Biophysics reports最新文献_第7页

A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. 一个基本的磷酸蛋白质组DIA工作流程，集成了系统生物学中磷酸位点的精确量化。

Biophysics reports Pub Date : 2023-04-30 DOI: 10.52601/bpr.2023.230007

Yi Di, Wenxue Li, Barbora Salovska, Qian Ba, Zhenyi Hu, Shisheng Wang, Yansheng Liu

{"title":"A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology.","authors":"Yi Di, Wenxue Li, Barbora Salovska, Qian Ba, Zhenyi Hu, Shisheng Wang, Yansheng Liu","doi":"10.52601/bpr.2023.230007","DOIUrl":"10.52601/bpr.2023.230007","url":null,"abstract":"Phosphorylation is one of the most important post-translational modifications (PTMs) of proteins, governing critical protein functions. Most human proteins have been shown to undergo phosphorylation, and phosphoproteomic studies have been widely applied due to recent advancements in high-resolution mass spectrometry technology. Although the experimental workflow for phosphoproteomics has been well-established, it would be useful to optimize and summarize a detailed, feasible protocol that combines phosphoproteomics and data-independent acquisition (DIA), along with follow-up data analysis procedures due to the recent instrumental and bioinformatic advances in measuring and understanding tens of thousands of site-specific phosphorylation events in a single experiment. Here, we describe an optimized Phos-DIA protocol, from sample preparation to bioinformatic analysis, along with practical considerations and experimental configurations for each step. The protocol is designed to be robust and applicable for both small-scale phosphoproteomic analysis and large-scale quantification of hundreds of samples for studies in systems biology and systems medicine.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 2","pages":"82-98"},"PeriodicalIF":0.0,"publicationDate":"2023-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10518521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41155098","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

Integrated proteomic and phosphoproteomic data-independent acquisition data evaluate the personalized drug responses of primary and metastatic tumors in colorectal cancer. 综合蛋白质组学和磷酸蛋白质组学数据独立采集数据评估癌症原发性和转移性肿瘤的个性化药物反应。

Biophysics reports Pub Date : 2023-04-30 DOI: 10.52601/bpr.2022.210048

Xumiao Li, Yiming Huang, Kuo Zheng, Guanyu Yu, Qinqin Wang, Lei Gu, Jingquan Li, Hui Wang, Wei Zhang, Yidi Sun, Chen Li

{"title":"Integrated proteomic and phosphoproteomic data-independent acquisition data evaluate the personalized drug responses of primary and metastatic tumors in colorectal cancer.","authors":"Xumiao Li, Yiming Huang, Kuo Zheng, Guanyu Yu, Qinqin Wang, Lei Gu, Jingquan Li, Hui Wang, Wei Zhang, Yidi Sun, Chen Li","doi":"10.52601/bpr.2022.210048","DOIUrl":"https://doi.org/10.52601/bpr.2022.210048","url":null,"abstract":"Mass spectrometry (MS)-based proteomics and phosphoproteomics are powerful methods to study the biological mechanisms, diagnostic biomarkers, prognostic analysis, and drug therapy of tumors. Data-independent acquisition (DIA) mode is considered to perform better than data-dependent acquisition (DDA) mode in terms of quantitative reproducibility, specificity, accuracy, and identification of low-abundance proteins. Mini patient derived xenograft (MiniPDX) model is an effective model to assess the response to antineoplastic drugs in vivo and is helpful for the precise treatment of cancer patients. Kinases are favorable spots for tumor-targeted drugs, and their functional completion relies on signaling pathways through phosphorylating downstream substrates. Kinase-phosphorylation networks or edge interactions are considered more credible and permanent for characterizing complex diseases. Here, we provide a workflow for personalized drug response assessment in primary and metastatic colorectal cancer (CRC) tumors using DIA proteomic data, DIA phosphoproteomic data, and MiniPDX models. Three kinase inhibitors, afatinib, gefitinib, and regorafenib, are tested pharmacologically. The process mainly includes the following steps: clinical tissue collection, sample preparation, hybrid spectral libraries establishment, MS data acquisition, kinase-substrate network construction, in vivo drug test, and elastic regression modeling. Our protocol gives a more direct data basis for individual drug responses, and will improve the selection of treatment strategies for patients without the druggable mutation.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"9 2","pages":"67-81"},"PeriodicalIF":0.0,"publicationDate":"2023-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10518519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41180699","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 hydrogen-deuterium exchange mass spectrometry-based protocol for protein-small molecule interaction analysis. 一种基于氢-氘交换质谱法的蛋白质小分子相互作用分析方案。

Biophysics reports Pub Date : 2023-04-30 DOI: 10.52601/bpr.2023.230006

Qian Meng, Yuan-Li Song, Chen Zhou, Han He, Naixia Zhang, Hu Zhou

引用次数: 0

Insights into human eNOS, nNOS and iNOS structures and medicinal indications from statistical analyses of their interactions with bound compounds 通过统计分析人类eNOS、nNOS和iNOS与结合化合物的相互作用，了解它们的结构和药物适应症

Biophysics reports Pub Date : 2023-01-01 DOI: 10.52601/bpr.2023.210045

Jianshu Dong, Dié Li, Lei Kang, Chenbing Luo, Jiangyun Wang

{"title":"Insights into human eNOS, nNOS and iNOS structures and medicinal indications from statistical analyses of their interactions with bound compounds","authors":"Jianshu Dong, Dié Li, Lei Kang, Chenbing Luo, Jiangyun Wang","doi":"10.52601/bpr.2023.210045","DOIUrl":"https://doi.org/10.52601/bpr.2023.210045","url":null,"abstract":"83 Structures of human nNOS, 55 structures of human eNOS, 13 structures of iNOS, and about 126 reported NOS-bound compounds are summarized and analyzed. Structural and statistical analysis show that, at least one copy of each analyzed compound binds to the active site (the substrate arginine binding site) of human NOS. And binding features of the three isoforms show differences, but the binding preference of compounds is not in the way helpful for inhibitor design targeting nNOS and iNOS, or for activator design targeting eNOS. This research shows that there is a strong structural and functional similarity between oxygenase domains of human NOS isoforms, especially the architecture, residue composition, size, shape, and distribution profile of hydrophobicity, polarity and charge of the active site. The selectivity and efficacy of inhibitors over the rest of isoforms rely a lot on chance and randomness. Further increase of selectivity via rational improvement is uncertain, unpredictable and unreliable, therefore, to achieve high selectivity through targeting this site is complicated and requires combinative investigation. After analysis on the current two targeting sites in NOS, the highly conserved arginine binding pocket and H4B binding pocket, new potential drug-targeting sites are proposed based on structure and sequence profiling. This comprehensive analysis on the structure and interaction profiles of human NOS and bound compounds provides fresh insights for drug discovery and pharmacological research, and the new discovery here is practically applied to guide protein-structure based drug discovery.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"293 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":"135444977","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

Reconstitution of membrane contact by unilamellar vesicles 单层囊泡重建膜接触

Biophysics reports Pub Date : 2023-01-01 DOI: 10.52601/bpr.2023.230011

Shulin Li, Min Zhang, Liang Ge

引用次数: 0

Isolation and proteomic study of fish liver lipid droplets 鱼肝脂滴的分离与蛋白质组学研究

Biophysics reports Pub Date : 2023-01-01 DOI: 10.52601/bpr.2023.230004

Yuwei Sun, Jian Heng, Feng Liu, Shuyan Zhang, Pingsheng Liu

{"title":"Isolation and proteomic study of fish liver lipid droplets","authors":"Yuwei Sun, Jian Heng, Feng Liu, Shuyan Zhang, Pingsheng Liu","doi":"10.52601/bpr.2023.230004","DOIUrl":"https://doi.org/10.52601/bpr.2023.230004","url":null,"abstract":"Lipid droplets (LDs) are a neutral lipid storage organelle that is conserved in almost all species. Excessive storage of neutral lipids in LDs is directly associated with many metabolic syndromes. Zebrafish is a better model animal for the study of LD biology due to its transparent embryonic stage compared to other organisms. However, the study of LDs in fish has been difficult due to the lack of specific LD marker proteins and the limitation of purification technology. In this paper, the purification and proteomic analysis of liver LDs of fish including zebrafish and Carassius auratus were performed for the first time. 259 and 267 proteins were identified respectively. Besides most of the identified proteins were reported in previous LD proteomes of mammals, indicating the similarity between mammal and fish LDs. We also identified many unique proteins of liver LDs in fish that are involved in the regulation of LD dynamics. Through morphological and biochemical analysis, we found that the marker protein Plin2 of zebrafish LD was located on LDs in Huh7 cells. These results will facilitate further study of LDs in fish and liver metabolic diseases using fish as a model animal.","PeriodicalId":93906,"journal":{"name":"Biophysics reports","volume":"162 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":"135444973","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