title: Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation.
abstract: Catalytic RNA molecules can achieve rate acceleration by shifting base pK(a) values toward neutrality. Prior evidence has suggested that base A38 of the hairpin ribozyme plays an important role in phosphoryl transfer, possibly functioning as a general acid, or by orienting a specific water molecule for proton transfer. To address the role of A38, we used Raman spectroscopy to measure directly the pK(a) of the N1-imino moiety in the context of hairpin ribozyme crystals representative of a "precatalytic" conformation. The results revealed that the pK(a) of A38 is shifted to 5.46 +/- 0.05 relative to 3.68 +/- 0.06 derived from a reference solution of the nucleotide AMP. The elevated pK(a) correlates well with the first titration point of the macroscopic pH-rate profile of the hairpin ribozyme in solution and strongly supports A38 as a general acid catalyst in bond scission. The results confirm that A38 is protonated before the transition state, which would promote phosphorane development. Overall, the results establish a cogent structure-function paradigm that expands our understanding of how RNA structure can enhance nucleobase reactivity to catalyze biological reactions.
authors.affiliation: Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
authors.forename: Man
authors.initials: M
authors.lastname: Guo
authors.forename: Robert C
authors.initials: RC
authors.lastname: Spitale
authors.forename: Rosaria
authors.initials: R
authors.lastname: Volpini
authors.forename: Jolanta
authors.initials: J
authors.lastname: Krucinska
authors.forename: Gloria
authors.initials: G
authors.lastname: Cristalli
authors.forename: Paul R
authors.initials: PR
authors.lastname: Carey
authors.forename: Joseph E
authors.initials: JE
authors.lastname: Wedekind
mesh_terms: D020134:Catalytic Domain; D003460:Crystallization; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000032:analysis*; D013059:Spectrum Analysis, Raman
chemical_list: D016337:RNA, Catalytic; C418481:hairpin ribozyme
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