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Shape-persistency and molecular function in heteromacrocycles: Creation of heteroarenecyclynes and arene - Azaarenecyclynes

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CHEMISTRY-A EUROPEAN JOURNAL 2003年第22期9卷 5430-5440页

作者： Yamaguchi, Y Yoshida, Z Kinki Univ Fac Sci & Engn Dept Chem Higashiosaka Osaka 5778502 Japan

On the basis of our concept that the introduction of heteroatoms and shape-persistency into the pi-macrocycles should bring forth striking functions or properties, heteroarenecyclynes (such as oxaarenecyclynes and thiaarenecyclynes) with semi-shape-persistent structure, and arene-azaarenecyclynes with shape-persistent structure have been prepared. Their novel functions and characteristic properties are disclosed. Noteworthy is that heteroarenecyclynes include C-60 to provide a Saturn-type complex with a N-2 binding function. A simple member of the oxaarenecyclyne compounds undergoes the Ag-I-induced cyclization leading to the quantitative formation of strongly luminescent perylene derivative. Arene-azaarenecyclynes are versatile compounds. For example, they exhibit intense luminescence in spite of the meta-bonding structure, providing the circular luminophore. Also they serve as receptors for special metal, organic, and inorganic substrates. The observed molecular functions are valuable for scientific and practical application.

关键词： cyclophanes heteroatoms macrocycles molecular function shape-persistency

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The subtype-specific molecular function of SPDEF in breast cancer and insights into prognostic significance

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JOURNAL OF CELLULAR AND molecular MEDICINE 2021年第15期25卷 7307-7320页

作者： Ye, Ting Li, Jingyuan Feng, Jia Guo, Jinglan Wan, Xue Xie, Dan Liu, Jinbo Southwest Med Univ Affiliated Hosp Dept Lab Med Luzhou Sichuan Peoples R China

Breast cancer (BC) is a molecular diverse disease which becomes the most common malignancy among women worldwide. There are four BC subtypes (Luminal A, Luminal B, HER2-enriched and Basal-like) robustly established following gene expression pattern-based characterization, behave significant differences in terms of their incidence, risk factors, prognosis and therapeutic sensitivity. Thus, there is an urgent need to provide mechanism research, treatment strategies and/or prognosis evaluation based on the patient stratification of BC subtypes. The prostate-derived ETS factor SPDEF was first identified as an activator of prostate specific antigen, and then, the involvements in many aspects of BC have been proposed. However, the subtype-specific molecular function of SPDEF in BC and insights into prognostic significance have not been clearly elucidated. This study demonstrated for the first time that SPDEF may play a diversity role in the expression levels, clinicopathologic importance, biological function and prognostic evaluation in BC via bioinformatics and experimental evidence, which mainly depends on different BC subtyping. In summary, our findings would help to better understand the possible mechanisms of various BC subtypes and to find possible candidate genes for prognostic and therapeutic usage.

关键词： breast cancer molecular function prognostic significance SPDEF subtype-specific

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Landscape of urine biomarkers for bladder cancer:molecular function,cell-of-origin,and bibliometric trend

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Oncology and Translational Medicine 2024年第3期10卷 132-142页

作者： Min Liu Shuo Li Yuan Rong Fei Long Wu-Shi Zhao Yu-Xuan Qin Ting Wang Fu-Bing Wang Xiang-Yu Meng Department of Laboratory Medicine Zhongnan Hospital of Wuhan UniversityWuhan 430071China Center for Single-Cell Omics and Tumor Liquid Biopsy Zhongnan Hospital of Wuhan UniversityWuhan 430071China School of Information Management Wuhan UniversityWuhan 430000China Department of Urology Zhongnan Hospital of Wuhan UniversityWuhan 430071China Wuhan Research Center for Infectious Diseases and Cancer Chinese Academy of Medical SciencesWuhan 430071China Health Science Center Hubei Minzu UniversityEnshi 445000China

Background:The effective management of bladder cancer(BCa)depends on the early diagnosis and *** studies have explored numerous urinary molecules as potential biomarkers of ***,the molecular functions and cell-of-origin profiles of these biomarkers are yet to be *** this study,we aimed to provide a comprehensive overview of the landscape of urinary biomarker genes for ***:We conducted an exhaustive literature search in PubMed,through which 555 biomarker genes were *** then analyzed the BCa single-cell atlas to infer the cellular origin of these BCa urine biomarker genes and performed functional enrichment analysis to gain insights into the functional molecular implications of these ***:These genes are involved in tumor proliferation,angiogenesis,cellmigration,and cell death and are predominantly expressed in epithelial and stromal ***,our analysis ofmultiomics tumor data revealed a discordance between tissue and urine in terms of differential methylation and RNA expression,suggesting that biomarker discovery for liquid biopsies should ideally begin with the analysis of bodily fluids rather than relying interest and that test strategies incorporating multiple molecular markers represent an ongoing ***:Collectively,our study has built a landscape of BCa urine biomarker genes,uncovered molecular insights into these biomarkers,and revealed the bibliometric trends in this field,which will contribute to the discovery of novel biomarkers in the future.

关键词： Bladder cancer Urine biomarker molecular function Cell-of-origin Bibliometric

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Shape-persistency and molecular function in heteromacrocyles: Creation of heteroarenecyclynes and arene - Azaarenecyclynes (vol 9, pg 5430, 2003)

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CHEMISTRY-A EUROPEAN JOURNAL 2004年第5期10卷 1070-1070页

作者： Yamaguchi, Y Yoshida, Z Kinki University Faculty of Science and Engineering Department of Chemistry 3-4-1 Kowakae Higashi-Osaka 577-8502 Japan Fax: (+81) 6-6723-2721 Kinki University Faculty of Science and Engineering Department of Chemistry 3-4-1 Kowakae Higashi-Osaka 577-8502 Japan Fax: (+81) 6-6723-2721

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Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

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Journal of Structural and functional Genomics 2007年第2-3期8卷 99-105页

作者： Shin, Dong Hae Hou, Jingtong Chandonia, John-Marc Das, Debanu Choi, In-Geol Kim, Rosalind Kim, Sung-Hou College of Pharmacy Ewha Womans University Seoul 120-750 South Korea Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley CA 94720 United States Department of Chemistry University of California Berkeley CA 94720 United States Department of Plant and Microbial Biology University of California Berkeley CA 94720 United States Division of Life Sciences and Biotechnology College of Life Sciences Korea University Seoul 136-713 South Korea

Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function. © 2007 Springer Science+Business Media B.V.

关键词： Berkeley Structural Genomics Center molecular function Structural genomics X-ray crystallography

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Identification and Validation of functional miRNAs and Their Main Targets in Sorghum bicolor

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molecular BIOTECHNOLOGY 2025年第1期67卷 123-137页

作者： Baqi, Abdul Samiullah Rehman, Wajid Bibi, Iram Menaa, Farid Khan, Yousaf Albalawi, Doha A. Sattar, Abdul Univ Balochistan Dept Chem Quetta 87300 Pakistan Hazara Univ Mansehra Dept Chem Mansehra Pakistan Calif Innovat Corp CIC Dept Biomed & Environm Engn BEE San Diego CA 92037 USA COMSATS Univ Islamabad Dept Chem Islamabad 45550 Pakistan Univ Tabuk Fac Sci Dept Biol Tabuk 71491 Saudi Arabia

MicroRNAs (miRNAs) are typically non-coding RNAs of 18-26 nucleotides (nts) that are produced endogenously and regulated post-transcriptionally through degradation or translational repression. Since miRNAs are evolutionarily conserved, their preservation is essential for important regulatory functions in plant development, growth, and responses to environmental stress. Sorghum bicolor (sbi) is a valuable food and fodder crop which is grown worldwide. A range of sbi miRNAs were identified so far as being connected to plant development and stress responses. Herein, we employed a variety of bioinformatics tools for miRNA profiling in sbi and a PCR-based platform for the validation of these miRNAs. In total, 74 new conserved sbi miRNAs from 52 miRNA families have been predicted. Using the psRNA Target method, 10613 different protein targets of these predicted miRNAs have been attained. These targets include 54 GO-terms which have substantial targets in the biological, molecular, and cellular processes. We particularly found that the sbi-miR1861c and sbi-miR5050 are involved to regulate sulphur compound biosynthetic process, while the significant spliceosomal complex is regulated by sbi-miR815b and sbi-miR7768b. Also, we report that the pre-ribosome, electron transport chain, cell communication, cellular respiration, protein localization, and photosynthesis are controlled by sbi-miR2907b, sbi-miR530, sbi-miR7749, sbi-miR1858a, sbi-mi7729a, and sbi-miR417, respectively. The identification and validation of these novel sbi miRNAs shall contribute a lot in improving the crop yield and ensure sustainable agriculture.

关键词： miRNA Sorghum bicolor RT-PCR Protein targets molecular function Sustainability

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Proteomic Analysis of Human Follicular Fluid-Derived Exosomes Reveals That Insufficient Folliculogenesis in Aging Women is Associated With Infertility

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molecular & CELLULAR PROTEOMICS 2025年第4期24卷 100930页

作者： Liu, Zhen Zhou, Qilin Zan, Jun Tian, Jingyan Zhang, Yangzhuohan Wu, Fanggui Zhao, Huan Peng, Qianwen Liu, Shangjie Chen, Qianjun Liu, Endong Liao, Zhengdong Zou, Pengfei Mei, Lin Wang, Wen Dong, Sen Niu, Luo Wu, Shengda He, Liangge Zhou, Xiaoyi Jin, Yanbo Li, Panpan Yang, Sheng Shenzhen Univ Affiliated Hosp 3 Shenzhen Luohu Hosp Grp Reprod Med Ctr Shenzhen Peoples R China Shenzhen Univ Sch Biomed Engn Guangdong Key Lab Biomed Measurements & Ultrasound Natl Reg Key Technol Engn Lab Med UltrasoundMed S Shenzhen Peoples R China Jiangxi Univ Sci & Technol Inst Addit Mfg Nanchang Peoples R China Hubei Univ Sci & Technol Dept Clin Med Xianning Peoples R China Shenzhen Univ Gen Hosp Med Sch Shenzhen Peoples R China

Although the risk of female infertility increases with advancing age, the underlying mechanisms remain unknown. Exosomes in follicular fluid are suggested to regulate folliculogenesis and influence oocyte quality, potentially playing a critical role in age-related infertility. Elucidating their content could enhance the understanding of the molecular mechanisms associated with female aging-induced infertility. In this study, we explored the proteomic profiles of exosomes derived from human follicular fluid to identify protein signatures associated with infertility in both young and aging women. Despite the lack of significant differences in the morphology and particle size of follicular fluid-derived exosomes between the two groups, proteomic analysis revealed a distinct pattern of differentially expressed proteins (DEPs). DEPs associated with B-cell activation, pathogen invasion, and disrupted metabolic processes were significantly more highly expressed in the aging group than in the young group, indicating their involvement in age-related infertility. In vivo experiments demonstrated that the application of exosomes, particularly those derived from young female group, facilitated the successful maturation of follicles. Key exosomal proteins, including ENO1, HSP90B1, fetuin-B, C7, and APOC4, were found to be associated with follicular maturation. Furthermore, the PI3K/AKT signaling pathway, which is known to be related to folliculogenesis, was activated by the application of exosomes in aging female mice. This study provides novel insights into the aging-associated protein signatures of follicular fluid-derived exosomes and their potential role in infertility. These findings suggest that aging-related protein signatures in exosomes could contribute to the treatment of age-related infertility.

关键词： aging exosomes folliculogenesis in vitro fertilization proteomic ACN Acetonitrile AFF-exos Follicular fluid-derived exosomes from aging women AKT Protein kinase B AMH Anti-mullerian hormone APC Adenomatous polyposis coli ATP Adenosine triphosphate BSA Bovine serum albumin CD Cluster of differentiation C1QA Complement component 1Q subcomponent chain A CCK-8 Cell counting Kit-8 DEP Differentially expressed protein DNA Deoxyribonucleic acid DTT Dithiothreitol E2 Estradiol ENO1 Alpha-enolase 1 FETUB Fetuin-B FSH Follicle-stimulating hormone FF-exos Follicular fluid-derived exosomes GAPDH Glyceraldehyde-3-phosphate dehydrogenase GnRH Gonadotropin-releasing hormone GO Gene Ontology HE Hematoxylin and eosin HSP90B1 Heat shock protein 90 beta family member 1 IVF In vitro fertilization IGHD Immunoglobulin heavy constant delta IGHM Immunoglobulin heavy mu IGHV Immunoglobulin heavy variable KEGG Kyoto Encyclopedia of Genes and Genomes LH Luteinizing hormone MF molecular function NLRP3 NOD-, LRR- and pyrin domain-containing protein 3 NTA Nanoparticle tracking analysis PCA Principal component analysis PI3K Phosphoinositide 3-kinase PCOS Polycystic ovary syndrome ROC Receiver operating characteristic SHP2 Src homology 2 domain-containing protein tyrosine phosphatase STRING Search tool for the retrieval of interacting genes TEM Transmission electron microscopy TSG101 Tumor susceptibility gene 101 UCHL1 Ubiquitin C-terminal hydrolase L1 WHO World Health Organization YFF-exos Follicular fluid-derived exosomes from young women

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Pipeline for inferring protein function from dynamics using coarse-grained molecular mechanics forcefield

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COMPUTERS IN BIOLOGY AND MEDICINE 2017年 83卷 134-142页

作者： Bhadra, Pratiti Pal, Debnath Indian Inst Sci Inst Math Initiat Bengaluru 560012 India Indian Inst Sci Computat & Data Sci Bengaluru 560012 India

Dynamics is integral to the function of proteins, yet the use of molecular dynamics (MD) simulation as a technique remains under-explored for molecular function inference. This is more important in the context of genomics projects where novel proteins are determined with limited evolutionary information. Recently we developed a method to match the query protein's flexible segments to infer function using a novel approach combining analysis of residue fluctuation-graphs and auto-correlation vectors derived from coarse-grained (CG) MD trajectory. The method was validated on a diverse dataset with sequence identity between proteins as low as 3%, with high function-recall rates. Here we share its implementation as a publicly accessible web service, named DynFunc (Dynamics Match for function) to query protein function from >= 1 mu s long CG dynamics trajectory information of protein subunits. Users are provided with the custom-developed coarse-grained molecular mechanics (CGMM) forcefield to generate the MD trajectories for their protein of interest. On upload of trajectory information, the DynFunc web server identifies specific flexible regions of the protein linked to putative molecular function. Our unique application does not use evolutionary information to infer molecular function from MD information and can, therefore, work for all proteins, including moonlighting and the novel ones, whenever structural information is available. Our pipeline is expected to be of utility to all structural biologists working with novel proteins and interested in moonlighting functions.

关键词： Simulation molecular function Dynamics Forcefield Database

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molecular functions of HAX1 during disease progress

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VIRUS GENES 2024年第5期60卷 435-445页

作者： Zhang, Dajun Yang, Jinke Huang, Qi Zhao, Dengshuai Wang, Tianyu Yu, Dixi Qin, Limei Zhang, Keshan Foshan Univ Coll Life Sci & Engn Foshan 528225 Guangdong Peoples R China Lanzhou Univ Lanzhou Vet Res Inst Chinese Acad Agr Sci Coll Vet MedState Key Lab Anim Dis Control & Prev Lanzhou 730000 Peoples R China

HCLS1-associated protein X-1 (HAX1) is a newly discovered multifunctional cell regulatory protein that is widely expressed in cells and has a close relationship with multiple cellular proteins. HAX1 plays important roles in various processes, including the regulation of apoptosis, maintenance of mitochondrial membrane potential stability and calcium homeostasis, occurrence and development of diseases, post-transcriptional regulation of gene expression, and host immune response after viral infection. In this article, we have reviewed the research progress on the biological functions of HAX1, thereby laying a theoretical foundation for further exploration of its underlying mechanisms and targeted application.

关键词： HAX1 Regulator Apoptosis molecular function Disease progress

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molecular functions of metallothionein and its role in hematological malignancies

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JOURNAL OF HEMATOLOGY & ONCOLOGY 2012年第1期5卷 1-8页

作者： Takahashi, Shinichiro Kitasato Univ Sch Allied Hlth Sci Div Hematol Minami Ku Sagamihara Kanagawa 2520373 Japan Kitasato Univ Grad Sch Med Sci Div Mol Hematol Minami Ku Sagamihara Kanagawa 2520373 Japan

Metallothionein (MT) was reported to be a potential negative regulator of apoptosis, and various reports have suggested that it may play roles in carcinogenesis and drug resistance, in at least a portion of cancer cells. The author summarizes the current understanding of the molecular functions of MT for tumor cell growth and drug resistance. These activities are regulated through intracellular metal ion modulation and free radical scavenging. Compared with analyses of solid tumors, few studies have analyzed the roles of MT in hematological malignancies. This review mainly describes the functions of MT in hematopoietic cells. Furthermore, through expression analyses of leukemias and lymphomas, the roles of MT in the biology of these diseases are particularly focused upon.

关键词： Metallothionein (MT) molecular function Hematological malignancies

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