Cited by Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands

Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules DOI

Daniel G.J. Smethurst,

Natalia Shcherbik

Journal of Biological Chemistry, Год журнала: 2021, Номер 297(6), С. 101374 - 101374

Опубликована: Окт. 31, 2021

Metal ions provide considerable functionality across biological systems, and their utilization within biomolecules has adapted through changes in the chemical environment to maintain activity they facilitate. While ancient earth's atmosphere was rich iron manganese low oxygen, periods of atmospheric oxygenation significantly altered availability certain metal ions, resulting ion replacement biomolecules. This adaptation mechanism given rise phenomenon cofactor interchangeability, whereby contemporary proteins nucleic acids interact with multiple interchangeably, different coordinated metals influencing activity, stability, toxic potential. The ability extant organisms adapt fluctuating remains relevant a number crucial biomolecules, including superoxide dismutases antioxidant defense systems ribonucleotide reductases. These well-studied enzymes illustrate potential for interchangeability adaptive utilization. More recently, ribosome also been demonstrated exhibit interchangeable interactions impacts on function, stress adaptation. Using these other examples, here we review significance from new angle that combines both biochemical evolutionary viewpoints. geochemical pressures properties underlie are discussed context impact modern disease states treatments. unique numerous facilitate extensive all areas cellular fundamental processes, such as respiration, metabolism, nitrogen fixation, photosynthesis, DNA replication, transcription, protein synthesis (1Bellenger J.P. Wichard T. Xu Y. Kraepiel A.M.L. Essential fixation free-living N2-fixing bacterium: Chelation, homeostasis high use efficiency.Environ. Microbiol. 2011; 13: 1395-1411Crossref PubMed Scopus (0) Google Scholar, 2Garcia-Diaz M. Bebenek K. Krahn J.M. Pedersen L.C. Kunkel T.A. Role catalytic during polymerization by polymerase lambda.DNA Repair. 2007; 6: 1333-1340Crossref 3Guth-Metzler R. Bray M.S. 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Sci. 2016; 17: 1-8Crossref Scholar), six d-block table: (Mn), (Fe), cobalt (Co), nickel (Ni), copper (Cu), zinc (Zn) ((10Crans D.C. Kostenkova Open questions roles first-row transition metals.Commun. Chem. 3: 1-4Crossref Scholar) Fig. 1A). characterized form partially filled d-subshells (shown 1A, blue). electron configuration facilitates oxidation states, defining many properties. called metals, biologically examples appearing first row table (Fig. dark cyan squares). Although important, Zn is excluded some definitions because possession complete d-subshell human body contains amounts magnesium (Mg), Fe, gram range, whereas milligram Mn, Cu, Co, molybdenum present 11Zoroddu M.A. Aaseth Crisponi Medici Peana Nurchi V.M. humans: A brief overview.J. Inorg. 2019; 195: 120-129Crossref (163) perform structure-stabilizing predominantly available divalent cations (possessing two fewer electrons than neutral state). 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Högbom Direct observation structurally encoded discrimination ether bond formation metalloprotein.Proc. 110: 17189-17194Crossref (27) and, such, can greatly influenced intracellular dictated particular or environmental condition. Therefore, flexibility preference more prevalent currently understood. Thus, view single native site may, unfavorably strict categorization. healthy cell, cytosolic organellar cation levels tightly regulated means protection against undesired elements, while imbalances manifest diseased states. identified link between non-native ion(s), which abolish correct leading mitigation disease, supports need further knowledge molecular mechanisms governing interchangeability. Such investigation will advance our understanding etiology progression, therapeutical intervention strategies. Particular progress revealing structure made recently technological developments. 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One prominent how mirrored host–pathogen interface. innate immune orchestrates assaults invading pathogens cases display responses. For example, connection biochemistry central phagocytic response, employs oxidant assault nutrient limitation (26Jakubovics N.S. Streptococcal stress.Biochem. 476: 699-703Crossref Many sensitive either side relatively narrow window, host exploit (27Hood M.I. Skaar E.P. Nutritional immunity: pathogen-host interface.Nat. 525-537Crossref (816) During infection organism, bacterial experience conditions, overload trace well severe (28Imlay Where world do bacteria stress?.Environ. 21: 521-530Crossref (70) 29Sultana Foti Dahl J.U. Bacterial neutrophilic hypochlorous acid.Infect. Immun. 88: 1-17Crossref 30Turner A.G. Djoko K.Y. Ong lynn Barnett T.C. Walker M.J. McEwan Group Streptococcus co-ordinates import efflux response hydrogen peroxide 595-611Crossref (8) viruses' survival pathogenesis. 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Язык: Английский

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Conoid extrusion regulates glideosome assembly to control motility and invasion in Apicomplexa DOI

Nicolas Dos Santos Pacheco, Lorenzo Brusini, Romuald Haase

и другие.

Nature Microbiology, Год журнала: 2022, Номер 7(11), С. 1777 - 1790

Опубликована: Сен. 15, 2022

Язык: Английский

Процитировано

Primary nutrient sensors in plants DOI

Dorina Podar, Frans J. M. Maathuis

iScience, Год журнала: 2022, Номер 25(4), С. 104029 - 104029

Опубликована: Март 4, 2022

Nutrients are scarce and valuable resources, so plants developed sophisticated mechanisms to optimize nutrient use efficiency. A crucial part of this is monitoring external internal levels adjust processes such as uptake, redistribution, cellular compartmentation. Measurement carried out by primary sensors that typically involve either transceptors or transcription factors. Primary only now starting be identified in for some nutrients. In particular, nitrate, there detailed insight concerning how the nitrate status sensed members transporter 1 (NRT1) family. Potential other macronutrients potassium sodium have also been recently, whereas micronutrients zinc iron, factor type reported. This review provides an overview interprets evaluates our current understanding sense macro rhizosphere root symplast.

Язык: Английский

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The past, present, and future of artificial zinc finger proteins: design strategies and chemical and biological applications DOI

Shigeru Negi, Miki Imanishi,

Mami Hamori

и другие.

JBIC Journal of Biological Inorganic Chemistry, Год журнала: 2023, Номер 28(3), С. 249 - 261

Опубликована: Фев. 7, 2023

Язык: Английский

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Upgrading and Validation of the AMBER Force Field for Histidine and Cysteine Zinc(II)-Binding Residues in Sites with Four Protein Ligands DOI

Marina Macchiagodena, Marco Pagliai, Claudia Andreini

и другие.

Journal of Chemical Information and Modeling, Год журнала: 2019, Номер 59(9), С. 3803 - 3816

Опубликована: Авг. 6, 2019

We developed and validated a novel force field in the context of AMBER parameterization for simulation zinc(II)-binding proteins. The proposed assumes nonbonded spherical interactions between central zinc(II) coordinating residues. A crucial innovative aspect our approach is to account polarization effects cation by redefining atomic charges residues an adjustment Lennard-Jones parameters Zn-interacting atoms reproduce mean distance distributions. optimal transferable parametrization was obtained performing accurate quantum mechanical calculations on training set high-quality protein structures, encompassing most common folds sites. addressed sites contain ion tetra-coordinated histidine cysteine represent about 70% all physiologically relevant Protein Data Bank. Molecular dynamics simulations with explicit solvent, carried out several proteins not included set, show that model preserves tetra-coordination metal site remarkable stability, yielding zinc(II)-X distances similar experimental data. Finally, tested evaluating affinities, using alchemical free energy perturbation approach. calculated dissociation constants correlate satisfactorily counterpart demonstrating validity transferability

Язык: Английский

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