“Proteins: Boil ’em, mash ’em, stick ’em in a stew”

A lot of headway has been made in understanding protein folding and stability from experimental and computational perspective. However, there is still a lack of understanding about how proteins interact with their surrounding and how these interactions affect protein folding and stability. This is especially important in the case of extremophiles where environmental conditions can vary rapidly, and adaptation is crucial for survival. I begin by describing the effect of environmental factors on protein in Chapter 1. I discuss the 5 major factors that affect protein namely – temperature, pressure, osmolytes, pH, macromolecular crowding. I briefly given an overview of the field and our particular interests in studying extreme pressure and temperature systems. In Chapter 2 I talk about using long range unbiased MD simulations to tease out nuances between weak interactions of proteins and osmolytes. Chapter 3 talks about phase diagram of a globular protein and how it gets modulated depending on its environment. This modulation might be critical for its function inside the cell. Then I finally combine all the learnings from my previous work to combine it altogether and put it in perspective with regards to extremophiles. In particular, I try to understand the role that sequence plays in interacting with environment to keep a protein stable and functions at extreme temperature and pressure (Chapter 4). In Chapter 5, I present the excerpt from my 3 min thesis talk, along with the image submission for SCS Image Challenge. These serve as an example of my attempt to communicate my science to a broader audience and some outreach activities. Finally in Chapter 6, I describe the issues with high-pressure systems, our setup along with the common issues that can be encountered and fixed with our setup. I also describe the high-pressure SAXS setup at CHESS.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Biophysics & Quant Biology

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2022

Author dc:creator

• Boob, Mayank

Contributors dc:contributor

• Gruebele, Martin
• Pogorelov, Taras
• Zimmerman, Steven C
• Shukla, Diwakar

• Protein Folding
• Extremophiles
• High Pressure Fluorescence Spectroscopy
• Molecular Dynamics Simulations

Statement dc:rights

• Copyright 2022 Mayank Boob

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/117624

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F117624