Proteopedia entry: “Tutorial: How we get the oxygen we breathe”


This Proteopedia page presents an interactive tutorial exploring the question “How do we get the oxygen we breathe?” While most pages in Proteopedia aim for an encyclopedic style of writing, this page has been created in the “Tutorial” area, as evidenced by its name, and instead aims for a style of writing appropriate for a tutorial or lesson plan. The reader is led through a brief explanation of the structure of hemoglobin and how it traffics oxygen through our body, along with the implications of the mutation in sickle-cell disease on hemoglobin structure. The key points illustrated are: (1) The basic distinction between cartoon and spacefilling representations as well as an introduction to the Corey-Pauling-Koltun and N-to-C rainbow coloring schemes. (2) Hemoglobin as a tetramer composed of two α monomer chains and two β monomer chains. (3) The structure of the heme group and how it associates with the monomer, along with the proximal and distal histidines. (4) Visualization of an oxygen molecule in spacefilling representation and comparison with carbon monoxide in the context of the problem of carbon monoxide binding to the heme. (5) The difference in conformation between an oxygenated and a deoxygenated monomer and how this gives rise to cooperative binding. (6) Visualization of the hydrophobic spot formed by the sickle-cell mutation, as well as the hydrophobic spot near the heme binding pocket in the deoxygenated state of both normal and sickle-cell hemoglobin, and how this causes aggregation of hemoglobin molecules into long fibers in sickle-cell disease.1

Figure 1.

Snapshots of two interactive scenes from the Proteopedia page “Tutorial: How we get the oxygen we breathe.” Left: the structure of hemoglobin with α monomer chains shown in light-blue, β monomer chains shown in light-green, and heme groups shown in CPK (Corey-Pauling-Koltun) coloring scheme (PDB entry 1hho). Right: an interpolated morph animation depicting a monomer transitioning from a deoxygenated state (PDB entry 1hga) to an oxygenated state (shown, PDB entry 1hho).