@book{Reuter2020, author = {Reuter, Bernhard}, title = {Generalisierte Markov-Modellierung}, publisher = {Springer Spektrum, Wiesbaden}, isbn = {978-3-658-29711-4}, doi = {10.1007/978-3-658-29712-1}, year = {2020}, abstract = {Markov State Models (MSM) sind der Goldstandard zur Modellierung biomolekularer Dynamik, da sie die Identifizierung und Analyse metastabiler Zust{\"a}nde erm{\"o}glichen. Die robuste Perron-Cluster-Cluster-Analyse (PCCA+) ist ein verbreiteter Spectral-Clustering-Algorithmus, der f{\"u}r das Clustering hochdimensionaler MSM verwendet wird. Da die PCCA+ auf reversible Prozesse beschr{\"a}nkt ist, wird sie zur Generalisierten PCCA+ (G-PCCA) verallgemeinert, die geeignet ist, nichtreversible Prozesse aufzukl{\"a}ren. Bernhard Reuter untersucht hier mittels G-PCCA die nichtthermischen Auswirkungen von Mikrowellen auf die Proteindynamik. Dazu f{\"u}hrt er molekulardynamische Nichtgleichgewichtssimulationen des Amyloid-β-(1-40)-Peptids durch und modelliert diese.}, language = {de} } @article{ThiesSunkaraRayetal.2023, author = {Thies, Arne and Sunkara, Vikram and Ray, Sourav and Wulkow, Hanna and Celik, M. {\"O}zg{\"u}r and Yerg{\"o}z, Fatih and Sch{\"u}tte, Christof and Stein, Christoph and Weber, Marcus and Winkelmann, Stefanie}, title = {Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design}, volume = {13}, journal = {Scientific Reports}, number = {607}, doi = {10.1038/s41598-023-27699-w}, year = {2023}, abstract = {We previously reported the successful design, synthesis and testing of the prototype opioid painkiller NFEPP that does not elicit adverse side effects. The design process of NFEPP was based on mathematical modelling of extracellular interactions between G-protein coupled receptors (GPCRs) and ligands, recognizing that GPCRs function differently under pathological versus healthy conditions. We now present an additional and novel stochastic model of GPCR function that includes intracellular dissociation of G-protein subunits and modulation of plasma membrane calcium channels and their dependence on parameters of inflamed and healthy tissue (pH, radicals). The model is validated against in vitro experimental data for the ligands NFEPP and fentanyl at different pH values and radical concentrations. We observe markedly reduced binding affinity and calcium channel inhibition for NFEPP at normal pH compared to lower pH, in contrast to the effect of fentanyl. For increasing radical concentrations, we find enhanced constitutive G-protein activation but reduced ligand binding affinity. Assessing the different effects, the results suggest that, compared to radicals, low pH is a more important determinant of overall GPCR function in an inflamed environment. Future drug design efforts should take this into account.}, language = {en} } @article{BauerWeberDiehlWieseneckeretal.2021, author = {Bauer, Wolfgang and Weber, Marcus and Diehl-Wiesenecker, Eva and Galtung, Noa and Prpic, Monika and Somasundaram, Rajan and Tauber, Rudolf and Schwenk, Jochen and Micke, Patrick and Kappert, Kai}, title = {Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection}, volume = {13}, journal = {Viruses}, number = {12}, doi = {10.3390/v13122456}, pages = {2456}, year = {2021}, abstract = {We evaluated how plasma proteomic signatures in patients with suspected COVID-19 can unravel the pathophysiology, and determine kinetics and clinical outcome of the infection. We identified distinct plasma proteins linked to the presence and course of COVID-19. These plasma proteomic findings may translate to a protein fingerprint, helping to assist clinical management decisions.}, language = {en} }