Article
Biochemistry & Molecular Biology
Xi Zhang, Cang Wu, Tianzi Wei, Yi Lu, Chuang Liu, Jian Zhang
Summary: IGF1R, a crucial protein in cellular metabolism and growth regulation, exhibits flexible structure as a single transmembrane protein. In this study, four distinct cryo-EM structures of IGF1R in apo states were reported, classified as Resting states and Active states based on the orientation of alpha-CT helices and structural symmetry. The active conformations revealed the formation of a Ligand-pocket, providing new insights into the conformational changes of apo-IGF1R and the binding mechanism of ligands.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Review
Biochemistry & Molecular Biology
Hao Huang
Summary: Receptor tyrosine kinases are crucial components of cell signaling pathways, playing important roles in regulating cellular processes. Dysregulation of RTK signaling is implicated in various human diseases, including cancer. Proteolytic cleavage phenomenon is commonly observed among multiple RTKs, providing valuable insights into their function and potential therapeutic targets.
Article
Virology
Jordan Anderson-Daniels, Jennifer Gribble, Mark Denison
Summary: In this study, it was discovered that cleavage between the nonstructural replicase proteins nsp13-14 and nsp14-15 is not necessary for replication of the murine hepatitis virus (MHV), but it does affect RNA synthesis and recombination. These findings provide new insight into the maturation of coronaviruses and the assembly of replication-transcription complexes, and they may reveal new therapeutic targets and strategies for attenuation.
JOURNAL OF VIROLOGY
(2022)
Article
Chemistry, Analytical
Jinghan Yang, Zhiqiang Gao, Xiuhan Ren, Jie Sheng, Ping Xu, Cheng Chang, Yan Fu
Summary: Proteolytic digestion of proteins is crucial in shotgun proteomics for further analysis, but the completion of digestion is often hindered by missed cleavage sites. DeepDigest, a deep learning algorithm, accurately predicts cleavage sites of various proteases, outperforming traditional machine learning algorithms. Transfer learning further enhances prediction accuracy and reveals interesting characteristics of different proteases.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Fengquan Dong, Cang Wu, Weipeng Jiang, Maocai Zhai, Haiying Li, Liting Zhai, Xi Zhang
Summary: This study determined the structural details of the human VPS10 domain-containing receptor SorCS3 and identified at least three distinct conformations in its apo state. Conserved amino acid residues may play key roles in its dimerization and protein/polypeptide binding, differentiating it from homologous proteins.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Geosciences, Multidisciplinary
Zexuan Xu, Rebecca Serata, Haruko Wainwright, Miles Denham, Sergi Molins, Hansell Gonzalez-Raymat, Konstantin Lipnikov, J. David Moulton, Carol Eddy-Dilek
Summary: In this study, a reactive transport model is developed to evaluate the impact of different climate change scenarios on contaminant plume conditions and groundwater well concentrations. The results indicate that the competition between dilution and remobilization significantly influences the sorption of uranium. By integrating climate modeling data and hydrogeochemistry models, the study enables the quantification of climate change impacts and assists in planning for climate resiliency efforts and site management.
HYDROLOGY AND EARTH SYSTEM SCIENCES
(2022)
Article
Biochemical Research Methods
Ying Peng, Xiaoying Wei, Kun Yang
Summary: Histones catalyze DNA strand incision at AP sites and form reversible but long-lived DPCs at 3'-DNA termini within single-strand breaks. This study developed a chemical approach to synthesize stable and site-specific 3'-histone-DPCs and their repair by nucleases. The efficiency of DPC repair is influenced by the local protein environment, and previous DPC proteolysis facilitates the repair.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Hisanori Domon, Tomoki Maekawa, Toshihito Isono, Kazuyuki Furuta, Chikara Kaito, Yutaka Terao
Summary: Bacterial and viral respiratory infections can cause acute lung injury and acute respiratory distress syndrome, with neutrophils and their granule enzymes playing a key role in the pathophysiology. Neutrophil elastase leakage into airway spaces may disrupt innate immune responses by cleaving Toll-like receptors and cytokines. Inhibition of neutrophil elastase could be a potential therapeutic option for bacterial and viral pneumonia.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Bailey Lubinski, Maureen H. Fernandes, Laura Frazier, Tiffany Tang, Susan Daniel, Diego G. Diel, Javier A. Jaimes, Gary R. Whittaker
Summary: The P681H mutation in the B.1.1.7 variant of SARS-CoV-2 does not significantly impact viral entry or cell-cell spread.
Article
Biochemistry & Molecular Biology
Wei Wang, Rui-Rui Yang, Lu-Yao Peng, Lu Zhang, Yue-Lin Yao, Yan-Yuan Bao
Summary: The study identified 15 homologues sequences of Rpn in the brown planthopper, revealing their significant role in proteolytic activity and reproductive processes. Knockdown of NlRpns led to impaired ovarian development, oocyte maturation, and reduced fecundity in females. This highlights the importance of proteasome activity in female reproductive strategies in insects.
Review
Biotechnology & Applied Microbiology
Jie Gu, Yan Xu, Yao Nie
Summary: This review highlighted the criticality of distal sites in enzyme engineering by discussing the effects of distal mutations on enzyme function, the influence of distal sites on enzyme function, and the methods for predicting and designing distal mutations. It provided insights into the catalytic mechanism of enzymes and offered strategies for protein engineering based on distal mutations.
BIOTECHNOLOGY ADVANCES
(2023)
Article
Endocrinology & Metabolism
Christoph Klenk, Leif Hommers, Martin J. Lohse
Summary: This study reveals that the extracellular domain of PTH1R is cleaved by metalloproteinases, leading to impaired stability of the receptor. The cleavage site is located in the first loop of the extracellular domain. A receptor mutant resistant to proteolytic cleavage showed reduced signaling to G(s) and increased activation of G(q).
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Chemistry, Analytical
Nan Yin, Ruihuan Zhao, Jie Zhang, Dingding Yang, Zhimin Guo, Rui Liu, Xin Yao
Summary: Abnormal O-GlcNAc concentrations have been linked to various diseases, but the lack of accurate detection methods has hindered its use as a biomarker in clinical diagnosis. OGT has emerged as a potential target for disease diagnosis due to its close relationship with O-GlcNAc levels. A label-free and sensitive SPR biosensor was developed for the accurate detection of OGT, utilizing a multi-functional peptide with three recognition sites. The method, which uses the change in peptide configuration as a signal probe, offers high sensitivity and selectivity, making it a promising tool for early clinical diagnosis of O-GlcNAc related diseases.
Article
Multidisciplinary Sciences
Shanshan Li, Kan-Yen Hsieh, Chiao- Kuo, Shih-Chieh Su, Kai-Fa Huang, Kaiming Zhang, Chung- Chang
Summary: Lon protease is able to degrade protein substrates in a processive fashion at each of its six proteolytic active sites, forming a deep groove that encloses the substrate polypeptide chain and allows for continuous cleavage in the C-to-N direction. An acidic residue at the binding groove exit is identified as essential for the proteolytic activity, likely promoting processive proteolysis through carboxyl-carboxylate interactions with cleaved intermediates. These findings reveal a previously unrecognized mechanism for processive substrate degradation by the Lon protease.
Article
Biochemical Research Methods
Zhen Sun, Weidi Xiao, Naikang Li, Lei Chang, Ping Xu, Yanchang Li
Summary: Trypsin is known for cleaving the C-terminus of lysine and arginine residues, but it often fails to cleave modified lysines, such as ubiquitination. This leads to the presence of uncleaved K-e-GG peptides, which are usually discarded as false positives. In this study, the ability of trypsin to cleave other ubiquitinated sites besides K48 chains was verified. A significant enrichment of lysine upstream of the cleaved modified K was observed. The findings suggest that cleaved K-e-GG sites with high post-translational modification probability (>=0.75) should be considered as true positives in future ubiquitome analyses.
JOURNAL OF PROTEOME RESEARCH
(2023)