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| - | ====== Journées du Centre Blaise Pascal : Exploring (Free) Energy Landscapes | ||
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| - | Location: Salle de réunion LR6 C 023, Centre Blaise Pascal, ENS-Lyon, France | ||
| - | November 20th, 2012 | ||
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| - | Organizing committee: | ||
| - | * **Paul Fleurat-Lessard**, | ||
| - | * **Claire Loison**, Laboratoire de Spectrométrie Ionique et Moléculaire - Université de Lyon / CNRS | ||
| - | * **Cerasela Calugaru**, Centre Blaise Pascal - ENS de Lyon | ||
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| - | Administrative coordination: | ||
| - | * **Samantha Barendson**, | ||
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| - | The workshop is supported by: | ||
| - | * the Centre Blaise Pascal | ||
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| - | La communauté des lyonnais utilisant l' | ||
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| - | Entre les objets d' | ||
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| - | Bien évidemment, | ||
| - | Nous chercherons à présenter des applications variées, des méthodes assez générales utilisées dans différents domaines, et des matériels toujours nouveaux et toujours plus performants. | ||
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| - | ===== 1. Program ===== | ||
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| - | 09h30 **Christophe Chipot** (UHP Nancy): // | ||
| - | 10h30 Coffee break \\ | ||
| - | 10h45 **Martin Spichty** (ENS Lyon): // | ||
| - | 11h15 **Chandan Patel** (ENS Lyon): //Complex DNA lesions : insights from QM/ | ||
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| - | 11h45 - 14h00 Buffet Lunch | ||
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| - | 14h00 **Ralf Everaers** (ENS Lyon): //A statistical mechanical framework for adaptive resolution multiscale simulations// | ||
| - | 15h00 Coffee break \\ | ||
| - | 15h15 **Benjamin Bouvier** (IBCP Lyon): // | ||
| - | 15h45 **Pawel Koziatek** (INP Grenoble): //Potential energy landscape of glasses: distributions of activation energies and attempt frequencies// | ||
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| - | ===== 2. Abstracts ===== | ||
| - | **Christophe Chipot (UHP Nancy)**: // | ||
| - | One of the current grand challenges of molecular modeling is the faithful description of the reaction coordinates that characterize processes of biological interest. Closely related to this endeavor, the determination of accurate free-energy changes along the model reaction coordinates constitutes an even greater challenge. Sampling the relevant degrees of freedom while circumventing hidden barriers will be illustrated in four case-studies, | ||
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| - | **Martin Spichty (ENS Lyon)**: // | ||
| - | Peptide aptamers, conceived to conceptually resemble antibodies, are man-made combinatorial protein reagents. They consist of a random sequence loop introduced into a scaffold protein (see Figure). The ends of the loop are restrained by a disulfide bond. When large libraries of random loops are expressed in living cells, certain loop sequences can adopt a conformation that is capable of interacting with a specific target protein and thereby modifying the functioning of the cell. Molecular biologists can determine the amino-acid sequence of such bioactive peptide aptamers but the three-dimensional structure remains unknown. This seminar will show how biomolecular computer simulations, | ||
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| - | **Chandan Patel (ENS Lyon)**: //Complex DNA lesions : insights from QM/MM--MD// \\ | ||
| - | DNA is continously exposed to a vast number of damaging events triggered by endogeneous and exogeneous agents.[4] Formation and structure variety of these lesions have been studied using exper- iments. Although experimental studies, within their confines, have provided very useful information regarding structural properties of some of the DNA lesions and their repair, they do not provide any mechanistic or energetic information pertaining to their formation. Computational Biochemistry has recently beneficiated from the advent of a large range methods [3], which rely on the increase of avail- able, highly-parallelized computational resources, but were first and foremost motivated by the utter need to describe as accurately as possible complex, strongly heterogeneous systems. Such multiscale and dynamical simulations have become routine for proteic systems [5], yet remain scarce on DNA. In the first seminal example in 2004, Parrinello and coworkers stressed out the importance of the B-helix environment on guanine radical cation structure. [2] QM/MM methodologies are particularly useful in this regard, as they can be used to study reaction mechanisms and electronic porperties in large systems. Here, we present our studies on oxidatively generated intrastrand crosslinks within DNA [1, 6]. In absence of NMR or X-ray structures, the B-helix distortion can be inspected purely on the basis of molecular simulations. Preliminary results obtained on other oxidative cross-link adducts, such as dCyd341, will also be discussed.[7] \\ | ||
| - | References : \\ | ||
| - | [1] Julian Garrec, Chandan Patel, Ursula Rothlisberger, | ||
| - | [2] Francesco Luigi Gervasio, Alessandro Laio, Marcella Iannuzzi, and Michele Parrinello. Influence of DNA Structure on the Reactivity of the Guanine Radical Cation. Chemistry A European Journal, 10(19): | ||
| - | [3] Eric H. Lee, Jen Hsin, Marcos Sotomayor, Gemma Comellas, and Klaus Schulten. Discovery Through the Computational Microscope. Structure, 17(10):1295 – 1306, 2009. \\ | ||
| - | [4] T. Lindahl and DE Barnes. Repair of endogenous DNA damage, 65. 2000. \\ | ||
| - | [5] J.A. McCammon, B.R. Gelin, M. Karplus, et al. Dynamics of folded proteins. Nature, 267(5612): | ||
| - | [6] C. Patel, J. Garrec, C. Dupont, and E. Dumont. What singles out the G[8-5]C intrastrand DNA cross-link ? Mechanistic and structural insights from hybrid Car-Parrinello simulations. submitted. \\ | ||
| - | [7] P. Regulus, B. Duroux, P.A. Bayle, A. Favier, J. Cadet, and J.L. Ravanat. Oxidation of the sugar moiety of DNA by ionizing radiation or bleomycin could induce the formation of a cluster DNA lesion. Proceedings of the National Academy of Sciences, 104(35): | ||
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| - | **Ralf Everaers (ENS Lyon), Rafael Delgado-Buscalioni (UAM, Madrid)**: //A statistical mechanical framework for adaptive resolution multiscale simulations// | ||
| - | Simultaneous multi-scale schemes directly couple parts of a system described with different models. The idea behind the embedding is to reduce finite size effects in the more finely resolved region compared to a one-level description with periodic or open boundary conditions. Classical examples are QM/MM and the reaction field method for long-range interactions. The particularity of the recently introduced AdResS scheme [1] is to allow a free exchange of particles across the interface between different regions. In the presentation, | ||
| - | References : \\ | ||
| - | [1] M. Praprotnik, L. Delle Site, and K. Kremer, The Journal of Chemical Physics 123, 224106 (2005); M. Praprotnik, L. Delle Site, and K. Kremer, Phys. Rev. E 73, 066701 (2006); M. Praprotnik, L. Delle Site, and K. Kremer, J. Chem. Phys. 126, 134902 (2007); M. Praprotnik, L. Delle Site, and K. Kremer, Annual Review of Physical Chemistry 59, 545 (2008); L. Delle Site, S. Leon, and K. Kremer, Journal of the American Chemical Society 126, 2944 (2004); S. Fritsch, C. Junghans, and K. Kremer, J. Chem. Theory Comput. 8, 398 (2012); A. B. Poma and L. D. Site, Physical Review Letters 104, 250201 (2010); R. Potestio and L. Delle Site, J. Chem. Phys. 136 (2012); S. Poblete, M. Praprotnik, K. Kremer, and L. Delle Site, J. Chem. Phys. 132, 114101 (2010); S. Fritsch, S. Poblete, C. Junghans, G. Ciccotti, L. Delle Site, and K. Kremer, Phys. Rev. Lett. 108 (2012). \\ | ||
| - | [2] R. Potestio, S. Fritsch, P. Espanol, R. Delgado-Buscalioni, | ||
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| - | **Benjamin Bouvier (IBCP Lyon)**: // | ||
| - | Biological macromolecules do not function isolatedly, but form intricate interaction networks featuring multi-partner complexes of diverse natures and binding strengths. The mechanisms driving the recognition between partners of such complexes are very efficient yet very subtle, allowing for instance faster-than-diffusion discrimination between similar DNA sequences. They often involve a combination of chemical interactions at an interface (direct recognition) and large-scale collective motion by which each partner probes the other’s ability to deform (indirect recognition). The amplitude of motion and binding free energies involved prevent the study of such recognition processes using standard molecular dynamics simulations on current computers. In this talk, we present examples of protein-DNA, | ||
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| - | **Pawel Koziatek (INP Grenoble), D. Rodney, J. L. Barrat**: //Potential energy landscape of glasses: distributions of activation energies and attempt frequencies// | ||
| - | Molecular dynamics is a powerful tool to simulate the atomic-scale processes that occur in bulk metallic glasses either at rest during aging or under plastic deformation. This technique is however limited to short-time dynamics and does not give access to the slow thermally-activated events that progressively dominate the glass dynamics when the temperature and/or the strain rate are decreased. We report here results obtained with a saddle-point search method, the Activation-Relaxation Technique, used to determine thermally-activated paths in glasses. From the paths, we determine the distributions of activation energies and attempt frequencies, | ||
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| - | ===== 3. Participants ===== | ||
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| - | ^ Family name ^ First name ^ Institution ^ | ||
| - | | Albaret | Tristan | Universite Lyon 1 | | ||
| - | | Bacchus | Marie-Christine | LASIM | | ||
| - | | Blanchet | Christophe | CNRS IBCP | | ||
| - | | Calugaru | Cerasela | ENS de Lyon | | ||
| - | | Caracas | Ema | ENS de Lyon | | ||
| - | | Caracas | Razvan | CNRS, ENS de Lyon | | ||
| - | | Cheaib | Bachar | ENS | | ||
| - | | Chuffart | Florent | CNRS | | ||
| - | | DELBECQ | Françoise | NRS-ENS | | ||
| - | | DONG | Wei | ENS-Lyon | | ||
| - | | Dumont | Elise | Laboratoire de Chimie, ENS de Lyon | | ||
| - | | Filbet | FRancis | univ Lyon 1 | | ||
| - | | Fleurat-Lessard | Paul | Laboratoire de Chimie de l'ENS de Lyon | | ||
| - | | FORSTER | Georg Daniel | LASIM at University Lyon 1 / Claude Bernard | | ||
| - | | Gebresilassie | Abel Gebreegziabher | INSA-Lyon | | ||
| - | | Giordano | Valentina | LPMCN | | ||
| - | | Houwaart | Torsten | ENS de Lyon | | ||
| - | | Ignacio | Maxime | LPMCN | | ||
| - | | Josh | Kaustubh | ENS de Lyon | | ||
| - | | Jost | Daniel | ENS de Lyon | | ||
| - | | Le Goff | Thomas | LPMCN | | ||
| - | | MERABIA | Samy | CNRS-université Lyon 1 | | ||
| - | | Meyer | Sam | ENS de Lyon | | ||
| - | | MICHON | Alexi | CNRS BMSSI | | ||
| - | | Renaut | Gilles-Alexis | ECL LMFA | | ||
| - | | STEBE | Pierre Nicolas | ENS de Lyon | | ||
| - | | TANGUY | Anne | Université Lyon 1 | | ||
| - | | VERDIER | Timothée | Labo de physique de l'ENS de Lyon | | ||
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