Phase Phenomena of Proteins in Living Matter

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dc.contributor.advisorCheung, Margaret S.
dc.contributor.committeeMemberBassler, Kevin E.
dc.contributor.committeeMemberGunaratne, Gemunu H.
dc.contributor.committeeMemberKolomeisky, Anatoly B.
dc.contributor.committeeMemberLubchenko, Vassiliy
dc.contributor.committeeMemberMorrison, Greg
dc.creatorGasic, Andrei G.
dc.creator.orcid0000-0003-4054-6545
dc.date.accessioned2021-08-06T18:31:19Z
dc.date.available2021-08-06T18:31:19Z
dc.date.createdDecember 2020
dc.date.issued2020-12
dc.date.submittedDecember 2020
dc.date.updated2021-08-06T18:31:20Z
dc.description.abstractProteins must fold and function in the immensely complex environment of a cell, i.e. the cytoplasm—this is far from the ideal test-tube setting of a dilute solution. Here, this thesis answers an important question at the interface of physics and biology: how does the crowded cellular environment influence the dynamics of individual proteins and their folding phases? This thesis is presented in two parts. First, we review protein folding and investigate the effects of hydrostatic pressure using coarse-grained molecular simulations. There are two common forms of pressure-dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for coarse-grained molecular simulations of protein folding and unfolding under hydrostatic pressure. We investigated the two different pressure-dependencies on the desolvation potential in a structure-based protein model using coarse-grained molecular simulations. We compared the simulation results to the known behavior of proteins based on experimental evidence. We showed that the protein’s folding transition curve on the pressure–temperature phase diagram depends on the relationship between the potential well minima and pressure. For a protein that reduces its total volume under pressure, the PMF needs to carry the feature that the direct contact well is less stable than the water-mediated contact well at high pressure. In the second part we move toward understanding the effects of crowded environment of the cell. Proteins have properties that are exhibited by systems near a critical point, where distinct phases merge. This concept goes beyond previous studies that propose proteins have a well-defined folded and unfolded phase boundary in the pressure-temperature plane. Here, by modeling the protein phosphoglycerate kinase (PGK) on the temperature ($T$), pressure ($P$), and crowding volume-fraction ($\phi$) phase diagram, we demonstrate a critical transition where phases merge, and PGK exhibits large structural fluctuations. Above the critical temperature ($T_c$), the difference between the intermediate and unfolded phases disappears. When $\phi$ increases, the $T_c$ moves to a lower $T$. With experiments mapping the $T$--$P$--$\phi$ space, we verify the calculations and reveal a critical point at 305 K and 170 MPa that moves to a lower $T$ as $\phi$ increases. Crowding shifts PGK closer to a critical line in its natural parameter space, where large conformational changes can occur without costly free-energy barriers. Specific structures are proposed for each phase based on the simulation. To understand the ``quniary'' interaction between cells, we examine the interplay between folding and inter-domain interactions of engineered FiP35 WW domain repeat proteins with $n = 1$ through 5 repeats using a coarse-grained simulated annealing with the AWSEM Hamiltonian. According to our simulations, misfolded structures become increasingly prevalent as one proceeds from monomer to pentamer, with extended inter-domain beta sheets appearing first, then multi-sheet `intramolecular amyloid' structures, and finally novel motifs containing alpha helices. Finally, in developing principles of protein behavior \emph{in vivo}, we discuss the implications and connection to the organization and dynamics of the cytoplasm, unifying the single protein scale with the many-protein architectures at the subcellular scale.
dc.description.departmentPhysics, Department of
dc.format.digitalOriginborn digital
dc.format.mimetypeapplication/pdf
dc.identifier.citationPortions of this document appear in: Gasic, Andrei G., and Margaret S. Cheung. "A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure." The Journal of Physical Chemistry B 124, no. 9 (2020): 1619-1627. And in: Cheung, Margaret S., and Andrei G. Gasic. "Towards developing principles of protein folding and dynamics in the cell." Physical biology 15, no. 6 (2018): 063001. And in: Gasic, Andrei G., Mayank M. Boob, Maxim B. Prigozhin, Dirar Homouz, Caleb M. Daugherty, Martin Gruebele, and Margaret S. Cheung. "Critical phenomena in the temperature-pressure-crowding phase diagram of a protein." Physical Review X 9, no. 4 (2019): 041035. And in: Dave, Kapil, Andrei G. Gasic, Margaret S. Cheung, and M. Gruebele. "Competition of individual domain folding with inter-domain interaction in WW domain engineered repeat proteins." Physical Chemistry Chemical Physics 21, no. 44 (2019): 24393-24405. And in: Zegarra, Fabio C., Dirar Homouz, Andrei G. Gasic, Lucas Babel, Michael Kovermann, Pernilla Wittung-Stafshede, and Margaret S. Cheung. "Crowding-induced elongated conformation of urea-unfolded apoazurin: investigating the role of crowder shape in silico." The Journal of Physical Chemistry B 123, no. 17 (2019): 3607-3617.
dc.identifier.urihttps://hdl.handle.net/10657/8010
dc.language.isoeng
dc.rightsThe author of this work is the copyright owner. UH Libraries and the Texas Digital Library have their permission to store and provide access to this work. UH Libraries has secured permission to reproduce any and all previously published materials contained in the work. Further transmission, reproduction, or presentation of this work is prohibited except with permission of the author(s).
dc.subjectprotein folding, critical phenomena, biopolymers, aggregation
dc.titlePhase Phenomena of Proteins in Living Matter
dc.type.dcmiText
dc.type.genreThesis
thesis.degree.collegeCollege of Natural Sciences and Mathematics
thesis.degree.departmentPhysics, Department of
thesis.degree.disciplinePhysics
thesis.degree.grantorUniversity of Houston
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy

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