This thesis is devoted to understanding solute-solvent interactions in folded and unfolded proteins. To this end, we have studied partial molar volume, Vo, and adiabatic compressibility, KoS, of 20 amino acid side chains using low weight molecular model compounds, N-acetyl amino acid amide and its derivatives, between 18 oC and 55 oC. We used our data to develop an additive scheme for calculating the partial specific volume and adiabatic compressibility of fully extended polypeptide chains as a function of pH and temperature. We compared our calculated volumetric characteristics of the fully extended conformations of apocytochrome c and apomyoglobin with the experimental values measured in neutral pH (for apocytochrome c) or acidic pH (for apomyoglobin). The comparison between the calculated and experimental volumetric characteristics suggested that neither apocytochrome c nor apomyoglobin are fully unfolded and retain solvent-inaccessible amino acid residues. To study cosolvent-solute interactions, we determined Vo and KoS of amino acid side chains and glycyl units as a function of urea concentration. We analyzed these data within the framework of a statistical thermodynamic formalism to determine the association constants, k, for the reaction in which urea binds to each of the amino acid side chains and the glycyl unit replacing two water molecules in solvation shell. Our determined k range from 0.04 to 0.39 M with the average of 0.16 ± 0.09 M. There was no apparent correlation between the values of k and the ratio of polar to nonpolar solvent accessible surface areas. This study supports a direct interaction model in which urea denatures a protein by concerted action via favorable interactions with a wide range of protein groups. In addition, we have presented buffer ionization effect on the volume of protein denaturation could be significant with the potential to affect not only its magnitude but also its sign using a pressure perturbation calorimetric technique. Our results identified buffer ionization as an important determinant of protein transition volume that needs to be carefully taken into account. Results described in this work provide fundamental understanding of solute-solvent interaction in both folded and unfolded proteins.
| Identifer | oai:union.ndltd.org:TORONTO/oai:tspace.library.utoronto.ca:1807/29789 |
| Date | 31 August 2011 |
| Creators | Lee, Soyoung |
| Contributors | Chalikian, Tigran |
| Source Sets | University of Toronto |
| Language | en_ca |
| Detected Language | English |
| Type | Thesis |
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