Master Thesis Defense: Gökçe Güven
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Gökçe Güven
Materials Science and Engineering, MSc, 2013 

Thesis Jury
Prof. Dr. Canan Atılgan (Thesis Supervisor), Prof. Dr. Ali Rana Atılgan (Thesis Co-Supervisor), Prof. Dr. Levent Demirel, Asst. Prof. Alpay Taralp, Asst. Prof. Elif Özkırımlı Sönmez 

Date &Time: August, 01st, 2013 – 10:00

Place: FENS L063

Keywords: Perturbation Response Scanning (PRS), Molecular Dynamics (MD), Gram-negative bacteria, Haemophilus Influenza, Periplasmic Ferric Bindin Proteins


Differences between the conformations of the ligand-bound and unbound forms of proteins provide clues on deciphering residues that have a direct effect on binding mechanisms. Using molecular dynamic (MD) simulations as a basis, conformational changes that take place on time scales much slower than those accessible by MD may be investigated by supplementary methods such as perturbation response scanning (PRS). Since proteins are complex macromolecules, to sample their conformational energy landscapes we applied both global and local perturbations with different combinations. Global pertubations are related with environmental changes such as (i) different scales of ionization strength (IS) of the solution which galvanize the protein as the main parameter to be able to function in vivo, (ii) or protonation of a group of residues to mimic a different pH environment. Local perturbations are related with specific point perturbations on protein such as, (i) protonation or (ii) mutation of a single residue to and locate the points that controls a conformational change in proteins.

In this work, the apo and holo (Fe3+ bound) forms of the periplasmic ferric binding protein systems -hFBP of the gram negative bacteria haemophilus influenzae-whose chromosome is the first completed genome sequence of a cellular life- was selected as the model system. PRS studies showed us that D52 and D47 residues are the ones that give the highest value  for the fractional contribution of the highest eigenvalue of the response matrix. Therewithal, using pKa calculations a particular charged residue (D52) (out of a total of 98) was found to be the most sensitive to subtle pH variations in the physiological range. The effect of single point protonation  (D52+) and mutation (D52A) is investigated via a series of MD simulations. The effect of IS (0.15 mM and ~0 mM) and pH (5 and 6.5) change is also studied to monitor the conformations sampled. For holo FBP, protonated and Ala mutants of D52 consistently triggers opening of the iron binding site in an ensemble of simulations, while elevated IS consistently traps the closed forms. We categorized our series of MD trajectories as open, partially open, and closed due to coordination level and mapping of iron ion inside the active site. Our results lend clues as to how the environment versus single residue perturbations may be utilized for regulation of binding modes in hFBP systems.