The secular debate on the origin of life on our planet represents one of the open challenges for the scientific community. In this endeavour, chemistry has a pivotal role in disclosing novel scenarios that allow us to understand how the formation of simple organic molecules would be possible in the early primitive geological ages of Earth. Amino acids play a crucial role in biological processes. They are known to be formed in experiments simulating primitive conditions and were found in meteoric samples retrieved throughout the years. Understanding their formation is a key step for prebiotic chemistry. Following this reasoning, we performed a computational investigation over 100'000 structural isomers of natural amino acids. The results we have found suggest that natural amino acids are among the most thermodynamically stable structures and, therefore, one of the most probable ones to be synthesised among their possible isomers.
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http://dx.doi.org/10.1007/s11084-021-09615-2 | DOI Listing |
J Phys Chem A
January 2025
Computer Modelling Group, 3710 33 St NW, Calgary, Alberta T2L 2M1, Canada.
Coarse-grained molecular dynamics simulation is widely accepted for assessment of a large complex biological system, but it may also lead to a misleading conclusion. The challenge is to simulate protein structural dynamics (such as folding-unfolding behavior) due to the lack of a necessary backbone flexibility. This study developed a standard coarse-grained model directly from the protein atomic structure and amino acid coarse-grained FF (such as MARTINI FF v2.
View Article and Find Full Text PDFNat Chem
January 2025
Department of Chemistry, Scripps Research, La Jolla, CA, USA.
Amino alcohols are vital in natural products, pharmaceuticals and agrochemicals, and as key building blocks for various applications. Traditional synthesis methods often rely on polar bond retrosynthetic analysis, requiring extensive protecting group manipulations that complicate direct access. Here we show a streamlined approach using a serine-derived chiral carboxylic acid in stereoselective electrocatalytic decarboxylative transformations, enabling efficient access to enantiopure amino alcohols.
View Article and Find Full Text PDFCell Death Differ
January 2025
Department of Hepatobiliary Surgery of the affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, China.
Lysine lactylation plays critical roles in various diseases, including cancer. Our previous study showed that lactylation of non-histone ABCF1 may be involved in hepatocellular carcinoma (HCC) progression. In this study, we evaluated the prognostic value of ABCF1-K430la in HCC using immunohistochemical staining and performed amino acid point mutations, multi-omics crossover, and biochemical experiments to investigate its biological role and underlying mechanism.
View Article and Find Full Text PDFNat Metab
January 2025
Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; School of Basic Medical Sciences, Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China.
Nutrient availability strongly affects intestinal homeostasis. Here, we report that low-protein (LP) diets decrease amino acids levels, impair the DNA damage response (DDR), cause DNA damage and exacerbate inflammation in intestinal tissues of male mice with inflammatory bowel disease (IBD). Intriguingly, loss of nuclear fragile X mental retardation-interacting protein 1 (NUFIP1) contributes to the amino acid deficiency-induced impairment of the DDR in vivo and in vitro and induces necroptosis-related spontaneous enteritis.
View Article and Find Full Text PDFNat Microbiol
January 2025
Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
Ecology and evolution are considered distinct processes that interact on contemporary time scales in microbiomes. Here, to observe these processes in a natural system, we collected a two-decade, 471-metagenome time series from Lake Mendota (Wisconsin, USA). We assembled 2,855 species-representative genomes and found that genomic change was common and frequent.
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