Date

2014

Document Type

Dissertation

Degree

Doctor of Philosophy

Department

Chemical Engineering

First Adviser

Mittal, Jeetain

Other advisers/committee members

Jagota, Anand; Snyder, Mark A.; Kim, Young C.; Vavylonis, Dimitrios

Abstract

The cellular environment is highly crowded owing to the presence of several kinds of macromolecules such as lipids, sugars, nucleic acids, and proteins, along with large organized macromolecular arrays such as the Chaperones. Thus, most of the in vivo processes such as the interaction between proteins and folding of proteins into their compact three-dimensional structures, that are of paramount biological importance, occur in restricted spaces. The primary focus of this dissertation is to broaden the understanding of protein folding and protein-protein interactions in a cell mimetic environment. We have reviewed the important developments that have furthered our understanding of the effects of macromolecular crowding on protein-protein interactions. We have outlined the development of a comprehensive crowding theory that can predict the binding thermodynamics considering both repulsive and attractive protein-crowder interactions. It has been observed that favorable weak interactions between proteins and crowders destabilize the protein complex formation in contrast to the traditional understanding that owing to the excluded volume effects, the primary effect of macromolecular crowding is to stabilize the bound complex. Additionally, we have performed replica exchange molecular dynamics (REMD) simulations to study the binding thermodynamics of proteins modeled as conformationally `flexible' entities under the influence of macromolecular crowding. We observe similar destabilization due to attractive interactions between proteins and crowders. Interestingly, we observe that the Scaled Particle Theory, originally developed for hard-sphere particles, can be utilized to predict the binding thermodynamics of flexible proteins.In order to study the effects of confinement, we have performed extensive REMD simulations using all-atom explicit solvent models to study the conformational stability of the sixteen residue GB1-hairpin confined between planar Lennard-Jones walls. We observe that confinement significantly alters the free-energy landscape. Under confinement, the misfolded state of the peptide is completely absent owing to the preferential adsorption of the hydrophobic residues on the confinement walls. Finally, in order to study the effect of cylindrical confinement, we have performed extensive REMD simulations of polyalanine helices confined within carbon nanotubes using all-atom explicit solvent models. We observe that the alpha-helix propensity of polyalanine is significantly reduced under confinement and that the effect is independent of the lengthscale of confinement.

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