@article {2019|2076, title = {Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates.}, journal = {Proc Natl Acad Sci U S A}, volume = {116}, year = {2019}, month = {2019 12 17}, pages = {26057-26065}, abstract = {

Protein aggregation is a complex physiological process, primarily determined by stress-related factors revealing the hidden aggregation propensity of proteins that otherwise are fully soluble. Here we report a mechanism by which glycolytic glyceraldehyde-3-phosphate dehydrogenase of (AtGAPC1) is primed to form insoluble aggregates by the glutathionylation of its catalytic cysteine (Cys149). Following a lag phase, glutathionylated AtGAPC1 initiates a self-aggregation process resulting in the formation of branched chains of globular particles made of partially misfolded and totally inactive proteins. GSH molecules within AtGAPC1 active sites are suggested to provide the initial destabilizing signal. The following removal of glutathione by the formation of an intramolecular disulfide bond between Cys149 and Cys153 reinforces the aggregation process. Physiological reductases, thioredoxins and glutaredoxins, could not dissolve AtGAPC1 aggregates but could efficiently contrast their growth. Besides acting as a protective mechanism against overoxidation, S-glutathionylation of AtGAPC1 triggers an unexpected aggregation pathway with completely different and still unexplored physiological implications.

}, issn = {1091-6490}, doi = {10.1073/pnas.1914484116}, author = {Zaffagnini, Mirko and Marchand, Christophe H and Malferrari, Marco and Murail, Samuel and Bonacchi, Sara and Genovese, Damiano and Montalti, Marco and Venturoli, Giovanni and Falini, Giuseppe and Marc Baaden and Lemaire, St{\'e}phane D and Fermani, Simona and Trost, Paolo} } @article {2016|1759, title = {Great interactions: How binding incorrect partners can teach us about protein recognition and function}, journal = {Proteins: Struct., Funct., Bioinf.}, year = {2016}, pages = {n/a-n/a}, keywords = {binding sites prediction, coarse grain models, docking, protein-protein interaction, protein-protein interfaces}, issn = {1097-0134}, doi = {10.1002/prot.25086}, author = {Vamparys, Lydie and B. Laurent and Carbone, A. and S Sacquin-Mora} } @article {2013|1528, title = {{G}ame on, science - how video game technology may help biologists tackle visualization challenges}, journal = {Plos One}, volume = {8}, number = {3}, year = {2013}, pages = {e57990}, author = {Lv, Z. and Tek, A. and Da Silva, F. and Empereur-mot, C. and Matthieu Chavent and Marc Baaden} } @article {2013|1974, title = {{A} gating mechanism of pentameric ligand-gated ion channels}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {110}, number = {42}, year = {2013}, month = {oct}, pages = {E3987{\textendash}3996}, author = {Calimet, N. and Simoes, M. and Changeux, J. P. and Karplus, M. and Antoine Taly and Cecchini, M.} } @article {2012|1960, title = {General Anesthetics Predicted to Block the {GLIC} Pore with Micromolar Affinity}, journal = {Plos Comput. Biol.}, volume = {8}, number = {5}, year = {2012}, pages = {e1002532}, publisher = {Public Library of Science}, abstract = {

Author Summary

Although general anesthesia is performed every day on thousands of people, its detailed microscopic mechanisms are not known. What is known is that general anesthetic drugs modulate the activity of ion channels in the central nervous system. These channels are proteins that open in response to binding of neurotransmitter molecules, creating an electric current through the cell membrane and thus propagating nerve impulses between cells. One possible mechanism for ion channel inhibition by anesthetics is that the drugs bind inside the pore of the channels, blocking ion current. Here we investigate such a pore block mechanism by computing the strength of the drugs{\textquoteright} interaction with the pore {\textendash} and hence the likelihood of binding, in the case of GLIC, a bacterial channel protein. The results, obtained from numerical simulations of atomic models of GLIC, indicate that the anesthetics isoflurane and propofol have a tendency to bind in the pore that is strong enough to explain blocking of the channel, even at low concentration of the drugs.

}, doi = {10.1371/journal.pcbi.1002532}, url = {http://dx.doi.org/10.1371\%2Fjournal.pcbi.1002532}, author = {LeBard, David N. and J{\'e}r{\^o}me H{\'e}nin and Roderic G Eckenhoff and Michael L Klein and Brannigan, Grace} } @article {2011|1972, title = {{A}gonist trapped in {A}{T}{P}-binding sites of the {P}2{X}2 receptor}, journal = {Proc. Natl. Acad. Sci. U.s.a.}, volume = {108}, number = {22}, year = {2011}, month = {may}, pages = {9066{\textendash}9071}, author = {Jiang, R. and Lemoine, D. and Martz, A. and Antoine Taly and Gonin, S. and Prado de Carvalho, L. and Specht, A. and Grutter, T.} } @article {2011|1437, title = {GPU-accelerated atom and dynamic bond visualization using HyperBalls: a unified algorithm for balls, sticks and hyperboloids}, journal = {J. Comput. Chem.}, volume = {32}, number = {13}, year = {2011}, month = {oct}, pages = {2924{\textendash}2935}, doi = {10.1002/jcc.21861/abstract}, author = {Matthieu Chavent and A. Vanel and A. Tek and B. L{\'e}vy and S. Robert and B. Raffin and Marc Baaden} } @article {2011|1393, title = {GPU-powered tools boost molecular visualization}, journal = {Briefings Bioinf.}, volume = {12}, year = {2011}, month = {feb}, pages = {689{\textendash}701}, author = {Matthieu Chavent and B. L{\'e}vy and M. Krone and K. Bidmon and J. P. Nomin{\'e} and T. Ertl and Marc Baaden} } @conference {2004|1423, title = {GenoMEDIA, a Midlleware Platform for Distributed Genomic Information}, booktitle = {International Conference on Information \& Communication Technologies: from Theory to Applications (ICTTA 2004 - IEEE)}, year = {2004}, month = {apr}, address = {Damascus - Syria}, author = {P.-E. Gros and Nicolas F{\'e}rey and J. H{\'e}risson and R. Gherbi} } @article {2003|1914, title = {Generating conformations for two zinc-binding sites of HIV-1 nucleocapsid protein from random conformations by a hierarchical procedure and polarizable force field}, journal = {J. Phys. Chem. B}, volume = {107}, number = {20}, year = {2003}, month = {may}, pages = {4862{\textendash}4870}, doi = {10.1021/jp022527z}, author = {Gresh, N and Philippe Derreumaux} } @article {2003|1761, title = {Geometry of the DNA strands within the RecA nucleofilament: role in homologous recombination}, journal = {Q. Rev. Biophys.}, volume = {36}, year = {2003}, month = {nov}, pages = {429{\textendash}53}, abstract = {

Homologous recombination consists of exchanging DNA strands of identical or almost identical sequence. This process is important for both DNA repair and DNA segregation. In prokaryotes, it involves the formation of long helical filaments of the RecA protein on DNA. These filaments incorporate double-stranded DNA from the cell\&$\#$39;s genetic material, recognize sequence homology and promote strand exchange between the two DNA segments. DNA processing by these nucleofilaments is characterized by large amplitude deformations of the double helix, which is stretched by 50\% and unwound by 40\% with respect to B-DNA. In this article, information concerning the structure and interactions of the RecA, DNA and ATP molecules involved in DNA strand exchange is gathered and analyzed to present a view of their possible arrangement within the filament, their behavior during strand exchange and during ATP hydrolysis, the mechanism of RecA-promoted DNA deformation and the role of DNA deformation in the process of homologous recombination. In particular, the unusual characteristics of DNA within the RecA filament are compared to the DNA deformations locally induced by architectural proteins which bind in the DNA minor groove. The possible role and location of two flexible loops of RecA are discussed.

}, author = {Chantal Pr{\'e}vost and M. Takahashi} } @article {2000|1958, title = {Generating ensemble averages for small proteins from extended conformations by Monte Carlo simulations}, journal = {Phys. Rev. Lett.}, volume = {85}, number = {1}, year = {2000}, month = {jul}, pages = {206{\textendash}209}, doi = {10.1103/PhysRevLett.85.206}, author = {Philippe Derreumaux} } @article {1992|1626, title = {Global optimization of conformation energy of polypeptides by tunnel algorithm}, journal = {Biophysics}, volume = {37}, year = {1992}, pages = {226{\textendash}230}, author = {M. G. Petuhov and V. E. Dorofeyev and R. A. Abagyan and Alexey K Mazur} } @article {1991, title = {{G}roove-backbone interaction in {B}-{D}{N}{A}. {I}mplication for {D}{N}{A} condensation and recombination}, journal = {J. Mol. Biol.}, volume = {221}, year = {1991}, month = {oct}, pages = {919{\textendash}940}, author = {Y Timsit and Moras, D.} } @article {1987|1991, title = {Gas-solution microcalorimeter for determining heat binding curves}, journal = {Rev. Sci. Instr.}, volume = {58}, year = {1987}, pages = {632{\textendash}638}, author = {Bishop, G. A. and Parody-Morreale, A. and Robert, C. and and Gill, S. J.} }