A comprehensive survey of scoring functions for protein docking models by Azam Shirali, Vitalii Stebliankin, Ukesh Karki, Jimeng Shi, Prem Chapagain, Giri Narasimhan

“…Abstract Background While protein-protein docking is fundamental to our understanding of how proteins interact, scoring protein-protein complex conformations is a critical component of successful docking programs. …”
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AFM observation of protein translocation mediated by one unit of SecYEG-SecA complex by Yui Kanaoka, Takaharu Mori, Wataru Nagaike, Seira Itaya, Yuto Nonaka, Hidetaka Kohga, Takamitsu Haruyama, Yasunori Sugano, Ryoji Miyazaki, Muneyoshi Ichikawa, Takayuki Uchihashi, Tomoya Tsukazaki

“…In the bacterial cytoplasmic membrane, the core proteins in this process are a membrane protein complex, SecYEG, corresponding to the eukaryotic Sec61 complex, and a cytoplasmic protein, SecA ATPase. …”
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A study on blocking store-operated Ca2+ entry in pulmonary arterial smooth muscle cells with xyloketals from marine fungi by Zhou Jie-Bin, Sun Ying-Ying, Zheng Ying-Lin, Yu Chu-Qin, Lin Hua-Qing, Pang Ji-Yan

“…Moreover, the molecular docking study of xyloketal A with activation region of the stromal interaction molecule (STIM) 1 and the calcium release-activated calcium modulator (ORAI) 1 (STIM1-ORAI1) protein complex, the key domain of SOCE, revealed that xyloketal A exhibited a noncovalent interaction with the key residue lysine 363 (LYS363) in the identified cytosolic regions in STIM1-C. …”
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A chemical genetic screen with the EXO70 inhibitor Endosidin2 uncovers potential modulators of exocytosis in Arabidopsis by Xiaohui Li, Diwen Wang, Xianglin Yin, Mingji Dai, Christopher J. Staiger, Chunhua Zhang

“…During exocytosis, an octameric protein complex named the exocyst facilitates the tethering of secretory vesicles to the plasma membrane. …”
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Genetics of Endometrial Cancers by Tsuyoshi Okuda, Akihiko Sekizawa, Yuditiya Purwosunu, Masaaki Nagatsuka, Miki Morioka, Masaki Hayashi, Takashi Okai

“…Lynch syndrome, which is an autosomal dominantly inherited disorder of cancer susceptibility and is characterized by a MSH2/MSH6 protein complex deficiency, is associated with the development of non-endometrioid carcinomas.…”
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Functional properties of the Su(Hw) complex are determined by its regulatory environment and multiple interactions on the Su(Hw) protein platform by L. S. Melnikova, M. V. Kostyuchenko, V. V. Molodina, P. G. Georgiev, A. K. Golovnin

“…The Su(Hw)-dependent protein complex is a unique model for studying the insulator, since its basic structural components affecting its activity are already known. …”
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Pancreatic Beta Cell Death: Novel Potential Mechanisms in Diabetes Therapy by Joselyn Rojas, Valmore Bermudez, Jim Palmar, María Sofía Martínez, Luis Carlos Olivar, Manuel Nava, Daniel Tomey, Milagros Rojas, Juan Salazar, Carlos Garicano, Manuel Velasco

“…They also include the action of proinflammatory cytokines, the production of reactive oxygen species, DNA fragmentation (typical of necroptosis in type 1 diabetic patients), excessive production of islet amyloid polypeptide with the consequent endoplasmic reticulum stress, disruption in autophagy mechanisms, and protein complex formation, such as the inflammasome, capable of increasing oxidative stress produced by mitochondrial damage. …”
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Hemorrhagic Shock Induces a Rapid Transcriptomic Shift of the Immune Balance in Leukocytes after Experimental Multiple Injury by Lisa Debler, Annette Palmer, Sonja Braumüller, Bettina Klohs, Tom Eirik Mollnes, Karlheinz Holzmann, Markus Huber-Lang, Rebecca Halbgebauer

“…After additional HS in PT mice, the gene expression of pathways related to the innate immunity, such as IL-6 production, neutrophil chemotaxis, cell adhesion, and toll-like receptor signaling was upregulated, whereas pathways of the adaptive immune system, such as B- and T-cell activation as well as the MHC class II protein complex, were downregulated. These results demonstrate that an additional HS plays an important role in the immune dysregulation early after PT by shifting the balance to increased innate and reduced adaptive immune responses.…”
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FBP1 Is an Interacting Partner of Menin by Shadia Zaman, Karen Sukhodolets, Patricia Wang, Jun Qin, David Levens, Sunita K. Agarwal, Stephen J. Marx

“…We describe the identification of FBP1 as an interacting partner of menin in a large-scale pull-down assay that also immunoprecipitated RBBP5, ASH2, and LEDGF, which are members of complex proteins associated with SET1 (COMPASS), a protein complex that methylates histone H3. This interaction was confirmed by coimmunoprecipitation and Flag-pull-down assays. …”
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Insights into the binding selectivity of harzianoic acids A and B to tetraspanin CD81 by Gérard Vergoten, Christian Bailly

“…Key H-bonds between the acid groups of Hz-B and the CD81-LEL domain stabilize the ligand-protein complex. A comparison of the interaction with the homologous tetraspanin CD9, which also presents a dynamic open/closed equilibrium, underlined the marked selectivity of Hz-A/B for CD81 over CD9. …”
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CitGATA7 interact with histone acetyltransferase CitHAG28 to promote citric acid degradation by regulating the glutamine synthetase pathway in citrus by Xiahui Lin, Shaojia Li, Yanna Shi, Yuchen Ma, Yinchun Li, Haohan Tan, Bo Zhang, Changjie Xu, Kunsong Chen

“…The findings demonstrate that the CitGATA7-CitHAG28 protein complex transcriptionally regulate the expression of the GS pathway genes, i.e., CitACO3, CitIDH1, and CitGS1, via histone acetylation, thus promoting citric acid catabolism. …”
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Investigating new drugs from marine seaweed metabolites for cervical cancer therapy by molecular dynamic modeling approach by Sk Injamamul Islam, Sheikh Sunzid Ahmed, Sarower Mahfuj, Gunjan Das, Md. Mohaimenul Islam Tareq, Mazen Almehmadi, Mamdouh Allahyani, Naif Alsiwiehri, Partha Biswas, Md. Nazmul Hasan, Foysal Ahammad

“…The MM/GBSA study revealed that the BC008-protein complex exhibited the most significant free binding energy, with a value of -57.41 kcal/mol. …”
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Crucial Genes in Aortic Dissection Identified by Weighted Gene Coexpression Network Analysis by Hongliang Zhang, Tingting Chen, Yunyan Zhang, Jiangbo Lin, Wenjun Zhao, Yangyang Shi, Huichong Lau, Yang Zhang, Minjun Yang, Cheng Xu, Lijiang Tang, Baohui Xu, Jianjun Jiang, Xiaofeng Chen

“…DEGs were rich in certain categories such as MHC class II receptor activity, MHC class II protein complex, and immune response genes. Gene coexpression networks via WGCNA identified 3 gene hub modules, with one positively and 2 negatively correlated with AD, respectively. …”
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New Resinogalea species from Araucaria araucana resin in Chile and reclassification of the genus in the Cryptocaliciomycetidae by Felipe Balocchi, Irene Barnes, Michael J. Wingfield, Rodrigo Ahumada, Cobus M. Visagie

“…Further analyses applying the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) based on ITS, mini chromosome maintenance protein complex (MCM7), RNA polymerase II second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF) gene regions, confirmed that strains represent two new species. …”
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Ellagic Acid Alleviates Rheumatoid Arthritis in Rats through Inhibiting MTA1/HDAC1-Mediated Nur77 Deacetylation by Huanjin Song, Hao Wu, Jun Dong, Sihua Huang, Jintao Ye, Ruoxi Liu

“…It was found that the level of metastasis-associated gene 1 (MTA1)/histone deacetylase 1 (HDAC1) protein complex was downregulated by polyphenols in several human disorders. …”
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Primary Study on Effect of Extraction Methods on the Properties and Activities of Polysaccharides from <i>Geum japonicum var. Chinense F. Bolle</i> by Xuan Chen, Ying-Bo Liu, Yong Deng, Jian-Yong Zhang

“…Meanwhile, AAE was preferable for extracting the polysaccharide–protein complex, achieving a yield of 14.21% and exhibiting superior thermal stability. …”
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Single-cell RNA-seq reveals immune cell heterogeneity and increased Th17 cells in human fibrotic skin diseases by Cheng-Cheng Deng, Xue-Yan Xu, Yan Zhang, Long-Can Liu, Xuan Wang, Jun-Yi Chen, Liu-Yi Yao, Ding-Heng Zhu, Bin Yang

“…However, upregulated genes in keloid M1 macrophages, M2 macrophages, and cDC2 are associated with the MHC class II protein complex assembly and antigen assembly, indicating that macrophages and cDC2 are active in keloids. …”
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A novel ARCN1 splice-site variant in a Chinese girl with central precocious puberty, intrauterine growth restriction, microcephaly, and microretrognathia by Guoying Chang, Fan Yang, Lingwen Ying, Qianwen Zhang, Biyun Feng, Yao Chen, Yu Ding, Tingting Yu, Ruen Yao, Kana Lin, Juan Li, Xiumin Wang

“…Abstract The ARCN1 gene encodes the delta subunit of the coatomer protein complex I (COPI), which is essential for mediating protein transport from the Golgi complex to the endoplasmic reticulum. …”
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Expression analysis of nuclear factor kappa B (NF-κB) in oral squamous cell carcinoma by Dev Arora, Dhanraj M. Ganapathy, Ashikha Shirin Usman Pp, K.P. Ameya, Durairaj Sekar, Kumaravel Kaliaperumal

“…Interestingly, nuclear factor kappa B (NF-κB) is a protein complex that controls transcription of DNA, cytokine production, and cell survival. …”
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Production of a new variant of soluble trimer Env of HIV-1 CRF63_02A6 SOSIP.664 by Nadezhda B. Rudometova, Andrey P. Rudometov, Anastasia A. Fando, Danil I. Vahitov, Alexander A. Ilyichev, Alexander P. Agafonov, Larisa I. Karpenko

“…Purification of the protein complex was performed using affinity chromatography and gel filtration. …”
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