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Document Type

Open Access Dissertation

Degree Name

Doctor of Philosophy (PhD)

Degree Program

Chemistry

Year Degree Awarded

2015

Month Degree Awarded

September

First Advisor

Igor A Kaltashov

Second Advisor

Anne Gershenson

Third Advisor

Scott Auerbach

Fourth Advisor

Richard Vachet

Subject Categories

Analytical Chemistry | Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology

Abstract

Haptoglobin (Hp), an acute phase protein, binds free hemoglobin (Hb) dimers in one of the strongest non-covalent interactions known in biology. This interaction protects Hb from causing potentially severe oxidative damage and limiting nitric oxide bioavailability. Once Hb/Hp complexes are formed, they proceed to bind CD163, a cell surface receptor on macrophages leading to complex internalization and catabolism. Myoglobin, (Mb) a monomeric protein, that is normally found in the muscle but can be released into the blood in high concentrations during myocardial injury, is homologous to Hb and shares many conserved Hb/Hp interface residues. Both monomeric Hb and Mb species present potential risks, yet their interactions with Hp have not been extensively studied or are a matter of controversy, respectively. To predict possible interactions of monomeric globins with Hp, we employed a variety of cost and time effective molecular modeling approaches. Native electrospray ionization mass spectrometry (ESI MS) experiments confirm the modeling results and show that monomeric Hb and Mb bind Hp with a stoichiometry of two globin monomers per Hp tetramer.

The ESI MS results also demonstrate the success of our computational approaches to Mb/Hp interactions, motivating us to model Hb/Hp/CD163 complexes. Both CD163 bound Ca2+ and specific CD163 acidic residues are known to be essential for binding specific Hp basic residues resulting in Hb/Hp/CD163 complex formation, but the structural details of Hb/Hp/CD163 interactions are unknown. We therefore constructed experimentally driven molecular models of Hb/Hp/CD163 complexes using molecular docking. In order to understand the role of Ca2+ in Hp/CD163 interactions and dynamics, all-atom molecular dynamics (MD) simulations were conducted for CD163 models in the presence and absence of Ca2+. The molecular models of Hb/Hp/CD163 suggest that Hp basic residues R252 and K262 each interact with a conserved acidic triad (E27, E28, D94) in CD163 domains 2 and 3. A calcium ion is postulated to stabilize this CD163 acidic cluster facilitating Hp recognition. Consistent with this, MD simulations on isolated CD163 domains suggest that Ca2+ bound at a specific site in CD163 preserves the arrangement of the acidic triad and protein structural stability. Our studies demonstrate how molecular modeling and molecular dynamics aided/correlated with mass spectrometry experiments can elucidate the structural basis and dynamics of interactions between Hp, globins and/or CD163. This approach may be useful for designing therapeutics that utilizes the Hb/Hp/CD263 endocytosis pathway and unraveling novel avenues for possible Hp-therapy administration for diseases or complications arising from Mb toxicity.

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