Conformational Switch of a Flexible Loop in Human Laminin Receptor Determines Laminin-1

Conformational Switch of a Flexible Loop in Human Laminin Receptor Determines Laminin-1 Interaction

Carmen Di Giovanni,† Alessandro Grottesi,‡ and Antonio Lavecchia†*

†Department of Pharmaceutical and Toxicological Chemistry, “Drug Discovery Laboratory”, University of Naples "Federico II", Via D. Montesano 49, 80131 Naples, Italy. ‡CASPUR (Supercomputing Consortium for Applications for University and Research), Computational Medicine and Biology Group, Via dei Tizii 6, 00185 Rome, Italy

*Address correspondence to this author at the Dipartimento di Chimica Farmaceutica e Tossicologica, “Drug Discovery” Laboratory, Università di Napoli “Federico II”, Facoltà di Farmacia, via D. Montesano 49, I-80131 Napoli, Italy; Phone: +39-081-678613; Fax: +39-081-678012; E-mail: [email protected]. Supplementary Material

Figure S1. (A): Cartoon representation of the LamR fold as determined by X-ray spectroscopy. Flexible loop and C-terminal α-helix are labeled and colored in yellow and green, respectively; Peptide G is represented in orange. (B): RMSD of Cα atoms as a function of simulation time of the Cα atoms for LamR in the 9-205 range (black curve) and in the 9-187 range (red curve). Figure S2. Root mean square fluctuations (RMSF) of the Cα atoms with respect to their average positions as measured for the first trajectory (black curve in Figure 1). The black line shows the RMSF calculated in the 5-100 ns range; red line shows the RMSF calculated in the 12-100 ns, after the main RMSD change. The 188-204 C-terminal loop contributes to the most striking difference due to its conformational change.

Figure S3. Secondary structure map of LamR as a function of simulation time (run 2). Each point is represents the secondary structure occurence of the n-th residues coloured according to the colour map showed at the bottom. Secondary structure was calculated using the DSSP software (see Methods for details). Figure S4. Convergence analysis of mean square fluctuations (MSF) of Cα atoms performed with a simular protocol as described in Faraldo-Gomez et al., 2004. Calculations were performed by averaging the MSF of atoms over 4 differently sampled trajectories (10, 50, 100 and 125 ps) and using different time windows (500, 1000, 2000 and 5000 ps). Error bars give standard deviations within each time window. Trajectories with different sampling frequency are colour coded as follows: black: 10 ps; red: 50 ps; green: 100 ps; blue: 125 ps. Top panel: Simulation one; Bottom panel: simulation two. Figure S5. Solvent Accessible Surface Area (SASA) of LamR as calculated on a per residue basis and at selected time frames along the simulation trajectory (run 2). Only the Peptide G sequence is reported, i.e., residues 161-184. The SASA per residue of the X-ray initial structure is shown as a black curve (solid circles). The time frames for the other curves are as follows: red: 15 ns; green: 50 ns; blue= 80 ns; magenta: 100 ns.

Movie M1: Sample movie of the MD simulation (run 2) of LamR in the 0-100 ns range. The protein structure is represented as light-grey cartoon. The flexible loop encompassing residues 187-198 is coloured in yellow; peptide G is in orange and the C-terminal helix is coloured in green. The K11, E192, and R184 side-chains are represented as green sticks. The W176 and V197 forming the hydrogen bond are represented as sticks and coloured according to atom types.

Movie M2: Sample movie of the MD simulation (run 2) of LamR in the 0-100 ns range. The protein structure is represented as a dark-grey cartoon. The flexible loop encompassing residues 187-198 is coloured in red; peptide G is in orange and the C-terminal helix is coloured in green. The K11, E192, and R184 side-chains are represented as green sticks. The W176 and V197 forming the hydrogen bond are represented as sticks and coloured according to atom types. Hot spot residues (see text) are represented as blue sticks.