Modeling and simulation of processes regulating protein binding in various environments
Abdizadeh, Haleh (2017) Modeling and simulation of processes regulating protein binding in various environments. [Thesis]
Conformational changes between structurally different forms of proteins are essential for their equilibrium and kinetic properties. Multiple conformers of the protein scaffolds are triggered by flexibility of the active site, local motions of the loops or allosteric response initiated by distal perturbations. It is our view that the conformational plasticity and allosteric regulations are essential contributors to protein stability, precise specificity and catalytic activity of the enzymes. The large-scale allosteric regulations are believed to involve some critical sites that mediate the conformational movements between different regions of the free energy landscape. In the first part of the thesis, we have employed Perturbation- Response Scanning (PRS) method unified with elastic network models to predict key residues that induce the dissociated state of 25 non-redundant protein-protein complexes over their bound states. We find that for a group of protein pairs, the functional sites are scattered on the protein surface while for another group the important residues are mainly confined to highly specific regions. We observe a rich mixture of both conservation and variability within the identified residues which we relate to their ability to alter the electrostatic potential distributions and their presence in helix-turn-helix motifs. In the second part of the thesis, we to provide insights into the dynamics of human transferrin (hTf) that transports ferric ions in blood stream with a high affinity and delivers them to cells via receptor mediated endocytosis. We study the effect of pH and salt via molecular dynamics (MD) simulations of total 3 μs, delineating large conformational changes occurring before and after the iron release process. Via PRS, we show that dynamics within a selected local minimum can lend clues on the global, large scale conformational transition of hTf alone and in its complexes with the human and bacterial receptors. Our studies provide a molecular level understanding of the full cycle of hTf-iron binding-release dynamics while resolving residues directly participating in each event in the cycle. In the third part of the thesis, we discuss the dynamics of dihydrofolate reductase, a ubiquitous enzyme with an essential role in cell growth and an important target by several drugs that act as inhibitors by competing with the ligand, dihydrofolate (DHF). We characterize Escherichia coli DHFR in its wild type (WT) and L28R survivor mutant in the presence of the substrate and its inhibitor (trimethoprim). We use extensive MD simulations to determine the conformational space, catalytic relevance of DHFR loop dynamics and hydrogen bond distributions near the active site. The study lays the framework to study the molecular mechanisms that control DHFR mutants conferring resistance to trimethoprim.
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