The computational analyses, molecular dynamics of fatty-acid transport mechanism to the CD36 receptor

Abstract

The transmembrane glycoprotein CD36, which is responsible of the metabolic disorders, and the elevated intake of fat induces lipid buildup, is a multifunctional scavenger receptor signaling those functions in high-affinity tissue uptake of long-chain fatty acids. In this study, we used series of molecular dynamics simulations of the wild type and mutants types K164A CD36 protein interacting with one palmitic acid (PLM) besides simulations of the wild type interacting with the three PLM to find out the mechanism of the functioning of the complex CD36/Fatty acids and the unraveling of the role of the mutation. Additionally we determined whether Lys164, mostly exposed to protein surface, played important roles in fatty acid uptake. These simulations revealed, the conformational changes induced by Lys164 residue and the altered interactions induced by the mutagenesis of surface lysine that was badly influencing the folding, utility, solubility, and stability form of the variant. Furthermore, Lys164 residue provided the structural basis of forming an opening at the region of principal portal for the dissociation of palmitic acid. The results of our simulations revealed hole two fatty acids found in CD36 cavity structure and it was the most preferred to CD36 structure stabilization.

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“…The small Rg values are harmonious to a tighter packing of atoms or vice versa. Throughout the simulation, (Figure 2C) the Mpro and other Mpro‐Peptide complexes exhibited almost similar type of unimodal violin plots in terms of Rg values holding discrete average values 68 . The Mpro‐DRAMP01342 took a sudden upward direction reaching up to 22.75 Å at 48 ns and then fluctuated a bit till 53 ns which suggested that the complex showed a weak structural compaction initially.…”

“…Throughout the simulation, (Figure 2C ) the Mpro and other Mpro‐Peptide complexes exhibited almost similar type of unimodal violin plots in terms of Rg values holding discrete average values. 68 The Mpro‐DRAMP01342 took a sudden upward direction reaching up to 22.75 Å at 48 ns and then fluctuated a bit till 53 ns which suggested that the complex showed a weak structural compaction initially. The average Rg values for Mpro, Mpro‐DRAMP01760, Mpro‐DRAMP01808, Mpro‐DRAMP018658, Mpro‐DRAMP01737, Mpro‐DRAMP01771 were calculated as 22.1, 22.30, 22.25, 22.20, and 22.35 Å respectively from the trajectory.…”

“…To evaluate the configurational compactness of Proteins, Radius of gyration is recommended as a formidable system. 68 The small Rg values are harmonious to a tighter packing of atoms or vice versa. Throughout the simulation, (Figure 2C ) the Mpro and other Mpro‐Peptide complexes exhibited almost similar type of unimodal violin plots in terms of Rg values holding discrete average values.…”

“…To evaluate the configurational compactness of Proteins, Radius of gyration is recommended as a formidable system 68 . The small Rg values are harmonious to a tighter packing of atoms or vice versa.…”

“…The post simulation trajectories were assessed considering a general analysis which incorporates RMSD, 65 Rg, 66 To evaluate the configurational compactness of Proteins, Radius of gyration is recommended as a formidable system. 68 The small Rg values are harmonious to a tighter packing of atoms or vice versa. Throughout with the least presence of non-polar residues (61.54%) which supports its highest SASA consistency among other complexes.…”