Compositional Effects on the Configuration of Water-soluble Polypeptide Copolymers of L-Glutamic Acid and L-Lysine1

Recent Progress in Ionic Coassembly of Cationic Peptides and Anionic Species

Peptide assembly has been extensively exploited as a promising platform for the creation of hierarchical nanostructures and tailor-made bioactive materials. Ionic coassembly of cationic peptides and anionic species is paving the way to provide particularly important contribution to this topic. In this review, the recent progress of ionic coassembly soft materials derived from the electrostatic coupling between cationic peptides and anionic species in aqueous solution is systematically summarized. The presentation of this review starts from a brief background on the general importance and advantages of peptide-based ionic coassembly. After that, diverse combinations of cationic peptides with small anions, macro- and/or oligo-anions, anionic polymers, and inorganic polyoxometalates are described. Emphasis is placed on the hierarchical structures, value-added properties, and applications. The molecular design of cationic peptides and the general principles behind the ionic coassembled structures are discussed. It is summarized that the combination of interesting and unique characteristics that arise both from the chemical diversity of peptides and the wide range of anionic species may contribute in a variety of output, including drug delivery, tissue engineering, gene transfection, and antibacterial activity. The emergent new phenomena and findings are illustrated. Finally, the outlook for the peptide-based ionic coassembly systems is also presented.

De novo protein design by citizen scientists

Online citizen science projects such as GalaxyZoo¹, Eyewire² and Phylo³ have been very successful for data collection, annotation, and processing, but for the most part have harnessed human pattern recognition skills rather than human creativity. An exception is the game EteRNA⁴, in which game players learn to build new RNA structures by exploring the discrete two-dimensional space of Watson-Crick base pairing possibilities. Building new proteins, however, is a more challenging task to present in a game, as both the representation and evaluation of a protein structure are intrinsically three-dimensional. We posed the challenge of de novo protein design in the online protein folding game Foldit⁵. Players were presented with a fully extended peptide chain and challenged to craft a folded protein structure with an amino acid sequence encoding that structure. After many iterations of player design, analysis of the top scoring solutions, and subsequent game improvement, Foldit players can now, starting from an extended polypeptide chain, generate a diversity of protein structures and sequences which encode them in silico. 146 Foldit player designs with sequences unrelated to naturally occurring proteins were encoded in synthetic genes; 56 were found to be expressed in E. coli with good solubility and to adopt stable monomeric folded structures in solution. The diversity of these structures is unprecedented in de novo protein design, representing 20 different folds—including a new fold not observed in natural proteins. High resolution structures were determined for four of the designs, and are nearly identical to the player models. This work makes explicit the considerable implicit knowledge contributing to success in de novo protein design, and shows that citizen scientists can discover creative new solutions to outstanding scientific challenges, such as the protein design problem.

Conformation-Directed Formation of Self-Healing Diblock Copolypeptide Hydrogels via Polyion Complexation

Synthetic diblock copolypeptides were designed to incorporate oppositely charged ionic segments that form β-sheet-structured hydrogel assemblies via polyion complexation when mixed in aqueous media. The observed chain conformation directed assembly was found to be required for efficient hydrogel formation and provided distinct and useful properties to these hydrogels, including self-healing after deformation, microporous architecture, and stability against dilution in aqueous media. While many promising self-assembled materials have been prepared using disordered or liquid coacervate polyion complex (PIC) assemblies, the use of ordered chain conformations in PIC assemblies to direct formation of new supramolecular morphologies is unprecedented. The promising attributes and unique features of the β-sheet-structured PIC hydrogels described here highlight the potential of harnessing conformational order derived from PIC assembly to create new supramolecular materials.

Polylysine-grafted Au144 nanoclusters: birth and growth of a healthy surface-plasmon-resonance-like band

Poly(amino acid)-coated gold nanoparticles hold promise in biomedical applications, particularly because they combine the unique physicochemical properties of the gold core, excellent biocompatibility, and easy functionalization of the poly(amino acid)-capping shell. Here we report a novel method for the preparation of robust hybrid core-shell nanosystems consisting of a Au144 cluster and a densely grafted polylysine layer. Linear polylysine chains were grown by direct N-carboxyanhydride (NCA) polymerization onto ligands capping the gold nanocluster. The density of the polylysine chains and the thickness of the polymer layer strongly depend on the amount and concentration of the NCA monomer and the initiator. The optical spectra of the so-obtained core-shell nanosystems show a strong surface plasmon resonance (SPR)-like band at 531 nm. In fact, despite maintenance of the gold cluster size and the absence of interparticle aggregation, the polylysine-capped clusters behave as if they have a diameter nearly 4 times larger. To the best of our knowledge, this is the first observation of the growth of a fully developed, very stable SPR-like band for a gold nanocluster of such dimensions. The robust polylysine protective shell makes the nanoparticles very stable under conditions of chemical etching, in the presence of glutathione, and at different pH values, without gold core deshielding or alteration of the SPR-like band. This polymerization method can conceivably be extended to prepare core-shell nanosystems based on other mono- or co-poly(amino acids).

Fine tuning of vesicle assembly and properties using dual hydrophilic triblock copolypeptides

The design, synthesis, and self-assembly of the first dual hydrophilic triblock copolypeptide vesicles, R(H)(m)E(n)L(o) and K(P)(m)R(H)(n)L(o), is reported. Variation of the two distinct hydrophilic domains is used to tune cellular interactions without disrupting the self-assembled structure. The aqueous self-assemblies of these triblock copolypeptides in water are characterized using microscopy and DLS. Cell culture studies are used to evaluate cytotoxicity as well as intracellular uptake of the vesicles. The ability of polypeptides to incorporate ordered chain conformations that direct self-assembly, combined with the facile preparation of functional, multiblock copolypeptide sequences of defined lengths, allow the design of vesicles attractive for development as drug carriers.

Large-scale models reveal the two-component mechanics of striated muscle

This paper provides a comprehensive explanation of striated muscle mechanics and contraction on the basis of filament rotations. Helical proteins, particularly the coiled-coils of tropomyosin, myosin and alpha-actinin, shorten their H-bonds cooperatively and produce torque and filament rotations when the Coulombic net-charge repulsion of their highly charged side-chains is diminished by interaction with ions. The classical "two-component model" of active muscle differentiated a "contractile component" which stretches the "series elastic component" during force production. The contractile components are the helically shaped thin filaments of muscle that shorten the sarcomeres by clockwise drilling into the myosin cross-bridges with torque decrease (= force-deficit). Muscle stretch means drawing out the thin filament helices off the cross-bridges under passive counterclockwise rotation with torque increase (= stretch activation). Since each thin filament is anchored by four elastic alpha-actinin Z-filaments (provided with force-regulating sites for Ca(2+) binding), the thin filament rotations change the torsional twist of the four Z-filaments as the "series elastic components". Large scale models simulate the changes of structure and force in the Z-band by the different Z-filament twisting stages A, B, C, D, E, F and G. Stage D corresponds to the isometric state. The basic phenomena of muscle physiology, i. e. latency relaxation, Fenn-effect, the force-velocity relation, the length-tension relation, unexplained energy, shortening heat, the Huxley-Simmons phases, etc. are explained and interpreted with the help of the model experiments.

From helix-coil transitions to protein folding

An evolution of procedures to simulate protein structure and folding pathways is described. From an initial focus on the helix-coil transition and on hydrogen-bonding and hydrophobic interactions, our original attempts to determine protein structure and folding pathways were based on an experimental approach. Experiments on the oxidative folding of reduced bovine pancreatic ribonuclease A (RNase A) led to a mechanism by which the molecule folded to the native structure by a minimum of four different pathways. The experiments with RNase A were followed by development of a molecular mechanics approach, first, making use of global optimization procedures and then with molecular dynamics (MD), evolving from an all-atom to a united-residue model. This hierarchical MD approach facilitated probing of the folding trajectory to longer time scales than with all-atom MD, and hence led to the determination of complete folding trajectories, thus far for a protein containing as many as 75 amino acid residues. With increasing refinement of the computational procedures, the computed results are coming closer to experimental observations, providing an understanding as to how physics directs the folding process.