Publications and patentsBiotec
We are experts in protein engineering with a focus on directed evolution approaches and semirational or rational design. Our research includes empirical and computational method development, and the application of the latter to ultimately generate enzyme variants with tailored characteristics. Computational methods further serve to solve structure/function relationships of targeted enzymes. The research output of the group is reflected by over 195 peer-reviewed articles and over 20 filed patents.
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A comparison of simultaneous OmniChange with iterative CAST for cpADH5 engineering
In Yunus´s new publication, the first comprehensive comparison regarding an improvement in enzymatic activity and required screening efforts during iterative and simultaneous site saturation mutagenesis experiment was performed. Screening of 7200 clones from 33 site saturation mutagenesis libraries (exploring 17 recombination paths) yielded the cpADH5 W286A variant with a 82-fold improved initial activity toward methyl 3- hydroxyhexanoate. Screening of 3500 clones from a single OmniChange library with four positions (C57, W116, L119, and W286; 1.8 % of the generated sequence space) yielded the cpADH5 C57V/W286S variant with a 108-fold improvement in initial activity toward methyl 3-hydroxyhexanoate. In conclusion, combination of high throughput screening system with simultaneous site saturation of four and more positions seems to be highly promising to take full advantage of nature’s diversity.
Ensari, Y., Dhoke, G., Davari, M., Ruff, A. J. and Schwaneberg, U. (2018), A comparative reengineering study of cpADH5 through iterative and simultaneous multi‐site saturation mutagenesis. ChemBioChem. Accepted Author Manuscript. doi:10.1002/cbic.201800159
Sortase-mediated ligation of purely artificial building blocks
The collaboration between the Schwaneberg and Böker groups resulted in the publication of a novel application of sortase A. Sortase A, an enzyme produced by Staphylococcus aureus, has long been studied as a catalyst for the ligation of proteins with various biomolecules, particles and surfaces. The present work shows an enzymatically catalyzed linkage of two synthetic blocks. First, the linkage between silica nanoparticles with polymer and between silica nanoparticles of different size by sortase A catalysis was investigated. Second, the linkage between two commercially available polymers by sortase A via MALDI-TOF-MS was proved. For this purpose, the building blocks were first equipped with the recognition sequence needed for sortase A reaction—the conserved peptide LPETG—and a pentaglycine motif. The linkage of the peptides to the nanoparticle surfaces and polymer functional end groups were performed by thiol click reaction between cysteine residues of the peptide motifs and C=C-decorated building blocks. These findings suggest a new ligation method for synthetic species.
Part of this work was performed at the Center for Chemical Polymer Technology in DWI, which was supported by the EU and the federal state of North Rhine–Westphalia.
Dai, X., Mate, D. M., Glebe, U., Mirzaei, Garakani, T., Körner, A., Schwaneberg, U., Böker, A.; Sortase-Mediated Ligation of Purely Artificial Building Blocks, Polymers, 2018, 10, 151; doi:10.3390/polym10020151
Directed Evolution of Hyaluronic Acid Synthase from Pasteurella multocida Towards High Molecular Weight Hyaluronic Acid
Mandawe, J., Infanzon, B., Eisele, A., Zaun, H., Kuballa, J., Davari, M.D., Jakob, F., Elling, L., Schwaneberg, U.; Directed Evolution of Hyaluronic Acid Synthase from Pasteurella multocida Towards High Molecular Weight Hyaluronic Acid; ChemBioChem, 2018
In John´s new publication, engineered hyaluronan synthase from Pasteurella multocida pmHAS-VF harbouring triple substitutions, T40L, V59M and T104A, exhibited improved N-terminal region flexibility and enhanced hyaluronic acid polymerizing activity. Production of high molecular weight hyaluronic acid up to 4.7 MDa at twice the normal output can now be achieved. Hyaluronic acid is the natural glycosaminoglycan product with diverse cosmetic and medical applications and a global market value of $8.3 billion. This protein engineering campaign not only demonstrates the applicability of protein engineering towards improved hyaluronic acid production, but also uncovers the potential involvement of the N-terminus in hyaluronic acid synthesis. This work was realized in the division Biohybrid System and it was possible through DBU funding.
To learn more, please access the full paper on Publications and patents
Exploring the full natural diversity of single amino acid exchange reveals that 40–60% of Bacillus subtilis Lipase A positions improve organic solvents resistanceBio VI
In Josiane´s new publication, protein engineering has been employed to successfully improve organic solvent resistance of Bacillus subtilis Lipase A. A systematic study covering the full natural diversity of Bacillus subtilis Lipase A with one amino acid exchange was performed to explore nature’s potential to improve organic solvent resistance of enzymes. The co-solvent resistance against 2,2,2‑trifluoroethanol, 1,4-dioxane, and dimethyl sulfoxide were improved by 41 to 59% of Bacillus subtilis Lipase A positions with a total of 4–10% of all possible substitutions. Charged substitutions were preferred to improve 1,4-dioxane and 2,2,2‑trifluoroethanol resistance whereas polar ones were preferred for dimethyl sulfoxide. Charged substitutions on the surface predominantly improved resistance, polar substitutions were preferred in buried regions and 58–93% of beneficial substitutions led to chemically different amino acids. This work was financially supported by Deutsche Forschungsgemeinschaft through the Research Training Group BioNoCo—Biocatalysis using non‑conventional media GRK 1166 and the Hundred Talents Program of Chinese Academy of Sciences to Prof. Leilei Zhu.
Frauenkron‑Machedjou, V. J., Fulton, A., Zhao J., Weber, L., Jaeger, K. E., Schwaneberg, U. and Zhu, L.: Exploring the full natural diversity of single amino acid exchange reveals that 40–60% of BSLA positions improve organic solvents resistance; Bioresour. Bioprocess. (2018) 5:2
A robust protocol for directed aryl sulfotransferase evolution towards GlcNAcBio VI
Sulfurylation is of biomolecules is well-spread in the nature, which plays an important role in biological events such as signal transduction, detoxification, molecular recognition, and hormone regulation. Chemical sulfurylation is performed in the industries that often requires several steps, hazardous chemicals and usually lacks regio- and chemoselectivity. On the other hand, the enzyme class, sulfotransferase catalyzes the selective transfer of a sulfuryl group from a donor to an acceptor molecule. Among the sulfotransferases, the class of bacterial aryl sulfotransferases are of growing interest because of their broad acceptor spectrum and cost-effective sulfuryl donor. As an alternative to chemical methods enzymatic sulfurylation is proposed, in which directed evolution can play an important role to improve the catalytic efficiency and substrate specificity of industrially relevant aryl sulfotransferases.
A directed aryl sulfotransferase evolution protocol was successfully validated to improve the specific activity towards a monosaccharide, N-acetylglucosamine – GlcNAc. A random mutagenesis library of aryl sulfotransferase B from Desulfitobacterium hafniense was generated using sequence saturation mutagenesis - SeSaM. The screening of 1760 clones was performed via advanced and optimized para-nitrophenylsulfate based screening system in 96-well format. The identified best variant, ASTB-V1 with a substitution Val579Asp showed an up to 3.4-fold increased specific activity and 2.4-fold higher monosulfurylated N-acetylglucosamine production determined via high-performance liquid chromatography and mass spectrometry.
Islam, S., Mate, D.M., Martínez, R., Jakob, F., Schwaneberg, U., 2018. A robust protocol for directed aryl sulfotransferase evolution toward the carbohydrate building block GlcNAc. Biotechnol. Bioeng., first published online Jan 22 2018, DOI: 10.1002/bit.26535.
Protein engineering of FhuA Δ1-160 to enhance pore sizeACS Publications
Biological membranes are perfect examples for a molecular filter that uses membrane channels to control the permeability of small water-soluble molecules. We started from the known mutant channel FhuA Δ1-160 in which the cork domain closing the channel had been removed to allow filtering of larger hydrophilic molecules. Here, we further expanded the pore diameter by copying the amino acid sequence of two β-strands in a stepwise manner increasing the total number of β-strands from 22 to 34. The pore size of the respective expanded channel protein was characterized by single-channel conductance analysis. Furthermore, polymer exclusion measurements were performed by analyzing single-channel conductance in the presence of differently sized polyethylene glycols of known polymer random coil radii.
The conclusion from channel conductance of small channel penetrating polymers versus larger excluded ones suggested an increase in pore radii from 1.6 nm for FhuA Δ1-160 up to a maximum of about 2.7 nm for FhuA Δ1-160 + 8 β. Integration of more β-strand caused instability of the channel and exclusion of smaller sized polymer. FhuA Δ1-160 + 10 β and FhuA Δ1-160 + 12 β effective radius decreased to 1.4 and 1.3 nm, respectively, showing the limitations of this approach.
Liu, Z., Ghai, I., Winterhalter, M., Schwaneberg, U., 2017. Engineering enhanced pore sizes using FhuA Δ1-160 from E. coli outer membrane as template. ACS Sens., 2, 1619-1626.
Directed evolution of polypropylene and polystyrene binding peptidesBio VI
Surface functionalization of biological inert polymers, for example polypropylene and polystyrene, with material binding peptides facilitates an efficient immobilization of enzymes, bioactive peptides or antigens at ambient temperature in water. The developed Peptide Polymer evolution protocol (PePevo) is robust directed evolution protocol that enables to tailor polymer binding anchor peptides for efficient binding under application conditions. Key for a successful directed evolution campaign was to develop an epPCR protocol with a very high mutation frequency, 60 mutations per kb, to ensure sufficient diversity in the peptides LCI and Tachystatin A2. LCI and Tachystatin A2 were genetically fused to the reporter eGFP to quantify peptide binding on polypropylene and polystyrene surfaces by fluorescence analysis. PePevo was validated in two directed evolution campaigns for both peptides and polymers, LCI and polypropylene as well as Tachystatin A2 and Polystyrene. The nonionic surfactant Triton X-100, 1 mM for LCI, and the anionic surfactant LAS, 0.5 mM for Tachystatin A2, were used as selection pressure for improved peptide binders. PePevo yielded in two up to three fold improved LCI polypropylene binders, I24T, Y29H, E42K and D31V, E42G and in two up to six fold stronger Tachystatin A2 polystyrene binders R3S, L6P, V12K, S15P, C29R, R30L, F33S, Y44H and F9C, C24S, G26D, S31G, C41S, Y44Q.
Rübsam*, K., Weber*, L., Jakob, F., Schwaneberg, U., 2017. Directed evolution of polypropylene and polystyrene binding peptides. Biotechnol. Bioeng., 115, 321–330. *shared first authorship
Electron transfer pathways in a light, oxygen, voltage (LOV) protein devoid of the photoactive cysteine
Blue-light absorption by the flavin chromophore in light, oxygen, voltage (LOV) photoreceptors triggers photochemical reactions that lead to the formation of a flavin-cysteine adduct. While it has long been assumed that adduct formation is essential for signaling, it was recently shown that LOV photoreceptor variants devoid of the photoactive cysteine can elicit a functional response and that flavin photoreduction to the neutral semiquinone is sufficient for signal transduction. Currently, the mechanistic basis of the underlying electron- (eT) and proton-transfer (pT) reactions is not well understood.
In this collaborative study, we reengineered pT into the naturally not photoreducible iLOV protein. A single amino acid substitution (Q489D) was sufficient to enable efficient photoreduction under aerobic conditions, which suggests that an eT pathway is naturally present in the protein. Employing this variant, we investigated the underlying eT and pT reactions using a combination of steady-state UV/Vis, transient absorption, electron paramagnetic resonance spectroscopy combined with site-directed mutagenesis. Our study provides strong evidence that several Tyrosine and Tryptophan residues, highly conserved in all LOV proteins, constitute the eT pathway for flavin photoreduction, suggesting that the propensity for photoreduction is evolutionary imprinted in all LOV domains, while efficient pT is needed to stabilize the neutral semiquinone radical.
Kopka, B., Magerl, K., Savitsky, A., Davari, M. D., Röllen, K., Bocola, M., Dick, B., Schwaneberg, U., Jaeger, K.-E., Krauss, U., 2017. Electron transfer pathways in a light, oxygen, voltage LOV protein devoid of the photoactive cysteine. Sci. Rep. UK, 7, 1-16.
Engineering of Candida parapsilosis alcohol dehydrogenase for conversion of methyl 3-hydroxyalkanoatesBio VI
Expanding the substrate scope of enzymes opens up new routes for the synthesis of valuable chemicals. Ketone-functionalized fatty acid derivatives and corresponding chiral alcohols are valuable building blocks for the synthesis of a variety of chemicals including pharmaceuticals.
Candida parapsilosis alcohol dehydrogenase wild type is an S-selective alcohol dehydrogenase that does not convert 3-hydroxy fatty acid methyl esters larger than methyl 3-hydroxypentanoate. Thus, methyl 3-hydroxyhexanoate and methyl (R)-3-hydroxybutyrate are not accepted as substrate by wild type Candida parapsilosis alcohol dehydrogenase. Enlarging the binding pocket of the wild type enzyme through substitution of tryptophan at position 286 by alanine led to a chain length specificity shift and oxidation of methyl 3-hydroxyhexanoate to the corresponding ketone. Furthermore, a second variant with double substitution on positions 119 and 286 exhibited inverted enantiopreference for methyl 3-hydroxybutyrate from the S-enantiomer to the R-enantiomer.
Ensari*, Y., Dhoke*, G. V., Davari, M. D., Bocola, M., Ruff, A. J., Schwaneberg, U., 2017. Inversion of cpADH5 enantiopreference and altered chain length specificity for methyl 3‑hydroxyalkanoates. Chem. Eur. J., 23, 12636-12645. *shared first authorship
Sortase-mediated functionalization of microgels with biomoleculesACS Publications
Microgels are colloidal macromolecular networks swollen in water while forming stable dispersions. They are highly porous, soft, deformable and exhibit a stimuli-responsiveness in aqueous solutions. Due to their interesting properties, microgels gained much attention in macromolecular and biomedical research fields.
In this work we developed a sortase-mediated method for chemo-selective and efficient decoration of aqueous microgels with biomolecules. Poly(N-vinylcaprolactam) (VCL) microgels with different amounts of glycidyl methacrylate (GMA) as a comonomer incorporated in the microgel shell were synthesized and characterized regarding to their size, swelling degree and temperature-responsiveness in aqueous solutions. The surface of the PVCL/GMA microgel was modified with the specific recognition peptide sequence (LPETG) for Sortase A. Sortase-mediated conjugation of oligoglycin-tagged enhanced Green Fluorescent Protein (eGFP) to the LPETG-modified microgels was successfully performed. Sortase-mediated bioconjugation can be used as a simple and powerful technique for the targeted surface functionalization of stimuli-responsive microgels with biomolecules.
Gau*, E., Mate*, D. M., Zou, Z., Oppermann, A., Töpel, A., Jakob, F., Wöll, D., Schwaneberg**, U., Pich**, A., 2017. Sortase-mediated surface functionalization of stimuli-responsive microgels. Biomacromolecules, 18, 2789-2798. *shared first authorship **shared corresponding authorship
High interfacial activity of a transmembrane protein leads to nano-thin walled micro-compartmentsRoyal Society of Chemistry
Protein-polymer conjugates have several applications in the field of biotechnology, medicine and nanotechnology. One example of conjugates is based on the transmembrane protein ferric hydroxamate uptake protein component A, FhuA, an outer membrane protein of Escherichia coli. These conjugates present properties such as high interfacial activity, which can be utilized for generation of Pickering emulsions. Instead of surfactant molecules, the conjugate particles are able to stabilize emulsions. We generated Pickering emulsions for the first time with the transmembrane protein FhuA. Stable micro-compartments made of these Pickering emulsions were later crosslinked by a newly synthesized UV-crosslinkable monomer, 3,4-dimethyl maleic imidobutyl acrylate, DMMIBA, to polymer chains. Characterization of the micro-compartments with scanning force microscopy determined membrane thickness of 11.1 ± 0.6 nm and fluorescent microscopy revealed the stability of the micro-compartments even after treatment with ethanol. These micro-compartments have potential application for drug delivery systems and bring us closer to the possibility of protein-polymer membrane generation, within which properties of membranes can be altered by temperature and pH stimuli.
Charan, H., Glebe, U., Anand, D., Kinzel, J., Zhu, L., Bocola, M., Mirazaei Garakani, T., Schwaneberg, U., Böker, A., 2017. Nano-thin walled micro-compartments from transmembrane protein-polymer conjugates. Soft matter, 13, 2866-2875.
Are Directed Evolution Approaches Efficient in Exploring Nature’s Potential to Stabilize a Lipase in Organic CosolventsMDPI AG
Despite the significant advances in the field of protein engineering, general design principles to improve organic cosolvent resistance of enzymes still remain undiscovered. Previous studies drew conclusions to engineer enzymes for their use in water-miscible organic solvents based on few amino acid substitutions. In this study, we compare a Bacillus subtilis lipase A - BSLA - library covering the full natural diversity of single amino acid substitutions at all 181 positions of BSLA with three state of the art random mutagenesis methods: error-prone PCR - epPCR - with low and high mutagenesis frequency as well as a transversion-enriched Sequence Saturation Mutagenesis - SeSaM-Tv P/P - method. Libraries were searched for amino acid substitutions that increase the enzyme’s resistance to the water-miscible organic cosolvents 1,4-dioxane, 2,2,2-trifluoroethanol, and dimethyl sulfoxide. Our analysis revealed that although a significant amount of all possible single substitutions contributes to improved cosolvent resistance, only a fraction of these substitutions could be detected in the three random mutagenesis libraries. This is the first study that quantifies the capability of these diversity generation methods generally employed in directed evolution campaigns and compares them to the entire natural diversity with a single substitution. Additionally, our investigation of the BSLA SSM library indicates the importance of introducing surface charges for organic cosolvent resistance.
Markel*, U., Zhu*, L., Frauenkron-Machedjou, V. J., Zhao, J., Bocola, M., Davari, M. D., Jaeger, K.-E., Schwaneberg, U., 2017. Are directed evolution approaches efficient in exploring nature’s potential to stabilize a lipase in organic cosolvents? Catalysts, 7, 142. *shared first authorship
2-Methyl-2,4-pentanediol boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerizationACS Publications
Transmembrane proteins have a hydrophobic middle part due to their presence in natural lipid bilayer. Therefore, stabilizing agents are essentially used to cover hydrophobic regions to solubilize purified transmembrane proteins for usage in aqueous media. 2-Methyl-2,4-pentanediol -MPD- a small molecule was applied for stabilization of ferric hydroxamate uptake protein component A, FhuA, which is a transmembrane protein found in the outer membrane of Escherichia coli. The β-barrel shaped protein was used for hosting a rhodium catalyst to perform a polymerization reaction of phenylacetylene as proof of concept. MPD does not form micelles compared to other commonly used detergents such as sodium dodecylsulfate and polyethylene polyethyleneglycol leading to higher polymer product yield and polymer masses. Computer-based simulations supported the suitability of the amphiphilic MPD molecules for successful stabilization of the transmembrane protein FhuA and enabling the functionality of the protein channel.
Kinzel*, J., Sauer*, D. F., Bocola, M., Arlt, M., Mirzaei Garakani, T., Thiel, A., Beckerle, K., Polen, T., Okuda, J., Schwaneberg, U. 2017. 2-Methyl-2,4-pentanediol (MPD) boosts as detergent-substitute the performance of ß-barrel hybrid catalyst for phenylacetylene polymerization. Beilstein J. Org. Chem., 13, 1498-1506. *shared first authorship
Green and versatile functionalization of polypropylene by anchor peptidesBio VI
Polypropylene is a wide spread commodity polymer used in medicine, textiles or packaging. Surface functionalization of polypropylene is performed to increase wettability, adhesion, or dyeing behavior, but it is challenging due to absent functional groups. Functionalization using peptides naturally evolved for surface interaction represents an attractive alternative to conventional modification techniques.
In this study polypropylene binding peptides were identified, characterized and used to successfully functionalize polypropylene surfaces. Anchor peptides bind to polypropylene at room temperature in water and show stability against treatment with surfactants. The presented anchor peptide toolbox enables easy to handle, green functionalization of polypropylene based materials.
Rübsam, K., Stomps, B., Böker, A., Jakob, F., Schwaneberg, U., 2017. Anchor peptides: A green and versatile method for polypropylene functionalization. Polymer, 116, 124-132.