bioRxiv : the preprint server for biology最新文献_第10页

QuickProt: A bioinformatics and visualization tool for DIA and PRM mass spectrometry-based proteomics datasets. QuickProt：用于基于 DIA 和 PRM 质谱的蛋白质组学数据集的生物信息学和可视化工具。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2025.03.24.645047

Omar Arias-Gaguancela, Carmen Palii, Mehar Un Nissa, Marjorie Brand, Jeff Ranish

{"title":"QuickProt: A bioinformatics and visualization tool for DIA and PRM mass spectrometry-based proteomics datasets.","authors":"Omar Arias-Gaguancela, Carmen Palii, Mehar Un Nissa, Marjorie Brand, Jeff Ranish","doi":"10.1101/2025.03.24.645047","DOIUrl":"https://doi.org/10.1101/2025.03.24.645047","url":null,"abstract":"Mass spectrometry (MS)-based proteomics focuses on identifying and quantifying peptides and proteins in biological samples. Processing of MS-derived raw data, including deconvolution, alignment, and peptide-protein prediction, has been achieved through various software platforms. However, the downstream analysis, including quality control, visualizations, and interpretation of proteomics results remains challenging due to the lack of integrated tools to facilitate the analyses. To address this challenge, we developed QuickProt, a series of Python-based Google Colab notebooks for analyzing data-independent acquisition (DIA) and parallel reaction monitoring (PRM) proteomics datasets. These pipelines are designed so that users with no coding expertise can utilize the tool. Furthermore, as open-source code, QuickProt notebooks can be customized and incorporated into existing workflows. As proof of concept, we applied QuickProt to analyze in-house DIA and stable isotope dilution (SID)-PRM MS proteomics datasets from a time-course study of human erythropoiesis. The analysis resulted in annotated tables and publication-ready figures revealing a dynamic rearrangement of the proteome during erythroid differentiation, with the abundance of proteins linked to gene regulation, metabolic, and chromatin remodeling pathways increasing early in erythropoiesis. Altogether, these tools aim to automate and streamline DIA and PRM-MS proteomics data analysis, making it more efficient and less time-consuming.","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974799/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805487","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

Secretory leukocyte protease inhibitor influences periarticular joint inflammation in B. burgdorferi-infected mice. 分泌性白细胞蛋白酶抑制剂对伯氏疏螺旋体感染小鼠关节周围炎症的影响。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2024.11.24.625079

Qian Yu, Xiaotian Tang, Thomas Hart, Robert Homer, Alexia A Belperron, Linda Bockenstedt, Aaron Ring, Akira Nakamura, Erol Fikrig

{"title":"Secretory leukocyte protease inhibitor influences periarticular joint inflammation in B. burgdorferi-infected mice.","authors":"Qian Yu, Xiaotian Tang, Thomas Hart, Robert Homer, Alexia A Belperron, Linda Bockenstedt, Aaron Ring, Akira Nakamura, Erol Fikrig","doi":"10.1101/2024.11.24.625079","DOIUrl":"10.1101/2024.11.24.625079","url":null,"abstract":"Lyme disease, caused by Borrelia burgdorferi , is the most common tick-borne infection in the United States. Arthritis is a major clinical manifestation of infection, and synovial tissue damage has been attributed to the excessive pro-inflammatory responses. The secretory leukocyte protease inhibitor (SLPI) promotes tissue repair and exerts anti-inflammatory effects. The role of SLPI in the development of Lyme arthritis in C57BL/6 mice, which can be infected with B. burgdorferi , but only develop mild joint inflammation, was therefore examined. SLPI -deficient C57BL/6 mice challenged with B. burgdorferi had a higher infection load in the tibiotarsal joints and marked periarticular swelling, compared to infected wild type control mice. The ankle joint tissues of B. burgdorferi -infected SLPI -deficient mice contained significantly higher percentages of infiltrating neutrophils and macrophages. B. burgdorferi -infected SLPI -deficient mice also exhibited elevated serum levels of IL-6, neutrophil elastase, and MMP-8. Moreover, using a recently developed BASEHIT (BActerial Selection to Elucidate Host-microbe Interactions in high Throughput) library, we found that SLPI directly interacts with B. burgdorferi . These data demonstrate the importance of SLPI in suppressing periarticular joint inflammation in Lyme disease.","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11623497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142804392","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

Identification of BET Inhibitors (BETi) Against Solitary Fibrous Tumor (SFT) Through High-Throughput Screening (HTS). 通过高通量筛选 (HTS) 鉴定抗单发纤维性肿瘤 (SFT) 的 BET 抑制剂 (BETi)。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2025.03.25.645256

Jose L Mondaza-Hernandez, David S Moura, Yi Li, Jesus Lopez-Marti, Paulino Gomez-Puertas, John T Nguyen, Shuguang Wei, Bruce A Posner, Clark A Meyer, Leonidas Bleris, Javier Martin-Broto, Heather Hayenga

{"title":"Identification of BET Inhibitors (BETi) Against Solitary Fibrous Tumor (SFT) Through High-Throughput Screening (HTS).","authors":"Jose L Mondaza-Hernandez, David S Moura, Yi Li, Jesus Lopez-Marti, Paulino Gomez-Puertas, John T Nguyen, Shuguang Wei, Bruce A Posner, Clark A Meyer, Leonidas Bleris, Javier Martin-Broto, Heather Hayenga","doi":"10.1101/2025.03.25.645256","DOIUrl":"https://doi.org/10.1101/2025.03.25.645256","url":null,"abstract":"Cancers, especially fusion oncoprotein (FO)-driven hematological cancers and sarcomas, often develop from a low number of key mutations. Solitary Fibrous Tumor (SFT) is a rare mesenchymal tumor driven by the NAB2-STAT6 oncofusion gene. Currently, the treatment options for SFT remain limited, with anti-angiogenic drugs providing only partial responses and an average survival of two years. To address this challenge, we constructed SFT cell models harboring specific NAB2-STAT6 fusion transcripts using the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology. High-throughput drug screens demonstrated that the BET inhibitor Mivebresib can differentially reduce proliferation in SFT cell models. Subsequently, BET inhibitors Mivebresib and BMS-986158 efficiently reduced tumor growth in an SFT patient-derived xenograft (PDX) animal model. Furthermore, our data showed that NAB2-STAT6 fusions may lead to higher levels of DNA damage in SFTs. Consequently, combining BET inhibitors with PARP (Poly (ADP-ribose) polymerase) or ATR inhibitors significantly enhanced anti-proliferative effects in SFT cells. Taken together, our study established BET inhibitors Mivebresib and BMS-986158 as promising anti-SFT agents.","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804788","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 split ALFA tag-nanobody system for protein localization and proximity proteomics in mycobacteria. 分枝杆菌中用于蛋白质定位和接近蛋白质组学的分裂ALFA标签-纳米体系统。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2025.03.22.644702

Allison Fay, Andrew P Kurland, Zhuoning Li, Mara Monetti, Jeffrey R Johnson, Michael S Glickman

{"title":"A split ALFA tag-nanobody system for protein localization and proximity proteomics in mycobacteria.","authors":"Allison Fay, Andrew P Kurland, Zhuoning Li, Mara Monetti, Jeffrey R Johnson, Michael S Glickman","doi":"10.1101/2025.03.22.644702","DOIUrl":"https://doi.org/10.1101/2025.03.22.644702","url":null,"abstract":"Tuberculosis remains a globally significant infection and new insights into the biology of Mycobacterium tuberculosis are badly needed. Discovery of protein localization and protein complex composition are powerful approaches to determine protein function, but have not been widely applied in mycobacteria, in part due to technical barriers. Here we develop a multi-functional system that utilizes the ALFA tag and functional protein fusions to an anti-ALFA nanobody (NBALFA) to target proteins in fast and slow growing mycobacteria. Insertion of the ALFA epitope tag on the target protein, coupled with conditional expression of the NBALFA fused to a fluorescent protein faithfully recapitulates cytosolic and membrane protein localization by fluorescent microscopy in living cells. Targeted NBALFA can relocalize an ALFA tagged protein to inclusion bodies or the cytoplasmic membrane, demonstrating enforced protein localization. Finally, conditional expression of the NBALFA fused to TurboID for proximity proteomics allowed identification of known partner proteins of the RNA polymerase complex and the PKS13 mycolic acid biosynthesis protein. We conclude that the split ALFA tag-nanobody system is a flexible platform for discovery protein biology in mycobacteria.","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805332","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

In vivo self-renewal and expansion of quiescent stem cells from a non-human primate. 非人灵长类静止干细胞的体内自我更新和扩增。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2025.03.27.645793

Jengmin Kang, Abhijnya Kanugovi, M Pilar J Stella, Zofija Frimand, Jean Farup, Andoni Urtasun, Shixuan Liu, Anne-Sofie Clausen, Heather Ishak, Summer Bui, Soochi Kim, Camille Ezran, Olga Botvinnik, Ermelinda Porpiglia, Mark Krasnow, Antoine de Morree, Thomas A Rando

{"title":"In vivo self-renewal and expansion of quiescent stem cells from a non-human primate.","authors":"Jengmin Kang, Abhijnya Kanugovi, M Pilar J Stella, Zofija Frimand, Jean Farup, Andoni Urtasun, Shixuan Liu, Anne-Sofie Clausen, Heather Ishak, Summer Bui, Soochi Kim, Camille Ezran, Olga Botvinnik, Ermelinda Porpiglia, Mark Krasnow, Antoine de Morree, Thomas A Rando","doi":"10.1101/2025.03.27.645793","DOIUrl":"https://doi.org/10.1101/2025.03.27.645793","url":null,"abstract":"The development of non-human primate models is essential for the fields of developmental and regenerative biology because those models will more closely approximate human biology than do murine models. Based on single cell RNAseq and fluorescence-activated cell sorting, we report the identification and functional characterization of two quiescent stem cell populations (skeletal muscle stem cells (MuSCs) and mesenchymal stem cells termed fibro-adipogenic progenitors (FAPs)) in the non-human primate Microcebus murinus (the gray mouse lemur). We demonstrate in vivo proliferation, differentiation, and self-renewal of both MuSCs and FAPs. By combining cell phenotyping with cross-species molecular profiling and pharmacological interventions, we show that mouse lemur MuSCs and FAPs are more similar to human than to mouse counterparts. We identify unexpected gene targets involved in regulating primate MuSC proliferation and primate FAP adipogenic differentiation. Moreover, we find that the cellular composition of mouse lemur muscle better models human muscle than does macaque ( Macaca fascicularis ) muscle. Finally, we note that our approach presents as a generalizable pipeline for the identification, isolation, and characterization of stem cell populations in new animal models.","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974844/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805377","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

Biosynthesis and Physiological Significance of Organ-Specific Flavonol Glycosides in Solanaceae. 茄科植物器官特异性黄酮醇苷的生物合成及其生理意义。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2025.03.27.645607

Doosan Shin, Haohao Zhao, Ethan Tucker, Keun Ho Cho, Dake Liu, Zhixin Wang, Scott Latimer, Gilles Basset, Yu Wang, Yousong Ding, Jeongim Kim

{"title":"Biosynthesis and Physiological Significance of Organ-Specific Flavonol Glycosides in Solanaceae.","authors":"Doosan Shin, Haohao Zhao, Ethan Tucker, Keun Ho Cho, Dake Liu, Zhixin Wang, Scott Latimer, Gilles Basset, Yu Wang, Yousong Ding, Jeongim Kim","doi":"10.1101/2025.03.27.645607","DOIUrl":"https://doi.org/10.1101/2025.03.27.645607","url":null,"abstract":"Flavonols are subclasses of flavonoids, with hundreds of structures identified in plants. This chemical diversity primarily arises from glycosylation, where sugars are selectively added to the flavonol backbone. While flavonol profiles vary across species and organs, the evolutionary forces shaping this chemodiversity and the physiological significance of specific glycosides remain a mystery. Here, we reveal that finely tuned transcriptional regulation and the sugar selectivity of glycosyltransferases drive the formation of distinct organ specific flavonol profiles and a specific flavonol is necessary for male fertility. In Solanaceae pollen, two flavonol glycosides, K2 (kaempferol 3- O -glucosyl(1 → 2)galactoside) and Q2 (quercetin 3- O -glucosyl(1 → 2)galactoside), are exclusively accumulated. K2 is evolutionarily conserved, while Q2 was lost over time. Consistently, K2 is essential for male fertility, whereas Q2 and aglycones fail to rescue fertility defects. These findings suggest that individual flavonol glycosides have distinct physiological roles, either actively maintained or discarded through evolutionary selection.","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805325","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

OctopusV and TentacleSV: a one-stop toolkit for multi-sample, cross-platform structural variant comparison and analysis. OctopusV和TentacleSV：用于多样本、跨平台结构变体比较和分析的一站式工具包。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2025.03.24.645012

Qingxiang Guo, Yangyang Li, Tingyou Wang, Abhi Ramakrishnan, Rendong Yang

引用次数: 0

T-World: A highly general computational model of a human ventricular myocyte. T-World：一个高度通用的人类心室肌细胞计算模型。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2025.03.24.645031

Jakub Tomek, Xin Zhou, Hector Martinez-Navarro, Maxx Holmes, Thomas Bury, Lucas Arantes Berg, Marketa Tomkova, Emily Jo, Norbert Nagy, Ambre Bertrand, Alfonso Bueno-Orovio, Michael Colman, Blanca Rodriguez, Donald Bers, Jordi Heijman

{"title":"T-World: A highly general computational model of a human ventricular myocyte.","authors":"Jakub Tomek, Xin Zhou, Hector Martinez-Navarro, Maxx Holmes, Thomas Bury, Lucas Arantes Berg, Marketa Tomkova, Emily Jo, Norbert Nagy, Ambre Bertrand, Alfonso Bueno-Orovio, Michael Colman, Blanca Rodriguez, Donald Bers, Jordi Heijman","doi":"10.1101/2025.03.24.645031","DOIUrl":"https://doi.org/10.1101/2025.03.24.645031","url":null,"abstract":"Cardiovascular disease is the leading cause of death, demanding new tools to improve mechanistic understanding and overcome limitations of stem cell and animal-based research. We introduce T-World, a highly general virtual model of human ventricular cardiomyocyte suitable for multiscale studies. T-World shows comprehensive agreement with human physiology, from electrical activation to contraction, and is the first to replicate all key cellular mechanisms driving life-threatening arrhythmias. Extensively validated on unseen data, it demonstrates strong predictivity across applications and scales. Using T-World we revealed a likely sex-specific arrhythmia risk in females related to restitution properties, identified arrhythmia drivers in type 2 diabetes, and describe unexpected pro-arrhythmic role of NaV1.8 in heart failure. T-World demonstrates strong performance in predicting drug-induced arrhythmia risk and opens new opportunities for predicting and explaining drug efficacy, demonstrated by unpicking effects of mexiletine in Long QT syndrome 2. T-World is available as open-source code and an online app.","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805541","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

Aggregation of the constitutively active K296E rhodopsin mutant contributes to retinal degeneration. 组成型活性 K296E rhodopsin 突变体的聚集导致视网膜变性。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2025.03.26.643112

Sreelakshmi Vasudevan, Vivek Prakash, Paul S-H Park

{"title":"Aggregation of the constitutively active K296E rhodopsin mutant contributes to retinal degeneration.","authors":"Sreelakshmi Vasudevan, Vivek Prakash, Paul S-H Park","doi":"10.1101/2025.03.26.643112","DOIUrl":"https://doi.org/10.1101/2025.03.26.643112","url":null,"abstract":"A K296E mutation in rhodopsin causes autosomal dominant retinitis pigmentosa, a progressive retinal degenerative disease. Early in vitro characterizations of this mutation studied on a bovine rhodopsin background indicated that the mutation causes the receptor to be constitutively active. This molecular defect has been the primary focus when considering the pathogenic mechanism of the mutation. Knockin mice expressing the K296E rhodopsin mutant were generated and characterized to better understand the pathogenic mechanism of the mutation. Knockin mice exhibited progressive retinal degeneration characteristic of retinitis pigmentosa. The K296E rhodopsin mutant mislocalized in photoreceptor cells and, surprisingly, appeared to aggregate, as indicated by the dye PROTEOSTAT, which binds protein aggregates. The propensity of the K296E rhodopsin mutant to aggregate was tested and confirmed in vitro but was dependent on the species background of rhodopsin. The K296E mutation on either murine or human rhodopsin backgrounds exhibited similar propensities to aggregate. The same mutation on a bovine rhodopsin background, however, exhibited a lower propensity to aggregate, indicating this species background does not adequately model the effects of the K296E mutation. In contrast to previous expectations, we demonstrate here that aggregation of the K296E rhodopsin mutant can promote photoreceptor cell loss.","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143804791","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

In vitro selection of cyclized, glycosylated peptide antigens that tightly bind HIV high mannose patch antibodies. 体外筛选能与 HIV 高甘露糖斑块抗体紧密结合的环化糖基化多肽抗原。

bioRxiv : the preprint server for biology Pub Date : 2025-03-28 DOI: 10.1101/2025.03.24.645033

Jennifer K Bailey, Satoru Horiya, Mahesh Neralkar, Viktor Horvath, Kosuke Nakamoto, J Sebastian Temme, Raphael J Turra, Isaac J Krauss

{"title":"In vitro selection of cyclized, glycosylated peptide antigens that tightly bind HIV high mannose patch antibodies.","authors":"Jennifer K Bailey, Satoru Horiya, Mahesh Neralkar, Viktor Horvath, Kosuke Nakamoto, J Sebastian Temme, Raphael J Turra, Isaac J Krauss","doi":"10.1101/2025.03.24.645033","DOIUrl":"https://doi.org/10.1101/2025.03.24.645033","url":null,"abstract":"In vitro selection is typically limited to discovery of peptides, proteins and nucleic acids. Given the importance of carbohydrate-protein interactions in diverse areas of biology including cell adhesion/recognition, immunoregulation and host-pathogen interactions, directed-evolution-based methods for discovery of potent glycoligands are greatly needed. We have previously reported a method for in vitro selection of glycopeptides that combines mRNA display, alkynyl amino acid incorporation, and CuAAC \"click\" glycosylation. Herein, we describe extensions of this method that incorporate chemical cyclization, removal of N-terminal glycosylation sites and next-generation sequencing; as an approach to HIV immunogen design, we have then used this method to develop mimics of the High Mannose Patch (HMP), which is the region on HIV envelope protein gp120 most commonly targeted by HIV broadly neutralizing antibodies (bnAbs). We prepared libraries of 10 12-14 glycopeptides about 50 amino acids in length, containing variable numbers of high mannose (Man 9 GlcNAc 2 ) glycans and cyclization at varied sites. We performed selections to obtain binders of HIV bnAbs PGT128, PGT122, and gl-PGT121, a germline precursor of PGT122, and prepared numerous glycopeptide hits by chemical synthesis. Selected glycopeptides in some cases bound very tightly to their target HIV bnAb, e.g., with a K D as low as 0.5 nM for PGT128. These glycopeptides are of interest as immunogens and tools for HIV vaccine design.","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143805316","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