No abstract

Protein engineering, chemical biology, and synthetic biology would benefit from toolkits of peptide and protein components that could be exchanged reliably between systems while maintaining their structural and functional integrity. Ideally, such components should be highly defined and predictable in all respects of sequence, structure, stability, interactions, and function. To establish one such toolkit, here we present a basis set of de novo designed α-helical coiled-coil peptides that adopt defined and well-characterized parallel dimeric, trimeric, and tetrameric states. The designs are based on sequence-to-structure relationships both from the literature and analysis of a database of known coiled-coil X-ray crystal structures. These give foreground sequences to specify the targeted oligomer state. A key feature of the design process is that sequence positions outside of these sites are considered non-essential for structural specificity; as such, they are referred to as the background, are kept non-descript, and are available for mutation as required later. Synthetic peptides were characterized in solution by circular-dichroism spectroscopy and analytical ultracentrifugation, and their structures were determined by X-ray crystallography. Intriguingly, a hitherto widely used empirical rule-of-thumb for coiled-coil dimer specification does not hold in the designed system. However, the desired oligomeric state is achieved by database-informed redesign of that particular foreground and confirmed experimentally. We envisage that the basis set will be of use in directing and controlling protein assembly, with potential applications in chemical and synthetic biology. To help with such endeavors, we introduce Pcomp, an on-line registry of peptide components for protein-design and synthetic-biology applications.

There are several approaches to creating synthetic-biological systems. Here, we describe a molecular-design approach. First, we lay out a possible synthetic-biology space, which we define with a plot of complexity of components versus divergence from nature. In this scheme, there are basic units, which range from natural amino acids to totally synthetic small molecules. These are linked together to form programmable tectons, for example, amphipathic alpha-helices. In turn, tectons can interact to give self-assembled units, which can combine and organize further to produce functional assemblies and systems. To illustrate one path through this vast landscape, we focus on protein engineering and design. We describe how, for certain protein-folding motifs, polypeptide chains can be instructed to fold. These folds can be combined to give structured complexes, and function can be incorporated through computational design. Finally, we describe how protein-based systems may be encapsulated to control and investigate their functions.

The protein beta-lactoglobulin (BLG) has been widely studied, in large part because of its importance to the food industry. Following denaturation during heating, under different conditions of pH it has been found to form either particulate (around the isoelectric point at pH 5.1) or fibrillar gels. The nature of the fibrils has recently been suggested to be the same as that identified with amyloid fibrils known for a wide-range of different proteins and implicated in many disease states. We confirm that the BLG fibrils show all the classical signatures of amyloid fibrils. In addition, the fibrils are capable themselves of aggregating further to form large-scale (many microns in size) spherulites. Polarized light microscopy and Environmental scanning electron microscopy (ESEM) have been used to explore the internal structure of these spherulites under conditions in which the solvent has not been dried off. The factors which determine whether or not the spherulites form have also been considered, together with implications for other amyloid-containing systems.

Small, apolar aromatic groups, such as phenyl rings, are commonly included in the structures of fluorophores to impart hindered intramolecular rotations, leading to desirable solid-state luminescence properties. However, they are not normally considered to take part in through-space interactions that influence the fluorescent output. Here, we report on the photoluminescence properties of a series of phenyl-ring molecular rotors bearing three, five, six, and seven phenyl groups. The fluorescent emissions from two of the rotors are found to originate, not from the localized excited state as one might expect, but from unanticipated through-space aromatic-dimer states. We demonstrate that these relaxed dimer states can form as a result of intra- or intermolecular interactions across a range of environments in solution and solid samples, including conditions that promote aggregation-induced emission. Computational modeling also suggests that the formation of aromatic-dimer excited states may account for the photophysical properties of a previously reported luminogen. These results imply, therefore, that this is a general phenomenon that should be taken into account when designing and interpreting the fluorescent outputs of luminescent probes and optoelectronic devices based on fluorescent molecular rotors.

We report the proteomes of four life cycle stages of the Apicomplexan parasite Eimeria tenella. A total of 1868 proteins were identified, with 630, 699, 845 and 1532 found in early oocysts (unsporulated), late oocysts (sporulated), sporozoites and second-generation merozoites, respectively. A MudPIT shotgun approach identified 812 sporozoite, 1528 merozoite and all of the oocyst proteins, whereas 2D gel proteomics identified 230 sporozoite and 98 merozoite proteins. Comparing the invasive stages, we find moving junction components RON2 in both, whilst AMA-1 and RON4 are found only in merozoites and AMA-2 and RON5 are only found in sporozoites, suggesting stage specific moving junction proteins. During early oocyst to sporozoite development, refractile body and most ‘glideosome’ proteins are found throughout, whilst microneme and most rhoptry proteins are only found after sporulation. Quantitative analysis indicates glycolysis and gluconeogenesis are the most abundant metabolic groups detected in all stages. The mannitol cycle ‘off shoot’ of glycolysis was not detected in merozoites but was well represented in the other stages. However, in merozoites we find more protein associated with oxidative phosphorylation, suggesting a metabolic shift mobilising greater energy production. We find a greater abundance of protein linked to transcription, protein synthesis and cell cycle in merozoites than in sporozoites, which may be residual protein from the preceding massive replication during schizogony.

The formation of amyloid-containing spherulite-like structures has been observed in some instances of amyloid diseases, as well as in amyloid fibril-containing solutions in vitro. In this article we describe the structure and kinetics of bovine insulin amyloid fibril spherulites formed in the presence and absence of different salts and at different salt concentrations. The general spherulite structure consists of radially oriented amyloid fibrils, as shown by optical microscopy and environmental scanning electron microscopy. In the center of each spherulite, a "core" of less regularly oriented material is observed, whose size decreases when the spherulites are formed in the presence of increasing concentrations of NaCl. Similarly, amyloid fibrils form faster in the presence of NaCl than in its absence. A smaller enhancement of the rate of formation with salt concentration is observed for spherulites. These data suggest that both amyloid fibril formation and random aggregation occur concurrently under the conditions tested. Changes in their relative rates result in the different-sized cores observed in the spherulites. This mechanism can be likened to that leading to the formation of spherulites of polyethylene, in agreement with observations that polypeptide chains under partially denaturing conditions can exhibit behavior not dissimilar to that of synthetic polymers.

Background: Although the genomes of many of the most important human and animal pathogens have now been sequenced, our understanding of the actual proteins expressed by these genomes and how well they predict protein sequence and expression is still deficient. We have used three complementary approaches (two-dimensional electrophoresis, gel-liquid chromatography linked tandem mass spectrometry and MudPIT) to analyze the proteome of Toxoplasma gondii, a parasite of medical and veterinary significance, and have developed a public repository for these data within ToxoDB, making for the first time proteomics data an integral part of this key genome resource.