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

Boob, Mayank

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

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

Language

eng

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.

Graduation Semester

2022-12

Type of Resource

Thesis

Handle URL

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

Copyright and License Information

Copyright 2022 Mayank Boob

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