Exploring the entry route of palmitic acid and palmitoylcarnitine into myoglobin

Abstract

Our previous studies confirmed the interaction of different chain lengths of fatty acids and their derivatives (acylcarnitines) with Oxy‐ and Deoxy‐Myoglobin, using both molecular dynamic simulations and Isothermal Titration Calorimetry experiments. However, those studies were limited to testing only the binding sites predicted from comparative studies of fatty acid binding protein homologs and pre‐calculated binding predictions using AutoDock grid maps. Also, those methods could not address the dynamic processes of the ligand entry into the binding pocket of the protein and the residues involved. To analyze the entry mechanisms of the lipid ligands into myoglobin, and to assess binding specificity at the proposed binding site, we have carried out 80 different molecular dynamic simulations (total length 4.4 microseconds) of murine Oxy‐ and Deoxy‐Mb structures with either the palmitate or palmitoylcarnitine initially placed at different positions near the protein surface. The simulations indicated that both ligands quickly enter the Oxy‐Mb structure through a dynamic area called the “portal region” near the heme group, which forms the entry point for small molecule gaseous ligands like O2, CO and NO. The same phenomenon is not observed with Deoxy‐Mb where the lipid ligands move away from the protein surface, due to a quick compaction of the entry portal and the heme‐containing crevice in the Mb protein upon O2 removal. On the other hand, random starting points for the ligands on the protein surface have shown an “alternate” interaction site which is common for both Oxy‐ and Deoxy‐Mb. The latter observations strongly suggest that spontaneous and “non‐specific” binding of long‐chain fatty acids and acylcarnitines to Mb is driven by hydrophobic forces, in contrast with the “portal region” crevice being a primary and specific binding spot that can be precluded by deoxygenation. Considering the importance of lipid metabolism and trafficking in oxidative, Mb‐rich tissues such as type 1 skeletal muscle and cardiomyocytes, identifying the mechanisms of entry, binding and off‐loading of long‐chain fatty acids and acylarnitines on Mb may have important ramifications for muscle management of bioactive lipids.Support or Funding InformationUSDA‐ARS Project 6026‐51000‐010‐05SThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.