Comparative study of binding pocket structure and dynamics in cardiac and skeletal myosin

Figures

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  Figure 1. OM binding site. (A) Cartoon representation of the x-ray structure of cardiac myosin bound to OM (orange spheres) (PDB: 5N69). The different subdomains are highlighted using different colors. OM is shown as orange spheres. (B) Close-up view of the OM binding site. (C) Alignment of the human MYH2 (skeletal) and MYH7 (cardiac) sequences in the OM binding region. The residues that differ in the two sequences are highlighted in red. To see this figure in color, go online.

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  Figure 2. Comparison of the pocket shape in the two isoforms. (A/B) MDpocket frequency grids. Points that are found to be part of a pocket for at least 45% of the frames are shown as points connected by edges for the combined skeletal M1 and M2 (A) and the cardiac (B) MD simulations (OM-free). The three residues that differ in the two sequences are shown as sticks. (C/D/E) Surface representation of the pocket in the M1 (C) and M2 (D) models, and in OM-bound cardiac myosin (E). Representative structures from the most populated clusters observed in 300-ns MD simulations are used for the skeletal models, whereas the energy-minimized structure of the complex from Hashem et al. (7) is used for the cardiac isoform. The residues lining pockets identified by fpocket in the OM binding region are shown as surface in (C and D), whereas residues within 0.8 nm of OM are shown in (E). The surface is clipped to show the internal shape of the pocket. The hydrophobicity score is color mapped on the surface from white (low hydrophobicity) to red (high hydrophobicity) using the Eisenberg scale (21). The position of the subpocket that becomes accessible in the skeletal models is indicated with a green arrow.…

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  Figure 3. Comparison of predicted OM affinity to skeletal and cardiac myosin. The distributions of OM binding affinity values to structures extracted from MD simulations are represented as light blue (skeletal M1), blue (skeletal M2), and orange (cardiac) boxplots. Red stars represent the affinity values of OM to the initial energy-minimized M1 and M2 models for skeletal myosin, and to the x-ray structure (PDB: 5N69) for cardiac myosin. To see this figure in color, go online.

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  Figure 4. Comparison of OM-myosin interactions in the two isoforms. Occurrence of hydrogen-bonding (A) and hydrophobic (B) interactions identified by PLIP (23) in the skeletal (blue) and cardiac (orange) complexes. Occurrence is calculated across all the cluster representatives of the OM complexes for each isoform. Residues are named using the skeletal MYH2 sequence and numbering (cardiac MYH7 names and numbers are indicated in parentheses where the two sequences differ). Residues in the native OM binding region (listed in Fig. 1C) are shown in bold. To see this figure in color, go online.

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  Figure 5. Comparison of OM binding modes in the two isoforms. OM-myosin complexes are represented to illustrate OM binding poses in (A) the cardiac-like OM-skeletal myosin complex (cluster 10 in Table S6), (B) the representative of the most populated OM-skeletal myosin cluster (cluster 17), and (C) the energy-minimized OM-cardiac myosin complex from Hashem et al. (7). The surface is clipped to show the internal shape of the pocket. The hydrophobicity score is color mapped on the surface from white (low hydrophobicity) to red (high hydrophobicity) using the Eisenberg scale (21). The position of the subpocket that becomes accessible in the skeletal models is indicated with a green arrow. To see this figure in color, go online.

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  Figure 6. Comparison of OM binding stability in MD simulations of the two isoforms. The time evolution of OM RMSD (non-hydrogen atoms) from the starting structure is plotted for a representative MD simulation of OM-bound skeletal (cardiac-like binding pose M1_OM1, light blue) and cardiac (orange) myosin. RMSD values were calculated after fitting the system to the initial structure using the protein C-alpha atoms to take into account the roto-translational motions of the ligand inside the pocket. To see this figure in color, go online.