{"entity": "researcher", "timestamp": "2026-09-27T16:01:28.640Z", "family": "Flori\u00e1n", "given": "Jan", "initials": "J", "orcid": "0000-0003-2669-4293", "affiliations": ["Department of Chemistry and Biochemistry, Loyola University Chicago , 1032 W. Sheridan Road, Chicago, Illinois 60660, United States."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/d87b22cfd27b43ee89e5a7c958a6ffab.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/d87b22cfd27b43ee89e5a7c958a6ffab"}}, "publications": [{"entity": "publication", "iuid": "cd062b7f5fa64a00baadaf78ea02f5ee", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cd062b7f5fa64a00baadaf78ea02f5ee.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cd062b7f5fa64a00baadaf78ea02f5ee"}}, "title": "Computer simulations of the catalytic mechanism of wild-type and mutant \u03b2-phosphoglucomutase.", "authors": [{"family": "Barrozo", "given": "Alexandre", "initials": "A"}, {"family": "Liao", "given": "Qinghua", "initials": "Q", "orcid": "0000-0002-2260-8493", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2cfe1da74631465d870b2cc2028442ab.json"}}, {"family": "Esguerra", "given": "Mauricio", "initials": "M", "orcid": "0000-0002-1775-586X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/beb7099f24f94eff965c1622d9ef008f.json"}}, {"family": "Marloie", "given": "Ga\u00ebl", "initials": "G"}, {"family": "Flori\u00e1n", "given": "Jan", "initials": "J", "orcid": "0000-0003-2669-4293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d87b22cfd27b43ee89e5a7c958a6ffab.json"}}, {"family": "Williams", "given": "Nicholas H", "initials": "NH", "orcid": "0000-0002-4457-4220", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ce19a540ded4ae2bb286e1d59c5f091.json"}}, {"family": "Kamerlin", "given": "Shina Caroline Lynn", "initials": "SCL", "orcid": "0000-0002-3190-1173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4540c85432f4cdf952b0ef7cfe1d875.json"}}], "type": "journal article", "published": "2018-03-28", "journal": {"title": "Org. Biomol. Chem.", "issn": "1477-0539", "volume": "16", "issue": "12", "pages": "2060-2073", "issn-l": "1477-0520"}, "abstract": "\u03b2-Phosphoglucomutase (\u03b2-PGM) has served as an important model system for understanding biological phosphoryl transfer. This enzyme catalyzes the isomerization of \u03b2-glucose-1-phosphate to \u03b2-glucose-6-phosphate in a two-step process proceeding via a bisphosphate intermediate. The conventionally accepted mechanism is that both steps are concerted processes involving acid-base catalysis from a nearby aspartate (D10) side chain. This argument is supported by the observation that mutation of D10 leaves the enzyme with no detectable activity. However, computational studies have suggested that a substrate-assisted mechanism is viable for many phosphotransferases. Therefore, we carried out empirical valence bond (EVB) simulations to address the plausibility of this mechanistic alternative, including its role in the abolished catalytic activity of the D10S, D10C and D10N point mutants of \u03b2-PGM. In addition, we considered both of these mechanisms when performing EVB calculations of the catalysis of the wild type (WT), H20A, H20Q, T16P, K76A, D170A and E169A/D170A protein variants. Our calculated activation free energies confirm that D10 is likely to serve as the general base/acid for the reaction catalyzed by the WT enzyme and all its variants, in which D10 is not chemically altered. Our calculations also suggest that D10 plays a dual role in structural organization and maintaining electrostatic balance in the active site. The correct positioning of this residue in a catalytically competent conformation is provided by a functionally important conformational change in this enzyme and by the extensive network of H-bonding interactions that appear to be exquisitely preorganized for the transition state stabilization.", "doi": "10.1039/c8ob00312b", "pmid": "29508879", "labels": [], "xrefs": [], "notes": [], "created": "2018-12-05T12:44:25.702Z", "modified": "2026-09-23T12:39:11.886Z"}, {"entity": "publication", "iuid": "4244f65ff8444e1a923ec41614ae79b4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/4244f65ff8444e1a923ec41614ae79b4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/4244f65ff8444e1a923ec41614ae79b4"}}, "title": "DNA Polymerase \u03bb Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study.", "authors": [{"family": "Maximoff", "given": "Sergey N", "initials": "SN", "orcid": "0000-0001-6783-6767", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/067a8e7a7a2c49fb9987e02cc3e0547e.json"}}, {"family": "Kamerlin", "given": "Shina Caroline Lynn", "initials": "SCL", "orcid": "0000-0002-3190-1173", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4540c85432f4cdf952b0ef7cfe1d875.json"}}, {"family": "Flori\u00e1n", "given": "Jan", "initials": "J", "orcid": "0000-0003-2669-4293", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d87b22cfd27b43ee89e5a7c958a6ffab.json"}}], "type": "journal article", "published": "2017-08-24", "journal": {"title": "J Phys Chem B", "issn": "1520-5207", "volume": "121", "issue": "33", "pages": "7813-7822", "issn-l": "1520-5207"}, "abstract": "Human DNA polymerase \u03bb is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase \u03bb, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an unexpected Watson-Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thymine in the DNA or guanine in the deoxyguanosine triphosphate analogue may spend a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the polymerase \u03bb mutant. The experiments do not determine particular forms of the nucleobases that contribute to this mutagenic mispair. Thus, we investigate the thermodynamics of formation of various mispairs between guanine and thymine in the ternary complex at a neutral pH using classical molecular dynamics simulations and the free energy perturbation method. Our free energy calculations, as well as a comparison of the experimental and computed structures of mispairs, indicate that the Watson-Crick-like mispair between the enol tautomer of guanine and the keto tautomer of thymine is dominant. The wobble mispair between the keto forms of guanine and thymine and the Watson-Crick-like mispair between the keto tautomer of guanine and the enol tautomer of thymine are less prevalent, and mispairs that involve deprotonated guanine or thymine are thermodynamically unlikely. These findings are consistent with the experiment and relevant for understanding mechanisms of spontaneous mutagenesis.", "doi": "10.1021/acs.jpcb.7b04874", "pmid": "28732447", "labels": [], "xrefs": [], "notes": [], "created": "2018-12-05T11:15:56.005Z", "modified": "2026-09-23T10:51:39.125Z"}]}