Molecular Dynamics Simulations of a Laminin and Elastin-Based Triblock Fusion Polypeptide | AIChE

Molecular Dynamics Simulations of a Laminin and Elastin-Based Triblock Fusion Polypeptide

Computer simulations offer unparalleled insight into microscopic phenomena, such as protein assembly. Simulations allow us to model complex molecular systems and provide a link between theory and experiment, as well as predictions to guide further experiments. Using molecular dynamics (MD) simulations, we are characterizing the structural and dynamical properties of an elastin-like fusion protein. Elastin-like polypeptide (ELP)-based biomaterials hold promise in the treatment of neurodegenerative diseases; for instance, the ability of ELP chains to self-assemble allows them to serve as scaffolds for tissue growth and regeneration1. This assembly behavior results from a reversible inverse temperature phase transition, wherein ELPs coacervate with increasing temperature2. ELP-based fusion proteins preserve this useful thermal response, and the phase transition temperature can be modified by adjusting protein sequence and amino acid composition3. We have designed a triblock system consisting of two ELP chains fused to the N- and C-termini, using a GVG linker, of the fifth globular domain of a key extracellular matrix protein known as laminin. Our ELP chains have a repeating (VPGXG)n sequence, where X denotes a guest residue and n denotes the number of pentapeptide repeats. We have begun simulating the triblock fusion protein using the ELP sequence (VPGKG)2(VPGLG)2(VPGIG)2(VPGKG)2. Our system was equilibrated for 10 ns (to 310 K) and underwent free dynamics for 200 ns. Our previous simulations of a diblock LG-ELP suggest that a temperature of 310 K promotes β-rich structure within the ELP chains4; our current results indicate formation of β-rich structure at 310 K in this triblock fusion protein, which is consistent with. The radius of gyration (Rg) also differs between the N-terminal and C-terminal ELP chains by 1 Å, and the Rg value for the N-terminal chain slightly increases following 150ns. Moreover, the number of inter-chain backbone contacts between the ELP chains remains constant at an average of 198 contacts per ns. Our data further indicates that the ELP chains interact intra-molecularly, with an average of nine hydrogen bonds forming in each of the N-terminal and C-terminal ELP regions. The information obtained from our analyses will guide ongoing computational and experimental studies of this protein design. Simulations of this ELP-LG-ELP system will both aid our understanding of ELP-based materials and elucidate the thermodynamic principles that govern the desired properties of various ELP-based materials.

[1] Zhang Y, Avery RK, Vallamjo-Martin Q, Assmann A, Vegh A, Memic A, Olsen BD, Annabi N, Khademhosseini A (2015) A Highly Elastic and Rapidly Crosslinkable Elastin-Like Polypeptide-Based Hydrogel for Biomedical Applications. Adv Funct Mater. 25:4814-4826.

[2] Tarakanova A, Huang W, Weiss AS, Kaplan DL, Buehler MJ (2017) Computational Smart Polymer Design based on Elastin Protein Mutability. Biomaterials 127:49-60.

[3] MacEwan SR, Chilkoti A (2010) Elastin-Like Polypeptides: Biomedical Applications of Tunable Biopolymers. Biopolymers 94:60–77.

[4] Tang J, McAnany C, Mura C, Lampe KJ (2016) Toward a Designable Extracellular Matrix: Molecular Dynamics Simulations of an Engineered Laminin-Mimetic, Elastin-Like Fusion Protein. Biomacromolecules 17:3222-3233.