@article {2022,
	title = {Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces.},
	journal = {Langmuir},
	volume = {38},
	year = {2022},
	month = {2022 Feb 01},
	pages = {1313-1323},
	abstract = {<p>The efficient immobilization of enzymes on surfaces remains a complex but central issue in the biomaterials field, which requires us to understand this process at the atomic level. Using a multiscale approach combining all-atom molecular dynamics and coarse-grain Brownian dynamics simulations, we investigated the adsorption behavior of β-glucosidase A (βGA) on bare and self-assembled monolayer (SAM)-functionalized gold surfaces. We monitored the enzyme position and orientation during the molecular dynamics (MD) trajectories and measured the contacts it forms with both surfaces. While the adsorption process has little impact on the protein conformation, it can nonetheless perturb its mechanical properties and catalytic activity. Our results show that compared to the SAM-functionalized surface, the adsorption of βGA on bare gold is more stable, but less specific, and more likely to disrupt the enzyme\&$\#$39;s function. This observation emphasizes the fact that the structural organization of proteins at the solid interface is a key point when designing devices based on enzyme immobilization, as one must find an acceptable stability-activity trade-off.</p>
},
	issn = {1520-5827},
	doi = {10.1021/acs.langmuir.1c01774},
	author = {Bourassin, Nicolas and Barbault, Florent and Marc Baaden and S Sacquin-Mora}
}
@article {2022|2156,
	title = {Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies},
	journal = {Frontiers in Molecular Biosciences},
	volume = {9},
	year = {2022},
	pages = {826136},
	abstract = {<p>Recent advances in structural biophysics and integrative modelling methods now allow us to decipher the structures of large macromolecular assemblies. Understanding the dynamics and mechanisms involved in their biological function requires rigorous integration of all available data. We have developed a complete modelling pipeline that includes analyses to extract biologically significant information by consistently combining automated and interactive human-guided steps. We illustrate this idea with two examples. First, we describe the ryanodine receptor, an ion channel that controls ion flux across the cell membrane through transitions between open and closed states. The conformational changes associated with the transitions are small compared to the considerable system size of the receptor; it is challenging to consistently track these states with the available cryo-EM structures. The second example involves homologous recombination, in which long filaments of a recombinase protein and DNA catalyse the exchange of homologous DNA strands to reliably repair DNA double-strand breaks. The nucleoprotein filament reaction intermediates in this process are short-lived and heterogeneous, making their structures particularly elusive. The pipeline we describe, which incorporates experimental and theoretical knowledge combined with state-of-the-art interactive and immersive modelling tools, can help overcome these challenges. In both examples, we point to new insights into biological processes that arise from such interdisciplinary approaches.</p>
},
	issn = {2296-889X},
	doi = {10.3389/fmolb.2022.826136},
	url = {https://www.frontiersin.org/article/10.3389/fmolb.2022.826136},
	author = {Molza, Anne-Elisabeth and Westermaier, Yvonne and Moutte, Magali and Ducrot, Pierre and Danilowicz, Claudia and Godoy-Carter, Veronica and Prentiss, Mara and Robert, Charles H. and Marc Baaden and Pr{\'e}vost, Chantal}
}
@inbook {2018|2082,
	title = {Biomimetic water channels: general discussion.},
	booktitle = {Faraday Discuss},
	volume = {209},
	year = {2018},
	month = {2018 09 28},
	pages = {205-229},
	issn = {1364-5498},
	doi = {10.1039/c8fd90020e},
	author = {Marc Baaden and Barboiu, Mihail and Bill, Roslyn M and Chen, Chun-Long and Davis, Jeffery and Di Vincenzo, Maria and Freger, Viatcheslav and Fr{\"o}ba, Michael and Gale, Philip A and Gong, Bing and H{\'e}lix-Nielsen, Claus and Hickey, Robert and Hinds, Bruce and Hou, Jun-Li and Hummer, Gerhard and Kumar, Manish and Legrand, Yves-Marie and Lokesh, Mahesh and Mi, Baoxia and Murail, Samuel and Pohl, Peter and Sansom, Mark and Song, Qilei and Song, Woochul and T{\"o}rnroth-Horsefield, Susanna and Vashisth, Harish and V{\"o}gele, Martin}
}
@article {2012|1382,
	title = {Bient{\^o}t dans votre amphith{\'e}{\^a}tre, la chimie fera son cin{\'e}ma. De la bonne utilisation des ressources informatiques pour l{\textquoteright}enseignement : visualisation mol{\'e}culaire, illustration de processus chimiques et de mod{\`e}les physiques},
	journal = {Actualit{\'e} Chimique},
	volume = {363},
	year = {2012},
	author = {Matthieu Chavent and Marc Baaden and E. H{\'e}non and S. Antonczak}
}
