicalIF":0.0,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10185486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9597307","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: 1

Cryogenic superresolution correlative light and electron microscopy of vitreous sections. 玻璃体切片的低温超分辨相关光学和电子显微镜。

生物物理学报:英文版 Pub Date : 2022-08-31 DOI: 10.52601/bpr.2022.220005

Buyun Tian, Maoge Zhou, Fengping Feng, Xiaojun Xu, Pei Wang, Huiqin Luan, Wei Ji, Yanhong Xue, Tao Xu

{"title":"Cryogenic superresolution correlative light and electron microscopy of vitreous sections.","authors":"Buyun Tian, Maoge Zhou, Fengping Feng, Xiaojun Xu, Pei Wang, Huiqin Luan, Wei Ji, Yanhong Xue, Tao Xu","doi":"10.52601/bpr.2022.220005","DOIUrl":"https://doi.org/10.52601/bpr.2022.220005","url":null,"abstract":"Fluorescence microscopy and electron microscopy complement each other as the former provides labelling and localisation of specific molecules and target structures while the latter possesses excellent revolving power of fine structure in context. These two techniques can combine as correlative light and electron microscopy (CLEM) to reveal the organisation of materials within the cell. Frozen hydrated sections allow microscopic observations of cellular components in situ in a near-native state and are compatible with superresolution fluorescence microscopy and electron tomography if sufficient hardware and software support is available and a well-designed protocol is followed. The development of superresolution fluorescence microscopy greatly increases the precision of fluorescence annotation of electron tomograms. Here, we provide detailed instructions on how to perform cryogenic superresolution CLEM on vitreous sections. From fluorescence-labelled cells to high pressure freezing, cryo-ultramicrotomy, cryogenic single-molecule localisation microscopy, cryogenic electron tomography and image registration, electron tomograms with features of interest highlighted by superresolution fluorescence signals are expected to be obtained.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":"8 4","pages":"193-204"},"PeriodicalIF":0.0,"publicationDate":"2022-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10185487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9597308","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

Brain structure and structural basis of neurodegenerative diseases. 脑结构与神经退行性疾病的结构基础。

生物物理学报:英文版 Pub Date : 2022-06-30 DOI: 10.52601/bpr.2022.220013

Jiawen Yang, Sen-Fang Sui, Zheng Liu

{"title":"Brain structure and structural basis of neurodegenerative diseases.","authors":"Jiawen Yang, Sen-Fang Sui, Zheng Liu","doi":"10.52601/bpr.2022.220013","DOIUrl":"https://doi.org/10.52601/bpr.2022.220013","url":null,"abstract":"The brain is one of the most complex organs in nature. In this organ, multiple neurons, neuron clusters, or multiple brain regions are interconnected to form a complex structural network where various brain functions are completed through interaction. In recent years, multiple tools and techniques have been developed to analyze the composition of different cell types in the brain and to construct the brain atlas on macroscopic, mesoscopic, and microscopic levels. Meanwhile, researchers have found that many neuropsychiatric diseases, such as Parkinson's disease, Alzheimer's disease, and Huntington's disease, are closely related to abnormal changes of brain structure, which means the investigation in brain structure not only provides a new idea for understanding the pathological mechanism of the diseases, but also provides imaging markers for early diagnosis and potential treatment. This article pays attention to the research of human brain structure, reviews the research progress of human brain structure and the structural mechanism of neurodegenerative diseases, and discusses the problems and prospects in the field.","PeriodicalId":59621,"journal":{"name":"生物物理学报:英文版","volume":"8 3","pages":"170-181"},"PeriodicalIF":0.0,"publicationDate":"2022-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10189650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9597792","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: 1