Marie Brut

23
Documents

Presentation

My general research interests include computational structural biology and its application to SAR study, protein/DNA motion and accommodation mechanisms. Specifically, my work is currently focused on the development of new computational methodologies to promote innovative in silico experiments and their application to:

  • structural flexibility of biomolecules and induced-fit mechanisms

  • oncoproteins as therapeutic targets

  • predictive physical models for bio-hybrid materials

  • protein machines to integrate active functions

  • nucleic acids for DNA technologies

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Publications

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Catalytic Cycle of Type II 4′-Phosphopantetheinyl Transferases

Sabine Gavalda , Alexandre Faille , Simone Fioccola , Minh Chau Nguyen , Coralie Carivenc et al.
ACS Catalysis, 2024, 14 (11), pp.8561-8575. ⟨10.1021/acscatal.3c06249⟩
Journal articles hal-04732713 v1
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Caractériser les cinétiques des diffusions atomiques - ART : l’explorateur de surfaces d’énergie potentielle

Antoine Jay , Normand Mousseau , Nicolas Salles , Miha Gunde , Matic Poberžnik et al.
Les Techniques de l'Ingenieur, 2023, pp.Réf : RE192 v1. ⟨10.51257/a-v1-re192⟩
Journal articles hal-04467976 v1
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Enhancing DFT-based energy landscape exploration by coupling quantum mechanics and static modes

Lionel Foulon , Anne Hémeryck , Georges Landa , Marie Brut
Physical Chemistry Chemical Physics, 2022, 24 (19), pp.12011-12026. ⟨10.1039/d1cp03562b⟩
Journal articles hal-03674113 v1

Unraveling cGAS catalytic mechanism upon DNA activation through molecular dynamics simulations

Jordi Soler , Pedro Paiva , Maria Joao Joao Ramos , Pedro Alexandrino Fernandes , Marie Brut
Physical Chemistry Chemical Physics, 2021, 23 (15), pp.9524-9531. ⟨10.1039/D1CP00378J⟩
Journal articles hal-03195928 v1

Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21 N-ras and the Resulting GTP Electronic Density

Ruth Elena Tichauer , Gilles Favre , Stéphanie Cabantous , Marie Brut
Journal of Physical Chemistry B, 2019, 123 (18), pp.3935-3944. ⟨10.1021/acs.jpcb.9b02660⟩
Journal articles hal-02634170 v1

Water Distribution within Wild-Type NRas Protein and Q61 Mutants during Unrestrained QM/MM Dynamics

Ruth Elena Tichauer , Gilles Favre , Stéphanie Cabantous , Georges Landa , Anne Hémeryck et al.
Biophysical Journal, 2018, 115 (8), pp.1417-1430. ⟨10.1016/j.bpj.2018.07.042⟩
Journal articles hal-01880032 v1
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Spatial Analysis of Nanofluidic-Embedded Biosensors for Wash-Free Single-Nucleotide Difference Discrimination

Jean Cacheux , Marie Brut , Aurélien Bancaud , Pierre Cordelier , Thierry Leichle
ACS Sensors, 2018, 3 (3), pp.606 - 611. ⟨10.1021/acssensors.7b00667⟩
Journal articles hal-01762631 v1
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Modeling of the interface formation during CuO deposition on Al(111) substrate: linking material design and elaboration process parameters through multi-levels approach

Mathilde Guiltat , Nicolas Salles , Marie Brut , Georges Landa , Nicolas Richard et al.
Modelling and Simulation in Materials Science and Engineering, 2017, Focus on MMM 2016, 25 (6), pp.064005. ⟨10.1088/1361-651X/aa7bbc⟩
Journal articles hal-01574744 v1
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Dioxygen molecule adsorption and oxygen atom diffusion on clean and defective Aluminum (111) surface using first principles calculations

Mathilde Guiltat , Marie Brut , Sébastien Vizzini , Anne Hémeryck
Surface Science : A Journal Devoted to the Physics and Chemistry of Interfaces, 2017, 657, pp.79-89. ⟨10.1016/j.susc.2016.11.010⟩
Journal articles hal-01407658 v1
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Binding modes of thrombin binding aptamers investigated by simulations and experiments

Ana Trapaidze , Aurélien Bancaud , Marie Brut
Applied Physics Letters, 2015, 106 (4), pp.043702. ⟨10.1063/1.4906594⟩
Journal articles hal-01137420 v1
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Thrombin detection in murine plasma using engineered fluorescence resonance energy transfer aptadimers

Marie Brut , Ana Trapaidze , Serge Mazères , Daniel Estève , Anne Marie Gué et al.
Applied Physics Letters, 2015, 107 (23), pp.233701-1-233701-4. ⟨10.1063/1.4937351⟩
Journal articles hal-01801826 v1

Toward in Silico Biomolecular Manipulation through Static Modes: Atomic Scale Characterization of HIV-1 Protease Flexibility

Marie Brut , Alain Estève , Georges Landa , Mehdi Djafari-Rouhani
Journal of Physical Chemistry B, 2014, 118 (11), pp.2821-2830. ⟨10.1021/jp4113156⟩
Journal articles hal-01481802 v1

Mimicking DNA stretching with the Static Mode method: Shear stress versus transverse pulling stress

Marie Brut , Alain Estève , Georges Landa , Mehdi Djafari-Rouhani
European Physical Journal E: Soft matter and biological physics, 2012, 35 (8), pp.art ID 75. ⟨10.1140/epje/i2012-12075-0⟩
Journal articles istex hal-01801823 v1

Bringing aptamers into technologies: Impact of spacer terminations

Marie Brut , Ana Trapaidze , Alain Estève , Aurélien Bancaud , Damien Estève et al.
Applied Physics Letters, 2012, 100 (16), pp.163702. ⟨10.1063/1.4704658⟩
Journal articles hal-01801821 v1

Atomic Scale Determination of Enzyme Flexibility and Active Site Stability through Static Modes: Case of Dihydrofolate Reductase

Marie Brut , Alain Estève , Georges Landa , Guillaume Renvez , Mehdi Djafari-Rouhani et al.
Journal of Physical Chemistry B, 2011, 115 (7), pp.1616-1622. ⟨10.1021/jp109874z⟩
Journal articles hal-01481808 v1

The electrostatic probe: a tool for the investigation of the A beta(1-16) peptide deformations using the static modes

Guillaume Renvez , Alain Estève , Georges Landa , Marie Brut , Mehdi Djafari-Rouhani et al.
Physical Chemistry Chemical Physics, 2011, 13 (32), pp.14611-14616. ⟨10.1039/c1cp20603f⟩
Journal articles hal-01481810 v1

Deformation of thiolated nucleic acid deposited on a silicon surface: A Static Mode approach

Marie Brut , Alain Estève , Georges Landa , Guillaume Renvez , Mehdi Djafari-Rouhani et al.
Materials Science and Engineering: B, 2010, 169 (1-3), pp.23-27. ⟨10.1016/j.mseb.2009.11.014⟩
Journal articles istex hal-01481814 v1

Atomic-scale determination of DNA conformational response to strained furanose a static mode approach

Marie Brut , Alain Estève , Georges Landa , Ahmed Dkhissi , Guillaume Renvez et al.
Tetrahedron, 2010, 66 (47), pp.9123-9128. ⟨10.1016/j.tet.2010.09.083⟩
Journal articles istex hal-01481815 v1

The Static Modes: An alternative approach for the treatment of macro- and bio-molecular induced-fit flexibility

Marie Brut , Alain Estève , Georges Landa , Guillaume Renvez , Mehdi Djafari-Rouhani
European Physical Journal E: Soft matter and biological physics, 2009, 28 (1), pp.17 - 25. ⟨10.1140/epje/i2008-10397-0⟩
Journal articles istex hal-01801802 v1

A new insight into the understanding of poly(N-isopropylacrylamide) the collapsed form of molecules

Alain Estève , Adeline Bail , Georges Landa , Ahmed Dkhissi , Marie Brut et al.
Chemical Physics, 2007, 340 (1-3), pp.12-16. ⟨10.1016/j.chemphys.2007.06.054⟩
Journal articles istex hal-01481821 v1