{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/117624"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/117624","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"“Proteins: Boil ’em, mash ’em, stick ’em in a stew”","abstract":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-12-01","abstract_html":"Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-12-01","abstract_has_math":false,"creators":["Boob, Mayank"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Biophysics & Quant Biology","degree_department":null,"school":null,"contributors":["Gruebele, Martin","Pogorelov, Taras","Zimmerman, Steven C","Shukla, Diwakar"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2022,"date_issued":"2022-12","date_published":"2022-12","updated_at":"2026-07-22T22:24:56Z","subjects":["Protein Folding","Extremophiles","High Pressure Fluorescence Spectroscopy","Molecular Dynamics Simulations"],"languages":["en","eng"],"rights":["Copyright 2022 Mayank Boob"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/2142/117624","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Gruebele, Martin","Pogorelov, Taras","Zimmerman, Steven C","Shukla, Diwakar"]},{"key":"dc:creator","label":"Author","values":["Boob, Mayank"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2022-12","2022-09-22"]},{"key":"dc:type","label":"Dc Type","values":["text","Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Biophysics & Quant Biology"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Protein Folding","Extremophiles","High Pressure Fluorescence Spectroscopy","Molecular Dynamics Simulations"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en","eng"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2022 Mayank Boob"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://hdl.handle.net/2142/117624"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-12-01","The student, Mayank Boob, accepted the attached license on 2022-08-17 at 13:56.","The student, Mayank Boob, submitted this Dissertation for approval on 2022-08-17 at 14:04.","This Dissertation was approved for publication on 2022-09-22 at 09:00.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18462 on 2023-04-12 at 08:10:22","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."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["“Proteins: Boil ’em, mash ’em, stick ’em in a stew”"]}]}],"canonical_facts":{"dc:contributor":["Gruebele, Martin","Pogorelov, Taras","Zimmerman, Steven C","Shukla, Diwakar"],"dc:creator":["Boob, Mayank"],"dc:date":["2022-12","2022-09-22"],"dc:description":["Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2024-12-01","The student, Mayank Boob, accepted the attached license on 2022-08-17 at 13:56.","The student, Mayank Boob, submitted this Dissertation for approval on 2022-08-17 at 14:04.","This Dissertation was approved for publication on 2022-09-22 at 09:00.","DSpace SAF Submission Ingestion Package generated from Vireo submission #18462 on 2023-04-12 at 08:10:22","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."],"dc:format":["application/pdf"],"dc:identifier":["https://hdl.handle.net/2142/117624"],"dc:language":["en","eng"],"dc:rights":["Copyright 2022 Mayank Boob"],"dc:subject":["Protein Folding","Extremophiles","High Pressure Fluorescence Spectroscopy","Molecular Dynamics Simulations"],"dc:title":["“Proteins: Boil ’em, mash ’em, stick ’em in a stew”"],"dc:type":["text","Thesis"],"thesis:degree_discipline":["Biophysics & Quant Biology"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:56Z"}