Browsing by Author "Makarov, Mikhail"

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    Enzyme catalysis prior to aromatic residues: Reverse engineering of a dephospho-CoA kinase
    (Wiley, 2021) Makarov, Mikhail; Meng, Jingwei; Tretyachenko, Vyacheslav; Srb, Pavel; Březinová, Anna; Giacobelli, Valerio Guido; Bednárová, Lucie; Vondrášek, Jiří; Dunker, A. Keith; Hlouchová, Klára; Biochemistry and Molecular Biology, School of Medicine
    The wide variety of protein structures and functions results from the diverse properties of the 20 canonical amino acids. The generally accepted hypothesis is that early protein evolution was associated with enrichment of a primordial alphabet, thereby enabling increased protein catalytic efficiencies and functional diversification. Aromatic amino acids were likely among the last additions to genetic code. The main objective of this study was to test whether enzyme catalysis can occur without the aromatic residues (aromatics) by studying the structure and function of dephospho-CoA kinase (DPCK) following aromatic residue depletion. We designed two variants of a putative DPCK from Aquifex aeolicus by substituting (a) Tyr, Phe and Trp or (b) all aromatics (including His). Their structural characterization indicates that substituting the aromatics does not markedly alter their secondary structures but does significantly loosen their side chain packing and increase their sizes. Both variants still possess ATPase activity, although with 150-300 times lower efficiency in comparison with the wild-type phosphotransferase activity. The transfer of the phosphate group to the dephospho-CoA substrate becomes heavily uncoupled and only the His-containing variant is still able to perform the phosphotransferase reaction. These data support the hypothesis that proteins in the early stages of life could support catalytic activities, albeit with low efficiencies. An observed significant contraction upon ligand binding is likely important for appropriate organization of the active site. Formation of firm hydrophobic cores, which enable the assembly of stably structured active sites, is suggested to provide a selective advantage for adding the aromatic residues.
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    Isotopic evidence for oligotrophication of terrestrial ecosystems
    (Nature, 2018) Craine, Joseph; Elmore, Andrew J.; Wang, Lixin; Aranibar, Julieta; Bauters, Marijn; Boeckx, Pascal; Crowley, Brooke E.; Dawes, Melissa A.; Delzon, Sylvain; Fajardo, Alex; Fang, Yunting; Fujiyoshi, Lei; Gray, Alan; Guerrieri, Rossella; Gundale, Michael J.; Hawke, David J.; Hietz, Peter; Jonard, Mathieu; Kearsley, Elizabeth; Kenzo, Tanaka; Makarov, Mikhail; Marañón-Jiménez, Sara; McGlynn, Terrence P.; McNeil, Brenden E.; Mosher, Stella G.; Nelson, David M.; Peri, Pablo L.; Roggy, Jean Christophe; Sanders-DeMott, Rebecca; Song, Minghua; Szpak, Paul; Templer, Pamela H.; Van der Colff, Dewidine; Werner, Christiane; Xu, Xingliang; Yang, Yang; Yu, Guirui; Zmudczyńska-Skarbek, Katarzyna; Earth Sciences, School of Science
    Human societies depend on an Earth system that operates within a constrained range of nutrient availability, yet the recent trajectory of terrestrial nitrogen (N) availability is uncertain. Examining patterns of foliar N concentrations and isotope ratios (δ15N) from more than 43,000 samples acquired over 37 years, here we show that foliar N concentration declined by 9% and foliar δ15N declined by 0.6–1.6‰. Examining patterns across different climate spaces, foliar δ15N declined across the entire range of mean annual temperature and mean annual precipitation tested. These results suggest declines in N supply relative to plant demand at the global scale. In all, there are now multiple lines of evidence of declining N availability in many unfertilized terrestrial ecosystems, including declines in δ15N of tree rings and leaves from herbarium samples over the past 75–150 years. These patterns are consistent with the proposed consequences of elevated atmospheric carbon dioxide and longer growing seasons. These declines will limit future terrestrial carbon uptake and increase nutritional stress for herbivores.