Toward the development of peptide nanofilaments and nanoropes as smart materials

Toward the development of peptide nanofilaments and nanoropes as smart materials
July 13, 2005 (received for review February 28, 2005)
Published online before print August 29, 2005,
Daniel E. Wagner , Charles L. Phillips , Wasif M. Ali , Grant E. Nybakken , Emily D. Crawford , Alexander D. Schwab , Walter F. Smith , and Robert Fairman
PNAS | September 6, 2005
Departments of Biology and Physics, Haverford College, 370 Lancaster Avenue, Haverford, PA 19041
Communicated by William F. DeGrado, University of Pennsylvania School of Medicine, Philadelphia, PA
Protein design studies using coiled coils have illustrated the potential of engineering simple peptides to self-associate into polymers and networks. Although basic aspects of self-assembly in protein systems have been demonstrated, it remains a major challenge to create materials whose large-scale structures are well determined from design of local proteinÒprotein interactions. Here, we show the design and characterization of a helical peptide, which uses phased hydrophobic interactions to drive assembly into nanofilaments and fibrils ("nanoropes"). Using the hydrophobic effect to drive self-assembly circumvents problems of uncontrolled self-assembly seen in previous approaches that used electrostatics as a mode for self-assembly. The nanostructures designed here are characterized by biophysical methods including analytical ultracentrifugation, dynamic light scattering, and circular dichroism to measure their solution properties, and atomic force microscopy to study their behavior on surfaces. Additionally, the assembly of such structures can be predictably regulated by using various environmental factors, such as pH, salt, other molecular crowding reagents, and specifically designed "capping" peptides. This ability to regulate self-assembly is a critical feature in creating smart peptide biomaterials.
biomaterial | coiled coil | protein design | circular dichroism | atomic force microscopy
Designed proteins are valuable paradigms for engineering at the nanoscale, offering favorable properties such as atomic-level precision and tight regulation of self-assembly by using a variety of environmental cues (i.e., pH, ionic strength, temperature) (1Ò3). As one of the most well studied and naturally abundant structural motifs in proteins, coiled coils are particularly suited to protein design. Their basic sequence feature, the heptad repeat, is a seven-residue pattern (abcdefg)n of nonpolar and polar residues that gives rise to amphipathic -helices. The hydrophobic effect drives the burial of nonpolar residues at the helix-pairing interface and influences geometric details of resulting structures (4). Electrostatic and polar residues at buried or solvent-exposed locations provide additional means to manipulate structural features by stabilization or destabilization (negative design) of key interactions (5Ò8).
Recent attempts to design self-assembling protein networks by using coiled coils have focused on simple systems, such as linear and branched fibrils (9Ò14), planar assemblies (15), and hydrogels (16Ò18). Specifically, filament formation has been achieved by stabilization of intermediate structures that foster intermolecular coiled-coil interactions (11Ò14). Previous studies have reported the design of short helical peptides, which interact via a dimeric coiled-coil motif and are stabilized by a combination of overlapping hydrophobic and electrostatic intermolecular interactions (9, 13, 14). These peptides do indeed self-assemble into filaments; however, these filaments also show evidence of extensive lateral association, to form fibrils; problems with such aggregation continue to pose a major obstacle toward the formation of well controlled nanoscale structures (9, 14). Here, we present a dual-component design strategy for the engineering of self-assembling peptides, using hydrophobic interactions to favor axial assembly and electrostatic forces to regulate lateral assembly in the formation of nanoropes. Evidence for self-assembled polymers in solution is provided by analytical ultracentrifugation and dynamic light scattering (DLS) experiments. The solution studies are complemented by atomic force microscopy (AFM) imaging of polymers deposited on mica surfaces. Additionally, CD experiments demonstrate that our system also fulfills another tenet of nanoengineering: reversible regulation of self-assembly using a variety of mechanisms, such as solvent or temperature factors.
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