Engineered Evolution of Self-Assembling Solid Binding Peptides Towards Simplicity

Using directed-evolution we have select 12-15 amino-acid (AAs) sequences that interact specifically with inorganic solids. Such sequences are called Solid-Binding-Peptides (SBPs) and have been used as tiny enzymes for nanoparticle-synthesis (metals, ceramics, semiconductors), as well as molecular-linkers, erectors, and assemblers in a variety of biomedical/biotechnological applications. Some of the SBPs spontaneously self-assemble under specific ranges of temperature, pH and concentration in aqueous solutions, to form long-range ordered two-dimensional (2D) molecular-lattices on atomically-flat surfaces of gold, graphene, MoS₂, and other 2D solids. Due to the absence of ionic or covalent interactions, the SBPs form a soft-interface on the atomic solid lattice. The soft interface is not only surface-specific but also electronically coherent due to enantiomorphic specificity because of complex 3D dynamical interactions of the peptides with the surface and among themselves. Since such behavior is dependent on the peptides’ sequence and conformation, understanding the role of individual AAs in the sequence becomes important. Additionally, since directed-evolution techniques impose a bound on the sequence’s length, and since the experimental methods to tease out the effects of each AA are impractical, there is a need to computationally-design shorter peptides that preserve the function of their longer counterparts. Here we choose a self-organizing graphene-binding dodecapeptide, WT-GrBP5, and perform metadynamics simulation of it and all its single-positional alanine-mutants to calculate the conformational energy-landscape of their interaction with single-layer Graphene. By dropping amino-acids from the WT-GrBP5 whose sidechains did not contribute much to the energy-landscape of WT-GrBP5, we created 8-AA, 7-AA and 5-AA SBPs that also self-assembled on Graphene. The method developed in this work not only sheds light on the role of individual AAs on peptide function but also establishes a method to design shorter peptides for a variety of uses where longer proteins are not suitable such as fluorescent probes, vaccines, and bioelectronic interfaces.