Proteases regulate various aspects of the life cycle in all organisms by cleaving specific peptide bonds. Their action is so central for biochemical processes that at least 2% of any known genome encodes for proteolytic enzymes. Here we show that selected proteases pairs, despite differences in oligomeric state, catalytic residues, and fold, share a common structural organization of functionally relevant regions which are further shown to undergo similar concerted movements. The structural and dynamical similarities found pervasively across evolutionarily distant clans point to common mechanisms for peptide hydrolysis.
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PLoS One
January 2025
Faculty of Education and Arts, Sohar University, Sohar, Oman.
Conjugate Gradient (CG) methods are widely used for solving large-scale nonlinear systems of equations arising in various real-life applications due to their efficiency in employing vector operations. However, the global convergence analysis of CG methods remains a significant challenge. In response, this study proposes scaled versions of CG parameters based on the renowned Barzilai-Borwein approach for solving convex-constrained monotone nonlinear equations.
View Article and Find Full Text PDFPLoS Biol
January 2025
Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan.
The unique architecture of the liver consists of hepatic lobules, dividing the hepatic features of metabolism into 2 distinct zones, namely the pericentral and periportal zones, the spatial characteristics of which are broadly defined as metabolic zonation. R-spondin3 (Rspo3), a bioactive protein promoting the Wnt signaling pathway, regulates metabolic features especially around hepatic central veins. However, the functional impact of hepatic metabolic zonation, regulated by the Rspo3/Wnt signaling pathway, on whole-body metabolism homeostasis remains poorly understood.
View Article and Find Full Text PDFMol Plant Pathol
January 2025
Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.
In the coevolutionary process between plant pathogens and hosts, pathogen effectors, primarily proteinaceous, engage in interactions with host proteins, such as plant transcription factors (TFs), during the infection process. This review delves into the intricate interplay between TFs and effectors, a key aspect in the prolonged and complex battle between plants and pathogens. Effectors strategically manipulate TFs using diverse tactics.
View Article and Find Full Text PDFBiomimetics (Basel)
January 2025
School of Petroleum Engineering, Yangtze University, Wuhan 430100, China.
Optimization algorithms play a crucial role in solving complex problems across various fields, including global optimization and feature selection (FS). This paper presents the enhanced polar lights optimization with cryptobiosis and differential evolution (CPLODE), a novel improvement upon the original polar lights optimization (PLO) algorithm. CPLODE integrates a cryptobiosis mechanism and differential evolution (DE) operators to enhance PLO's search capabilities.
View Article and Find Full Text PDFBiomimetics (Basel)
January 2025
School of Mathematics and Information Science, North Minzu University, Yinchuan 750021, China.
The Whale Optimization Algorithm (WOA) is recognized for its simplicity, few control parameters, and effective local optima avoidance. However, it struggles with global search efficiency and slow convergence. This paper introduces the Improved WOA (ImWOA) to overcome these challenges.
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