Welcome
Welcome to my thesis! To navigate: Sections are listed on the left of the screen, and subsections on the right; you may also click on the button at the bottom of the page to advance section by section.
To view/download the PDF output, click here. Scripts, raw results, and all project-related material are available at my GitHub.
Enjoy!
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Abstract
Hemoproteins are able to catalyze an extraordinarily broad range of reactions. This class of proteins includes cytochrome P450s and peroxidases, among many others. Hemoproteins by definition include heme to achieve their chemistry; but heme molecules themselves vary considerably, and different heme molecules are employed depending on the function of a particular hemoprotein. At present, there is a knowledge gap in the literature of the structural features required to bind heme in hemoprotein binding sites.
In this study, we investigated the binding environments of heme-b, heme-c, siroheme, and verdoheme. A high-throughput framework was developed to generate, process, and analyze data derived from the Protein Data Bank (PDB) files used in the study. Amino acid frequencies, volume, surface areas, and angular relations within the heme binding sites were all obtained and examined for a diverse set of hemoproteins. Overall, we find that nonpolar residues and their interactions with heme may be of greater importance to heme binding than previously thought, suggesting that polar interactions, while necessary, are insufficient to efficiently bind heme. We also report several values for binding pocket volumes, surface areas, and angular data that may be of utility in artificial metalloenzyme design. The framework developed for this study is highly adaptable and may facilitate similar investigations for other proteins and ligands.
Acknowledgments
In case anyone reads this in the future, some context may be appreciated: I attended and (hopefully) completed this Master’s program during the COVID-19 global pandemic from September 2020 to September 2021.
Thanks to everyone who taught me something during this program.
Thanks to those in the research group who helped me understand what a heme is and got me this far; they tolerated and attempted to alleviate my ignorance: Laura Tiessler Sala, José Emilio Sánchez Aparicio and JeanDi.
Thanks to the UAB for having me; and thanks to our professors for providing a mercilessly thorough education.
Thanks to Spain, and Catalonia, for even allowing me into the country, and, I emphasize, thanks for implementing public health measures.
Thanks to my classmates for sharing in the suffering.
Thanks to my family and friends for supporting me, often over the phone, throughout this program and interesting time.
Thanks to whatever media I consumed and the creators of that media that facilitated the survival of my sanity through the pandemic.
Finally, I’d like to quote a well-known artist from California. He was referencing his own work, but I wholly identify with his appreciation for the subject of his esteem:
“Last but not least, I wanna thank me. I wanna thank me for believing in me. I wanna thank me for doing all this hard work. I wanna thank me for having no days off. I wanna thank me for, for never quitting. I wanna thank me for always being a giver, and trying to give more than I receive. I wanna thank me for trying to do more right than wrong. I wanna thank me for just being me at all times.” – Calvin Cordozar Broadus Jr.