Gergely Katona

University of Gothenburg

gergely.katona@gu.se

0709123309

Keywords

Bayesian inference, Bioinformatics, Biophysics, collective dynamics, Machine learning, miscibility, protein dynamics, protein folding, protein-protein interactions, small angle X-ray scattering, Structural biology, time-resolved, time-resolved X-ray crystallography, X-ray crystallography

Key Publications

Anindya, A.L., Olsson, T.N., Jensen, M., Garcia-Bonete, M.-J., Wheatley, S.P., Bokarewa, M.I., Mezzasalma, S.A. & Katona, G. (2024) Deciphering peptide-protein interactions via composition-based prediction: a case study with survivin/BIRC5. Machine Learning: Science and Technology, 5(2), 025081.

Jensen, M., Chandrasekaran, V., Garcia-Bonete, M.-J., Li, S., Anindya, A. L., Andersson, K. M. E., Erlandsson, M.C., Oparina, N. Y., Burmann, B. M., Brath, U., Panchenko, A. R., Bokarewa I., M. & Katona, G. (2023) Survivin prevents the polycomb repressor complex 2 from methylating histone 3 lysine 27. iScience, 26(7), 106976.

nindya, A. L., Garcia-Bonete, M.-J., Jensen, M., Recktenwald, C. V., Bokarewa I., M. & Katona, G. (2022) Bayesian Progress Curve Analysis of MicroScale Thermophoresis Data. Digital discovery, 1, 325-332.

Gagnér, V. A., Lundholm, I., Garcia-Bonete, M.-J., Rodilla, H., Friedman, R., Zhaunerchyk, V., Bourenkov, G., Schneider, T., Stake, J. & Katona, G. (2019) Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties. Scientific reports, 9, 19281.

Jensen, M., Ahlberg Gagner, V., Cabello Sanchez, J., Bengtsson, A. U. J., Ekstrom, J. C., Bjorg Ulfarsdottir, T., Garcia-Bonete, M.-J., Jurgilaitis, A., Kroon, D., Pham, V. T., Checcia, S., Coudert-Alteirac, H., Schewa, S., Rossle, M., Rodilla, H., Stake, J., Zhaunerchyk, V., Larsson, J. & Katona, G. (2021) High-resolution macromolecular crystallography at the FemtoMAX beamline with time-over-threshold photon detection. J. Synchrotron Radiat., 28(1), 64-70.

Lundholm, I.V., Rodilla, H., Wahlgren, W.Y., Duelli, A., Bourenkov, G., Vukusic, J., Friedman, R., Stake, J., Schneider, T. & Katona, G. (2015) Terahertz radiation induces non-thermal structural changes associated with Fröhlich condensation in a protein crystal. Structural Dynamics, 2(5), 054702

Garcia-Bonete, M.-J., Jensen, M., Recktenwald, C. V., Rocha, S., Stadler, V., Bokarewa I., M. & Katona, G. (2017) Bayesian Analysis of MicroScale Thermophoresis Data to Quantify Affinity of Protein: Protein Interactions with Human Survivin. Scientific reports, 7(1), 16816.

SciLifeLab / Contact / Gergely Katona

I am interested in the interface between structural biology, protein interactions and assembly, and polymer science, with a focus on how molecular dynamics establish interactions between biomolecules.

This research involves identifying suitable fine-grained units for describing biological macromolecules and deriving preferably closed-form mean-field thermodynamic equations that can predict biological association and dissociation.

We also apply concepts of miscibility to describe protein protein interactions. The method has been successful in predicting survivin binding on peptide microarrays and in associating groups of proteins with functional annotations.

Ultimately, we aim to explain the molecular mechanisms and dynamics that underlie the mean-field parameters, and how these same mechanisms can sometimes drive folded structure formation.

Group Members

Torbjörn Nur Olsson