(Georgia Institute of Technology, 2020-08)
Meade, Caeden Daniel
RiboVision is a collection of applications housed on servers at the Georgia Institute of Technology which serves to facilitate the development of publication-quality diagrams of ribosomal RNA (rRNA) and ribosomal protein (rProtein) structures (Petrov et. al, 2014). In particular, RiboVision seeks to promote analysis of key properties of rRNA and rProteins in primary, secondary, and tertiary structures.
As key semantides (ubiquitous macromolecules which carry genetic equivalent to the information intrinsic to DNA molecules and may be used by comparison to inform phylogenetic relationships), comparison of the primary and secondary structures of 16S and 18S RNA allows for the phylogenetic comparison of prokaryotic species and eukaryotic species, respectively (Fuerst, 2001). Sequence alignments are housed on the RiboVision server and stored in a MySQL database. Over the next two semesters, major improvements will be made to the server resulting in the newest edition, RiboVision3, which will feature improvements over the preceding RiboVision2 including the integration of XRNA, a program responsible for the generation of rRNA secondary structures and their exportation of their data into common computer-file formats (CSV, SVG, PDF, etc.) and the PDB Topology Viewer, a program responsible for production of protein secondary structures and their exportation into SVG image files.
The core functionality of XRNA - demonstration and editing tools of rRNA secondary structures needs to be iterated upon to allow for a more diverse set of purposes, including processing of high-quality hand-edited images into formats which are compatible with on-server management and conversion into formats native to web browsers.
(Georgia Institute of Technology, 2017-05)
Kwon, Michelle S.
Olfactomedin (OLF) domain-containing proteins, first identified in relation to bullfrog olfactory chemoreception, are part of a superfamily of proteins implicated in many important biological functions and human diseases. The myocilin OLF domain (mOLF), one of the best studied, is closely associated with the ocular disease glaucoma. Nearly 100 myocilin mutations have been reported in glaucoma patients; >90% are missense mutations within mOLF. Disease-associated mutant myocilins are destabilized and aggregation prone, leading to toxicity and death of cells that maintain the anatomical trabecular meshwork extracellular matrix in the eye. The Lieberman lab solved the crystal structures of OLF domains from myocilin and gliomedin (gOLF), a peripheral nervous system OLF domain. While both are similar five-bladed β-propellers, only mOLF contains a stabilizing calcium ion. Remarkably, gOLF is ~20 °C more stable than mOLF, even though it doesn't have a calcium ion and is phylogenetically more primitive. The goal of this project was to use insights from mOLF and gOLF to create a thermostable mOLF. Surprisingly, mutagenesis of a calcium-coordinating aspartate (D478) to alanine abolished calcium binding but increased mOLF thermal stability to near gOLF levels. Addition of D478A to the destabilized, glaucoma-associated variant D380A rescued thermal stability to that of wild-type (WT) mOLF. Structures of thermostable mOLF variants reveal unexpected changes in tertiary structure compared to WT mOLF, which were confirmed by solution biophysical measurements. The findings from this study expand our understanding of the structure-stability relationship of mOLF and provide further insight into the evolution of the OLF β-propeller.