Biology subjects

Hoecker, B.

Publications and source records attributed to Hoecker, B..

5 recordsLinked to original sources

bioRxiv2025

Customizing the Structure of a Minimal TIM Barrel to Craft a De Novo Enzyme

The TIM barrel is the most prevalent fold in natural enzymes, supporting efficient catalysis of diverse chemical reactions. While de novo TIM barrels have been successfully designed, their minimalistic architecture lacks structural elements essential for substrate binding and catalysis. Here, we present CANVAS, a computational workflow that introduces a structural lid into a minimal de novo TIM barrel to anchor catalytic residues and form an active-site pocket for enzymatic function. Starting from two de novo TIM barrels, we designed nine variants with distinct lids to form active sites for the Kemp elimination. Four designs showed measurable activity, with the most active reaching a catalytic efficiency of 21,000 M-{superscript 1} s-{superscript 1} at its optimal pH. A co-crystal structure of this variant bound to a transition-state analogue confirmed the accuracy of the designed lid and active site. Using the X-ray structure of a lower-activity variant (19 M-{superscript 1} s-{superscript 1}), we applied ensemble-based design to optimize its active site, increasing catalytic efficiency by >1,600-fold to 32,000 M-{superscript 1} s-{superscript 1}. These results demonstrate that de novo TIM barrels can be endowed with substrate binding pockets supporting efficient catalytic function, establishing a platform for building enzymes on demand from minimal protein scaffolds.

biochemistry↗

bioRxiv2020

Protlego: A Python package for the analysis and design of chimeric proteins

MotivationGene duplication and recombination of protein fragments have led to the highly diverse protein space that we observe today. By mimicking this natural process, the design of protein chimeras via fragment recombination has proven experimentally successful and has opened a new era for the design of customizable proteins. The in-silico building of structural models for these chimeric proteins, however, remains a manual task that requires a considerable degree of expertise and is not amenable for high-throughput studies. Energetic and structural analysis of the designed proteins often require the use of several tools, each with their unique technical difficulties and available in different programming languages or web servers. ResultsWe have implemented a Python package that enables automated, high-throughput design of chimeras and their structural analysis. First, it is possible to fetch evolutionarily conserved fragments from a built-in database (also available at fuzzle.uni-bayreuth.de). These relationships can then be represented via networks or further selected for chimera construction via recombination. Designed chimeras or natural proteins are then scored and minimised with the Charmm and Amber forcefields and their diverse structural features can be analysed at ease. Here, we showcase Protlegos pipeline by exploring the relationships between the P-loop and Rossmann superfolds and building and characterising their offspring chimeras. We believe that Protlego provides a powerful new tool for the protein design community. Availability and implementationProtlego is freely available at (https://hoecker-lab.github.io/protlego/) with tutorials and documentation.

bioinformatics↗

bioRxiv2020

An Artificial Cofactor catalyzing the Baylis-Hillman Reaction using Designed Streptavidin as Protein Host

An artificial cofactor based on an organocatalyst embedded in a protein was used to conduct the Baylis-Hillman reaction in a buffered system. As protein host we chose streptavidin, since it can be easily crystallized and thereby supports the design process. The protein host around the cofactor was rationally designed based on high-resolution crystal structures obtained after each variation of the amino acid sequence. Additionally, DFT-calculated intermediates and transition states were used to rationalize activity. Finally, repeated cycles of structure determination and redesign led to a system with 24 to 35-fold increased activity over the bare cofactor and to the most active proteinogenic catalyst for the Baylis-Hillman reaction known today.

synthetic biology↗

bioRxiv2020

Ligand promiscuity in the tryptophan repressor - from structural understanding towards rational design

Receptors that promiscuously bind a range of ligands provide insights into how nature mediates affinity and biological functioning. Moreover, such receptors provide vantage points for the rational design of specific binding for biotechnological applications. Here we describe the molecular details of the ligand binding promiscuity of the well-known tryptophan repressor TrpR. We elucidated high-resolution structures of TrpR bound to the co-repressors 5-methyl-tryptophan and 5-methyl-tryptamine as well as the pseudo-repressors indole-3-propionic and indole-3-acetic acid. Furthermore, using isothermal titration calorimetry we procure the corresponding thermodynamic parameters. Together this data provides molecular explanations for the strongly varied affinities and biological effects of the ligands providing insights into how nature shapes specificity and affinity. Beyond this we use these insights to exemplarily showcase knowledge-based design of TrpR by swapping its specificity from its native ligand tryptophan to indole-3-acetic acid. Finally, we elucidate the structures of the variant bound to indole-3-acetic and indole-3-propionic acid to retrace our design rationale.

synthetic biology↗

bioRxiv2020

Design of a biosensor for direct visualisation of auxin

In plants, one of the most important regulative small molecules is indole-3-acetic acid (IAA) known as auxin. Its dynamic redistribution plays an essential role in virtually every aspect of plant life, ranging from cell shape and division to organogenesis and responses to light and gravity1,2. So far, the spatial and temporal distribution of auxin at cellular resolution could not be determined directly. Instead it has been inferred from visualisation of irreversible processes involving the endogenous auxin response machinery3-7. This detection system failed to record transient changes. Here we report on a genetically encoded biosensor for quantitative in vivo visualisation of auxin distributions. The sensor is based on the E. coli tryptophan repressor (TrpR)8 whose binding pocket was engineered for specific IAA binding and coupled to fluorescent proteins to employ FRET as readout. This sensor, unlike previous systems, enables direct monitoring of the fast uptake and clearance of auxin by individual cells in the plant as well as the graded spatial distribution along the root axis and its perturbation by transport inhibitors. Thus, our auxin sensor enables mapping of auxin concentrations at (sub)cellular resolution and their changes in time and space during plant life.

plant biology↗