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Title:Computational studies of the self-cleavage mechanism in the glmS ribozyme
Author(s):Zhang, Sixue
Director of Research:Hammes-Schiffer, Sharon
Doctoral Committee Chair(s):Hammes-Schiffer, Sharon
Doctoral Committee Member(s):Gruebele, Martin; Martinis, Susan A; Lu, Yi
Department / Program:Chemistry
Discipline:Chemistry
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):glmS ribozyme
self-cleavage
free energy simulations
Abstract:Ribozymes are catalytically functional RNA molecules. To overcome the lack of structural and chemical diversity, ribozymes employ several interesting strategies for catalysis. The glmS ribozyme regulates the level of glucosamine-6-phosphate (GlcN6P) in bacteria by catalyzing a self-cleavage reaction. Namely, the GlcN6P bonds to the glmS ribozyme and triggers a cleavage of a phosphodiester bond at a certain position via a general acid-base mechanism. This work explored the following aspects of its self-cleavage mechanism: general acid-base species, multiple roles of the cofactor GlcN6P, as well as the beneficial and deleterious effects of metal ions. Computational approaches including classical molecular dynamics (MD), quantum mechanical/molecular mechanical (QM/MM) calculations, and free energy simulations were employed to study the cleavage mechanisms and explain experimental observations such as the thio effects and metal ion rescue effects. A concerted yet asynchronous cleavage mechanism with an active site guanine as the general base and the cofactor as the general acid was elucidated. The calculated free energy barrier associated with this mechanism was consistent with experimental measurements. Additional catalytic roles of the cofactor such as disrupting an inhibitory hydrogen bond were revealed by simulations together with the large thio effect found in the ribozyme-cofactor complex and the inverse thio effect found in the apo ribozyme. Metal ion rescue experiments indicated the direct participation of an active site Mg2+ ion in the catalysis in the apo ribozyme but not in the ribozyme-cofactor complex. Therefore, the beneficial and deleterious effects of the active site Mg2+ ion were examined by computational approaches. The findings in this work have provided insights for general ribozyme catalysis. All of these findings have implications for general ribozyme catalysis.
Issue Date:2016-09-16
Type:Thesis
URI:http://hdl.handle.net/2142/95279
Rights Information:Copyright 2016 Sixue Zhang
Date Available in IDEALS:2017-03-01
Date Deposited:2016-12


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