Topological constraints of structural elements in regulation of catalytic activity in HDV-like self-cleaving ribozymes.

Abstract:

: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.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Webb CH,Nguyen D,Myszka M,Lupták A

doi

10.1038/srep28179

subject

Has Abstract

pub_date

2016-06-15 00:00:00

pages

28179

issn

2045-2322

pii

srep28179

journal_volume

6

pub_type

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