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.

Figure 1

(a) Scheme of the molecular dynamics simulation procedure that the CD36 transporter (blue) and ligand plamitic acid PLM (reed). MD0 The wild type CD36 protein was simulated in the absence of palmitic acid (PLM), MD1 the wild type CD36 protein was simulated in the presence of a single PLM, MD2 the mutant type CD36 protein was simulated in the presence of a single PLM, MD3 the wild type protein was simulated in the presence of a three PLM put outside, MD4 the wild type protein was simulated in the presence of a three PLM (two PLM put inside and one PLM outside). (b) Scheme of molecular dynamic results that the CD36 transporter (blue) and ligand plamitic acid PLM (reed) including the efflux of the substrate PLM along with the uptake across the CD36 receptor. (c) Evaluation of the mutant K164A CD36 (3D) structure by ERRAT2 and Prove and Ramachandran plot.

Figure 2

(a) Dynamics analyses of plamitic acid (PLM) uptake across the wild and mutant type CD36 receptor. RMSD plot, Backbone residual fluctuations (RMSF) plot, time evolution of Radius of Gyration (Rg), Solvent Accessible Surface (SASA), Gromacs Energies and Hydrogen Bonds for wild and mutant type of CD36 in presence and absence of PLM a function of time during 100,000 ps (100 ns). Black, blue, and red, represent values obtained for Wild type CD36 in absence of PLM, wild type CD36 in presence of a single PLM, mutant K164A type CD36 in e of in presence of a single PLM respectively. (b) DSSP analysis for the secondary structure fluctuations as a function of time from 0 to 100 ns of plamitic acid (PLM) uptake across the wild and mutant type CD36 receptor.

Figure 3

(a–c) Model and motion produced by principal component analysis for wild and mutant type of CD36 in presence and absence of PLM a function of time during 100,000 ps (100 ns). (a) Principal component analysis, PC2 vs PC1, PC2 vs PC3, PC3 vs PC1 and an eigenvalue rank plot. (b) Visualization of the motions along PC1. (c) Motion of two different modes by ANM Analyze, the red arrows show the direction and amplitudes of the movements occurred from first trajectory of holo and apo form in (gray) and (pink) color respectively. (d,e) Cross-correlation Analysis matrix of the fluctuations of the C α atoms of the residue from their average during 100 ns for wild and mutant type of CD36 in presence and absence of PLM. (d) Cross-correlation map for MD simulation. Cyan color indicates a positive correlation between residue fluctuations, while the pink color depicts a negative correlation. (e) Residue cross-correlations. CD36 is depicted by gray cartoon. Red and blue lines indicate correlated and anti-correlation motions.

Figure 4

Structure of the studied CD36 with their respective tunnels. (a) PLM-bound snapshot, with the crystal structure of the wild-type CD36 (CD36-CIDRα, PDB-ID: 5LGD) depicting fully formed tunnel (identified using CAVER 3.0 PyMOL plugin). The main tunnel is shown by the blue and green surface. (b) CHEXVIS was used to analyze snapshots from 50 and 100 ns molecular dynamics simulation for six simulations for wild and mutant type of CD36 in presence and absence of PLM. (c) The transport channel of the fatty acid in the apo and holo conformations were identified based on the PCA analysis using CHEXVIS for CD36 WT, CD36WT–PLM and CD36MT–PLM.

Figure 5

Properties of Protein helice during MD simulations. (a) Motion analysis based on the PCA analysis in apo (pink color) and holo (gray color) form of CD36 WT and MT in presence of PLM. (b) The geometrical parameters used for the analysis of the upper helix conformations. The values of the rotation angle calculated for the upper helices are plotted as a function of time for one of the MD simulations of CD36 WT (I) and MT (II) in presence of PLM. The angle is estimated with respect to the original inward facing structure. The blue ticks in the source and on the side of the circles measured the angle value for the first and last trajectory frames respectively; the red line corresponds to the mean angle value along the trajectory. (c,d) Analyze a static peptide’s local angles along the length of the helix and heatmap color represented a angle-indicative graphics of CD36 wild type (c) and CD36 mutant type (d) in presence of PLM.

Figure 6

A snapshots representing the pathway of palmitic acid al transport at the portal of the CD36. (a) The snapshots correspond with 100 ps, 800 ps, 15 ns, 21 ns, 23 ns, 25 ns, 100 ns, 200 ns with one FA adsorbed to the protein. (b) The RMSD of the system, as they evolve with time. A is representation of Fatty acids at the starting point of the simulation 200 ns.

Figure 7

(a) Snapshots representing of Fatty acid transport rates, snapshots at 100 ps, 50, 100, 150, and 200 ns taken during each simulation, which depicted the pathway, transport mode and rate of three PLM to the portal CD36 receptor. (b) MD analyses of three PLM (three put outside two PLM put inside (green color) and one PLM outside (pink color)) Uptake across the wild type CD36 receptor. RMSD plot, Backbone residual fluctuations (RMSF) plot, time evolution of radius of gyration (Rg).