Backbone Modification in a Protein Hydrophobic Core

Targeted protein backbone modification can recreate tertiary structures reminiscent of folds found in nature on artificial scaffolds with improved biostability. Incorporation of altered monomers in such entities is typically limited to sites distant from the hydrophobic core to avoid potential disruptions to folding. This is limiting, as it is advantageous in some applications to incorporate artificial connectivity at buried sites. Here, we report an examination of protein backbone modification targeted specifically to hydrophobic core positions and its impacts on tertiary folded structure and fold stability. Different artificial monomer types are placed at core, core-flanking, or solvent-exposed positions in a compact three-helix protein. Effects on structure and folding energetics are assessed by NMR spectroscopy and biophysical methods. Results show that artificial residues can be well accommodated in the hydrophobic core of a defined tertiary fold, with effects on stability only modestly larger than identical changes at solvent-exposed sites. Collectively, these results provide new insights into folding behavior of protein-like artificial chains as well as strategies for the design of such molecules.

Toward Artificial Mussel-Glue Proteins: Differentiating Sequence Modules for Adhesion and Switchable Cohesion

Artificial mussel-glue proteins with pH-triggered cohesion control were synthesized by extending the tyrosinase activated polymerization of peptides to sequences with specific modules for cohesion control. The high propensity of these sequence sections to adopt β-sheets is suppressed by switch defects. This allows enzymatic activation and polymerization to proceed undisturbed. The β-sheet formation is regained after polymerization by changing the pH from 5.5 to 6.8, thereby triggering O→N acyl transfer rearrangements that activate the cohesion mechanism. The resulting artificial mussel glue proteins exhibit rapid adsorption on alumina surfaces. The coatings resist harsh hypersaline conditions, and reach remarkable adhesive energies of 2.64 mJ m-2 on silica at pH 6.8. In in situ switch experiments, the minor pH change increases the adhesive properties of a coating by 300 % and nanoindentation confirms the cohesion mechanism to improve bulk stiffness by around 200 %.

A proposed treatment for pathogenic enveloped viruses having high rates of mutation or replication

Several enveloped viruses, particularly some RNA viruses, have high rates of mutation or replication, which can make them virulent pathogens in humans and other mammals. A proposed treatment could use synthesized proteins to mask pathogenic viral surface proteins to quickly induce an immune attack on specific enveloped viruses by using existing immune cells. One treatment could inject dual‐protein ligand masks into patients' bloodstreams to mask pathogenic surface proteins used to infect mammalian cells. The mammalian immune system already uses an analogous, more complex structure called a pentraxin to neutralize some pathogens by connecting their surface proteins to immune cells. And several types of antiviral peptides have already experimentally demonstrated effectiveness in blocking various viral pathogen infections. These treatments offer advantages, especially for currently untreatable viral pathogens. Furthermore, using dual‐protein ligands and the antigenic memory of some sub‐populations of NK cells would also allow the creation of defacto vaccines based on a host's NK cells, instead of vaccines utilizing CD4 and CD8 α:β T cells, which are limited by the requirement of MHC presentation of the target antigens to α:β T cells. Targeted NK cell vaccines could attack host cells latently or actively infected by intracellular pathogens, even host cells having pathogen downregulated MHC antigen presentation. Eight postulates concerning the effects of pathogen mutation, or change in phenotype from genetic recombination or rearrangement, and replication rates on pathogen vs host dominance are also listed, which should be applicable to viral and non‐viral pathogens.

Synthetic biology and therapeutic strategies for the degenerating brain: Synthetic biology approaches can transform classical cell and gene therapies, to provide new cures for neurodegenerative diseases

Synthetic biology is an emerging engineering discipline that attempts to design and rewire biological components, so as to achieve new functions in a robust and predictable manner. The new tools and strategies provided by synthetic biology have the potential to improve therapeutics for neurodegenerative diseases. In particular, synthetic biology will help design small molecules, proteins, gene networks, and vectors to target disease-related genes. Ultimately, new intelligent delivery systems will provide targeted and sustained therapeutic benefits. New treatments will arise from combining ‘protect and repair’ strategies: the use of drug treatments, the promotion of neurotrophic factor synthesis, and gene targeting. Going beyond RNAi and artificial transcription factors, site-specific genome modification is likely to play an increasing role, especially with newly available gene editing tools such as CRISPR/Cas9 systems. Taken together, these advances will help develop safe and long-term therapies for many brain diseases in human patients.

Single-chain self-folding of synthetic polymers induced by metal-ligand complexation

The controlled folding of a single polymer chain is for the first time realized by metal- complexation. α,ω-Bromine functional linear polymers are prepared via activators regenerated by electron transfer (ARGET) ATRP (M¯n,SEC = 5900 g mol(-1) , Đ = 1.07 and 12 000 g mol(-1) , Đ = 1.06) and the end groups of the polymers are subsequently converted to azide functionalities. A copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction is carried out in the presence of a novel triphenylphosphine ligand and the polymers to afford homotelechelic bis-triphenylphosphine polymeric-macroligands (MLs) (M¯n,SEC = 6600 g mol(-1) , Đ = 1.07, and 12 800 g mol(-1) , Đ = 1.06). Single-chain metal complexes (SCMCs) are formed in the presence of Pd(II) ions in highly diluted solution at ambient temperature. The results derived via (1) H and (31) P{(1) H} NMR experiments, SEC, and DLS unambiguously evidence the efficient formation of SCMCs via metal ligand complexation.

Synthetic biology and personalized medicine

Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task.

Preparing semisynthetic and fully synthetic histones h3 and h4 to modify the nucleosome core

The purpose of this chapter is to provide practical chemical ligation procedures to prepare histone proteins suitable for the reconstitution of nucleosomes with specific posttranslational modifications in the nucleosome core. Detailed methods are described for the efficient preparation of semisynthetic histones H3 and H4 with modifications near the C-terminus of the proteins by expressed protein ligation and desulfurization. Additionally, we present optimized protocols for solid phase peptide synthesis combined with sequential native chemical ligation to generate fully synthetic modified histone H3, here in the context of H3 lysine 56 acetylation (H3K56ac).