Biology subjects

Gerhards, L.

Publications and source records attributed to Gerhards, L..

3 recordsLinked to original sources

bioRxiv2026

Revealing properties for enhanced quantum sensing in engineered proteins

Genetically encoded flavoproteins have emerged as optically readable radical pair quantum sensors, but the molecular basis of the differing magnetic responses of closely related variants remains unresolved. Here, we analyse parental AsLOV2 and three evolved MagLOV variants using molecular dynamics, quantum chemical hyperfine calculations, Marcus electron transfer theory, and trajectory-based spin relaxation analysis. The mutations preserve the LOV fold and FMN-binding core but progressively reshape the conformational landscape of the W89 electron donor, with broader rigid-body libration yet increasingly restricted internal torsional motion and predominant occupation of a single rotameric basin in MagLOV2f. These distinct motions have different magnetic consequences: dipolar coupling modulation increases strongly in the later variants, whereas hyperfine modulation rates vary non-monotonically and decrease from MagLOV2 to MagLOV2f. The mutations also alter the radical pair free energy landscape and donor-acceptor orientation, producing variant-dependent back electron transfer rates, with MagLOV2f combining comparatively fast calculated recombination with reduced hyperfine relaxation relative to MagLOV2. Thus, directed evolution redistributes competing recombination and relaxation pathways rather than optimising a single kinetic parameter. This molecular picture rationalises the distinct magnetic-response amplitudes and saturation dynamics of closely related MagLOV proteins and identifies donor conformational control as a practical design variable for protein-based radical pair quantum sensors.

biophysics↗

bioRxiv2023

How do antimicrobial peptides interact with the outer membrane of Gram-negative bacteria? Role of lipopolysaccharides in the peptide binding, anchoring and penetration

Gram-negative bacteria possess a complex structural cell envelope that constitutes a barrier for antimicrobial peptides which neutralize the microbes by disrupting their cell membranes. Computational and experimental approaches were used to study a model outer membrane interaction with an antimicrobial peptide, melittin. The investigated membrane included di[3-deoxy-D-manno-octulosonyl]-lipid A (KLA) in the outer leaflet and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) in the inner leaflet. Molecular dynamics simulations revealed, that the positively charged helical C-terminus of melittin anchors rapidly into the hydrophilic head-group region of KLA, while the flexible N-terminus makes contacts with the phosphate groups of KLA moving melittin into the boundary between the hydrophilic and hydrophobic regions of the lipids. Electrochemical techniques confirmed binding of melittin to the model membrane. To probe the peptide conformation and orientation during interaction with the membrane, polarization modulation infrared reflection absorption spectroscopy was used. The measurements revealed conformational changes in the peptide accompanied by reorientation and translocation of the peptide at the membrane surface. The study suggests that melittin insertion into the outer membrane affects its permeability and capacitance, but does not disturb the membranes integrity, indicating a distinct mechanism of the peptide action on the outer membrane of Gram-negative bacteria.

biochemistry↗

bioRxiv2022

Across atoms to crossing continents: Application of similarity measures to biological location data

Biological processes involve movements across all measurable scales. Similarity measures can be applied to compare and analyze these movements but differ in how differences in movement are aggregated across space and time. The present study reviews frequently-used similarity measures, such as the Hausdorff distance, Frechet distance, Dynamic Time Warping, and Longest Common Subsequence, jointly with several measures less used in biological applications (Wasserstein distance, weak Frechet distance, and Kullback-Leibler divergence), and provides computational tools for each of them that may be used in computational biology. We illustrate the use of the selected similarity measures in diagnosing differences within two extremely contrasting sets of biological data, which, remarkably, may both be relevant for magnetic field perception by migratory birds. Specifically, we assess and discuss cryptochrome protein conformational dynamics and extreme migratory trajectories of songbirds between Alaska and Africa. We highlight how similarity measures contrast regarding computational complexity and discuss those which can be useful in noise elimination or, conversely, are sensitive to spatiotemporal scales.

bioinformatics↗