Design of Peptides that Fold and Self-Assemble on Graphite

Abstract

The graphite–water interface provides a unique environment for polypeptides that generally favors ordered structures more than in solution. Therefore, systems consisting of designed peptides and graphitic carbon might serve as a convenient medium for controlled self-assembly of functional materials. Here, we computationally designed cyclic peptides that spontaneously fold into a β-sheet-like conformation at the graphite–water interface and self-assemble, and we subsequently observed evidence of such assembly by atomic force microscopy. Using a novel protocol, we screened nearly 2000 sequences, optimizing for formation of a unique folded conformation while discouraging unfolded or misfolded conformations. A head-to-tail cyclic peptide with the sequence GTGSGTGGPGGGCGTGTGSGPG showed the greatest apparent propensity to fold spontaneously, and this optimized sequence was selected for larger scale molecular dynamics simulations, rigorous free-energy calculations, and experimental validation. In simulations ranging from hundreds of nanoseconds to a few microseconds, we observed spontaneous folding of this peptide at the graphite–water interface under many different conditions, including multiple temperatures (295 and 370 K), with different initial orientations relative to the graphite surface, and using different molecular dynamics force fields (CHARMM and Amber). The thermodynamic stability of the folded conformation on graphite over a range of temperatures was verified by replica-exchange simulations and free-energy calculations. On the other hand, in free solution, the folded conformation was found to be unstable, unfolding in tens of picoseconds. Intermolecular hydrogen bonds promoted self-assembly of the folded peptides into linear arrangements where the peptide backbone exhibited a tendency to align along one of the six zigzag directions of the graphite basal plane. For the optimized peptide, atomic force microscopy revealed growth of single-molecule-thick linear patterns of 6-fold symmetry, consistent with the simulations, while no such patterns were observed for a control peptide with the same amino acid composition but a scrambled sequence.

Molecular Scale Structure and Kinetics of Layer-by-Layer Peptide Self-Organization at Atomically Flat Solid Surfaces

“…Furthermore, studying the inter-and intramolecular interactions is highly challenging as the key contributors to the self-organized nanostructures on surfaces. 6,18,19 The solid binding peptides, selected through directed evolution methodologies, [1][2][3][4]9 may provide a means to address these questions, as demonstrated by previous studies. Normally, the peptide is selected, from the pool of peptides with billions of different sequences, for its exclusive affinity to the relevant solid surface.…”

“…The structural and self-organization characteristics of these small biomolecules are largely unknown, and the structures formed are unpredictable, thereby, making the design of such self-organized molecular architectures currently impractical. One of the reasons for this unpredictability, until recently, has been due to the uncoupled nature of the peptide–solid systems studied so far, i.e., random peptide sequence used that assemble in solution and land on the surface, or self-organize, often by chance, on arbitrary solid surfaces. − More importantly, short peptides are labile and have intrinsically disordered structural folding patterns, which limits the prediction of their conformation characteristics and, therefore, their interaction with solid surfaces. Furthermore, studying the inter- and intramolecular interactions is highly challenging as the key contributors to the self-organized nanostructures on surfaces. ,, …”

An Electrochemistry and Computational Study at an Electrified Liquid–Liquid Interface for Studying Beta-Amyloid Aggregation

“…We note in passing that recent work [ 45 ] has indicated that even short peptides can require run lengths well in excess of 300 ns to fold. However, in the case of Aβ 1-42 , the structure transforms quickly and completely from the initial PDB secondary structure containing two α-helices (see Figure S3a , which was obtained as a 3D NMR structure in an apolar solution) to a β-sheet folded structure in SPC water.…”

Computational design of a cyclic peptide that inhibits the CTLA4 immune checkpoint

“…Before these simulations, we cyclized the peptides using a head-to-tail amide linkage, which can improve proteolytic and conformational stability. [23][24][25][26][27][28] We characterized the strength of binding by tracking the time that the peptide stayed bound during the simulation and estimated binding free energy using the MM-GBSA method. 49 While neither of these characterizations are rigorous, they provided an efficient means to eliminate unpromising candidates with a small investment of computer time.…”

“…23,25 Furthermore, crosslinks of various chemistries (referred to as "staples") can be used to cyclize peptides in ways never found in nature. 18,24 Cyclization also helps to stabilize the secondary structure of peptides [26][27][28] and can also improve binding affinity by reducing the entropy of the unbound state and therefore the entropy lost upon binding. 12,29,30 Computational protein design tools have matured over the last decade, enabling rational design of peptides with desired structure and function.…”