Advances in the design and engineering of peptide-binding repeat proteins

The specific recognition of peptides, which we define to include unstructured regions or denatured forms of proteins, is an intrinsic part of a multitude of biochemical assays and procedures. Many cellular interactions are also based on this principle as well. While it would be highly desirable to have a stockpile of sequence-specific binders for essentially any sequence, a de novo selection of individual binders against every possible target peptide sequence would be rather difficult to reduce to practice. Modular peptide binders could overcome this problem, as preselected and/or predesigned modules could be reused for the generation of new binders and thereby revolutionize the generation of binding proteins. This minireview summarizes advances in the development of peptide binders and possible scaffolds for their design

Improving in vivo folding and stability of a single-chain Fv antibody fragment by loop grafting

The complementary determining regions (CDRs) from the fluorescein-binding antibody 4-4-20, which yields almost no soluble protein in periplasmic expression in Escherichia coli, were transplanted to the framework of the humanized antibody 4D5. The resulting single-chain Fv fragment (scFv) 4D5Flu showed both a dramatic improvement in soluble expression, even at 37 degrees C, and an improved thermodynamic stability. Antigen affinity was maintained upon this engineering by paying attention to crucial framework-CDR contacts. This demonstrates that the use of superior frameworks is a robust strategy to improve the physical properties of scFv fragments. We also report that the grafted version was selected in phage display over several competing variants of the same antibody with identical binding constant but poorer folding or stability properties. The selection required four panning rounds and a temperature of 37 degrees C and we show that the underlying reason for this selection is a higher fraction of phages carrying functional scFv molecule

Engineered turns of a recombinant antibody improve its in vivo folding

Using recombinant antibodies functionally expressed by secretion to the periplasm in Escherichia coli as a model system, we identified mutations located in turns of the protein which reduce the formation of aggregates during in vivo folding or which influence cell stability during expression. Unexpectedly, the two effects are based on different mutations and could be separated, but both mutations act synergistically in vivo. Neither mutation increases the thermodynamic stability in vitro. However, the in vivo folding mutation correlates with the yield of oxidative folding in vitro, which is limited by the side reaction of aggregation. The in vivo folding data also correlate with the rate and activation entropy of thermally induced aggregation. This analysis shows that it is possible to engineer improved frameworks for semi-synthetic antibody libraries which may be important in maintaining library diversity. Moreover, limitations in recombinant protein expression can be overcome by single amino acid substitution

Strategies for Selection from Protein Libraries Composed of de Novo Designed Secondary Structure Modules

As more and more protein structures are determined, it has become clear that there is only a limited number of protein folds in nature. To explore whether the protein folds found in nature are the only solutions to the protein folding problem, or that a lack of evolutionary pressure causes the paucity of different protein folds found, we set out to construct protein libraries without any restriction on topology. We generated different libraries (all α-helix, all β-strand and α-helix plus β-strand) with an average length of 100 amino acid residues, composed of designed secondary structure modules (α-helix, β-strand and β-turn) in various proportions, based primarily on the patterning of polar and non-polar residues. From the analysis of proteins chosen randomly from the libraries, we found that a substantial portion of pure α-helical proteins show properties similar to native proteins.Using these libraries as a starting point, we aim to establish a selection system which allows us to enrich proteins with favorable folding properties (non-aggregating, compactly folded) from the libraries. We have developed such a method based on ribosome display. This selection is based on two concepts: (1) misfolded proteins are more sensitive to proteolysis, (2) misfolded and/or aggregated proteins are more hydrophobic. We show that by applying each of these selection criteria proteins that are compactly folded and soluble can be enriched over insoluble and random coil protein

Transfer of engineered biophysical properties between different antibody formats and expression systems

Recombinant antibodies and their derivatives are receiving ever increasing attention for many applications. Nevertheless, they differ widely in biophysical properties, from stable monomers to metastable aggregation-prone mixtures of oligomers. Previous work from our laboratory presented the combination of structure-based analysis with family consensus alignments as being able to improve the properties of immunoglobulin variable domains. We had identified a series of mutations in the variable domains that greatly influenced both the stability and the expression level of single-chain Fv (scFv) fragments produced in the periplasm of Escherichia coli. We now investigated whether these effects are transferable to Fab fragments and immunoglobulin G (IgG) produced in bacteria, Pichia pastoris, and mammalian cells. Taken together, our data indicate that engineered mutations can increase functional expression levels only for periplasmic expression in prokaryotes. In contrast, stability against thermal and denaturant-induced unfolding is improved by the same mutations in all formats tested, including scFv, Fab and IgG, independent of the expression system. The mutations in VH also influenced the structural homogeneity of full-length IgG, and the reducibility of the distant CH1-CL inter-chain disulfide bond. These results confirm the potential of structure-based protein engineering in the context of full-length IgGs and the transferability of stability improvements discovered with smaller antibody fragment

Construction and characterization of a kappa opioid receptor devoid of all free cysteines

We have constructed an optimized mutant of the kappa opioid receptor (KOR), which is devoid of its 10 free cysteines. It was necessary to test different amino acid replacements at various positions and we used a structural model and homology with other receptor family members as a guide. This mutant binds ligands and couples to the cognate G‐proteins in a very similar fashion to wild‐type KOR. The addition of the antagonist naloxone during cell growth greatly enhances heterogeneous expression of the mutant in mammalian cells, such that amounts similar to wild‐type could be produced. We showed by fluorescence microscopy that naloxone stabilizes the mutant in the plasma membrane. This mutant, which now permits the insertion of single cysteines, was designed for use in spectroscopic studies of ligand‐induced receptor conformational changes as well as to simplify folding studie

Investigating the effect of the compression rate on the kinetic response of diamond anvil cell experiments

In this work, the high pressure behavior of cubic and hexagonal symmetric samples: Au, Pt, Re, Zn, Fe, [Fe,Mg]O were investigated by means of dynamic compression. The simultaneous use of hard X-ray radiation at synchrotron and free-electron laser (XFEL) facilities allowed time-resolved investigation of the lattice response of these materials. Here, using the membrane-driven and the novel piezo-driven dynamic diamond anvil cell enabled the possibility to directly compare the effect of quasi-static or intermediate compression rates.In dieser Arbeit wurde das Hochdruckverhalten von kubisch und hexagonal symmetrischen Proben: Au, Pt, Re, Zn, Fe, [Fe,Mg]O mit Hilfe von dynamischer Kompression untersucht. Die gleichzeitige Verwendung harter Röntgenstrahlung eines Synchrotrons oder Freie-Elektronen-Lasers (XFEL) ermöglichte eine zeitaufgelöste Untersuchung der Gitterstruktur dieser Materialien. Dabei erlaubt die Verwendung der membranangetriebenen und der neuartigen piezoangetriebenen dynamischen Diamantstempelzelle einen direkten Vergleich der Auswirkungen von quasi-statisch oder mittleren Kompressionsraten

Assessment of ab initio models of protein complexes by molecular dynamics.

Determining how proteins interact to form stable complexes is of crucial importance, for example in the development of novel therapeutics. Computational methods to determine the thermodynamically stable conformation of complexes from the structure of the binding partners, such as RosettaDock, might potentially emerge to become a promising alternative to traditional structure determination methods. However, while models virtually identical to the correct experimental structure can in some cases be generated, the main difficulty remains to discriminate correct or approximately correct models from decoys. This is due to the ruggedness of the free-energy landscape, the approximations intrinsic in the scoring functions, and the intrinsic flexibility of proteins. Here we show that molecular dynamics simulations performed starting from a number top-scoring models can not only discriminate decoys and identify the correct structure, but may also provide information on an initial map of the free energy landscape that elucidates the binding mechanism

G-quadruplexes are specifically recognized and distinguished by selected designed ankyrin repeat proteins

We introduce designed ankyrin repeat binding proteins (DARPins) as a novel class of highly specific and structure-selective DNA-binding proteins, which can be functionally expressed within all cells. Human telomere quadruplex was used as target to select specific binders with ribosome display. The selected DARPins discriminate the human telomere quadruplex against the telomeric duplex and other quadruplexes. Affinities of the selected binders range from 3 to 100 nM. CD studies confirm that the quadruplex fold is maintained upon binding. The DARPins show different specificity profiles: some discriminate human telomere quadruplexes from other quadruplex-forming sequences like ILPR, c-MYC and c-KIT, while others recognize two of the sequences tested or even all quadruplexes. None of them recognizes dsDNA. Quadruplex-binding DARPins constitute valuable tools for specific detection at very small scales and for the in vivo investigation of quadruplex DN