“Proteins: Boil ’em, mash ’em, stick ’em in a stew”
Boob, Mayank
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https://hdl.handle.net/2142/117624
Description
Title
“Proteins: Boil ’em, mash ’em, stick ’em in a stew”
Author(s)
Boob, Mayank
Issue Date
2022-09-22
Director of Research (if dissertation) or Advisor (if thesis)
Gruebele, Martin
Pogorelov, Taras
Doctoral Committee Chair(s)
Gruebele, Martin
Pogorelov, Taras
Committee Member(s)
Zimmerman, Steven C
Shukla, Diwakar
Department of Study
School of Molecular & Cell Bio
Discipline
Biophysics & Quant Biology
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Protein folding, extremophiles, High pressure fluorescence spectroscopy, Molecular dynamics simulations
Abstract
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.
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