Toward a Designable Extracellular Matrix: Molecular Dynamics Simulations of an Engineered Laminin-Mimetic, Elastin-Like Fusion Protein

Native extracellular matrices (ECMs) exhibit networks of molecular interactions between specific matrix proteins and other tissue components. Guided by these naturally self-assembling supramolecular systems, we have designed a matrix-derived protein chimera that contains a laminin globular-like (LG) domain fused to an elastin-like polypeptide (ELP). This bipartite design offers a flexible protein engineering platform: (i) laminin is a key multifunctional component of the ECM in human brains and other neural tissues, making it an ideal bioactive component of our fusion, and (ii) ELPs, known to be well-tolerated in vivo, provide a self-assembly scaffold with tunable physicochemical (viscoelastic, thermoresponsive) properties. Experimental characterization of novel proteins is resource-intensive, and examining many conceivable designs would be a formidable challenge in the laboratory. Computational approaches offer a way forward: molecular dynamics (MD) simulations can be used to analyze the structural/physical behavior of candidate LG-ELP fusion proteins, particularly in terms of conformational properties salient to our design goals, such as assembly propensity in a temperature range spanning the inverse temperature transition. As a first step in examining the physical characteristics of a model LG-ELP fusion protein, including its temperature-dependent structural behavior, we simulated the protein over a range of physiologically relevant temperatures (290–320 K). We find that the ELP region, built upon the archetypal (VPGXG)₅ scaffold, is quite flexible and has a propensity for β-rich secondary structures near physiological (310–315 K) temperatures. Our trajectories indicate that the temperature-dependent burial of hydrophobic patches in the ELP region, coupled to the local water structure dynamics and mediated by intramolecular contacts between aliphatic side chains, correlates with the temperature-dependent structural transitions in known ELP polymers. Because of the link between compaction of ELP segments into β-rich structures and differential solvation properties of this region, we posit that future variation of ELP sequence and composition can be used to systematically alter the phase transition profiles and, thus, the general functionality of our LG-ELP fusion protein system.