Association between ABCB4 variants and intrahepatic cholestasis of pregnancy by Dekun Zhang, Yuhong Li, Shufeng He, Jing Shu, Tiechen Li, Qing Sun

“…PolyPhen2, Mutation Taster, Provean, SIFT and Mutpred2 were used to predict protein structure, and Pymol software was used to predict the impact of missense variant c.1954 A > G(p.Arg652Gly) on proteins. …”
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Integration of ATAC-seq and RNA-seq reveals signal regulation during post-molt and inter-molt stages in muscle of Eriocheir sinensis by Bin Wang, Bin Wang, Jingjing Li, Mingzhi Zhang, Mingzhi Zhang, Anqi Li, Zhentao Song, Zhentao Song, Zhen He, Zhen He, Ruiqi Zhang, Ruiqi Zhang, Tong Hao, Tong Hao, Jinsheng Sun, Jinsheng Sun

“…In all the enriched signaling pathways, GPCR signaling pathway includes the most differentially expressed genes (8 genes), which underlines its importance in the signal transduction from the post-molt stage to the inter-molt stage. Further protein structure analysis and RT-qPCR validation confirmed five GPCR genes related to molting process, in which four genes (GRM7, FMRFaR, mth2, gpr161) are active during the post-molt stage and one gene (moody) functions during the inter-molt stage.DiscussionThese findings highlight the key regulatory proteins and pathways involved in E. sinensis muscle during molting and also offer foundational data for studying the mechanisms of molting and discontinuous growth in crustaceans.…”
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A rare deleterious missense mutation in the AXIN2 gene in Chinese women with polycystic ovary syndrome by Ying Zhang, Yu Chen, Fa-Ying Liu, Jing-Wen Fu, Xian-Xian Liu, Jun Tan, Ou-Ping Huang, Yang Zou

“…The evolutionary conservation analysis of the identified Axin-2 mutant was analyzed among 15 vertebrates from human to zebrafish. The protein structure change was analyzed between the wild-type and mutation-type. …”
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Tat-fimbriae (“tafi”): An unusual type of haloarchaeal surface structure depending on the twin-arginine translocation pathway by Anna V. Galeva, Dahe Zhao, Alexey S. Syutkin, Marina Yu Topilina, Sergei Yu Shchyogolev, Elena Yu Pavlova, Olga M. Selivanova, Igor I. Kireev, Alexey K. Surin, Gennady L. Burygin, Jingfang Liu, Hua Xiang, Mikhail G. Pyatibratov

“…Molecular genetic evidence demonstrates TafA was transported through the twin-arginine translocation pathway (Tat-pathway). Based on protein structure prediction (including AlphaFold 3), tafi exhibits a linear structure: TafC at the tip, TafE acting as an adapter, TafA forming the core filament, and they link the fourth subunit TafF, anchoring tafi to the cell wall. …”
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From structure prediction to function: defining the domain on the African swine fever virus CD2v protein required for binding to erythrocytes by Ana Luisa Reis, Anusyah Rathakrishnan, Vlad Petrovan, Muneeb Islam, Lynnette Goatley, Katy Moffat, Mai Tuyet Vuong, Yuan Lui, Simon J. Davis, Shinji Ikemizu, Linda K. Dixon

“…A combination of protein structure modeling and extensive mutagenesis was used to identify residues mediating binding of transiently expressed CD2v to erythrocytes. …”
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Deciphering the role of flutamide, fluorouracil, and furomollugin based ionic liquids in potent anticancer agents: Quantum chemical, medicinal, molecular docking and MD simulation... by Danish Ali, Muhammad Arif Ali, Muhammad Sarfraz, Afifa Yousuf, Rasham Zulfiqar, Abdul Rauf, Hong-Liang Xu, Muhammad Arshad

“…In addition, Ramachandran plots indicate that >90 % of residues occupy the favored regions supporting the protein structure stability. Thus, these analyses confirm that the newly identified ILs exhibit superior binding affinities and acceptable bioinformatics profiles, making them attractive candidates for the development of anticancer drugs.…”
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Application of copy number variation sequencing combined with whole exome sequencing in prenatal left–right asymmetry disorders by Yu Qin, Muon Senglong, Koksear Touch, Juan Xiao, Ruijie Fang, Qingling kang, Lei Fan, Shufang Li, Jing Liu, Jianli Wu, Yuanyuan Wu, Xinwei Shi, Haiyi Liu, Xun Gong, Xingguang Lin, Ling Feng, Suhua Chen, Wei Li

“…Further bioinformatics scrutiny was conducted to assess the protein structure and function prediction of these variants, ultimately indicating their potential pathogenicity. …”
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Cucumeropsis mannii seed oil shields against cyclophosphamide-induced hepatorenal toxicity by modulating redox imbalance and iNOS/IL-β1 signalling in rats by Amaka Cecilia Agbara, Ejike Daniel Eze, Christian Emeka Offor, Adam Moyosore Afodun, Ezebuilo Ugbala Ekpono, Peter Chinedu Agu, Chinyere Aloke, Nkeiru Nwaamaka Ezeani, Emmanuel Orire Ikuomola, Ekom Monday Etukudo, Ilemobayo Victor Fasogbon, Angela Mumbua Musyoka, Patrick Maduabuchi Aja

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Simulations of pH and thermal effects on SARS-CoV-2 spike glycoprotein by Ziyuan Niu, Georgios Kementzidis, Miriam Rafailovich, Marcia Simon, Evangelos Papadopoulos, Bertal H. Aktas, Yuefan Deng

“…This study elucidates the complex interplay between pH and thermal effects on S-protein structures, with implications for its behavior under diverse conditions, and identifies the RBD as a primary region of the structural deviations. …”
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Ribosome pausing in amylase producing Bacillus subtilis during long fermentation by Yaozu Han, Biwen Wang, Alberto Agnolin, Gaurav Dugar, Frans van der Kloet, Christopher Sauer, Paul Igor Costea, Max Fabian Felle, Mathis Appelbaum, Leendert W. Hamoen

“…Since these sites can neither be predicted based on codon specificity nor on secondary protein structures, we speculate that secondary mRNA structures are responsible for these translation pausing sites. …”
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Representing and Quantifying Conformational Changes of Kinases and Phosphatases Using the TSR-Based Algorithm by Tarikul I. Milon, Krishna Rauniyar, Sara Furman, Khairum H. Orthi, Yingchun Wang, Vijay Raghavan, Wu Xu

“…In conclusion, this study presents an advanced computational methodology with significant advantages in not only representing and quantifying conformational changes of protein structures but also having the capability of directly linking protein structures to their functions.…”
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Predicting the impact of missense mutations on an unresolved protein’s stability, structure, and function: A case study of Alzheimer’s disease-associated TREM2 R47H variant by Joshua Pillai, Kijung Sung, Chengbiao Wu

“…However, AF2 falls short of predicting the effects of missense mutations on unresolved protein structures that may be informative to efforts in personalized medicine. …”
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Influence of Polymorphism on Glycosylation of Serum Amyloid A4 Protein by Toshiyuki Yamada, Jyunji Sato, Kazuhiko Kotani, Masafumi Tanaka

“…These findings suggest that the changes in protein structures alter the efficiency of glycosylation in the SAA4 molecule. …”
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Nonprotein Structures from Mycobacteria: Emerging Actors for Tuberculosis Control by Luz M. Lopez-Marin

“…For many decades, consistent to classical biochemistry, most studies regarding immunity to the tubercle bacilli focused mainly on protein structures. But the atypical, highly impermeable and waxy coat of mycobacteria captured the interest of structural biologists very early, allowing the description of amazing molecules, such as previously unknown carbohydrates or fatty acids of astonishing lengths. …”
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AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation by Matteo Manfredi, Gabriele Vazzana, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio

“…AlphaFold2 predicts protein structures from structural and functional knowledge. …”
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Effects of Ozone Treatments on the Physicochemical Changes of Myofibrillar Proteins from Silver Carp (Hypophthalmichthys molitrix) during Frozen Storage by Rongrong Zhang, Shanbai Xiong, Juan You, Yang Hu, Ru Liu, Tao Yin

“…To2 did not significantly (P>0.05) affect these physicochemical properties, indicating that myofibrillar proteins structure was well maintained. Consequently, To1 significantly (P>0.05) decreased breaking force of surimi gels while To2 did not significantly (P>0.05) affect gel breaking force. …”
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Effects of Drying Temperature and Relative Humidity on Quality Properties of Chinese Dried Noodles by Ying-Quan Zhang, Ying Hui, Yuan Wang, Bo Zhang, Bo-Li Guo, Guo-Quan Zhang, Yi-Min Wei

“…The influence of the drying conditions on protein structural properties and its impact on Chinese dried noodles (CDN) quality properties is addressed in this study. …”
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Advancements in electron paramagnetic resonance (EPR) spectroscopy: A comprehensive tool for pharmaceutical research by Bešić Erim, Rajić Zrinka, Šakić Davor

“…Electron paramagnetic resonance (EPR) spectroscopy has long been established across various scientific disciplines for characterizing organic radicals, organometallic complexes, protein structures and dynamics, polymerization processes, and radical degradation phenomena. …”
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Genetic Algorithm-Enhanced Direct Method in Protein Crystallography by Ruijiang Fu, Wu-Pei Su, Hongxing He

“…We systematically tested the method on 15 protein structures from different space groups with diffraction resolutions of 1.35∼2.5 Å. …”
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Future trends in plant-based meat: Consumer perception, market growth and health benefits by Janifer Raj Xavier, Sahana Hevlin Shashikumar, Dimple Vats, Om Prakash Chauhan

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