Computational analysis reveals unique binding patterns of oxygenated and deoxygenated myoglobin to the outer mitochondrial membrane

Authors: ANISHKIN, ANDRIY - University Of Maryland School Of Medicine; ADEPU, KIRAN KUMAR - Arkansas Children'S Nutrition Research Center (ACNC); BHANDARI, DIPENDRA - Arkansas Children'S Nutrition Research Center (ACNC); ADAMS, SEAN - Uc Davis Medical Center; CHINTAPALLI, SREE - Arkansas Children'S Nutrition Research Center (ACNC)

Submitted to: Biomolecules
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/13/2023
Publication Date: 7/17/2023
Citation: Anishkin, A., Adepu, K., Bhandari, D., Adams, S.H., Chintapalli, S.V. 2023. Computational analysis reveals unique binding patterns of oxygenated and deoxygenated myoglobin to the outer mitochondrial membrane. Biomolecules. 13(7):1138. https://doi.org/10.3390/biom13071138.
DOI: https://doi.org/10.3390/biom13071138

Interpretive Summary: Myoglobin (Mb), a protein abundantly found in muscle tissues plays an important role in storing and transporting the oxygen and lipids to mitochondria in the cells for energy production. The contact of myoglobin with outer mitochondrial surface is known to promote oxygen release from myoglobin into the mitochondria. However, the molecular details of the process is yet to be described. Here, we use computational and modeling techniques to explore the process of oxygen release from myoglobin into the mitochondria. Our study shows that contact of oxygen carrying myoglobin to the outer mitochondrial membrane with heme group of myoglobin facing the membrane at some small angle facilitates the release and diffusion of oxygen into the mitochondria. The oxygen release process is fairly stable for the myoglobin's contact at the position of mitochondrial cristae as compared to other contact sites. Further, this contact is also dictated by the protein geometry and the transient local interactions between the charges on the protein and lipid residues of the outer mitochondrial membrane.

Technical Abstract: Myoglobin serves as a buffer for cytoplasmic oxygen as well as a vehicle that delivers it, along with the lipids, to mitochondria for oxidative phosphorylation. It is known that myoglobin associates with the outer mitochondrial membrane and that contact promotes oxygen release, however the molecular descriptions of these processes are missing. Here, we used molecular dynamics simulations to explore the interactions of oxy- and deoxy-myoglobin with the lipids of the outer mitochondrial membrane in two lipid compositions - one typical for the whole membrane on average, and another specifically for the contact sites with the cristae. The approach involved establishing of the contact between myoglobin and the membrane using gentle constant force, followed by unrestrained relaxation of the complex and then steered detachment aimed to estimate relative stability of the binding. Multiple repetitions with different myoglobin orientations (in total, 48 starting arrangements and over 3 µs of simulations) showed that on average, myoglobin establishes more stable contacts with the lipids typical for the contact sites rather than the average outer membrane. The regions of the myoglobin that contributed the most for the initial contact were the N-terminal helix and loop regions at the outer “corners” of the protein, whereas the residues on the side of the heme crevice added significantly to the stabilization of the attachment later in the process. Analysis of the contacts indicates non-specific binding mediated by local electrostatic interactions between the charged or polar groups of the protein and the membrane, many of them stable on the scale beyond of tens of nanoseconds. Simulations suggest variability in the orientation of the bound myoglobin, while the most stable steered detachment simulations show the heme crevice side usually positioned at some angle in proximity to the membrane thus leaving only a narrow solute layer mediating the potential release of the bound ligands.