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protein acetylation sites with complex-valued polynomial model

Frontiers of Computer Science 2024年第3期18卷 217-226页

作者： Wenzheng BAO Bin YANG School of Information Engineering Xuzhou University of TechnologyXuzhou 221018China School of Information Science and Engineering Zaozhuang UniversityZaozhuang 277160China

protein acetylation refers to a process of adding acetyl groups(CH3CO-)to lysine residues on protein *** one of the most commonly used protein post-translational modifications,lysine acetylation plays an important role in different *** our study,we developed a humanspecific method which uses a cascade classifier of complexvalued polynomial model(CVPM),combined with sequence and structural feature descriptors to solve the problem of imbalance between positive and negative *** gene expression programming and differential evolution are utilized to search the optimal CVPM *** also made a systematic and comprehensive analysis of the acetylation data and the prediction *** performances of our proposed method are 79.15%in Sp,78.17%in Sn,78.66%in ACC 78.76%in F1,and 0.5733 in MCC,which performs better than other state-of-the-art methods.

关键词： protein acetylation complex-valued polynomial model machine learning

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protein acetylation as a mechanism for Nostoc flagelliforme adaptation to drought stress

Protein acetylation as a mechanism for Nostoc flagelliforme ...

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中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Lingxia Wang Yang Liu Fengkun Yan Xiaoxu Li Miaomiao Ding Men Wang Jing Shi Tingting Xu Wenyu Liang School of Life Sciences Ningxia University Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China School of Agriculture Ningxia University

Nostoc flagelliforme,a terrestrial cyanobacterium,is well adapted to *** explore the adaptation mechanisms of *** in response to drought condition,a large-scale quantitative lysine acetylome was carried out using immunoaffinity enrichment of Lys-acetylated peptides and liquid chromatography linked to tandem mass spectrometry.A total of 1340 lysine acetylation（LysAc） sites,1340 Lysacetylated peptides and 653 Lys-acetylated proteins were *** conserved sequence motifs of the LysAc sites,including a new motif KxxK,were *** analyses revealed that the differentially acetylated proteins involved in response to drought condition were preferentially predicted to participate in glutathione metabolism and carbon metabolism and photosynthesis pathways based on KEGG pathway category enrichment *** found that GSH accumulation played important roles as stress protectant and reactive oxygen species scavenger,and soluble sugar accumulation improved the osmotic regulation ability in response to drought condition in *** energy metabolism-related proteins of *** were regulated by the LysAc modification under the environment of extreme drought to maintain lower *** with a large number of accumulation the energy metabolism of raw materials（glucose,pyruvic acid） are advantageous to quickly restore physiological activity under the condition of *** of physiological parameters and mRNA expression levels related to glutathione metabolism and carbon metabolism and photosynthesis were found to be significantly affected by drought *** together,reversible protein LysAc is likely to be a post-translational mechanism contributing to the ***’s adaptation to drought condition.

关键词： Nostoc flagelliforme drought condition protein acetylation

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HDACs,histone deacetylation and gene transcription: from molecular biology to cancer therapeutics

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Cell Research 2007年第3期17卷 195-211页

作者： PaolaGallinari StefaniaDiMarco PhillipJones MichelePallaoro ChristianSteinkühler Istituto di Ricerche di Biologia Molecolare“P.Angeletti”-IRBM-Merck Research Laboratories Rome Via Pontina Km 3060000040 PomeziaItaly

Histone deacetylases(HDACs)and histone acetyl transferases(HATs)are two counteracting enzyme families whoseenzymatic activity controls the acetylation state of protein lysine residues,notably those contained in the N-terminalextensions of the core *** of histones affects gene expression through its influence on chromatin *** addition,several non-histone proteins are regulated in their stability or biological function by the acetylationstate of specific lysine *** intervene in a multitude of biological processes and are part of a multiproteinfamily in which each member has its specialized *** addition,HDAC activity is tightly controlled throughtargeted recruitment,protein-protein interactions and post-translational *** of cell cycle progression,cell survival and differentiation are among the most important roles of these *** these processes are affectedby malignant transforlnation,HDAC inhibitors were developed as antineoplastic drugs and are showing encouragingefficacy in cancer patients.

关键词： histone deacetylase histone post-translational modification transcription histone deacetylase inhibitors protein acetylation

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Interplay between the bacterial protein deacetylase CobB and the second messenger c-di-GMP

Interplay between the bacterial protein deacetylase CobB and...

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中国生物工程学会第十三届学术年会暨2019年全国生物技术大会

作者： Zhaowei Xu Hainan Zhang Xingrun Zhang Hewei Jiang Chengxi Liu Fanlin Wu Lili Qian Bingbing Hao Daniel M Czajkowsky Shujuan Guo Zhijing Xu Lijun Bi Shihua Wang Haitao Li Minjia Tan Wei Yan Lei Feng Jingli Hou Sheng-ce Tao Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University MOE Key Laboratory of protein Sciences Center for Structural Biology School of Life Sciences Tsinghua University Department of Basic Medical Sciences School of Medicine Tsinghua University The Chemical Proteomics Center and State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences School of Biomedical Engineering Shanghai Jiao Tong University College of Life Sciences Shanghai Normal University National Key Laboratory of Biomacromolecules Key Laboratory of Non-Coding RNA and Key Laboratory of Protein and Peptide Pharmaceuticals Institute of Biophysics Chinese Academy of Sciences School of Stomatology and Medicine Foshan University School of Life Science Fujian Agriculture and Forestry University Instrumental Analysis Center Shanghai Jiao Tong University State Key Laboratory of Oncogenes and Related Genes

As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis, and DNA supercoiling in many bacteria. Using an Escherichia coli proteome microarray, we found that c-di-GMP strongly binds to CobB. Further, protein deacetylation assays showed that c-di-GMP inhibits the activity of CobB and thereby modulates the biogenesis of acetyl-CoA. Interestingly, we also found that one of the key enzymes directly involved in c-di-GMP production, DgcZ, is a substrate of CobB. Deacetylation of DgcZ by CobB enhances its activity and thus the production of cdi-GMP. Our work establishes a novel negative feedback loop linking c-di-GMP biogenesis and CobB-mediated protein deacetylation.

关键词： c-di-GMP CobB diguanylate cyclase negative feedback loop protein acetylation

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结合多特征算法和信息熵预测蛋白质乙酰化位点

结合多特征算法和信息熵预测蛋白质乙酰化位点

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第十一届全国计算（机）化学学术会议

作者：索生宝孙兴玉邱建丁南昌大学化学系

＜正＞蛋白质乙酰化作为蛋白质翻译后修饰的一种重要形式,在各种生命活动中起着重要的作用。其基本原理是在乙酰基转移酶的作用下,在蛋白质的特定位置添加乙酰基,是细胞控制基因表达、调节蛋白质活性或生理过程的一种机制,已成为基因表... 详细信息

＜正＞蛋白质乙酰化作为蛋白质翻译后修饰的一种重要形式,在各种生命活动中起着重要的作用。其基本原理是在乙酰基转移酶的作用下,在蛋白质的特定位置添加乙酰基,是细胞控制基因表达、调节蛋白质活性或生理过程的一种机制,已成为基因表达、蛋白组学、酶动力学以及药物设计等研究的重要方面。预测蛋白质乙酰化修饰位点,对研究蛋白质的性质和功

关键词： protein acetylation multi-feature extraction algorithm jackknife test support vector machine

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