Computational Investigation of the Molecular Mechanisms Regulating Nucleic Acid Processing Metalloenzymes

Donati, Elisa (2022) Computational Investigation of the Molecular Mechanisms Regulating Nucleic Acid Processing Metalloenzymes, [Dissertation thesis], Alma Mater Studiorum Università di Bologna. Dottorato di ricerca in Data science and computation, 33 Ciclo. DOI 10.48676/unibo/amsdottorato/10119.
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Polymerases and nucleases are enzymes processing DNA and RNA. They are involved in crucial processes for cell life by performing the extension and the cleavage of nucleic acid chains during genome replication and maintenance. Additionally, both enzymes are often associated to several diseases, including cancer. In order to catalyze the reaction, most of them operate via the two-metal-ion mechanism. For this, despite showing relevant differences in structure, function and catalytic properties, they share common catalytic elements, which comprise the two catalytic ions and their first-shell acidic residues. Notably, recent studies of different metalloenzymes revealed the recurrent presence of additional elements surrounding the active site, thus suggesting an extended two-metal-ion-centered architecture. However, whether these elements have a catalytic function and what is their role is still unclear. In this work, using state-of-the-art computational techniques, second- and third-shell elements are showed to act in metallonucleases favoring the substrate positioning and leaving group release. In particular, in hExo1 a transient third metal ion is recruited and positioned near the two-metal-ion site by a structurally conserved acidic residue to assist the leaving group departure. Similarly, in hFEN1 second- and third-shell Arg/Lys residues operate the phosphate steering mechanism through (i) substrate recruitment, (ii) precise cleavage localization, and (iii) leaving group release. Importantly, structural comparisons of hExo1, hFEN1 and other metallonucleases suggest that similar catalytic mechanisms may be shared by other enzymes. Overall, the results obtained provide an extended vision on parallel strategies adopted by metalloenzymes, which employ divalent metal ion or positively charged residues to ensure efficient and specific catalysis. Furthermore, these outcomes may have implications for de novo enzyme engineering and/or drug design to modulate nucleic acid processing.

Tipologia del documento
Tesi di dottorato
Donati, Elisa
Dottorato di ricerca
Settore disciplinare
Settore concorsuale
Parole chiave
Nucleic Acids, Nucleases, Metalloenzymes, Polymerases, two-metal-ion mechanism, DNA, catalysis, Molecular dynamics, enhanced sampling
Data di discussione
21 Marzo 2022

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