Structure and identification of the native PLP synthase complex from Methanosarcina acetivorans lysate by Angela Agnew, Ethan Humm, Kang Zhou, Robert P. Gunsalus, Z. Hong Zhou

“…ABSTRACT Many protein-protein interactions behave differently in biochemically purified forms as compared to their in vivo states. …”
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Investigation of the Mechanism of Complement System in Diabetic Nephropathy via Bioinformatics Analysis by Bojun Xu, Lei Wang, Huakui Zhan, Liangbin Zhao, Yuehan Wang, Meng Shen, Keyang Xu, Li Li, Xu Luo, Shasha Zhou, Anqi Tang, Gang Liu, Lu Song, Yan Li

“…Then, the protein-protein interactions (PPIs) of DEGs were performed by STRING database, the result was integrated and visualized via applying Cytoscape software, and the hub genes in this PPI network were selected by MCODE and topological analysis. …”
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Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins by E. A. Antropova, T. M. Khlebodarova, P. S. Demenkov, A. S. Venzel, N. V. Ivanisenko, A.  D.  Gavrilenko, T.  V. Ivanisenko, A. V. Adamovskaya, P. M. Revva, I. N. Lavrik, V. A. Ivanisenko

“…The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, protein activity, stability, and transport regulations, the expression regulation pathways being statistically significant. …”
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Overexpression of miR-21-5p as a potential pathogenesis marker for ovarian endometriosis by Mohamed Mahmoud, Amr Ahmed WalyEldeen, Mohamed A. Samie, Ahmed M. Sadek, Sayed Elakhras, Mohamed Samir, Osama Ahmed, Rasha Mohamed Samir Sayed, Ahmed Abdelaziz Baiomy, Sherif Abdelaziz Ibrahim, Hebatallah Hassan

“…Using bioinformatics tools, Gene Ontology Kyoto Encyclopedia of Genes and Genomes pathways, and protein–protein interactions, we identified differentially expressed genes and several pathways regulated by miR-21-5p that may contribute to endometriosis progression. …”
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Noncoding RNA profiling in omentum adipose tissue from obese patients and the identification of novel metabolic biomarkers by Yongjiao Zhang, Yongjiao Zhang, Ao Chen, Ao Chen, Sumei Lu, Dong Liu, Xiaolei Xuan, Xiaofei Lei, Mingwei Zhong, Fei Gao

“…Subsequent analyses included functional annotation with GO and KEGG pathway mapping, validation via real-time quantitative polymerase chain reaction (qRT‒PCR), the exploration of protein‒protein interactions (PPIs), and the identification of key regulatory genes through network analysis.ResultsThe results indicated that, compared with those in healthy individuals, various lncRNAs, circRNAs, and miRNAs were significantly differentially expressed in obese subjects. …”
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High-Pressure Treatment in Combination with Reduced Sodium for Improving the Physicochemical Properties and Sensory Qualities of Pork Gels by Weitong Wang, Jingying Cai, Satomi Tsutsuura, Tadayuki Nishiumi

“…Protein analysis by sodium dodecyl sulfate–polyacrylamide gel electrophoresis showed a reduction in the <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>α</mi></semantics></math></inline-formula>-actinin band with increased pressure, which suggested protein interactions were enhanced. Differential scanning calorimetry analysis indicated that protein denaturation occurred more readily at higher pressures (0.071 J/g at 0.1 MPa, 0.057 J/g at 150 MPa, and 0.039 J/g at 200 MPa). …”
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YAP K236 acetylation facilitates its nucleic export and deprived the protection against cardiac hypertrophy in mice by Panxia Wang, Luping Wang, Cui Liu, Yuehuai Hu, Guodong Feng, Zuqian Lian, Jing Lu, Ping He, Hexin Cai, Xiaohui Liang, Peiqing Liu, Xiaoqian Wu

“…Co-immunoprecipitation and immunofluorescence assays were used to elucidate the protein interactions and subcellular colocalization. We found that YAP protected against ISO-induced pathological cardiac hypertrophy both in vivo and in vitro. …”
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Metformin blocks BIK1-mediated CPK28 phosphorylation and enhances plant immunity by Yazhou Bao, Qian Zhang, Hai Zhu, Yong Pei, Yaning Zhao, Yixin Li, Peiyun Ji, Dandan Du, Hao Peng, Guangyuan Xu, Xiaodan Wang, Zhiyuan Yin, Gan Ai, Xiangxiu Liang, Daolong Dou

“…Additionally, surface plasmon resonance (SPR) and microscale thermophoresis (MST) techniques were employed to identify MET targets. Protein-protein interactions were analyzed using a luciferase complementation assay and a co-immunoprecipitation assay. …”
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HPGCN: A graph convolutional network-based prediction model for herbal heat/cold properties by Qikai Niu, Jing’ai Wang, Hongtao Li, Lin Tong, Haiyu Xu, Weina Zhang, Ziling Zeng, Sihong Liu, Wenjing Zong, Siqi Zhang, Siwei Tian, Huamin Zhang, Bing Li

“…Based on protein-protein interactions (PPI) and herb-herb networks, 30 target genes were selected as features for herbal heat/cold property prediction. …”
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Tumor CEMIP drives immune evasion of colorectal cancer via MHC-I internalization and degradation by Ying Zhu, Jiao Li, Tao Zhang, Lei Zhao, Min Jin, Jinghua Ren, Jing Tang, Haihong Wang, Zhenyu Lin, Qing Liang, Ruiqi Li, Biying Zhang, Qingling Hua, Guojie Xu, Jiayuan Chen, Lanqing Wang, Dejun Zhang, Dandan Yu

“…Flow cytometry analysis was used to examine immune cells. Protein–protein interactions were investigated by co-immunoprecipitation and proximity ligation assays. …”
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Deciphering the functional roles of PE18 and PPE26 proteins in modulating Mycobacterium tuberculosis pathogenesis and immune response by Aquib Ehtram, Mohd Shariq, Neha Quadir, Neha Quadir, Salma Jamal, Manjunath Pichipalli, Sheeba Zarin, Sheeba Zarin, Javaid Ahmad Sheikh, Nasreen Z. Ehtesham, Seyed E. Hasnain, Seyed E. Hasnain

“…Despite their importance, the roles and molecular interactions of PE18 and PPE26 in Mtb pathogenesis require further investigation.MethodsWe explored the roles of PE18 and PPE26 using recombinant Mycobacterium smegmatis (Msmeg) as a model organism. Protein-protein interactions were analyzed biochemically to identify partners within the ESX-5 secretion system, including EspG5 and other PE/PPE proteins. …”
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Microcephaly protein ANKLE2 promotes Zika virus replication by Adam T. Fishburn, Cole J. Florio, Thomas N. Klaessens, Brian Prince, Neil A. B. Adia, Nicholas J. Lopez, Nitin Sai Beesabathuni, Sydney S. Becker, Liubov Cherkashchenko, Sophia T. Haggard Arcé, Vivian Hoang, Traci N. Shiu, R. Blake Richardson, Matthew J. Evans, Claudia Rückert, Priya S. Shah

“…We previously mapped ZIKV-host protein interactions and identified the interaction between ZIKV non-structural protein 4A (NS4A) and host microcephaly protein ankyrin repeat and LEM domain-containing 2 (ANKLE2). …”
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Elucidating the pharmacological foundations and mechanisms of the Sihai Shuyu formula in treating Graves’ disease through integrated serum metabolomics and network pharmacology wit... by Xiaoju Liu, Xingjia Li, Wenbin Huang, Yifan Cui, Fengyun Cheng, Guofang Chen, Guofang Chen, Xiaodong Mao, Chao Liu, Chao Liu, Shuhang Xu

“…A comprehensive analysis of the multi-level bioinformatic analysis, including protein-protein interactions (PPI) and functional pathways of the targets, was conducted, followed by verification through immunohistochemistry (IHC) to clarify SHSY’s pharmacological basis and action mechanisms in treating GD.ResultsAfter 8 weeks of treatment, SHSY significantly reduced serum T4 and TRAb levels in GD mice and enhanced the morphology of thyroid tissues. …”
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Enhanced motivated behavior mediated by pharmacological targeting of the FGF14/Nav1.6 complex in nucleus accumbens neurons by Nolan M. Dvorak, Paul A. Wadsworth, Guillermo Aquino-Miranda, Pingyuan Wang, Douglas S. Engelke, Jingheng Zhou, Nghi Nguyen, Aditya K. Singh, Giuseppe Aceto, Zahra Haghighijoo, Isabella I. Smith, Nana Goode, Mingxiang Zhou, Yosef Avchalumov, Evan P. Troendle, Cynthia M. Tapia, Haiying Chen, Reid T. Powell, Timothy J. Baumgartner, Jully Singh, Leandra Koff, Jessica Di Re, Ann E. Wadsworth, Mate Marosi, Marc R. Azar, Kristina Elias, Paul Lehmann, Yorkiris M. Mármol Contreras, Poonam Shah, Hector Gutierrez, Thomas A. Green, Martin B. Ulmschneider, Marcello D’Ascenzo, Clifford Stephan, Guohong Cui, Fabricio H. Do Monte, Jia Zhou, Fernanda Laezza

“…Abstract Protein/protein interactions (PPI) play crucial roles in neuronal functions. …”
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Identification of biomarkers for the diagnosis of type 2 diabetes mellitus with metabolic associated fatty liver disease by bioinformatics analysis and experimental validation by Guiling Wu, Guiling Wu, Sihui Wu, Sihui Wu, Tian Xiong, Tian Xiong, Tian Xiong, You Yao, You Yao, Yu Qiu, Yu Qiu, Yu Qiu, Liheng Meng, Cuihong Chen, Xi Yang, Xi Yang, Xi Yang, Xinghuan Liang, Yingfen Qin

“…We utilised protein–protein interactions (PPIs), Gene Ontology, and the Kyoto Encyclopedia of Genes and Genomes to identify T2DM-associated MAFLD genes and potential mechanisms. …”
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Identification of reproductive performance in Bali-polled bulls using computer-assisted semen analysis and plasma seminal proteomics by Athhar Manabi Diansyah, Sanstoso Santoso, Herdis Herdis, Muhammad Yusuf, Tri Puji Priyatno, Tulus Maulana, Abdul Latief Toleng, Muhammad Ihsan Andi Dagong, Syahruddin Said, Hikmayani Iskandar, Aeni Nurlatifah, Puji Lestari, Lukman Affandy, Abdullah Baharun

“…Seminal plasma proteins were analyzed through liquid chromatography–tandem mass spectrometry (LC-MS/MS) and annotated using the UniProt database, PANTHER for gene ontology, and STRING database for protein interactions. Results: Post-thaw sperm kinematics showed satisfactory results, with a mean S/C of 1.52. …”
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Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes by Peter Vo, Denise M. Imai-Leonard, Benjamin Yang, Andrew Briere, Andy Shao, M. Isabel Casanova, David Adams, Takanori Amano, Oana Amarie, Zorana Berberovic, Lynette Bower, Robert Braun, Steve Brown, Samantha Burrill, Soo Young Cho, Sharon Clementson-Mobbs, Abigail D’Souza, Mary Dickinson, Mohammad Eskandarian, Ann M. Flenniken, Helmut Fuchs, Valerie Gailus-Durner, Jason Heaney, Yann Hérault, Martin Hrabe de Angelis, Chih-Wei Hsu, Shundan Jin, Russell Joynson, Yeon Kyung Kang, Haerim Kim, Hiroshi Masuya, Hamid Meziane, Steve Murray, Ki-Hoan Nam, Hyuna Noh, Lauryl M. J. Nutter, Marcela Palkova, Jan Prochazka, Miles Joseph Raishbrook, Fabrice Riet, Jennifer Ryan, Jason Salazar, Zachery Seavey, John Richard Seavitt, Radislav Sedlacek, Mohammed Selloum, Kyoung Yul Seo, Je Kyung Seong, Hae-Sol Shin, Toshihiko Shiroishi, Michelle Stewart, Karen Svenson, Masaru Tamura, Heather Tolentino, Uchechukwu Udensi, Sara Wells, Jacqueline White, Amelia Willett, Janine Wotton, Wolfgang Wurst, Atsushi Yoshiki, The International Mouse Phenotyping Consortium, Louise Lanoue, K. C. Kent Lloyd, Brian C. Leonard, Michel J. Roux, Colin McKerlie, Ala Moshiri

“…Phenotypes of human orthologues of mouse candidate genes were compared with known human CD genes to identify protein-protein interactions and molecular pathways using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Protein Analysis Through Evolutionary Relationships (PANTHER), and Kyoto Encyclopedia of Genes and Genomes. …”
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Optimasi Data Tidak Seimbang pada Interaksi Drug Target dengan Sampling dan Ensemble Support Vector Machine by Nabila Sekar Ramadhanti, Wisnu Ananta Kusuma, Annisa Annisa

“…This research is focusing on handling imbalanced data problem for drug-target (compound-protein) interaction data. There are many target protein and drug compound existed in compound-protein interaction databases, which many interactions are not validated yet by experiment. …”
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Immunoinformatics Approach for Multiepitope Vaccine Prediction from H, M, F, and N Proteins of Peste des Petits Ruminants Virus by Bothina B. M. Gaafar, Sumaia A. Ali, Khoubieb Ali Abd-elrahman, Yassir A. Almofti

“…For instance, the epitope 45MFLSLIGLL53 from the H protein interacted with four BoLA alleles, while 276FKKILCYPL284 predicted from the M protein interacted with two alleles. …”
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Potential Therapeutic Drugs for Parkinson’s Disease Based on Data Mining and Bioinformatics Analysis by Chuan Xu, Jiajun Chen, Xia Xu, Yingyu Zhang, Jia Li

“…Method differential gene candidates were obtained based on data mining of genes of PD brain tissue, original gene data analysis, differential gene crossover, pathway enrichment analysis, and protein interaction, and potential therapeutic drugs for Parkinson’s disease were obtained through drug-gene relationship. …”
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