@inproceedings{IgdeWoelkRoeblitzetal., author = {Igde, Sinaida and W{\"o}lk, Hendrik and R{\"o}blitz, Susanna and Reidelbach, Marco and Weber, Marcus and Hartmann, Laura}, title = {Identifying Multivalent Binding Kinetics of Precision Glycomacromolecules: A Kinetic Study Using kinITC}, series = {M{\"u}nster Symposium on Cooperative Effects 2015 - SFB 858, at Westf{\"a}lische Wilhelms-Universit{\"a}t M{\"u}nster, 2015}, booktitle = {M{\"u}nster Symposium on Cooperative Effects 2015 - SFB 858, at Westf{\"a}lische Wilhelms-Universit{\"a}t M{\"u}nster, 2015}, abstract = {Multivalent sugar/protein interactions are well-known to proceed through different binding modes 1-5 which in turn can be described by their binding kinetics 3-5. This study provides additional insight into the association and dissociation reaction rates of complex multivalent sugar/protein interactions. Binding kinetics of recently introduced multivalent precision glycomacromolecules 6-8 to Concanavalin A (Con A) were studied by " kinetic Isothermal Titration Calorimetry " (kinITC) 9-11. The effect of multivalency is evaluated by comparing rate constants of glycomacromolecules obtaining the same and different valency of mannose ligands and by variation of the overall backbone properties, such as hydrophilic/ hydrophoboc. In addition, binding kinetics were studied using different conformations of Con A (homodimer vs.-tetramer) and thus a different protein valency. Our results show that precision glycomacromolecule/Con A binding proceeds non-cooperatively. Further, association and dissociation rates are mainly described by intermolecular complex formation. Together with the so-called functional valency, we can discriminate between " bound " and " unbound " states for macroscopic on-and off-rates, even for such complex glycooligomer/protein systems. By comparing e.g. a mono-to a divalent glycomacromolecule for their binding to dimeric Con A, we see a lower dissociation rate for the latter. As both bind monovalently to Con A, this is a strong indication for a statistical rebinding event. Further, there is a strong dependence of multivalent binding kinetics on the ligand density of glycomacromolecules as well as the Con A conformation and thus the overall on-and off-rates.}, language = {en} } @misc{WeberDurmazSabrietal., author = {Weber, Marcus and Durmaz, Vedat and Sabri, Peggy and Reidelbach, Marco}, title = {Supplementary simulation data for Science Manuscript ai8636}, doi = {10.12752/5.MWB.1.0}, abstract = {The simulation data has been produced by Vedat Durmaz, Peggy Sabri and Marco Reidelbach inside the "Computational Molecular Design" Group headed by Marcus Weber at Zuse-Institut Berlin, Takustr. 7, D-14195 Berlin, Germany. The file contains classical simulation data for different fentanyl derivates in the MOR binding pocket at different pHs. It also includes instruction files for quantum-chemical pKa-value estimations and a description of how we derived the pKa-values from the Gaussian09 log-files.}, language = {en} } @article{SpahnDelVecchioLabuzetal., author = {Spahn, Viola and Del Vecchio, Giovanna and Labuz, Dominika and Rodriguez-Gaztelumendi, Antonio and Massaly, N. and Temp, Julia and Durmaz, Vedat and Sabri, P. and Reidelbach, Marco and Machelska, Halina and Weber, Marcus and Stein, Christoph}, title = {A nontoxic pain killer designed by modeling of pathological receptor conformations}, series = {Science}, volume = {355}, journal = {Science}, number = {6328}, doi = {10.1126/science.aai8636}, pages = {966 -- 969}, language = {en} } @article{ReidelbachWeberImhof, author = {Reidelbach, Marco and Weber, Marcus and Imhof, Petra}, title = {Prediction of perturbed proton transfer networks}, series = {PLoS ONE}, volume = {13}, journal = {PLoS ONE}, number = {12}, doi = {https://doi.org/10.1371/journal.pone.0207718}, pages = {e0207718 -- e0207718}, abstract = {The transfer of protons through proton translocating channels is a complex process, for which direct samplings of different protonation states and side chain conformations in a transition network calculation provide an efficient, bias-free description. In principle, a new transition network calculation is required for every unsampled change in the system of interest, e.g. an unsampled protonation state change, which is associated with significant computational costs. Transition networks void of or including an unsampled change are termed unperturbed or perturbed, respectively. Here, we present a prediction method, which is based on an extensive coarse-graining of the underlying transition networks to speed up the calculations. It uses the minimum spanning tree and a corresponding sensitivity analysis of an unperturbed transition network as initial guess and refinement parameter for the determination of an unknown, perturbed transition network. Thereby, the minimum spanning tree defines a sub-network connecting all nodes without cycles and minimal edge weight sum, while the sensitivity analysis analyzes the stability of the minimum spanning tree towards individual edge weight reductions. Using the prediction method, we are able to reduce the calculation costs in a model system by up to 80\%, while important network properties are maintained in most predictions.}, language = {en} } @phdthesis{Reidelbach, author = {Reidelbach, Marco}, title = {Optimal Network Generation for the Simulation of Proton Transfer Processes}, language = {en} } @article{SpahnDelVecchioRodriguezGaztelumendietal., author = {Spahn, Viola and Del Vecchio, Giovanna and Rodriguez-Gaztelumendi, Antonio and Temp, Julia and Labuz, Dominika and Kloner, Michael and Reidelbach, Marco and Machelska, Halina and Weber, Marcus and Stein, Christoph}, title = {Opioid receptor signaling, analgesic and side effects induced by a computationally designed pH-dependent agonist}, series = {Scientific Reports}, volume = {8}, journal = {Scientific Reports}, publisher = {Springer Nature}, pages = {8965}, abstract = {Novel pain killers without adverse effects are urgently needed.}, language = {en} } @misc{ReidelbachWeber, author = {Reidelbach, Marco and Weber, Marcus}, title = {MaRDI - The mathematical Research Data Initiative}, series = {Aktionstag Forschungsdaten}, journal = {Aktionstag Forschungsdaten}, doi = {10.5281/zenodo.7397588}, language = {en} } @article{ReidelbachBaiZoellneretal., author = {Reidelbach, Marco and Bai, Mei and Z{\"o}llner, Martin Sebastian and Schneeberger, Michaela and Kubicek, Katharina and Kirchberg, Henning and Bressler, Christian and Thorwart, Michael and Herrmann, Carmen}, title = {Solvent dynamics of aqueous halides before and after photoionization}, series = {Journal of Physical Chemistry}, journal = {Journal of Physical Chemistry}, language = {en} } @article{BennerBurgerGoeddekeetal., author = {Benner, Peter and Burger, Michael and G{\"o}ddeke, Dominik and G{\"o}rgen, Christiane and Himpe, Christian and Heiland, Jan and Koprucki, Thomas and Ohlberger, Mario and Rave, Stephan and Reidelbach, Marco and Saak, Jens and Sch{\"o}bel, Anita and Tabelow, Karsten and Weber, Marcus}, title = {Die mathematische Forschungsdateninitiative in der NFDI: MaRDI (Mathematical Research Data Initiative)}, series = {GAMM Rundbrief}, journal = {GAMM Rundbrief}, number = {1}, pages = {40 -- 43}, language = {de} } @article{BoegeFritzeGoergenetal., author = {Boege, Tobias and Fritze, Ren{\´e} and G{\"o}rgen, Christiane and Hanselmann, Jeroen and Iglezakis, Dorothea and Kastner, Lars and Koprucki, Thomas and Krause, Tabea and Lehrenfeld, Christoph and Polla, Silvia and Reidelbach, Marco and Riedel, Christian and Saak, Jens and Schembera, Bj{\"o}rn and Tabelow, Karsten and Weber, Marcus}, title = {Research-Data Management Planning in the German Mathematical Community}, series = {Eur. Math. Soc. Mag.}, volume = {130}, journal = {Eur. Math. Soc. Mag.}, doi = {10.4171/mag/152}, pages = {40 -- 47}, abstract = {In this paper we discuss the notion of research data for the field of mathematics and report on the status quo of research-data management and planning. A number of decentralized approaches are presented and compared to needs and challenges faced in three use cases from different mathematical subdisciplines. We highlight the importance of tailoring research-data management plans to mathematicians' research processes and discuss their usage all along the data life cycle.}, language = {en} }