A molecular dynamics study and free energy analysis of complexes between the Mlc1p protein and two IQ motif peptides

Abstract

The Mlc1p protein from the budding yeast Saccharomyces cerevisiae is a Calmodulin-like protein, which interacts with IQ-motif peptides located at the yeast's myosin neck. In this study, we report a molecular dynamics study of the Mlc1p-IQ2 protein-peptide complex, starting with its crystal structure, and investigate its dynamics in an aqueous solution. The results are compared with those obtained by a previous study, where we followed the solution structure of the Mlc1p-IQ4 protein-peptide complex by molecular dynamics simulations. After the simulations, we performed an interaction free-energy analysis using the molecular mechanics Poisson-Boltzmann surface area approach. Based on the dynamics of the Mlc1p-IQ protein-peptide complexes, the structure of the light-chain-binding domain of myosin V from the yeast S. cerevisiae is discussed.

FIGURE 1

Cartoon diagrams of the crystal and the simulated structures of the Mlc1p protein when it binds the IQ2 peptide (PDB 1M45), and the IQ4 peptide (PDB 1M46). The N-lobe (residues 1–59), the interdomain (residues 60–92), the C-lobe (residues (93–148), and the IQ peptides are shown in blue, red, green, and yellow, respectively. Both crystal structures, and both simulated solution structures, are presented with the same orientation, where the N-lobes are structurally aligned. (A) The crystal structure of the Mlc1p-IQ2 complex; (B) the simulated structure of the Mlc1p-IQ2 complex after 12-ns simulation; (C) the crystal structure of the Mlc1p-IQ4 complex; and (D) the simulated structure of the Mlc1p-IQ4 complex after 12-ns simulation. The black arrows in frames B and D mark the kink of helix D.

FIGURE 2

(A) The RMSD of the backbone atoms of the Mlc1p-IQ2 complex (black), the Mlc1p protein (dark gray), and the IQ2 peptide (light gray) as a function of the simulation time. (B) The RMSD of the backbone atoms of the different domains of the Mlc1p protein as a function of the simulation time. The domains of the protein are defined as follows: residues 1–59 for the N-lobe (black), 60–92 for the interdomain (dark gray), and 93–148 for the C-lobe (light gray).

FIGURE 3

Matrix representation of mutual C-α atoms' RMSD of the Mlc1p protein obtained upon comparison of the two simulations. The RMSD values of the Mlc1p protein for the Mlc1p-IQ4 simulation's trajectory were calculated in relation to those of the Mlc1p protein obtained from the Mlc1p-IQ2 simulation's trajectory and vice versa. The values are given by color codes; blue and red represent high and low similarity, respectively.

FIGURE 4

The root mean-square fluctuation (RMSF) as a function of the residue number of the Mlc1p protein. The RMSF was calculated for the backbone atoms of the Mlc1p protein for each residue at both simulations. The solid line represents the RMSF of the Mlc1p protein at the simulation of the Mlc1p-IQ2 structure, while the dashed line represents the RMSF of the Mlc1p protein at the simulation of the Mlc1p-IQ4 structure. The bold horizontal bars, drawn in parallel to the abscissa, represent the α-helices that the Mlc1p protein comprises. The RMSF of both MD trajectories is presented for the entire simulations time (A), and for the timeframe t = 10 ns until t = 12 ns (B).

FIGURE 5

The electrostatic potential surface around the IQ2 peptide (A) and the IQ4 peptide (B). Both peptides are presented in yellow with the same orientation, while their positive and negative residues are drawn in blue and red, respectively. The Coulomb cages for the positive (transparent blue) and negative (transparent red) domains are drawn at the distance where the electrostatic potential equals 1 k_BT/e.

FIGURE 6

Contacts (<4 Å) between residues of the Mlc1p protein and the bound IQ peptides obtained from the MD simulations at t > = 6 ns. Data regarding the Mlc1p-IQ4 structure simulation (60) are presented at the upper half of the illustration, whereas data regarding the Mlc1p-IQ2 structure simulation are presented at its lower half. The IQ peptides, the N-lobe of the protein, the interdomain of the protein, and the C-lobe of the protein are colored in black, blue, red, and green, respectively. Residues of the Mlc1p protein that interact with both peptides are underlined. Only contacts that persist at least 80% of the examined period are presented.