Binding Kinetics I Conformational Changes
|Affinity, dose response||KD, IC50, fM sensitivity||Protein diameter||DH, ΔDH = 0.1 nm|
|Kinetics||kON, kOFF||Thermodynamics||ΔH, ΔS, ΔG|
|Avidity, bispecifics||Two-color detection||Nucleic acid enzyme activity||kcat, KM, kEXO|
|Conformational changes||% friction change|
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Dr. Michael Schraeml, Head Protein and Enzyme Technologies
ROCHE DIAGNOSTICS GMBH
Browse through the latest publications.
Paper in Nature Portfolio (under review) I 28 April 2022
They investigated peptide-based effectors inhibiting protein-protein interactions (PPI) and demonstrated the value of switchSENSE® to analyse structure-activity relationships. They synthesized >100 unique multivalent peptide binders and used switchSENSE® to systematically evaluate their binding kinetics.
In this paper they show that specific peptide architectures influence the binding dynamics, which enabled them to identify highly inhibitory peptides. The binding affinity was increased for higher-order multimers, which was mainly driven by increased on-rates. Precise on- and off-rate determination is thus key to engineer optimized multivalent binders.
switchSENSE® was demonstrated to be a viable method for high-throughput PPI characterization in order to optimize peptide architectures and engineer most efficient multivalent effectors. More specifically, switchSENSE® showed superior accuracy and low sample consumption when compared to alternative biophysical methods.
Paper in Nature Nanotechnology I 28 April 2022
Congratulations to Yongzheng Xing and our collaborators from Stefan Howorka’s lab for their notable publication in Nature Nanotechnology!
They designed synthetic nanopores using molecular design with DNA. Nanopores can be used to perform single-molecule analyses by measuring changes in current as individual molecules block the pore. Their nanopore design consists of bundles of DNA duplexes which form subunits and can be arranged in a modular way to create versatile polygonal shapes and sizes that do not exist in nature.
They confirmed the applicability of their pores as sensors by detecting single molecules of anti-biotin antibodies within pores modified with biotin tags. They further attached SARS-CoV-2 spike proteins into the pore lumen and demonstrated the usage as a sensor for SARS-CoV-2 antibodies. Due to its high validity, the switchSENSE® technology was used to verify the kinetic data of the biotin antibody binding experiment.
Paper in Science Advances I 05 Jan 2022
Congratulations to Richard Kosinski and our collaborators from Barbara Saccà’s group at the University of Duisburg-Essen for this outstanding Science Advances paper.
This work addresses key questions on kinetic properties of DNA-scaffolded enzymes using thrombin, a model of allosterically regulated serine proteases, encaged into DNA origami cavities with distinct structural and electrostatic features.
Besides demonstrating how DNA nanostructures affect charge-dependent mechanisms of encaged enzymes, thereby offering an alternative strategy to regulate allosteric processes through spatial confinement, the kinetic binding properties of thrombin were also characterized with switchSENSE® technology. The switchSENSE® biosensor is ideal to study DNA-protein interaction, and it was used to support the findings on the thrombin binding properties to the thrombin-binding DNA aptamers.
Paper in Advanced Materials Technologies I 29 Oct 2021
The peptide called “PeB” specifically binds the viral surface protein hemagglutinin and is coupled to a three-armed DNA nanostructure, which is optimized for hybridization in the switchSENSE® biosensor.
The oligovalent arrangement mirrors the homo-trimeric structure of the target protein hemagglutinin. Virus binding to peptide-DNA-nanostructures can be observed directly as a decrease in fluorescence intensity in static mode measurements.
Subsequently, the immobilized viruses are used as ligands to determine rate constants of the individual peptide-protein interactions. Furthermore, influenza virus subtypes are varied, and their binding behavior is compared.
The switchSENSE® method is shown to be applicable to characterize virus-receptor interactions.
Paper in Nature Communications I 18 June 2021
The paper shows that an engineered anti-Her2 tetravalent antibody construct that binds to two different Her2 epitopes (biparatopic) significantly increases the anti-tumoral efficacy over trastuzumab or pertuzumab treatments. The biparatopic tetravalent antibody induces cluster formation of Her2 molecules on the cancer cell surface by its crosslinking capabilities leading to enhanced Her2 growth factor receptor internalization and degradation.
Besides determination of precise binding kinetics of all constructs, the superior distance-dependent crosslinking capabilities of the tetravalent construct over its parental antibody constructs at different Her2 surface densities were measured and quantified by the switchSENSE® technology. A dynamicBIOSENSORS’ internal simulation algorithm confirmed the measured crosslinking effects at different Her2 densities.