Photochemical Sciences Ph.D. Dissertations


Analyzing and classifying bimolecular interactions: I. Effects of metal binding on an iron-sulfur cluster scaffold protein II. Automatic annotation of RNA-protein interactions for NDB

Date of Award


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Photochemical Sciences

First Advisor

Neocles Leontis (Committee Co-Chair)

Second Advisor

Andrew Torelli (Committee Co-Chair)

Third Advisor

H. Peter Lu (Committee Member)

Fourth Advisor

Vipaporn Phuntumart (Other)


This dissertation comprises two distinct parts; however the different research agendas are thematically linked by their complementary approaches to investigate the nature of important intermolecular interactions. The first part is the study of interactions between an iron-sulfur cluster scaffold protein, IscU, and different transition metal ions. Interactions between IscU and specific metal ions are investigated and compared with those of SufU, a homologous Fe-S cluster biosynthesis protein from Gram-positive bacteria whose metal-dependent conformational behavior remains unclear. These studies were extended with additional metal ions selected to determine whether coordination geometry at the active sites of IscU and its homolog influence metal ion selectivity. Comparing the conformational behavior and affinity for different transition metal ions revealed that metal-dependent conformational transitions exhibited by IscU may be a recurring strategy exhibited by U-type proteins involved in Fe-S cluster biosynthesis.

The second part of the thesis focuses on automated detection and annotation of specific interactions between nucleotides and amino acid residues in RNA-protein complexes. RNA-protein interactions play crucial roles in all stages of transcription, translation and gene regulation. In order to systematically detect, annotate, and query these non-covalent interactions, we have developed programs that are integrated into the RNA.BGSU.EDU data pipeline to provide RNA-protein interaction annotations to the NDB website. Our programs were then used to identify RNA-protein interactions in the mammalian mitochondrial (mmt) ribosome. Mmt ribosomes have evolved from ancestral bacterial ribosomes by large-scale reduction of ribosomal RNAs (rRNAs), loss of guanosine (G) nucleotides, and an increased prevalence of ribosomal proteins. Systematic comparisons of recently solved structures of small-subunits (SSU) mmt-ribosomes with those of bacteria, and of high-quality rRNA sequence alignments, allowed us to deduce rules for folding a complex RNA with far fewer Gs. Via specific RNA-protein interactions, mmt rProteins (i) substitute for truncated rRNA helices, (ii) maintain the mutual spatial orientations of the remaining helices, (iii) compensate for lost RNA-RNA interactions, (iv) reduce the solvent accessibility of exposed bases, and (v) stabilize the RNA loop motifs lacking Gs that are conserved in bacteria.