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Computational Study of Bovine β-Lactoglobulin Complexes with Fatty Acids

  • Author / Creator
    jalili, Nobar
  • This thesis presents studies aimed at delivering a deeper understanding of protein-fatty acids recognition and dissociation processes using molecular dynamics simulations. The focus of this thesis is on theoretical modeling of β-lactoglobulin protein in complex with fatty acid ligands (fluorinated and non-fluorinated). The dynamics of ligand exit from protein binding site is unclear and it is desired to understand whether ligands dissociate from the protein binding site along a well defined dissociation pathway or through a collection of exit pathways. This computational study of β-lactoglobulin and fatty acid complexes was inspired by recent mass spectrometry experiments using blackbody infrared radiative dissociation technique where the dissociation kinetics of these complexes was measured. Potential of mean force calculations and transition state theory were utilized to compute the dissociation rate constant of β-lactoglobulin-fatty acids complexes. Analysis of the calculated free energy profiles provided a more complete picture of the probable intermolecular interactions. The carboxyl group of the fatty acids interacts with variety of the residues on the flexible loops via hydrogen bonds but it is not involved in the interactions with the charged amino acids. There is a late transition state for the dissociation of β-lactoglobulin-fatty acid complexes and most probably the cleavage of the nonpolar interactions of the fatty acid aliphatic chain with protein residues lined in binding cavity is the last step of the activation process. It is not clear how fluorination influences the stability of protein-ligand complexes. Recently, quantitative investigation of the energetics of β-lactoglobulin complex with fluorinated fatty acids proved that fluorocarbon binding within the binding cavity of β-lactoglobulin is stronger than hydrocarbon binding. MD simulations were performed on β-lactoglobulin-fluorinated fatty acids complexes to probe the nature of stabilizing intermolecular interactions in further details. Analysis of the trajectory files revealed fluorine bonding to the polar hydrogen atoms is primarily responsible for the stabilizing effects of fluorination.

  • Subjects / Keywords
  • Graduation date
    2014-11
  • Type of Item
    Thesis
  • Degree
    Master of Science
  • DOI
    https://doi.org/10.7939/R3XK84W2D
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
    English
  • Institution
    University of Alberta
  • Degree level
    Master's
  • Department
    • Department of Chemistry
  • Supervisor / co-supervisor and their department(s)
    • Klassen, John (Chemistry)
  • Examining committee members and their departments
    • Klobukowski, Mariusz (Chemistry)
    • Hanna, Gabriel (Chemistry)