The Development and Application of Methods to Study the Evolution of Specificity, Allostery, and RNA -Protein Interactions in Translation
Sethi, Anurag
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https://hdl.handle.net/2142/84296
Description
Title
The Development and Application of Methods to Study the Evolution of Specificity, Allostery, and RNA -Protein Interactions in Translation
Author(s)
Sethi, Anurag
Issue Date
2008
Doctoral Committee Chair(s)
Zaida Luthey-Schulten
Department of Study
Chemistry
Discipline
Chemistry
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Biology, Molecular
Language
eng
Abstract
We have developed the sequence QR algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. These biasless profiles were used to identify a putative class II cysteinyl-tRNA synthetase (CysRS) in several archaea that eluded previous annotation studies. This enzyme was found to be involved in the indirect pathway of cysteine aminoacylation that is shown to exist in the last universal common ancestral state. We have developed a network analysis based on molecular dynamics simulations in order to probe the mechanism and identify residues critical for allosteric regulation in a bacterial glutamyl tRNA-synthetase (GluRS):tRNA complex. In addition, our evolutionary analysis shows that the ancestral core of the class I AARS family consists only of the catalytic domain while the anticodon binding domain and the editing domain were later additions that evolved as specificity emerged in the AARSs. In the second step of translation, the elongation factor Tu (EF-Tu) binds to all the standard aminoacyl-transfer RNAs and transports them to the ribosome. Combined energetic and evolutionary analyses reveal the coevolution of residues in EF-Tu and CysRS with the charged tRNA at the binding interface. The final step of translation involves protein synthesis at the ribosome where the anticodon of the charged tRNA is matched with the sequence of the mRNA and the aminoacid on the aminoacyl-tRNA gets added onto the growing nascent polypeptide. We present evidence that domain specific r-proteins and signatures in universal r-proteins have coevolved with rRNA signatures, which are often in close proximity. We have combined equilibrium and steered molecular dynamics (SMD) simulations with principal component and correlation analyses to probe the mechanism of allosteric regulation in imidazole glycerol phosphate (IGP) synthase, which is involved in histidine biosynthesis. An evolutionary analysis of IGP synthase revealed a conserved network of interactions leading from the effector binding site to the glutaminase active site, forming conserved communication pathways between the remote active sites.
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