Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes.
Self-cleaving ribozymes fold into intricate structures, which orient active site groups into catalytically competent conformations. Most ribozyme families have distinct catalytic cores stabilized by tertiary interactions between domains peripheral to those cores. We show that large hepatitis delta virus (HDV)-like ribozymes are activated by peripheral domains that bring two helical segments, P1 and P2, into proximity - a "pinch" that results in rate acceleration by almost three orders of magnitude. Kinetic analysis of ribozymes with systematically altered length and stability of the peripheral domain revealed that about one third of its free energy of formation is used to lower an activation energy barrier, likely related to a rate-limiting conformational change leading to the pre-catalytic state. These findings provide a quantitative view of enzyme regulation by peripheral domains and may shed light on the energetics of allosteric regulation.
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.
Chiu-Ho T
CH
Webb
Department of Chemistry, University of California, Irvine, CA 92697, USA.
Dang
D
Nguyen
Department of Chemistry, University of California, Irvine, CA 92697, USA.
Marie
M
Myszka
Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.|Department of Chemistry, University of California, Irvine, CA 92697, USA.|Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA.
Andrej
A
Lupták
D003698:Hepatitis Delta Virus / Q000235:genetics*; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D009690:Nucleic Acid Conformation; D020871:RNA Stability; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
D016337:RNA, Catalytic; D008274:Magnesium