@article {2023|2163, title = {Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology}, journal = {J Chem Inf Model}, year = {2023}, month = {Jun}, author = {Graille, M and S Sacquin-Mora and Antoine Taly} } @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 = {

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.

}, 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 = {

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.

}, 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} } @article {2021|2148, title = {Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry}, journal = {The Journal of Chemical Physics}, volume = {154}, year = {2021}, pages = {204101}, doi = {10.1063/5.0046853}, url = {https://doi.org/10.1063/5.0046853}, author = {Elise Dubou{\'e}-Dijon and J{\'e}r{\^o}me H{\'e}nin} } @article {2020|2145, title = {Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy}, journal = {Phys. Chem. Chem. Phys.}, volume = {22}, year = {2020}, pages = {24014-24027}, chapter = {24014}, abstract = {

In spite of the biological importance of the binding of Zn2+, Ca2+, and Mg2+ to the carboxylate group, cation\–acetate binding affinities and binding modes remain actively debated. Here, we report the first use of Raman multivariate curve resolution (Raman-MCR) vibrational spectroscopy to obtain self-consistent free and bound metal acetate spectra and one-to-one binding constants, without the need to invoke any a priori assumptions regarding the shapes of the corresponding vibrational bands. The experimental results, combined with classical molecular dynamics simulations with a force field effectively accounting for electronic polarization via charge scaling and ab initio simulations, indicate that the measured binding constants pertain to direct (as opposed to water separated) ion pairing. The resulting binding constants do not scale with cation size, as the binding constant to Zn2+ is significantly larger than that to either Mg2+ or Ca2+, although Zn2+ and Mg2+ have similar radii that are about 25\% smaller than Ca2+. Remaining uncertainties in the metal acetate binding free energies are linked to fundamental ambiguities associated with identifying the range of structures pertaining to non-covalently bound species.

}, doi = {10.1039/D0CP02987D}, url = {https://pubs.rsc.org/en/content/articlelanding/2020/cp/d0cp02987d$\#$!divAbstract}, author = {Mendes de Oliveira, Denilson and Samual R. Zukowski and Vladimir Palivec and J{\'e}r{\^o}me H{\'e}nin and Hector Martinez-Seara and Dor Ben-Amotz and Pavel Jungwirth and Elise Dubou{\'e}-Dijon} } @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} } @conference {2018|2069, title = {Is the boundary of fun redefined in a mixed-reality serious game?}, year = {2018}, author = {Antoine Taly} } @article {2018|2112, title = {Breaking down cellulose fibrils with a mid-infrared laser}, journal = {Cellulose}, volume = {25}, year = {2018}, pages = {5553{\textendash}5568}, author = {Domin, Dominik and Man, Viet Hoang and Van-Oanh, Nguyen-Thi and Wang, Junmei and Kawasaki, Takayasu and Philippe Derreumaux and Phuong Hoang Nguyen} } @inbook {2016|1721, title = {Bridging Enzymatic Structure Function via Mechanics: A Coarse-Grain Approach}, booktitle = {Methods in Enzymology}, year = {2016}, pages = {227{\textendash}248}, publisher = {Academic Press}, organization = {Academic Press}, keywords = {Coarse-grain simulations}, issn = {0076-6879}, doi = {10.1016/bs.mie.2016.05.022}, url = {http://www.sciencedirect.com/science/article/pii/S007668791630057X}, author = {S Sacquin-Mora} } @proceedings {2014|1577, title = {{BIOIMAGING} 2014 - Proceedings of the International Conference on Bioimaging, ESEO, Angers, Loire Valley, France, 3-6 March, 2014}, year = {2014}, publisher = {SciTePress}, editor = {M{\'a}rio Forjaz Secca and Jan Schier and Guy Plantier and Tanja Schultz and Ana L. N. Fred and Hugo Gamboa} } @article {2013|1797, title = {Biomolecular hydration dynamics: a jump model perspective}, journal = {Chem. Soc. Rev.}, volume = {42}, number = {13}, year = {2013}, pages = {5672{\textendash}5683}, author = {Fogarty, Aoife C. and Elise Dubou{\'e}-Dijon and Sterpone, Fabio and Hynes, James T. and Laage, Damien} } @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} } @article {2011|1834, title = {{B}inding modes of noncompetitive {G}{A}{B}{A}-channel blockers revisited using engineered affinity-labeling reactions combined with new docking studies}, journal = {J. Agric. Food Chem.}, volume = {59}, number = {7}, year = {2011}, month = {apr}, pages = {2803{\textendash}2807}, author = {Charon, S. and Antoine Taly and Rodrigo, J. and Perret, P. and Goeldner, M.} } @article {2008|1615, title = {The beta-strand-loop-beta-strand conformation is marginally populated in beta(2)-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations}, journal = {Biophys. J.}, volume = {95}, number = {2}, year = {2008}, month = {jul}, pages = {510{\textendash}517}, doi = {10.1529/biophysj.107.125054}, author = {Liang, Chungwen and Philippe Derreumaux and Mousseau, Normand and Wei, Guanghong} } @article {2005|1980, title = {The beta alpha beta alpha beta alpha elementary Supersecondary structure of the Rossmann fold from porcine lactate dehydrogenase exhibits characteristics of a molten globule}, journal = {Proteins: Struct., Funct., Bioinf.}, volume = {60}, number = {4}, year = {2005}, month = {sep}, pages = {740{\textendash}745}, doi = {10.1002/prot.20507}, author = {Coincon, M and Heitz, A and Chiche, L and Philippe Derreumaux} } @article {1991|1503, title = {{B}ase-pairing shift in the major groove of ({C}{A})n tracts by {B}-{D}{N}{A} crystal structures}, journal = {Nature}, volume = {354}, year = {1991}, month = {nov}, pages = {167{\textendash}170}, author = {Y Timsit and Vilbois, E. and Moras, D.} } @article {1989|1821, title = {Binding of oxygen and carbon monoxide to the hemocyanin from the spiny lobster}, journal = {J. Mol. Biol.}, volume = {207}, number = {4}, year = {1989}, month = {jun}, pages = {829{\textendash}832}, author = {Connelly, P R and Johnson, C R and Robert, C H and Bak, H J and Gill, S J} }