Frits A. de Wolf

High-yield secretion of recombinant gelatins by Pichia pastoris.

Recombinant non‐hydroxylated gelatins based on mouse type I and rat type III collagen sequences were secreted from the methylotrophic yeast Pichia pastoris, using the Saccharomyces cerevisiae α‐mating factor prepro signal. Proteolytic degradation could be minimized to a large extent by performing fermentations at pH 3·0 and by adding casamino acids to the medium, even though gelatin is extremely susceptible to proteolysis due to its open, unfolded structure. Proteolytic cleavage at specific mono‐arginylic sites, by a putative Kex2‐like protease, could be successfully abolished by site‐directed mutagenesis of these sites. Production levels as high as 14·8 g/l clarified both were obtained, using multicopy tranformants. To our knowledge, this represents the highest level of heterologous protein secretion reported to date for P. pastoris. Copyright

One-step photochemical attachment of NHS-terminated monolayers onto silicon surfaces and subsequent functionalization.

N-Hydroxysuccinimide (NHS)-ester-terminated monolayers were covalently attached in one step onto silicon using visible light. This mild photochemical attachment, starting from omega-NHS-functionalized 1-alkenes, yields a clean and flat monolayer-modified silicon surface and allows a mild and rapid functionalization of the surface by substitution of the NHS-ester moieties with amines at room temperature. Using a combination of analytical techniques (infrared reflection absorption spectroscopy (IRRAS), extensive X-ray photoelectron spectroscopy (XPS) in combination with density functional theory calculations of the XPS chemical shifts of the carbon atoms, atomic force microscopy (AFM), and static contact angle measurements), it was shown that the NHS-ester groups were attached fully intact onto the surface. The surface reactivity of the NHS-ester moieties toward amines was qualitatively and quantitatively evaluated via the reaction with para-trifluoromethyl benzylamine and biotin hydrazide.

Design and self-assembly of simple coat proteins for artificial viruses

Viruses are among the simplest biological systems and are highly effective vehicles for the delivery of genetic material into susceptible host cells. Artificial viruses can be used as model systems for providing insights into natural viruses and can be considered a testing ground for developing artificial life. Moreover, they are used in biomedical and biotechnological applications, such as targeted delivery of nucleic acids for gene therapy and as scaffolds in material science. In a natural setting, survival of viruses requires that a significant fraction of the replicated genomes be completely protected by coat proteins. Complete protection of the genome is ensured by a highly cooperative supramolecular process between the coat proteins and the nucleic acids, which is based on reversible, weak and allosteric interactions only. However, incorporating this type of supramolecular cooperativity into artificial viruses remains challenging. Here, we report a rational design for a self-assembling minimal viral coat protein based on simple polypeptide domains. Our coat protein features precise control over the cooperativity of its self-assembly with single DNA molecules to finally form rod-shaped virus-like particles. We confirm the validity of our design principles by showing that the kinetics of self-assembly of our virus-like particles follows a previous model developed for tobacco mosaic virus. We show that our virus-like particles protect DNA against enzymatic degradation and transfect cells with considerable efficiency, making them promising delivery vehicles.

Precision gels from collagen-inspired triblock copolymers.

Gelatin hydrogels find broad medical application. The current materials, however, are from animal sources, and their molecular structure and thermal properties cannot be controlled. This study describes recombinant gelatin-like polymers with a general design that inherently offers independent tuning of the cross-link density, melting temperature, and biocompatibility of the gel. The polymers contain small blocks with thermoreversible trimerization capacity and defined melting temperature, separated by hydrophilic nontrimerizing blocks defining the distance between the knot-forming domains. As an example, we report the secreted production in yeast at several g/L of two nonhydroxylated approximately 42 kDa triblock copolymers with terminal trimerizing blocks. Because only the end blocks formed cross-links, the molecular architecture of the gels is much more defined than that of traditional gelatins. The novel hydrogels had a approximately 37 degrees C melting temperature, and the dynamic elasticity was independent of the thermal history. The concept allows to produce custom-made precision gels for biomedical applications.

Physical gels of telechelic triblock copolymers with precisely defined junction multiplicity

We study transient networks formed by monodisperse telechelic polypeptides with collagen-like end blocks and a random-coil-like middle block. These artificial proteins are created using recombinant DNA techniques. Upon cooling, the end blocks associate reversibly into triple helices, leading to gels with a well-defined junction multiplicity of three. Both the storage modulus and the relaxation time of the gel increase very strongly as a function of concentration, and decrease with increasing temperature. All the experimental results are described quantitatively by an analytical model, based on classical gel theory, that requires no adjustable parameters, and accounts for the molecular structure of the gel, and the presence of loops and dangling ends.

Reduced proteolysis of secreted gelatin and Yps1-mediated alpha-factor leader processing in a Pichia pastoris kex2 disruptant.

ABSTRACT Heterologous proteins secreted by yeast and fungal expression hosts are occasionally degraded at basic amino acids. We cloned Pichia pastoris homologs of the Saccharomyces cerevisiae basic residue-specific endoproteases Kex2 and Yps1 to evaluate their involvement in the degradation of a secreted mammalian gelatin. Disruption of the P. pastoris KEX2 gene prevented proteolysis of the foreign protein at specific monoarginylic sites. The S. cerevisiae α-factor preproleader used to direct high-level gelatin secretion was correctly processed at its dibasic site in the absence of the prototypical proprotein convertase Kex2. Disruption of the YPS1 gene had no effect on gelatin degradation or processing of the α-factor propeptide. When both the KEX2 and YPS1 genes were disrupted, correct precursor maturation no longer occurred. The different substrate specificities of both proteases and their mutual redundancy for propeptide processing indicate that P. pastoris kex2 and yps1 single-gene disruptants can be used for the α-factor leader-directed secretion of heterologous proteins otherwise degraded at basic residues.

“Clickable” elastins: elastin-like polypeptides functionalized with azide or alkyne groups

Elastin-like polypeptides (ELPs) functionalized with azide or alkyne groups were produced biosynthetically and coupled via the Cu-catalyzed azide-alkyne cycloaddition to a variety of (bio)molecules.

Coating of single DNA molecules by genetically engineered protein diblock copolymers.

Coating DNA is an effective way to modulate its physical properties and interactions. Current chemosynthetic polymers form DNA aggregates with random size and shape. In this study, monodisperse protein diblock copolymers are produced at high yield in recombinant yeast. They carry a large hydrophilic colloidal block (≈400 amino acids) linked to a short binding block (≈12 basic amino acids). It is demonstrated that these protein polymers complex single DNA molecules as highly stable nanorods, reminiscent of cylindrical viruses. It is proposed that inter- and intramolecular bridging of DNA molecules are prevented completely by the small size of the binding block attached to the large colloidal stability block. These protein diblocks serve as a scaffold that can be tuned for application in DNA-based nanotechnology.

From micelles to fibers: balancing self-assembling and random coiling domains in pH-responsive silk-collagen-like protein-based polymers

We study the self-assembly of genetically engineered protein-based triblock copolymers consisting of a central pH-responsive silk-like middle block (SHn, where SH is a silk-like octapeptide, (GA)3GH and n is the number of repeats) flanked by hydrophilic random coil outer blocks (C2). Our previous work has already shown that triblocks with very long midblocks (n = 48) self-assemble into long, stiff protein filaments at pH values where the middle blocks are uncharged. Here we investigate the self-assembly behavior of the triblock copolymers for a range of midblock lengths, n = 8, 16, 24, 48. Upon charge neutralization of SHn by adjusting the pH, we find that C2SH8C2 and C2SH16C2 form spherical micelles, whereas both C2SH24C2 and C2SH48C2 form protein filaments with a characteristic beta-roll secondary structure of the silk midblocks. Hydrogels formed by C2SH48C2 are much stronger and form much faster than those formed by C2SH24C2. Enzymatic digestion of much of the hydrophilic outer blocks is used to show that with much of the hydrophilic outer blocks removed, all silk-midblocks are capable of self-assembling into stiff protein filaments. In that case, reduction of the steric repulsion by the hydrophilic outer blocks also leads to extensive fiber bundling. Our results highlight the opposing roles of the hydrophilic outer blocks and central silk-like midblocks in driving protein filament formation. They provide crucial information for future designs of triblock protein-based polymers that form stiff filaments with controlled bundling, that could mimick properties of collagen in the extracellular matrix.

Polypeptide nanoribbon hydrogels assembled through multiple supramolecular interactions

We investigated the formation of nanoribbon hydrogels in a mixed system of zinc ions, bis(ligand)s, and triblock peptide copolymers. Using a combination of experimental techniques: dynamic light scattering, cryo-transmission electron microscopy, small-angle X-ray scattering and circular dichroism, we arrived at a model for the formation of nanoribbon hydrogels in which well-defined nanoribbons are formed out of multiple supramolecular interactions: (1) metal coordination that yields supramolecular polyelectrolytes; (2) electrostatic complexation between the supramolecular polyelectrolytes and the oppositely charged blocks of the peptide copolymers; (3) hydrogen bond and (4) hydrophobic interactions that support the secondary and ternary structure of the ribbons; (5) van der Waals interactions that enable bundling of the ribbons.