Controlled assembly of artificial protein-protein complexes via DNA duplex formation.

DNA-protein conjugates have found a wide range of applications. This study demonstrates the formation of defined, non-native protein-protein complexes via the site specific labeling of two proteins of interest with complementary strands of single-stranded DNA in vitro. This study demonstrates that the affinity of two DNA-protein conjugates for one another may be tuned by the use of variable lengths of DNA allowing reversible control of complex formation.

Nanoparticle-induced folding and fibril formation of coiled-coil-based model peptides.

Nanomedicine is a rapidly growing field that has the potential to deliver treatments for many illnesses. However, relatively little is known about the biological risks of nanoparticles. Some studies have shown that nanoparticles can have an impact on the aggregation properties of proteins, including fibril formation. Moreover, these studies also show that the capacity of nanoscale objects to induce or prevent misfolding of the proteins strongly depends on the primary structure of the protein. Herein, light is shed on the role of the peptide primary structure in directing nanoparticle-induced misfolding by means of two model peptides. The design of these peptides is based on the alpha-helical coiled-coil folding motif, but also includes features that enable them to respond to pH changes, thus allowing pH-dependent beta-sheet formation. Previous studies showed that the two peptides differ in the pH range required for beta-sheet folding. Time-dependent circular dichroism spectroscopy and transmission electron microscopy are used to characterize peptide folding and aggregate morphology in the presence of negatively charged gold nanoparticles (AuNPs). Both peptides are found to undergo nanoparticle-induced fibril formation. The determination of binding parameters by isothermal titration calorimetry further reveals that the different propensities of both peptides to form amyloid-like structures in the presence of AuNPs is primarily due to the binding stoichiometry to the AuNPs. Modification of one of the peptide sequences shows that AuNP-induced beta-sheet formation is related to the structural propensity of the primary structure and is not a generic feature of peptide sequences with a sufficiently high binding stoichiometry to the nanoparticles.

Towards understanding secondary structure transitions: phosphorylation and metal coordination in model peptides.

Secondary structure transitions are important modulators of signal transduction and protein aggregation. Phosphorylation is a well known post-translational modification capable of dramatic alteration of protein secondary structure. Additionally, phosphorylated residues can induce structural changes through metal binding. Data derived from the Protein Data Bank demonstrate that magnesium and manganese are metal ions most favored by phosphate. Due to the complexity of molecular interactions as well as the challenging physicochemical properties of natural systems, simplified peptide models have emerged as a useful tool for investigating the molecular switching phenomenon. In this study using a coiled coil model peptide, we show structural consequences of phosphorylation and subsequent magnesium and manganese ions coordination. In the course of our experiment we obtained a switch cascade starting from a stable helical conformation of the control peptide, continuing through the phosphorylation-induced unfolded structure, and ending with a metal-stabilized alpha-helix (Mg(2+)) or helical fibers (Mn(2+)), each of which could be transferred back to the unfolded form upon EDTA chelation. This study demonstrates how small peptide models can aid in the evaluation and a better understanding of protein secondary structure transitions.

How post-translational modifications influence amyloid formation: a systematic study of phosphorylation and glycosylation in model peptides.

A reciprocal relationship between phosphorylation and O-glycosylation has been reported for many cellular processes and human diseases. The accumulated evidence points to the significant role these post-translational modifications play in aggregation and fibril formation. Simplified peptide model systems provide a means for investigating the molecular changes associated with protein aggregation. In this study, by using an amyloid-forming model peptide, we show that phosphorylation and glycosylation can affect folding and aggregation kinetics differently. Incorporation of phosphoserines, regardless of their quantity and position, turned out to be most efficient in preventing amyloid formation, whereas O-glycosylation has a more subtle effect. The introduction of a single beta-galactose does not change the folding behavior of the model peptide, but does alter the aggregation kinetics in a site-specific manner. The presence of multiple galactose residues has an effect similar to that of phosphorylation.

Enzymatically triggered amyloid formation: an approach for studying peptide aggregation.

A strategy has been demonstrated that utilizes a phosphatase as a natural tool for the triggering and control of amyloid formation in a coiled coil peptide model under conditions that closely approximate a physiological environment.

Switchable electrostatic interactions between gold nanoparticles and coiled coil peptides direct colloid assembly.

The nanoparticle-peptide interaction described here is based on electrostatic forces and the pH value can act as a trigger to direct the organization of functionalized nanoparticles in a reversible and repeatable manner. The ability of the peptide to interact with the charged gold nanoparticles is directly related to its helical structure and was not found for a random coil peptide with the same net charge. Interestingly, the interaction with nanoparticles seems to induce a fibrillation of the coiled coil peptide.

Intramolecular charge interactions as a tool to control the coiled-coil-to-amyloid transformation.

Under the influence of a changed environment, amyloid-forming proteins partially unfold and assemble into insoluble beta-sheet rich fibrils. Molecular-level characterization of these assembly processes has been proven to be very challenging, and for this reason several simplified model systems have been developed over recent years. Herein, we present a series of three de novo designed model peptides that adopt different conformations and aggregate morphologies depending on concentration, pH value, and ionic strength. The design strictly follows the characteristic heptad repeat of the alpha-helical coiled-coil structural motif. In all peptides, three valine residues, known to prefer the beta-sheet conformation, have been incorporated at the solvent-exposed b, c, and f positions to make the system prone to amyloid formation. Additionally, pH-controllable intramolecular electrostatic repulsions between equally charged lysine (peptide A) or glutamate (peptide B) residues were introduced along one side of the helical cylinder. The conformational behavior was monitored by circular dichroism spectroscopic analysis and thioflavin T fluorescence, and the resulting aggregates were further characterized by transmission electron microscopy. Whereas uninterrupted alpha-helical aggregates are found at neutral pH, Coulomb repulsions between lysine residues in peptide A destabilize the helical conformation at acidic pH values and trigger an assembly into amyloid-like fibrils. Peptide B features a glutamate-based switch functionality and exhibits opposite pH-dependent folding behavior. In this case, alpha-helical aggregates are found under acidic conditions, whereas amyloids are formed at neutral pH. To further validate the pH switch concept, peptide C was designed by including serine residues, thus resulting in an equal distribution of charged residues. Surprisingly, amyloid formation is observed at all pH values investigated for peptide C. The results of further investigations into the effect of different salts, however, strongly support the crucial role of intramolecular charge repulsions in the model system presented herein.

Random coils, beta-sheet ribbons, and alpha-helical fibers: one peptide adopting three different secondary structures at will.

To potentially cure neurodegenerative diseases, we need to understand on a molecular level what triggers the complex folding mechanisms and shifts the equilibrium from functional to pathological isoforms of proteins. The development of small peptide models that can serve as tools for such studies is of paramount importance. We describe the de novo design and characterization of an alpha-helical coiled coil based model peptide that contains structural elements of both alpha-helical folding and beta-sheet formation. Three distinct secondary structures can be induced at will by adjustment of pH or concentration. Low concentrations at pH 4.0 yield globular particles of the unfolded peptide, while at the same pH, but at higher concentration, defined beta-sheet ribbons are formed. In contrast, at high concentrations and pH 7.4, the peptide forms highly ordered alpha-helical fibers. Thus, this system allows one to systematically study now the consequences of the interplay between peptide and protein primary structure and environmental factors for peptide and protein folding on a molecular level.