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Rationally designed synthetic peptide as versatile calibrant to improve the accuracy of protein sequence analysis using MALDI mass spectrometry

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Chinese Chemical Letters 2024年第3期35卷 214-220页

作者： Lingpeng Zhan Yanyi Huang guanbo wang Institute for Cell Analysis Shenzhen Bay LaboratoryShenzhen 518132China Biomedical Pioneering Innovation Center Peking UniversityBeijing 100871China

Matrix-assisted laser desorption/ionization(MALDI)mass spectrometry(MS)plays an indispensable role in analyzing protein covalent *** reliable identification of amino acid residues and modifications relies on the mass accuracy,which is highly dependent on ***,the accuracy provided by the currently available calibrants still needs further improvement in terms of compatibility with multiple tandem MS modes or ion polarity modes,calibratable range,and minimizing suppression of and interference with analyte *** aiming at developing a versatile calibrant to solve these problem,we designed a synthetic peptide format of calibrant R_x(GDP_n)_m(referred to as“Gly-Asp-Pro,GDP”)according to the chemical natures of amino acids and polypeptide fragmentation rules in tandem *** four types of amino acid residues selected and arranged through rational designs,a GDP peptide produces highly regulated fragments that give rise to evenly spaced signals in each tandem MS mode and is compatible with both positive and negative ion *** internal calibration,its regulated fragmentation pattern minimizes interference with analyte signals,and using a single peptide as the input minimizes suppression of the analyte *** demonstrated by analyses of proteins including monoclonal antibody and Aβ-42,these features allowed significant increase of the mass accuracy and precision,which improved sequence coverage and sequence resolution in sequence analyses(including de novo sequencing).This rational design strategy may also inspire further development of synthetic calibrants that benefit structural analysis of biomolecules.

关键词： Biomolecule design Synthetic peptide Protein sequencing Covalent structure De novo sequencing Mass spectrometry Gas-phase fragmentation

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Screening and identifying natural products with SARS-CoV-2 infection inhibitory activity from medicinal fungi

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Biosafety and Health 2024年第1期6卷 12-20页

作者： Shuang Zhao Amelia Siqi Huang Weibo Zhang Lili Ren Hexiang wang Jianbin wang Xinyang Shao guanbo wang Institute of Agri-Food Processing and Nutrition Institute of Plant ProtectionBeijing Academy of Agriculture and Forestry SciencesBejing 100097China Bejing Key Laboratory of Fruits and Vegetable Storage and Processing Key Laboratory of Vegetable Postharvest ProcessingMinistry of AgricultureBejing 100097China Dalton Academy The Affliated High School of Peking UniversityBeijing 100190China NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory National Institute of Pathogen BiologyBejing 100730China Key Laboratory of Respiratory Disease Pathogenomics Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100730China College of Biological Sciences China Agricultural UniversityBejing 100193China School of Life Sciences Tsinghua UniversityBeijing 100084China Changping Laboratory Beijing 102206China Institute for Cell Analysis Shenzhen Bay LaboratoryShenzhen 518132China

The coronavirus disease of 2019(COVID‐19),a global pandemic caused by the severe acute respiratory syndrome coronavirus 2(SARS‐CoV‐2),can result in severe health *** addition to physical preventative measures,pharmaceutical intervention is also *** natural products from medicinal fungi have shown promise as potential antiviral drugs and may serve as a source of effective components with antiviral activity against SARS‐CoV‐2 and other *** this study,we developed a workflow that integrates viral infection inhibition assays at both cellular and molecular levels,as well as molecular separation and characterization,to screen and identify natural products with antiviral *** this workflow,we screened 167 extracts extracted from 36 medicinal fungi using optimized extraction *** assessed the antiviral effects of these extracts by measuring their ability to inhibit SARS‐CoV‐2 infection and receptor binding domain‐human angiotensin‐converting enzyme 2(RBD‐hACE2)binding in *** charge‐and size‐based characterization of the active compounds through filtration and chromatographic fractionation,mass spectrometry characterization of the fractionated compounds revealed that the active components are polysaccharides and determined their monosaccharide residue *** findings provide new insights into the antiviral potential of natural products and their screening strategies and may contribute to the development of effective antiviral therapeutics against COVID‐19 and other diseases.

关键词： Medicinal fungi Natural products Antiviral activity COVID‐19 Polysaccharides

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Federated Offline Reinforcement Learning with Proximal Policy Evaluation

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Chinese Journal of Electronics 2024年

作者： Sheng YUE Yongheng DENG guanbo wang Ju REN Yaoxue ZHANG Department of Computer Science and Technology BNRist Tsinghua University Zhongguancun Laboratory

Offline reinforcement learning (RL) has gathered increasing attention in recent years, which seeks to learn policies from static datasets without active online exploration. However, the existing offline RL approaches often require a large amount of pre-collected data and hence are hardly implemented by a single agent in practice. Inspired by the advancement of federated learning (FL), this paper studies federated offline reinforcement learning(FORL), whereby multiple agents collaboratively carry out offline policy learning with no need to share their raw trajectories. Clearly, a straightforward solution is to simply retrofit the off-the-shelf offline RL methods for FL, whereas such an approach easily overfits individual datasets during local updating, leading to instability and subpar performance. To overcome this challenge, we propose a new FORL algorithm, named model-free (MF)-FORL, thatexploits novel “proximal local policy evaluation” to judiciously push up action values beyond local data support, enabling agents to capture the individual information without forgetting the aggregated knowledge. Further, we introduce a model-based variant, MB-FORL, capable of improving the generalization ability and computational efficiency via utilizing a learned dynamics model. We evaluate the proposed algorithms on a suite of complex and high-dimensional offline RL benchmarks, and the results demonstrate significant performance gains over the baselines.

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基于纯自注意力机制的毫米波雷达手势识别

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系统工程与电子技术 2024年第3期46卷 859-867页

作者：张春杰王冠博陈奇邓志安哈尔滨工程大学信息与通信工程学院黑龙江哈尔滨150001 先进船舶通信与信息技术工业和信息化部重点实验室黑龙江哈尔滨150001

在构建智慧控制,万物互联的背景下,通过手势远程控制设备,进行人机交互逐渐成为研究热点。对此,提出了一种以毫米波雷达为传感器,采用基于纯自注意力机制模型实现手势识别的方法。首先,采集正面视角的13类手势的时序回波数据。接着,对... 详细信息

在构建智慧控制,万物互联的背景下,通过手势远程控制设备,进行人机交互逐渐成为研究热点。对此,提出了一种以毫米波雷达为传感器,采用基于纯自注意力机制模型实现手势识别的方法。首先,采集正面视角的13类手势的时序回波数据。接着,对数据进行三维快速傅里叶变换(three-dimension fast Fourier transform,3D-FFT)、动目标显示(moving target indication,MTI)、恒虚警率(constant false alarm rate,CFAR)检测操作并进行固定种类特征提取,将这些特征传入基于纯自注意力机制网络的雷达特征变换(radar feature transformer,RFT)网络。最后,基于实测数据完成了数据特征提取、网络训练、手势识别等步骤。实验结果表明,所提方法在测试集上准确率达到95.38%,网络训练时间短,模型复杂度低,泛化性好,为现有研究提供了新的研究思路。

关键词：毫米波雷达手势识别自注意力机制噪声抑制

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ODS MA754合金传热界面接触热阻实验研究

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西安交通大学学报 2024年第2期58卷 100-108页

作者：杨万奎郭啸宇曾和荣郭玉川唐彬王冠博严睿豪孟兆明郭斯茂中国工程物理研究院核物理与化学研究所四川绵阳621900 黑龙江省核动力装置性能与设备重点实验室哈尔滨150001 哈尔滨工程大学核科学与技术学院哈尔滨150001

鉴于ODS MA754合金传热界面的接触热阻参数对全固态堆芯空间反应堆系统的热量导出具有重要影响,研发和设计了高温高压接触热阻实验装置,测量了不同温度(20~800℃)、压力(0~80 MPa)、气体氛围(He、CO_(2))以及试件表面粗糙度(1.6、3.2μm... 详细信息

鉴于ODS MA754合金传热界面的接触热阻参数对全固态堆芯空间反应堆系统的热量导出具有重要影响,研发和设计了高温高压接触热阻实验装置,测量了不同温度(20~800℃)、压力(0~80 MPa)、气体氛围(He、CO_(2))以及试件表面粗糙度(1.6、3.2μm)下ODS MA754合金传热界面的接触热阻,并基于测试获得的宽量程数据点,建立了ODS MA754合金的接触热阻数据库。实验结果表明:随着接触面温度和压力的升高,界面接触热阻降低,且热阻降低的速率逐渐减小;相较于表面粗糙度为1.6μm的试件,粗糙度为3.2μm试件表面的界面接触热阻明显偏大,实验得到的定量关系可为工程样件的加工粗糙度要求提供依据;He气氛下的接触热阻远小于CO_(2)气氛,在0.1 MPa、100℃工况下,He气氛接触热阻约为CO_(2)气氛接触热阻的1/4。该研究结果可为空间反应堆的热工设计提供数据参考。

关键词：空间反应堆 ODS MA754合金接触热阻高温高压表面粗糙度

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Cr3和Cr5系支承辊大型锻件脱氧工艺研究

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江西冶金 2024年第1期44卷 25-33页

作者：何川张延玲王冠博戴乐张威风石如星北京科技大学钢铁冶金新技术国家重点实验室北京100083 洛阳中重铸锻有限责任公司洛阳471039

由于Cr3和Cr5系支承辊钢液中铬含量增加会抑制铝脱氧反应的进行。本文以Cr3和Cr5系支承辊冶金过程中脱氧工艺为研究背景,通过实验室脱氧实验,利用FactSage 8.1软件计算Cr3和Cr5系轧辊钢中氧含量,绘制铝脱氧平衡曲线,将Wagner模型与炉渣... 详细信息

由于Cr3和Cr5系支承辊钢液中铬含量增加会抑制铝脱氧反应的进行。本文以Cr3和Cr5系支承辊冶金过程中脱氧工艺为研究背景,通过实验室脱氧实验,利用FactSage 8.1软件计算Cr3和Cr5系轧辊钢中氧含量,绘制铝脱氧平衡曲线,将Wagner模型与炉渣共存理论相结合,建立了钢渣反应模型,探讨铬含量对钢液中铝脱氧效果的影响。结果表明,钢液中铬含量在一定范围内增加会抑制铝脱氧反应进行;在精炼过程中,当Cr3系支承辊中铝含量控制在0.03%左右、Cr5系支承辊中铝含量控制在0.05%左右时,可将氧含量有效控制在10^(-5)以下;而与之相匹配的最佳炉渣成分的碱度为2.5~3.0,w(Al_(2)O_(3))>20%。

关键词：轧辊钢脱氧工艺铬含量钢渣反应模型炉渣共存理论

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Characterization of co-existing protein conformers and dynamic assembly of protein machineries using hybrid mass spectrometry approaches

Characterization of co-existing protein conformers and dynam...

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2018年中国质谱学术大会（CMSC2018）

作者： guanbo wang School of Chemistry and Materials Science Nanjing Normal University

Characterization of structure and dynamics of various protein states is important for understanding molecular mechanisms of processes including assembly of protein machineries, protein denaturation, aggregation, and enzyme catalysis. Top-down mass spectrometry(MS) coupled with hydrogen/deuterium exchange(HDX) allows a distinction to be made among multiple protein conformers that coexist in solution via isolation of individual conformers in the gas phase. However, separation of conformers with subtle differences remains a problem due to their similar degrees of deuterium uptake. We made effort to carry out conformer separation in the solution phase using modified capillary electrophoresis, whereby conformers are labeled with deuterium during the separation process, followed by deuteration-level determination and label localization with online top-down MS analysis. With this approach we performed conformer-specific characterization of a panel of proteins, and disulfide mapping of individual isomers of disulfide-rich proteins with re-arranged disulfide patterns. Some biochemical reactions relevant to protein conformation, such as disulfide reduction/rearrangement, were also monitored with this approach in a timeresolved fashion. To decipher the relationship between subtle conformational changes and assembly of protein complexes, we extended the scope of the temperature-controlled MS technique, which we previously developed to study protein aggregation as a function of temperature or heat-exposure, to systems that undergo multi-step denaturation and oligomerization. Combination of these approaches enables conformer-specific and time-resolved characterization of complex protein systems.

关键词： hydrogen/deuterium exchange (HDX) capillary electrophoresis (CE) stopped-flow top-down native MS

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Multi-omics for COVID-19:driving development of therapeutics and vaccines

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National Science Review 2023年第9期10卷 307-336页

作者： Mengyu Guo Muya Xiong Jinying Peng Tong Guan Haixia Su Yanyi Huang Cai-Guang Yang Yang Li Diana Boraschi Thanigaimalai Pillaiyar guanbo wang Chengqi Yi Yechun Xu Chunying Chen CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology of China State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences University of Chinese Academy of Sciences State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Biomedical Pioneering Innovation Centre Peking University 6. Institute for Cell AnalysisShenzhen Bay Laboratory Peking-Tsinghua Center for Life Sciences Peking University College of Chemistry and Molecular Engineering Beijing National Laboratory for Molecular SciencesPeking University 9. State Key Laboratory of Drug Research Centre for Chemical BiologyShanghai Institute of Materia MedicaChinese Academy of Sciences 10. Laboratory of Immunology and Nanomedicine and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical ImmunomodulationShenzhen Institute of Advanced TechnologyChinese Academy of Sciences 11. Institute of Biochemistry and Cell Biology National Research Council 12. Institute of PharmacyPharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery Eberhard Karls University Tübingen 13. Department of Chemical Biology and Synthetic and Functional Biomolecules CenterCollege of Chemistry and Molecular Engineering Peking University 14. GBA National Institute for Nanotechnology Innovation

The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and *** development of therapeutics and vaccines to combat this virus is continuously ***-omics approaches,including genomics,transcriptomics,proteomics,metabolomics,epigenomics and metallomics,have helped understand the structural and molecular features of the virus,thereby assisting in the design of potential therapeutics and accelerating vaccine development for ***,we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19,in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines.

关键词： COVID-19 SARS-CoV-2 multi-omics antibodies small-molecule drugs vaccines

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TREM-1 multimerization is essential for its activation on monocytes and neutrophils

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Cellular & Molecular Immunology 2019年第5期16卷 460-472页

作者： Kevin Carrasco Amir Boufenzer Lucie Jolly Helene Le Cordier guanbo wang Albert JR Heck Adelheid Cerwenka Emilie Vinolo Alexis Nazabal Alexandre Kriznik Pierre Launay Sebastien Gibot Marc Derive INOTREM Vandœuvre-les-NancyFrance UMR-S 1116 Defaillance cardiovasculaire aigue et chroniqueVandœuvre-les-NancyFrance UMR7365 Ingénierie Moléculaire et Physiopathologie Articulaire(IMoPA)CNRS-Universitéde LorraineVandœuvre-les-NancyFrance Biomolecular Mass Spectrometry and Proteomics Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences and Netherlands Proteomics CenterUtrecht UniversityUtrechtThe Netherlands Innate Immunity German Cancer Research Center(DKFZ)HeidelbergGermany CovalX ZurichSwitzerland Service Commun de Biophysique Interactions Moléculaires(SCBIM) FR3209Biopole de l’Universitede LorraineVandœuvre-les-NancyFrance Inatherys Evry CedexFrance

The triggering receptor expressed on myeloid cells-1(TREM-1)is a receptor expressed on innate immune *** promoting the amplification of inflammatory signals that are initially triggered by Toll-like receptors(TLRs),TREM-1 has been characterized as a major player in the pathophysiology of acute and chronic inflammatory diseases,such as septic shock,myocardial infarction,atherosclerosis,and inflammatory bowel ***,the molecular events leading to the activation of TREM-1 in innate immune cells remain ***,we show that TREM-1 is activated by multimerization and that the levels of intracellular Ca 2+release,reactive oxygen species,and cytokine production correlate with the degree of TREM-1 ***-1 activation on primary human monocytes by LPS required a two-step process consisting of upregulation followed by clustering of TREM-1 at the cell surface,in contrast to primary human neutrophils,where LPS induced a rapid cell membrane reorganization of TREM-1,which confirmed that TREM-1 is regulated differently in primary human neutrophils and *** addition,we show that the ectodomain of TREM-1 is able to homooligomerize in a concentration-dependent manner,which suggests that the clustering of TREM-1 on the membrane promotes its *** further show that the adapter protein DAP12 stabilizes TREM-1 surface expression and ***-1 multimerization at the cell surface is also mediated by its endogenous ligand,a conclusion supported by the ability of the TREM-1 inhibitor LR12 to limit TREM-1 *** results provide evidence for ligand-induced,receptor-mediated dimerization of ***,our findings uncover the mechanisms necessary for TREM-1 activation in monocytes and neutrophils.

关键词： TREM-1 multimerization activation monocytes neutrophils

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A deep learning-based global tropical cyclogenesis prediction model and its interpretability analysis

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Science China Earth Sciences 2024年

作者： Bin MU Xin wang Shijin YUAN Yuxuan CHEN Guansong wang Bo QIN guanbo ZHOU School of Software Engineering Tongji University Department of Atmospheric and Oceanic Sciences & Institute of Atmospheric Sciences Fudan University National Meteorological Center Shanghai Typhoon Institute China Meteorological Administration

Tropical cloud clusters (TCCs) can potentially develop into tropical cyclones (TCs),leading to significant casualties and economic *** prediction of tropical cyclogenesis (TCG) is crucial for early *** traditional deep learning methods applied to TCG prediction rely on predictors from a single time point,neglect the ocean-atmosphere interactions,and exhibit low model *** study proposes the Tropical Cyclogenesis Prediction-Net (TCGP-Net) based on the Swin Transformer,which leverages convolutional operations and attention mechanisms to encode spatiotemporal features and capture the temporal evolution of *** model incorporates the coupled ocean-atmosphere interactions,including multiple variables such as sea surface ***,causal inference and integrated gradients are employed to validate the effectiveness of the predictors and provide an interpretability analysis of the model’s decision-making *** model is trained using GridSat satellite data and ERA5 reanalysis *** results demonstrate that TCGP-Net achieves high accuracy and stability,with a detection rate of 97.9%and a false alarm rate of 2.2%for predicting TCG 24 hours in advance,significantly outperforming existing *** indicates that TCGP-Net is a reliable tool for tropical cyclogenesis prediction.

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