(715a) Biomaterial Properties of Aggregating Tripeptides Designed Using a De Novo Multimeric Protein Design Framework
Computational protein design has had great success in the development of novel therapeutics, novel protein folds, and protein-based biomaterials. Much of this design has focused on the design of protein tertiary structure, but as computing power improves it becomes increasingly possible to shift this focus to the quaternary structure of protein complexes. In nature any number of identical or non-identical proteins can self-assemble into ordered (amyloid) or disordered (hydrogel) complexes. Biologically these complexes can be either essential or disrupting to cell function. Additionally, they have application in the design of self-assembling biomaterial. There has been much effort in the design of protein-protein interfaces, which is generally restricted to the design of a single monomer in a multimeric complex [1-9]. Recently, we have developed a novel de novo design method capable of designing for multimeric peptides/proteins simultaneously. This method has been applied to the design of aggregating peptides with success and we present the designed peptides and the properties of the resulting designed hydrogel and crystal structures.
The novel protein design method involves three stages and is capable of improving the aggregation affinity of a multimeric system. The first stage is a Mixed Integer Linear Optimization model [10-12] Sequence Selection stage capable of designing multiple identical or non-identical protein chains simultaneously. A flexible template structure for the protein complex is initially determined through Molecular Dynamics (MD) simulations. The potential energy of the system is minimized to generate a rank-ordered list of designed peptide sequences. The second stage calculates the Fold Specificity of each designed sequence for the flexible aggregation template. The third stage employs MD simulations in CHARMM  to predict the assembly of multiple peptides into a macromolecular structure. From these MD generated structure ensembles, we calculate approximate molecular partition functions of the structures, which are used to calculate an approximate aggregation affinity of the designed proteins . This approximate aggregation affinity is used as a matric in choosing the peptides that will be tested experimentally.
The work detailed in the presentation shows the application of the novel Multimeric Protein Design method to the design of aggregating peptide systems. Experimental validation of the designed aggregating tripeptides has been carried out successfully and demonstrates aggregation into hydrogel and crystal structures. Several of the hydrogel aggregating peptides demonstrate higher stability, aggregation rate, and storage moduli than the template tripeptide. Additionally, one of the designed peptides demonstrates rapid self-assembly into large crystals that lend themselves well to crystallographic analysis. The biomaterial properties of the designed peptides provide important information for the understanding of which properties control peptide hydrogel aggregation and crystallization.
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