Publications | Matthieu Chavent

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Peer-reviewed scientific articles:

36- Supramolecular organization and dynamics of mannosylated phosphatidylinositol lipids in the mycobacterial plasma membrane
C. M. Brown, R. A. Corey, A. Grélard, Y. Gao, Y. K. Choi, E. Luna, M. Gilleron, N. Destainville, J. Nigou, A. Loquet, E. Fullam, W. Im+, P J. Stansfeld+, M. Chavent+(+ co-corresponding authors)
PNAS, 2023, 120, e2212755120 BioRxiv version

35- GPC3-Unc5 receptor complex structure and role in cell migration
O. Akkermans, C. Delloye-Bourgeois, C. Peregrina, M. Carrasquero-Ordaz, M. Kokolaki, M. Beibeira-Santana, M. Chavent, F. Reynaud, R. Raj, J. Agirre, M. Aksu, E. S. White, E. Lowe, D. Ben Amar, S. Zaballa, J. Huo, I. Pakos, P. T. N. McCubbin, D Comoletti, R. J. Owens, C. V. Robinson, V. Castellani+, E. Seiradake+ (+ co-corresponding authors)
Cell, 2022, 185, 21, 3931-3949 BioRxiv version

34- The guidance and adhesion protein FLRT2 dimerizes in cis via dual small-X3-small transmembrane motifs
V. Jackson, J. Hermann, C. J. Tynan, D. Rolfe, R. A. Corey, A. L. Duncan, M. Noriega, A. Chu, A. Kalli, E. Y. Jones, M. S. P. Sansom, M. L. Martin-Fernandez+, E. Seiradake+, M. Chavent+ (+ co-corresponding authors)
Structure, 2022, 30, 9, 1354-1365 BioRxiv version

33- Proteasome complexes experience profound structural and functional rearrangements throughout mammalian spermatogenesis
D. Zivkovic, A. Sanchez Dafun, T. Menneteau, A. Schahl, S. Lise, C. Kervarrec, A. Toste Rego, P. C. A. da Fonseca, M. Chavent, C. Pineau, O. Burlet-Schiltz, J. Marcoux, M. P. Bousquet
PNAS, 2022, 119 (15) e2116826119

32- Visualizing protein structures — tools and trends
X. Martinez, M. Chavent, M. Baaden
Biochem Soc Trans (2020) 48 (2): 499–506

31- Structural Basis of Teneurin-Latrophilin Interaction in Repulsive Guidance of Migrating Neurons
J. D. del Toro, M. A. Carrasquero-Ordaz, A. Chu, T. Ruff, M. Shahin, V. A. Jackson, M. Chavent, M. Berbeira-Santana, G. Seyit-Bremer, S. Brignani, R. Kaufmann, E. Lowe, R. Klein, E. Seiradake
Cell, 2020, 180 (2), 323–339 Open Access

30- The conical shape of DIM lipids promotes Mycobacterium tuberculosis infection of macrophages
J. Augenstreich, E. Haanappel, G. Ferré, G. Czaplicki, F. Jolibois, N. Destainville, C. Guilhot, A. Milon+, C. Astarie-Dequeker+, M. Chavent+ (+ co-corresponding authors)
PNAS, 2019, 116 (51), 25649-25658 BioRxiv version pdf
Paper highlighted by K. Gawrisch in the same PNAS issue: Mycobacterium tuberculosis enters macrophages with aid from a bacterial lipid

29- Sharing Data from Molecular Simulations
M. Abraham, R. Apostolov, J.n Barnoud, P. Bauer, C. Blau, A. M.J.J. Bonvin, M. Chavent, J. Chodera, K. Čondić-Jurkić, L. Delemotte, H. Grubmüller, R. J. Howard, E. J. Jordan, E. Lindahl, O. H. S. Ollila, J. Selent, D. G. A. Smith, P. J. Stansfeld, J. K. S. Tiemann, M. Trellet, C. Woods, A. Zhmurov
JCIM, 2019, 59 (10), 4093-4099 ChemRxiv version
Paper based on Bioexcel workshop held in Stockholm Nov 2018: videos of the discussions available here

28- Molecular Graphics: Bridging Structural Biologists and Computer Scientists
X. Martinez, M. Krone, N. alharbi, A. Rose, R. Laramee, S. O'Donoghue, M. Baaden, M. Chavent
Structure, 2019, 27 (11), 1617-1623

27- Cholesterol Interaction Sites on the Transmembrane Domain of the Hedgehog Signal Transducer and Class F G Protein-Coupled Receptor Smoothened
G. Hedger, H. Koldso, M. Chavent, , E. Y. Jones, M. S. P. Sansom
Structure, 2018, 27 (3), 549-559

26- Nanoscale protein interactions determine the mesoscale dynamic organization of bacterial outer membranes
M. Chavent+, A. Duncan+, P. Rassam+, O. Birkholz, J. Hélie, T. Reddy, D. Belayev, B. Hambly, J. Piehler, C. Kleanthous, M. S. P. Sansom (+ co-1st authors)
Nature Communications, 2018, 9, Article number: 2846

25- Interactions of the EphA2 kinase domain with PIPs in membranes: Implications for receptor function
M. Chavent, D. Karia, A. Kalli, J. Domanski, A. Duncan, G. Hedger, P. Stansfeld, E. Seiradake, E. Y. Jones, M. S. P. Sansom
Structure, 2018, 26 (7), 1025-1034

24- Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes
A. Duncan, T. Reddy, H. Koldsø, J. Hélie, P. W. Fowler, M. Chavent, M. S. P. Sansom
Scientific Reports, 2017, 7, Article number: 16647

23- Molecular visualization of computational biology data: A survey of surveys
N. Alharbi, M. Alharbi, X. Martinez, M. Krone, A. Rose, M. Baaden, R.S. Laramee, M. Chavent
Eurovis conference, 2017, conference paper

22- Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes
G. Hedger, S. L. Rouse, J. Domański, M. Chavent, H. Koldsø, M. S. P. Sansom
Biochemistry, 2016, 55 (45), 6238-6249

21- MolPathFinder: interactive multi-dimensional path filtering of molecular dynamics simulation data
N. Alharbi, R. S. Laramee, M. Chavent
Proceedings of the conference on Computer Graphics & Visual Computing, 2016, 9-16

20- Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale
M. Chavent, A. Duncan, M. S. P. Sansom
Current opinion in structural biology, 2016, 40, 8-16.

19- Membrane stiffness is modified by integral membrane proteins
P.W. Fowler, J. Hélie, A. Duncan, M. Chavent, H. Koldsø, M. S. P. Sansom
Soft matter, 2016, 12 (37), 7792-7803.

18- Super-complexes of adhesion GPCRs and neural guidance receptors
V. A. Jackson, S. Mehmood+, M. Chavent+, P. Roversi, M. Carrasquero, D. del Toro, G. Seyit-Bremer, F. M. Ranaivoson, D. Comoletti, M. S.P. Sansom, C. V. Robinson, R. Klein, E. Seiradake (*equal contributions)
Nature Communications, 2016, 7, 11184.

17- Structures of the EphA2 receptor at the membrane: role of lipid interactions
M. Chavent, E. Seiradake, E. Y. Jones, M. S. P. Sansom
Structure, 2016, 24(2), 337-347

16- Molecular dynamics simulations of Gram-negative membranes: a vignette of some recent successes
J. Parkin, M. Chavent, S. Khalid
Biophysical Journal, 2015, 109(3), 461-468

15- Supramolecular assemblies underpin turnover of outer membrane proteins in bacteria
P. Rassam, N. A. Copeland, O. Birkholz, C. Toth, M. Chavent, A. Duncan, N. G. Housden, U. Seger, S. J. Cross, D. M. Quinn, T. J. Garrod, M. S. P. Sansom, J. Piehler, C. G. Baumann and C. Kleanthous
Nature, 2015, 523(7560), 333-336

14- Nothing to sneeze at: a dynamic and integrative computational model of an influenza A virion
T. Reddy, D. Shorthouse, D. Parton, E. Jefferys, P. W. Fowler, M. Chavent, M. Baaden, M. S. P. Sanson
Structure, 2015, 23, 1-14

13- Epock: Speedy analysis of protein pocket dynamics
B. Laurent+, M. Chavent+, T. Cragnolini, A. C. E. Dahl, S. Pasquali, P. Derreumaux, M. S. P. Sansom, M. Baaden (+ co-1st author)
Bioinformatics, 2015, 31(9), 1478-1480.

12- Dimerization of the EphA1 receptor tyrosine kinase transmembrane domain: Insights into the Mechanism of Receptor Activation
M. Chavent, A. Chetwyn, P. Stansfeld, M.S.P. Sansom
Biochemistry, 2014, 53(42), 6641-6652.

11- Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems
M. Chavent+, T. Reddy, J. Goose, A. C. E. Dahl, J. Stone, B. Jobard, M. S.P. Sansom (+corresponding author)
Faraday Discussion, 2014, 169, 455-475.

10- Blind prediction of Interfacial water positions in CAPRI
M. Lensink, ... , M. Chavent, D. Ritchie, ... , S. J. Wodak
Proteins: Structure, Function and Bioinformatics, 2014, 82(4), 620-632.

9- Interactive Molecular Dynamics: Scaling up to Large Systems
M. Dreher, M. Piuzzi, A. Turki, M. Chavent, M. Baaden, N. Férey, S. Limet, B. raffin, S. Robert
Procedia Computer Science, 2013, 18, 20-29.

8- Game on, Science - how video game technology may help biologists tackle visualization challenges
L. Zihan, A. Tek, F. Dasilva, C. Empereur-mot, M. Chavent+, M. Baaden+ (+ co-corresponding author)
PLoS ONE, 2013, 8 (3), e57990.

7- Bendix: Intuitive helix geometry analysis and abstraction
A.C.E. Dahl, M. Chavent, M.S.P. Sansom
Bioinformatics, 2012, 28 (16): 2193-2194.

6- Soon in your lecture halls, chemistry will go to Hollywood
M. Chavent, M. Baaden, E. Hénon, S. Antonczak
L’actualité Chimique 2012, 363, 42-46

5- Unified molecular representations accelerated by graphics processors : balls, sticks and hyperboloids from macro- to meso-scale dynamics
M. Chavent, A. Vanel, A. Tek, B. Levy, B. Raffin, M. Baaden
Journal of Computational Chemistry 2011, 32 (13), 2924-2935.

4- GPU-powered tools boost molecular visualization
M. Chavent, B. Levy, M. Krone, K. Bidmon, J. P. Nominé, T. Ertl, M. Baaden
Briefings in Bioinformatics, 2011, 12 (6), 689-701.

3- Biochemical studies and Molecular Dynamics Simulations of Smad3-Erbin interaction identify a non-classical erbin PDZ binding
N. Déliot+, M. Chavent+, C. Nourry, P. Lécine, C. Arnaud, A. Hermant, B. Maigret, J.-P. Borg (+ co-1st author)
Biochemical and Biophysical Research Communications 2009, 378 (3), 360-365.

2- MetaMol: high quality visualization of molecular skin surface.
M. Chavent+, B. Levy, B. Maigret (+ corresponding author)
Journal of Molecular Graphics and Modelling, 2008, 27 (2), 209-216.

1- Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment
A. Beautrait, V. Leroux, M. Chavent, L. Ghemtio, M.-D. Devignes, M. Smaïl-Tabbone, W. Cai, X. Shao, G. Moreau, P. Bladon, J. Yao, B. Maigret
Journal of Molecular Modeling, 2008, 14 (5), pp. 393-401.