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Predicting dynamic cellular protein-RNA interactions by deep learning using in vivo RNA structures

细胞研究（英文版） 2021年第5期31卷 495-516页

作者： Lei Sun Kui Xu Wenze Huang Yucheng T.Yang Pan Li Lei Tang Tuanlin Xiong Qiangfeng Cliff Zhang MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological StructureCenter for Synthetic and Systems BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China Program in Computational Biology and Bioinformatics Yale UniversityNew HavenCT 06520USA Department of Molecular Biophysics and Biochemistry Yale UniversityNew HavenCT 06520USA

Interactions with RNA-binding proteins (RBPs) are integral to RNA function and cellular regulation,and dynamically reflect specific cellular ***,presently available tools for predicting RBP-RNA interactions employ RNA sequence and/or predicted RNA structures,and therefore do not capture their condition-dependent ***,after profiling transcriptome-wide in vivo RNA secondary structures in seven cell types,we developed PrismNet,a deep learning tool that integrates experimental in vivo RNA structure data and RBP binding data for matched cells to accurately predict dynamic RBP binding in various cellular *** results for 168 RBPs support its utility for both understanding CUP-seq results and largely extending such interaction data to accurately analyze additional cell ***,PrismNet employs an 'attention' strategy to computationally identify exact RBP-binding nucleotides,and we discovered enrichment among dynamic RBP-binding sites for structure-changing variants(riboSNitches),which can link genetic diseases with dysregulated RBP *** rich profiling data and deep learning-based prediction tool provide access to a previously inaccessible layer of cell-type-specific RBP-RNA interactions,with clear utility for understanding and treating human diseases.

关键词： Bioinformatics Mechanisms of disease molecular biology

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structural insights into the role of N-terminal integrity in PhoSL for core-fucosylated N-glycan recognition

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International Journal of Biological Macromolecules 2024年 255卷 128309页

作者： Lou, Yuan-Chao Tu, Cheng-Fen Chou, Chun-Chi Yeh, Hsin-Hong Chien, Chia-Yu Sadotra, Sushant Chen, Chinpan Yang, Ruey-Bing Hsu, Chun-Hua Institute of Biomedical Sciences Academia Sinica Taipei115 Taiwan Department of Agricultural Chemistry National Taiwan University Taipei106 Taiwan Chemical Biology and Molecular Biophysics Taiwan International Graduate Program Academia Sinica Taipei115 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300 Taiwan Biomedical Translation Research Center Academia Sinica Taipei115 Taiwan Ph.D. Program in Drug Discovery and Development Industry College of Pharmacy Taipei Medical University Taipei110 Taiwan Genome and Systems Biology Degree Program National Taiwan University and Academia Sinica Taipei106 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei106 Taiwan Center for Computational and Systems Biology National Taiwan University Taipei106 Taiwan

PhoSL (Pholiota squarrosa Lectin) has an exceptional binding affinity for biomolecules with core-fucosylated N-glycans. This modification involves the addition of fucose to the inner N-acetylglucosamine within the N-glycan structure and is known to influence many physiological processes. Nevertheless, the molecular interactions underlying high-affinity binding of native PhoSL to core-fucosylated N-glycans remain largely unknown. In this study, we devised a strategy to produce PhoSL with the essential structural characteristics of the native protein (n-PhoSL). To do so, a fusion protein was expressed in E. coli and purified. Then, enzymatic cleavage and incubation with glutathione were utilized to recapitulate the native primary structure and disulfide bonding pattern. Subsequently, we identified the residues crucial for n-PhoSL binding to core-fucosylated chitobiose (N2F) via NMR spectroscopy. Additionally, crystal structures were solved for both apo n-PhoSL and its N2F complex. These analyses suggested a pivotal role of the N-terminal amine in maintaining the integrity of the binding pocket and actively contributing to core-fucose recognition. In support of this idea, the inclusion of additional residues at the N-terminus considerably reduced binding affinity and PhoSL cytotoxicity toward breast cancer cells. Taken together, these findings can facilitate the utilization of PhoSL in basic research, diagnostics and therapeutic strategies. © 2023 Elsevier B.V.

关键词： Proteins

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Graph-based information diffusion method for prioritizing functionally related genes in protein-protein interaction networks 25

Graph-based information diffusion method for prioritizing fu...

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25th Pacific Symposium on Biocomputing, PSB 2020

作者： Pham, Minh Lichtarge, Olivier Integrative Molecular and Biomedical Sciences Graduate Program Department of Molecular and Human Genetics Baylor College of Medicine One Baylor Plaza HoustonTX77030 United States Departments of Molecular and Human Genetics Structural and Computational Biology and Molecular Biophysics Biochemistry and Molecular Biology and Pharmacology One Baylor Plaza HoustonTX77030 United States

Shortest path length methods are routinely used to validate whether genes of interest are functionally related to each other based on biological network information. However, the methods are computationally intensive, impeding extensive utilization of network information. In addition, nonweighted shortest path length approach, which is more frequently used, often treat all network connections equally without taking into account of confidence levels of the associations. On the other hand, graph-based information diffusion method, which employs both the presence and confidence weights of network edges, can efficiently explore large networks and has previously detected meaningful biological patterns. Therefore, in this study, we hypothesized that the graph-based information diffusion method could prioritize genes with relevant functions more efficiently and accurately than the shortest path length approaches. We demonstrated that the graph-based information diffusion method substantially differentiated not only genes participating in same biological pathways (p 0.0001) but also genes associated with specific human drug-induced clinical symptoms (p 0.0001) from random. Furthermore, the diffusion method prioritized these functionally related genes faster and more accurately than the shortest path length approaches (pathways: p = 2.7e-28, clinical symptoms: p = 0.032). These data show the graph-based information diffusion method can be routinely used for robust prioritization of functionally related genes, facilitating efficient network validation and hypothesis generation, especially for human phenotypespecific genes. © 2019 The Authors.

关键词： Genes

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Alternatively spliced MAP4 isoforms have key roles in maintaining microtubule organization and skeletal muscle function

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iScience 2024年第11期27卷 111104页

作者： Lucas, Lathan Nitschke, Larissa Nguyen, Brandon Loehr, James A. Rodney, George G. Cooper, Thomas A. Chemical Physical Structural Biology Graduate Program Baylor College of Medicine Houston TX United States Department of Pathology & Immunology Baylor College of Medicine Houston TX United States Department of Molecular Physiology and Biophysics Baylor College of Medicine Houston TX United States Department of Molecular and Cellular Biology Baylor College of Medicine Houston TX United States University of Otago Te Tari Matai Whaiariaro Department of Physiology Dunedin New Zealand

Skeletal muscle cells (myofibers) are elongated non-mitotic, multinucleated syncytia that have adapted a microtubule lattice. Microtubule-associated proteins (MAPs) play roles in regulating microtubule architecture. The most abundant MAP in skeletal muscle is MAP4. MAP4 consists of a ubiquitous MAP4 isoform (uMAP4), expressed in most tissues, and a striated-muscle-specific alternatively spliced isoform (mMAP4) that includes a 3,180-nucleotide exon (exon 8). To determine the role of mMAP4 in skeletal muscle, we generated mice that lack mMAP4 and express only uMAP4 due to genomic deletion of exon 8. We demonstrate that loss of mMAP4 leads to disorganized microtubule architecture and intrinsic loss of force generation. We show that mMAP4 exhibits enhanced association with microtubules compared to uMAP4 and that both the loss of mMAP4 and the concomitant gain of uMAP4 cause loss of muscle function. These results demonstrate the critical role for balanced expression of mMAP4 and uMAP4 for skeletal muscle homeostasis. © 2024 The Author(s)

关键词： Cellular physiology Functional aspects of cell biology molecular physiology molecular Structure

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Single-image example-based superresolution of hyperpolarized 13C images

arXiv

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arXiv 2023年

作者： Deh, Kofi Coffee, Elizabeth Zhang, Guannan Kim, Nathaniel Miloushev, Vesselin Keshari, Kayvan R. Department of Radiology Memorial Sloan Kettering Cancer Center New York CityNY United States Department of Neurology Memorial Sloan Kettering Cancer Center New York CityNY United States Department of Physiology & Biophysics Weill Cornell Graduate School New York CityNY United States Department of Biochemistry & Structural Biology Weill Cornell Graduate School NYCNY United States Molecular Pharmacology Program Memorial Sloan Kettering Cancer Center NYCNY United States

The transient signal available for hyperpolarized (HP) 13C imaging limits the image spatial resolution. This paper demonstrates a method of increasing spatial resolution by post-processing the HP 13C metabolic map using a corresponding anatomic image as a high-resolution example. The proposed method is tested with a Shepp-Logan digital phantom and for an MR image of a tumor in a mouse brain acquired at 3 Tesla using 13C Chemical Shift Imaging. The results are compared to the results of standard image rescaling methods using peak-signal-to-noise ratio and structural similarity index (SSIM) image quality metrics. In vivo, the method reduced blur resulting in a better match between the metabolite biodistribution and the anatomy. It is concluded that the image quality of hyperpolarized 13C MRI in vivo images can be improved with single image superresolution using the anatomic image as an example. © 2023, CC0.

关键词： Magnetic resonance imaging

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An adapted cardioprotective diet with or without phytosterol and/or krill oil supplement in familial hypercholesterolemia: A pilot study protocol

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Clinical Nutrition Open Science 2024年 54卷 127-139页

作者： de Abreu-Silva, Erlon Oliveira Machado, Rachel Helena Vieira dos Santos, Bianca Rodrigues Kojima, Flávia Soares Santos, Renato Hideo Nakagawa Murizine, Gabriela Souza Homsi, Jordana Rosa Negrelli, Karina Leal Barbante, Letícia Galvão de Barros e Silva, Pedro G.M. de Lima, Andressa Gusmão Tramujas, Lucas Bersch-Ferreira, Ângela Cristine Carvalho, Adriana Bastos de Oliveira, Thaís Martins Izar, Maria Cristina Sampaio, Geni Rodrigues Damasceno, Nágila Raquel Teixeira Rogero, Marcelo Macedo da Silva Torres, Elizabeth Aparecida Ferraz Costa, Rosana Perim de Souza Mota, Luís Gustavo Krey, Julia Pinheiro da Silva, Lucas Ribeiro de Luca, Patrícia Vieira Amaral, Cristiane Kovacs de Oliveira, Patricia Rodrigues da Silva, Renata Alves Moreira, Priscila dos Santos, Elisa Maia de Melo, Rodrigo Morel Vieira Lima, Eduardo Gomes de Luca, André Heck, Thiago Gomes Carvalho, Ana Paula Perillo Ferreira Garofallo, Silvia Bueno Cavalcanti, Alexandre Biasi Marcadenti, Aline Hcor Research Institute SP São Paulo Brazil Division of Health Care Sciences Dresden International University Dresden Germany Department of Education and Research BP - A Beneficência Portuguesa de São Paulo SP São Paulo Brazil Carlos Chagas Filho Biophysics Institute Federal University of Rio de Janeiro RJ Rio de Janeiro Brazil National Institute of Cardiology RJ Rio de Janeiro Brazil Graduate Program in Genetics and Molecular Biology Federal University of Rio Grande do Sul RS Porto Alegre Brazil Paulista School of Medicine Federal University of São Paulo SP São Paulo Brazil Department of Nutrition School of Public Health University of São Paulo SP São Paulo Brazil Hcor Outpatient Nutrition Service SP São Paulo Brazil Hcor Nutrition Service SP São Paulo Brazil Brazilian Association of Familial Hypercholesterolemia SP São Paulo Brazil Dante Pazzanese Institute of Cardiology SP São Paulo Brazil Graduate Program in Cardiovascular Sciences (Professional Master's Degree) National Institute of Cardiology RJ Rio de Janeiro Brazil Graduate Program in Medicine and Health Federal University of Bahia BA Salvador Brazil Hospital Ana Nery BA Salvador Brazil Atherosclerosis Clinical Unit Hospital das Clínicas Heart Institute School of Medicine University of São Paulo SP São Paulo Brazil Dasa Cardiology Unit (Hospital 9 de Julho) SP São Paulo Brazil Clinical Research Center Hospital São José SC Criciúma Brazil Graduate Program in Integral Health Care and Graduate Program in Mathematical and Computational Modeling Regional University of the Northwest of the State of Rio Grande do Sul (UNIJUÍ) RS Ijuí Brazil Health and Nutrition Research Improvement Group /Clinical Hospital Federal University of Goiás GO Goiânia Brazil Feevale University RS Novo Hamburgo Brazil Graduate Program in Health Sciences (Cardiology) Rio Grande do Sul Cardiology Institute/University Foundation of Cardiology RS Porto Alegre Brazil Graduate Program in Epidemiology University

Background and aims: A healthy diet is one of the pillars of familial hypercholesterolemia (FH) treatment. However, the best dietary pattern and indication for specific supplementation have not been established. Our aim is to conduct a pilot study to assess the effect of an adapted cardioprotective diet with or without phytosterol and/or krill oil supplement in participants with a probable or definitive diagnosis of FH, treated with moderate/high potency statins. Methods: A national, multicenter, factorial, and parallel placebo-controlled randomized clinical trial with a superiority design and 1:1:1:1 allocation rate will be conducted. The participants will undergo whole exome sequencing and be allocated into four treatment groups: 1) a cardioprotective diet adapted for FH (DICA-FH) + phytosterol placebo + krill oil placebo;2) DICA-FH + phytosterol 2 g/day + krill oil placebo;3) DICA-FH + phytosterol placebo + krill oil 2 g/day;or 4) DICA-FH + phytosterol 2 g/day + krill oil 2 g/day. The primary outcomes will be low-density lipoprotein (LDL)-cholesterol and lipoprotein (a) levels and adherence to treatment after a 120-day follow-up. LDL- and high-density lipoprotein (HDL)-cholesterol subclasses, untargeted lipidomics analysis, adverse events, and protocol implementation components will also be assessed. Results: A total of 58 participants were enrolled between May–August 2023. After the end of the follow-up period, the efficacy and feasibility results of this pilot study will form the basis of the design of a large-scale randomized clinical trial. Conclusions: This study's overall goal is to recommend dietary treatment strategies in the context of FH. © 2024 The Author(s)

关键词： Diet Fatty acids Healthy Hypercholesterolemia Omega-3 Phytosterols

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Development of label-free triboelectric nanosensors as screening platforms for anti-tumor drugs

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Nano Energy 2024年 125卷

作者： Cheng, Yu-Ying Ganguly, Anindita Cheng, Yi-Yun Ortiz, Christopher Llynard D. Pal, Arnab Shah, Pramod Kaswan, Kuldeep Yang, Lee-Wei Lin, Zong-Hong Department of Biomedical Engineering National Taiwan University Taipei10617 Taiwan Institute of Biomedical Engineering National Tsing Hua University Hsinchu30013 Taiwan Internet of Senses Research Center National Tsing Hua University Hsinchu30013 Taiwan Praexisio Taiwan Inc. New Taipei221425 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300044 Taiwan Chemical Biology and Molecular Biophysics Program Taiwan International Graduate Program Institute of Biological Chemistry Academia Sinica Taipei115 Taiwan Department of Chemistry National Tsing Hua University Hsinchu300044 Taiwan International Intercollegiate PhD Program National Tsing Hua University Hsinchu300044 Taiwan Department of Power Mechanical Engineering National Tsing Hua University Hsinchu300044 Taiwan Biomedical Artificial Intelligence PhD Program National Tsing Hua University Hsinchu300044 Taiwan Physics Division National Center for Theoretical Sciences Taipei Taiwan

This study introduces a general label-free drug screening platform with potential to support high-throughput drug screening for any protein target. Its innovation lies in quantifying the affinity of molecule-molecule interactions via voltage output variation, which achieves unprecedented selectivity and sensitivity. It combines computational analysis complemented by experimental substantiation with a solid-liquid triboelectric nanosensor. Owing to its high binding affinity, FKBP-rapamycin is used as a model system to demonstrate the platform's sensitivity. Subsequently, the research is extended to study drug interactions with an oncogenic protein ATG4B. The findings unveil the binding of S130 and Tioconazole to ATG4B, a critical cysteine protease involved in autophagy, while revealing that Dexamethasone does not bind ATG4B. This binding exerts a specific inhibitory effect on autophagic flux and triggers cancer cell apoptosis. The results support the previously verified inhibitory effects of these drugs and the effectiveness of a newly developed self-powered drug screening platform, leveraging the principles of solid-liquid contact electrification. This approach adeptly confronts enduring challenges in traditional drug development methods where biochemical assays need to be designed for each individual protein target or only time-consuming and concentration-demanding molecular interaction measurements were made available. © 2024 Elsevier Ltd

关键词： Nanosensors

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Identifying topologically associating domains using differential kernels

arXiv

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arXiv 2023年

作者： Maisuradze, Luka King, Megan C. Surovtsev, Ivan V. Mochrie, Simon G.J. Shattuck, Mark D. O’Hern, Corey S. Department of Molecular Biophysics and Biochemistry Yale University New HavenCT United States Department of Cell Biology Yale School of Medicine New HavenCT United States Department of Physics Yale University New HavenCT United States Benjamin Levich Institute Physics Department The City College of New York New YorkNY United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT United States Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT United States

Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture techniques generate Hi-C maps that can provide insight into the 3D structure of chromatin. Hi-C maps can be represented as a symmetric matrix Aij, where each element represents the average contact probability or number of contacts between chromatin loci i and j. Previous studies have detected topologically associating domains (TADs), or self-interacting regions in Aij within which the contact probability is greater than that outside the region. Many algorithms have been developed to identify TADs within Hi-C maps. However, most TAD identification algorithms are unable to identify nested or overlapping TADs and for a given Hi-C map there is significant variation in the location and number of TADs identified by different methods. We develop a novel method to identify TADs, KerTAD, using a kernel-based technique from computer vision and image processing that is able to accurately identify nested and overlapping TADs. We benchmark this method against state-of-the-art TAD identification methods on both synthetic and experimental data sets. We find that the new method consistently has higher true positive rates (TPR) and lower false discovery rates (FDR) than all tested methods for both synthetic and manually annotated experimental Hi-C maps. The TPR for KerTAD is also largely insensitive to increasing noise and sparsity, in contrast to the other methods. We also find that KerTAD is consistent in the number and size of TADs identified across replicate experimental Hi-C maps for several organisms. Thus, KerTAD will improve automated TAD identification and enable researchers to better correlate changes in TADs to biological phenomena, such as enhancer-promoter interactions and disease states. © 2023, CC BY.

关键词： Topology

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Phosphoproteomic analysis reveals distinctive responses in Mangrovibacter phragmatis under high-salinity condition

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Biochemical and biophysical research communications 2024年 736卷 150514页

作者： Hong Soon Chin Narendrakumar Ravi Varadharajulu Zhi-Han Lin Chuan-Chih Hsu Steve S-F Yu Institute of Chemistry Academia Sinica Taipei Taiwan Chemical Biology and Molecular Biophysics Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu Taiwan. Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Department of Chemistry National Tsing Hua University Hsinchu Taiwan. Institute of Biochemical Sciences National Taiwan University Taipei Taiwan. Institute of Plant and Microbial Biology Academia Sinica Taipei Taiwan. Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan. Electronic address: sfyu@gate.sinica.edu.tw.

We conducted a thorough genome-wide investigation of protein phosphorylation in the halotolerant bacterium Mangrovibacter phragmitis (MPH) ASIOC01, using the Fe-IMAC enrichment method combined with tandem mass spectrometry under low- and high-salinity conditions. The phosphoproteome comprises 86 unique phosphorylated proteins, crucially involving pathways such as glycolysis/gluconeogenesis, the citrate cycle, chaperones, ribosomal proteins, and cell division. This study represents the first and most extensive investigation to-date comparing the bacterial phosphoproteome under different osmotic conditions using a gel-free approach. We identified 45 unique phosphoproteins in MPH cultured in media containing 1 % NaCl, and 33 exclusive phosphoproteins in MPH cultured in media containing 5 % NaCl. Eight phosphoproteins were detected in both growth conditions. Analysis of high-confidence phosphosites reveals that phosphorylation predominantly occurs on serine residues (52.3 %), followed by threonine (35.1 %) and tyrosine (12.6 %) residues. Interestingly, 34 % of the phosphopeptides display multiple phosphosites. Currently, prokaryotic phosphorylation site prediction platforms like MPSite and NetPhosBac 1.0 demonstrate an average prediction accuracy of only 21 % when applied to our dataset. Fourteen phosphoproteins did not yield matches when compared against dbPSP 2.0 (database of Phosphorylation Sites in Prokaryotes), indicating that these proteins may be novel phosphoproteins. These unique proteins undergoing phosphorylation under high salinity growth conditions potentially enhance their adaptive capabilities to environmental challenges.

关键词： Halotolerance LC-MS/MS Mangrovibacter phragmitis Osmotic-stress Phosphoproteomes Ser/thr/tyr phosphorylation

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Biomedical data and AI

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Science China Life Sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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