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Electron transfer in polysaccharide monooxygenase catalysis.
Proc Natl Acad Sci U S A
January 2025
California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720.
Polysaccharide monooxygenase (PMO) catalysis involves the chemically difficult hydroxylation of unactivated C-H bonds in carbohydrates. The reaction requires reducing equivalents and will utilize either oxygen or hydrogen peroxide as a cosubstrate. Two key mechanistic questions are addressed here: 1) How does the enzyme regulate the timely and tightly controlled electron delivery to the mononuclear copper active site, especially when bound substrate occludes the active site? and 2) How does this electron delivery differ when utilizing oxygen or hydrogen peroxide as a cosubstrate? Using a computational approach, potential paths of electron transfer (ET) to the active site copper ion were identified in a representative AA9 family PMO from (PMO9E).
View Article and Find Full Text PDFTungsten is utilized for lactate consumption and SCFA production by a dominant human gut microbe .
Proc Natl Acad Sci U S A
January 2025
Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602.
is a dominant member of the human gut microbiome and produces short-chain fatty acids (SCFAs). These promote immune system function and inhibit inflammation, making this microbe important for human health. Lactate is a primary source of gut SCFAs but its utilization by has not been explored.
View Article and Find Full Text PDFPredicting the polyspecificity of aminoacyl-tRNA synthetase for non-canonical amino acids using molecular dynamics simulation and MM/PBSA.
PLoS One
January 2025
Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, Republic of Korea.
With the advancement of genetic code expansion, the field is progressing towards incorporating multiple non-canonical amino acids (ncAAs). The specificity of aminoacyl-tRNA synthetases (aaRSs) towards ncAAs is a critical factor, as engineered aaRSs frequently show polyspecificity, complicating the precise incorporation of multiple ncAAs. To address this challenge, predicting binding affinity can be beneficial.
View Article and Find Full Text PDFAn optimized approach for container deployment driven by a two-stage load balancing mechanism.
PLoS One
January 2025
School of Humanities, Ningbo University of Finance and Economics, Ningbo, Zhejiang, China.
Lightweight container technology has emerged as a fundamental component of cloud-native computing, with the deployment of containers and the balancing of loads on virtual machines representing significant challenges. This paper presents an optimization strategy for container deployment that consists of two stages: coarse-grained and fine-grained load balancing. In the initial stage, a greedy algorithm is employed for coarse-grained deployment, facilitating the distribution of container services across virtual machines in a balanced manner based on resource requests.
View Article and Find Full Text PDFThe ability of pentose pathways to form all essential metabolites provides clues to the origins of metabolism.
PLoS Biol
January 2025
Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany.
The structure of the early metabolic network is unknown. Here, we report that when considered together, pentose utilization pathways form all life-essential precursors. We speculate that the chemistry preserved in pentose metabolism could therefore have been a central structural element in early metabolism.
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