Poster abstracts
Poster number 47 submitted by Ella Yi
RevProtFinder: detecting reverse protonation in RNA from hydrogen bond geometry
Andrew J. Veenis (Dept of Chemistry, Pennsylvania State Univ, Univ Pk, PA 16802; Center for RNA Molecular Biology, Pennsylvania State Univ), Gayoung E. Yi (Dept of Chemistry, Pennsylvania State Univ, Univ Pk, PA 16802; Center for RNA Molecular Biology, Pennsylvania State Univ), Sreeja Thota (Center for RNA Molecular Biology, Pennsylvania State Univ; Dept of Biochemistry and Molecular Biology, Pennsylvania State Univ), Philip C. Bevilacqua (Dept of Chemistry, Pennsylvania State Univ, Univ Pk, PA 16802; Center for RNA Molecular Biology, Pennsylvania State Univ; Dept of Biochemistry and Molecular Biology, Pennsylvania State Univ)
Abstract:
Reverse protonation refers to a proton either being added to or removed from a certain nitrogen on the nucleobases (1). When reverse protonation happens, it flips which atom acts as a hydrogen bond donor or acceptor, as well as placing a formal charge on the nucleobase. The change in protonation state of a nucleobase can influence the catalytic activity of RNA (2). However, hydrogen atoms are rarely resolved in experimental structures, making it difficult to observe the protonation state directly (3). Therefore, we developed RevProtFinder, a lightweight Python application that infers hydrogen positions from heavy-atom coordinates in experimentally determined mmCIF structures. The program then evaluates the resulting hydrogen bond geometry to identify candidate reverse-protonated sites.
For the case study, we applied RevProtFinder to 2,170 representative RNA structures curated by the BGSU non-redundant list (4), spanning 1,832 unique PDB entries, and identified over 600,000 hydrogen bonds. Among them, 1,204 were cases where reverse-protonated cytosine N3 (C(N3)+) acts as a hydrogen bond donor. These include well-known C+•GC base triples and C+•C pairs as well as novel and unexpected pairs. RevProtFinder's hydrogen bond detection ability was validated against a well-established hydrogen bond calculation tool, HBPlus (3), on RNA, DNA, small proteins, and their complexes.
References:
1. Sims, P.A., Larsen, T.M., Poyner, R.R., Cleland, W.W. and Reed, G.H. (2003) Reverse protonation is the key to general acid-base catalysis in enolase. Biochemistry, 42, 8298-8306.
2. Frankel, E.A. and Bevilacqua, P.C. (2018) Complexity in pH-dependent ribozyme kinetics: dark pKa shifts and wavy rate-pH profiles. Biochemistry, 57, 1819-1828.
3. McDonald, I.K. and Thornton, J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
4. Leontis, N.B. and Zirbel, C.L. (2012) Nonredundant 3D structure datasets for RNA knowledge extraction and benchmarking. In Leontis, N. and Westhof, E. (eds), RNA 3D Structure Analysis and Prediction. Nucleic Acids and Molecular Biology, Vol. 27. Springer, Berlin, Heidelberg, pp. 281-298.
Keywords: Reverse-protonation, Hydrogen bond, Cheminformatics