title: Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations.
abstract: X-ray crystallography can provide important insights into the structure of RNA enzymes (ribozymes). However, the details of a ribozyme's active site architecture are often altered by the inactivating chemical modifications necessary to inhibit self-cleavage. Molecular dynamics (MD) simulations are able to complement crystallographic data and model the conformation of the ribozyme's active site in its native form. However, the performance of MD simulations is driven by the quality of the force field used. Force fields are primarily parametrized and tested for a description of canonical structures and thus may be less accurate for noncanonical RNA elements, including ribozyme catalytic cores. Here, we show that our recent reparametrization of ε/ζ torsions significantly improves the description of the hairpin ribozyme's scissile phosphate conformational behavior. In addition, we find that an imbalance in the force field description of the nonbonded interactions of the ribose 2'-OH contributes to the conformational behavior observed for the scissile phosphate in the presence of a deprotonated G8(-). On the basis of the new force field, we obtain a reactive conformation for the hairpin ribozyme active site that is consistent with the most recent mechanistic and structural data.
authors.affiliation: †Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic.
authors.forename: Vojtěch
authors.initials: V
authors.lastname: Mlýnský
authors.affiliation: †Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic.
authors.forename: Petra
authors.initials: P
authors.lastname: Kührová
authors.affiliation: †Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic.
authors.forename: Marie
authors.initials: M
authors.lastname: Zgarbová
authors.affiliation: †Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic.
authors.forename: Petr
authors.initials: P
authors.lastname: Jurečka
authors.affiliation: ‡Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States.
authors.forename: Nils G
authors.initials: NG
authors.lastname: Walter
authors.affiliation: †Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic.
authors.forename: Michal
authors.initials: M
authors.lastname: Otyepka
authors.affiliation: †Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic.|§Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.|∥CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic.
authors.forename: Jiří
authors.initials: J
authors.lastname: Šponer
authors.affiliation: †Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic.|§Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Banáš
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D010710:Phosphates / Q000737:chemistry; D011522:Protons; D011789:Quantum Theory; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D012266:Ribose / Q000737:chemistry
chemical_list: D010710:Phosphates; D011522:Protons; D016337:RNA, Catalytic; C418481:hairpin ribozyme; D012266:Ribose; D004247:DNA