Life on Earth fundamentally and indispensably relies on proper regulation and metabolism of inorganic molecules such as dioxygen (O2), nitric oxide (NO), carbon dioxide (CO2) and ammonia (NH3). These chemical species often act as substrates of enzymes and/or as ligands modulating biochemical cascades, so elucidating their delivery and transport is imminent towards understanding cellular functions. Destinated targets (i.e. proteins and enzymes) of these molecules are often separated from exterior environments by layers or shells coated not only membrane lipids but also, in some cases, proteins, effectively forming physical barriers against their passage. For instance, catalytic site of many enzymes are sequestered deeply inside, while there is no clearly defined pathways for substrate delivery and product removal. Since gaseous molecules such as O2, NO, CO2 and NH3 have tiny volumes, probing their interactions with their surroundings within a medium requires techniques that provide both atomic spatial and small temporal resolutions. To fulfill these purposes, I have employed molecular dynamics (MD) simulation to characterize delivery pathways of O2, NO and CO2 in aerobic respiratory terminal oxidases (cytochrome ba3 and cytochrome aa3), nitric oxide reductase (cNOR) and bacterial carboxysome, and to describe the movement of O2, CO2 and NH3 through lipid membranes and membrane channels. In the first part of this dissertation, I illustrated the necessity of pathways in assuring optimal delivery of O2 or NO to the terminal oxidases and cNOR, which are homologous enzymes, under physiological conditions. The conclusions from the studies are correlated to the experimental measurements. Although O2 and NO are readily dissolved in membrane lipids, they migrate to the reduction site exclusively via a pre-formed hydrophobic tunnel. The unobstructed pathway in cytochrome ba3 ultimately permits the substrate(s) to migrate at the maximum diffusion rate (10^9 M^−1 s^−1), which is faster than through partially constricted pathways in cytochrome aa3 and cNOR. I then characterized the permeation of CO2 fixation substrates through the carboxysome shell of cyanobacteria, which is an assembled layer of shell proteins. The results of energetic analysis characterized a pore within each shell protein to be permeable to bicarbonate (HCO3- ) rather than CO2 and O2. The preferred uptake of HCO3- is advantageous of enhancing the incorporation of CO2 into biomass and mitigating the wasteful O2 fixation. The enzyme carbonic anhydrase inside the carboxysomal lumen can readily convert HCO3- to CO2. In the second part of this dissertation, I examined the permeability of O2 and CO2 across lipid membranes varied by ratios of glycerolphospholipids, cholesterol and sphinogomyelins, which are major constituents of mammalian membranes. This study shows that membrane lipid compositions modulate the permeability of nonpolar gases, emphasizing the existence of gas-impermeable membranes and significance of membrane-facilitated gas channels. I have also provided preliminarily structural insights into the selectivity of aquaporins for NH3, CO2 and glycerol. Aquaporins, widely known as membrane-facilitated water channels, also facilitate the permeation of gases and other molecules such as glycerol but with different degrees in selectivity. The recent crystal structure of human AQP7, an aquaglyceroporin, provided by colleagues at the Case Western Reserve University, has enabled further elucidations of AQPs in their permeability to glycerol.
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Microscopic description of gas permeation and delivery pathways in biological macromolecules
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