FG Biokatalyse

15 Items

Recent Submissions
Dendronylation: Residue-specific chemoselective attachment of oligoglycerol dendrimers on proteins with noncanonical amino acids

Ma, Ying ; Thota, Bala N. S. ; Haag, Rainer ; Budisa, Nediljko (2015)

Polyglycerol dendrimers as an important class of polymeric materials especially attractive for covalent attachment to therapeutic proteins as a useful alternative to traditional PEGylation procedures. Herein, we combine in vivo noncanonical amino acid (ncAA) incorporation and chemoselective conjugation in vitro to produce novel hybrid protein–dendrimer conjugates with the defined architectures....

Construction of a polyproline structure with hydrophobic exterior using octahydroindole-2-carboxylic acid

Kubyshkin, Vladimir ; Budisa, Nediljko (2016)

The proline analogue (2S,3aS,7aS)-octahydroindole-2-carboxylic acid (Oic) has been previously applied as a proline substitute in pharmocologically active peptides and as a structural component of the antihypertensive drug Perindopril. Herein, we describe the formation of an oligoproline structure by an Oic oligomer. A series of Oic oligomers were investigated to show the structural and energeti...

Proteome characterization of Escherichia coli cells evolved to tolerate elongation factor P deletion

Wang, Mingjian (2017)

Elongation factor P (EF-P) is an essential translation factor in bacteria, it has been reported that EF-P plays an important role in rescuing the translation stalling caused by the oligo-proline containing peptides stretch. The growth rate of E. coli was significantly restricted when EF-P was knocked out. However, through a continuous directed evolution in the turbidostatic model, both the wild...

gamma-(S)-Trifluoromethyl proline: evaluation as a structural substitute of proline for solid state F-19-NMR peptide studies

Kubyshkin, Vladimir ; Afonin, Sergii ; Kara, Sezgin ; Budisa, Nediljko ; Mykhailiuk, Pavel K. ; Ulrich, Anne S. (2015)

gamma-(4S)-Trifluoromethyl proline was synthesised according to a modified literature protocol with improved yield on a multigram scale. Conformational properties of the amide bond formed by the amino acid were characterised using N-acetyl methyl ester model. The amide populations (s-trans vs. s-cis) and thermodynamic parameters of the isomerization were found to be similar to the corresponding...

Site-specific conjugation of 8-ethynyl-BODIPY to a protein by [2+3] cycloaddition

Albrecht, Marcel ; Lippach, Andreas ; Exner, Matthias P. ; Jerbi, Jihene ; Springborg, Michael ; Budisa, Nediljko ; Wenz, Gerhard (2015)

We report a straightforward synthesis of 8-ethynyl-BODIPY derivatives and their potential as fluorescent labeling compounds using an alkyne-azide click chemistry approach. The ethynyl substituted BODIPY dyes at the meso-position were reacted under Cu+ catalysis and mild physiological conditions in organic and biological model systems using benzyl azide and a Barstar protein which was selectivel...

Photochemical formation of quinone methides from peptides containing modified tyrosine

Husak, Antonija ; Noichl, Benjamin P. ; Ramljak, Tatjana Šumanovac ; Sohora, Margareta ; Škalamera, Đani ; Budiša, Nediljko ; Basarić, Nikola (2016)

We have demonstrated that quinone methide (QM) precursors can be introduced in the peptide structure and used as photoswitchable units for peptide modifications. QM precursor 1 was prepared from protected tyrosine in the Mannich reaction, and further used as a building block in peptide synthesis. Moreover, peptides containing tyrosine can be transformed into a photoactivable QM precursor by the...

Energetic contribution to both acidity and conformational stability in peptide models

Kubyshkin, Vladimir ; Durkin, Patrick ; Budisa, Nediljko (2016)

The acidity of N-acyl amino acids is dependent upon the rotameric state of the amide bond. In this work we systematically investigated the acidity difference of the rotamers (Delta pK(a)) in the frames of various acetylated amino acids. Our results indicated a mutual interaction of two carbonyl groups of an attractive type. We observed conservative Delta pK(a)s for acyclic amino acids (2.2-3.0 ...

Metabolic engineering of O-acetyl-L-homoserine sulfhydrylase and Met-biosynthetic pathway in Escherichia coli

Ma, Ying (2017)

The application of non-canonical amino acids (ncAAs) offers a new approach for the post-translational modification of proteins [1–4]. Especially the incorporation of ncAAs containing different functional groups such as azides, alkynes or olefins, provides a covalent site on the protein. Subsequently the attachment of other small molecules (fluorescent dye, biotin, sugar, PEG, etc.) brings more ...

Evolution of fluorinated enzymes: an emerging trend for biocatalyst stabilization

Biava, Hernan ; Budisa, Nediljko (2014)

Nature uses remarkably limited sets of chemistries in its repertoire, especially when compared to synthetic organic chemistry. This limits both the chemical and structural diversity that can ultimately be achieved with biocatalysis, unless the powers of chemical synthesis are merged with biological systems by integrating nonnatural synthetic chemistries into the protoplasma of living cells. Of ...

Xenomicrobiology: a roadmap for genetic code engineering

Acevedo-Rocha, Carlos G. ; Budisa, Nediljko (2016)

Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high-throughput and low-cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processe...

Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids

Bohlke, Nina ; Budisa, Nediljko (2014)

One of the major challenges in contemporary synthetic biology is to find a route to engineer synthetic organisms with altered chemical constitution. In terms of core reaction types, nature uses an astonishingly limited repertoire of chemistries when compared with the exceptionally rich and diverse methods of organic chemistry. In this context, the most promising route to change and expand the f...

Adaptation of E. coli towards tryptophan analog usage

Oehm, Stefan (2016)

The presented study set out to change the amino acid set of the genetic code in two different Trp-auxotrophic E. coli strains with the help of the serial transfer regime under constant evolutionary pressure. By increasing the stringency of the system as the source for the canonical amino acid is depleted, the bacteria were forced to incorporate the Trp surrogate [3,2]Tpa at all Trp-positions in...

Evaluation of bicinchoninic acid as a ligand for copper(I)-catalyzed azide-alkyne bioconjugations

Christen, Erik H. ; Gübeli, Raphael J. ; Kaufmann, Beate ; Merkel, Lars ; Schoenmakers, Ronald ; Budisa, Nediljko ; Fussenegger, Martin ; Weber, Wilfried ; Wiltschi, Birgit (2012)

The Cu(I)-catalyzed cycloaddition of terminal azides and alkynes (click chemistry) represents a highly specific reaction for the functionalization of biomolecules with chemical moieties such as dyes or polymer matrices. In this study we evaluate the use of bicinchoninic acid (BCA) as a ligand for Cu(I) under physiological reaction conditions. We demonstrate that the BCA–Cu(I)-complex represents...

Organic fluorine as a polypeptide building element: in vivo expression of fluorinated peptides, proteins and proteomes

Merkel, L. ; Budisa, Nediljko (2012)

Traditionally, the biological fluorination of complex biological systems like proteins is achieved through substitution of canonical amino acids or addition of fluorinated amino acids in the context of the standard genetic code. Ribosomal translation of monofluorinated amino acids into proteins often yields structures with minimal local changes in the interior but, on the same time, results in ...

Non-canonical amino acids as a useful synthetic biological tool for lipase-catalysed reactions in hostile environments

Acevedo-Rocha, Carlos G. ; Hoesl, Michael G. ; Nehring, Sebastian ; Royter, Marina ; Wolschner, Christina ; Wiltschi, Birgit ; Antranikian, Garabed ; Budisa, Nediljko (2013)

The incorporation of several non-canonical amino acids into the Thermoanaerobacter thermohydrosulfuricus lipase confers not only activity enhancement upon treatment with organic solvents (by up to 450%) and surfactants (resp. 1630%), but also protective effects against protein reducing (resp. 140%), alkylating (resp. 160%), and denaturing (resp.190%) agents as well as inhibitors (resp. 40%). Th...