Publications

ARTICLES

2021

43. M.T. Degiacomi , S. Tian, H.C. Greenwell, V. Erastova (2021), DynDen: Assessing convergence of molecular dynamics simulations of interfaces, Computer Physics Communications

42. L.S.P. Rudden & M.T. Degiacomi (2021), Transmembrane protein docking with JabberDock, Journal of Chemical Information and Modelling

41. V.K. Ramaswamy, S.C. Musson, C.G. Willcocks, M.T. Degiacomi (2021). Learning protein conformational space with convolutions and latent interpolations, Physical Review X 11

40. A. Olerinyova, A. Sonn-Segev, J. Gault, C. Eichmann, J. Schimpf, A.H. Kopf, L.S.P. Rudden, D. Ashkinadze, R. Bomba, J. Greenwald, M.T. Degiacomi, J.A. Killian, T. Friedrich, R. Riek, W.B. Struwe, P. Kukura (2021). Mass Photometry of Membrane ProteinsChem 7(1)

2020

39. A. Leach, L.S.P. Rudden, S. Bond-Taylor, J.C. Brigham, M.T. Degiacomi , C.G. Willcocks (2020). Shape tracing: An extension of sphere tracing for 3D non-convex collision in protein docking, 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE)

38. T. Allison, P. Barran, S. Cianferani, M.T. Degiacomi, V. Gabelica, R. Grandori, E. Marklund, T. Menneteau, L. Migas, A. Politis, M. Sharon, F. Sobott, K. Thalassinos, J.L.P. Benesch (2020). Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural BiologyAnalytical Chemistry

37. T. Allison, P. Barran, J.L.P. Benesch, S. Cianferani, M.T. Degiacomi, V. Gabelica, R. Grandori, E. Marklund, T. Menneteau, L. Migas, A. Politis, M. Sharon, F. Sobott, K. Thalassinos (2020). Software requirements for the analysis and interpretation of native mass spectrometry dataAnalytical Chemistry

36. M. Landreh, C. Sahin, J. Gault, S. Sadeghi, C.L. Drum, P. Uzdavinys, D. Drew, T.M. Allison, M.T. Degiacomi , E.G. Marklund (2020). Predicting the shapes of protein complexes through collision cross section measurements and database searchesAnalytical Chemistry

2019

35. L.P. Rudden & M.T. Degiacomi (2019), Protein docking using a single representation for protein surface, electrostatics and local dynamics. Journal of Chemical Theory and Computation

34. M.P. Collier, T.R. Alderson, C.P. de Villiers, D. Nicholls, H.Y. Gastall, T.M. Allison, M.T. Degiacomi, H. Jiang, G. Mlynek, D.O. Fürst, P.F.M. van der Ven, K. Djinovic-Carugo, A.J. Baldwin, H. Watkins, K. Gehmlich, J.L.P. Benesch. (2019). HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C. Science Advances. 5(5)

33. M.T. Degiacomi (2019), Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space. Structure. datasets

32. Y.A. Lyon, M.P. Collier, D.L. Riggs, M.T. Degiacomi, J.L.P. Benesch, R.R. Julian (2019). Structural and functional consequences of age-related isomerization in α-crystallins. Journal of Biological Chemisty. Editors’ Pick

31. M.T. Degiacomi (2019). On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies. Journal of the American Mass Spectrometry Society

2018
JBC_cover

30. Santhanagopalan I., Degiacomi M.T., Shepherd D.A., Hochberg G.K.A., Benesch J.L.P.,  Vierling E., (2018). It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate, Journal of Biological Chemisty

29. Finelli M.J., Aprile D., Castroflorio E., Jeans A., Moschetta M., Chessum L., Degiacomi M.T., Grasegger J., Lupien-Meilleur A., Bassett A., Rossignol E., Campeau P.M., Bowl M.R., Benfenati F., Fassio A., Oliver P.L. (2018). The epilepsy-associated protein TBC1D24 is required for normal development, survival and vesicle trafficking in mammalian neurons. Human Molecular Genetics 28 (4), 584–597

28. Liko, I., Degiacomi, M.T., Lee, S., Newport, T.D., Gault, J., Reading, E., Hopper, J.T.S., Housden, N.G., White, P., Colledge, M., Sula, A., Wallace, B.A., Kleanthous, C., Stansfeld, P.J., Bayley, H., Benesch, J.L.P., Allison, T.M., Robinson, C.V., (2018). Lipid binding attenuates channel closure of the outer membrane protein OmpFProceedings of the National Academy of Sciences of the United States of America, 115 (26), 6691-6696

27. Hochberg, G.K.A., Shepherd, D.A., Marklund, E.G., Santhanagoplan, I., Degiacomi M.T., Laganowsky, A., Allison, T.M., Basha, E.,  Marty, M.T., Galpin, M.R., Struwe, W.B., Baldwin, A.J., Vierling, E., Benesch, J.L.P. (2018). Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions, Science,  359 (6378), 930-935. datasets

2017

26. Erastova, V. *, Degiacomi, M.T. *, Fraser, D.G., Greenwell, H.C. (2017). Mineral surface control for origin of prebiotic peptides, Nature Communications 8 (1): 2033 datasets.

25. Degiacomi, M.T. , Schmidt, C. , Baldwin, A.J., Benesch, J.L.P. (2017). Accommodating Protein Dynamics in the Modeling of Chemical Crosslinks, Structure, 25(11), 1751-1757. datasets

24. Pritisanac, I., Degiacomi, M.T., Alderson, T.R., Carneiro, M.G., AB, E., Siegal, Gregg & Baldwin, Andrew J (2017). Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph TheoryJournal of the American Chemical Society

23. Tamò, G., Maesani, A., Träger, S., Degiacomi, M.T., Floreano, D. & Dal Peraro, M. (2017). Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assembliesScientific reports 7(1): 235.

22. Landreh, M., Marklund, E.G., Uzdavinys, P., Degiacomi, M.T., Coincon, M., Gault, J., Gupta, K., Liko, I., Benesch, J.L.P., Drew, D. & Robinson, C.V. (2017). Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiportersNature Communications 8.

21. Hopper, J.T.S., Ambrose, S., Grant, O.C., Krumm, S.A., Allison, T.M., Degiacomi, M.T., Tully, M.D., Pritchard, L.K., Ozorowski, G., Ward, A.B., Crispin, M., Doores, K.J., Woods, R.J., Benesch, J.L.P., Robinson, C.V. & Struwe, W.B. (2017). The Tetrameric Plant Lectin BanLec Neutralizes HIV through Bidentate Binding to Specific Viral GlycansStructure 25(5): 773-782.e5.

20. Erastova, V., Degiacomi, M. T., O’Hare, D. & Greenwell, H.C. (2017). Understanding surface interactions in aqueous miscible organic solvent treated layered double hydroxidesRSC Advances 7(9): 5076-5083.

2016

19. McDowell, M.A., Marcoux, J., Mcvicker, G., Johnson, S., Fong, Y.H., Stevens, R., Bowman, L.A.H., Degiacomi, M.T., Yan, J., Wise, A., Friede, M.E., Benesch, J.L.P., Deane, J.E., Tang, C.M., Robinson, C.V. & Lea, S.M. (2016). Characterisation of ShigellaSpa33 and ThermotogaFliM/N reveals a new model for C-ring assembly in T3SSMolecular Microbiology 99(4): 749-766.

18. Liko, I., Degiacomi, M.T., Mohammed, S., Yoshikawa, S., Schmidt, C. & Robinson, C.V. (2016). Dimer interface of Bovine cytochrome c oxidase is influenced by local posttranslational modifications and lipid bindingProceedings of the National Academy of Sciences of the United States of America 113(29): 8230-8235.

17. Degiacomi, M.T.*, Erastova, V. * & Wilson, M.R. (2016). Easy creation of polymeric systems for molecular dynamics with Assemble!Computer Physics Communications 202: 304-309.

16. Degiacomi, M.T. & Benesch, J.L.P. (2016). EM∩IM: Software for relating ion mobility mass spectrometry and electron microscopy dataAnalyst 141(1): 70-75.

2015

15. Marcoux, J., Mangione, P.P., Porcari, R., Degiacomi, M.T., Verona, G., Taylor, G.W., Giorgetti, S., Raimondi, S., Sanglier-Cianférani, S., Benesch, J.L., Cecconi, C., Naqvi, M.M., Gillmore, J.D., Hawkins, P.N., Stoppini, M., Robinson, C.V., Pepys, M.B. & Bellotti, V. (2015). A novel mechano-enzymatic cleavage mechanism underlies transthyretin amyloidogenesisEMBO Molecular Medicine 7(10): 1337-1349.

14. Bechara, C., Nöll, A., Morgner, N., Degiacomi, M.T., Tampé, R. & Robinson, C.V. (2015). A subset of annular lipids is linked to the flippase activity of an ABC transporterNature Chemistry 7(3): 255-262.

13. Marklund, E.G., Degiacomi, M.T., Robinson, C.V., Baldwin, A.J. & Benesch, J.L.P. (2015). Collision cross sections for structural proteomicsStructure 23(4): 791-799.

2014

12. Laganowsky, A., Reading, E., Allison, T.M., Ulmschneider, M.B., Degiacomi, M.T., Baldwin, A.J. & Robinson, C.V. (2014). Membrane proteins bind lipids selectively to modulate their structure and functionNature 510(7503): 172-175.

11. Spiga, E.*, Degiacomi, M.T. *  & Dal Peraro, M. (2014). New strategies for integrative dynamic modeling of macromolecular assemblyAdvances in Protein Chemistry and Structural Biology 96: 77-111.

10. Bovigny, C., Degiacomi, M.T., Lemmin, T., Dal Peraro, M. & Stenta, M. (2014). Reaction mechanism and catalytic fingerprint of allantoin racemaseJournal of Physical Chemistry B 118(27): 7457-7466.

2013 and earlier

9. Hofmeyer, T., Schmelz, S., Degiacomi, M.T., Dal Peraro, M., Daneschdar, M., Scrima, A., Van Den Heuvel, J., Heinz, D.W. & Kolmar, H. (2013). Arranged sevenfold: Structural insights into the C-terminal oligomerization domain of human C4b-binding proteinJournal of Molecular Biology 425(8): 1302-1317.

8. Spiga, E., Alemani, D., Degiacomi, M.T., Cascella, M. & Peraro, M.D. (2013). Electrostatic-consistent coarse-grained potentials for molecular simulations of proteinsJournal of Chemical Theory and Computation 9(8): 3515-3526.

7. Kudryashev, M., Stenta, M., Schmelz, S., Amstutz, M., Wiesand, U., Castaño-Díez, D., Degiacomi, M.T., Münnich, S., Bleck, C.K.E., Kowal, J., Diepold, A., Heinz, D.W., Dal Peraro, M., Cornelis, G.R. & Stahlberg, H. (2013). In situ structural analysis of the Yersinia enterocolitica injectisomeeLife 2013(2).

6. Degiacomi, M.T. & Dal Peraro, M. (2013). Macromolecular symmetric assembly prediction using swarm intelligence dynamic modelingStructure 21(7): 1097-1106.

5. Degiacomi, M.T.*, Iacovache, I.*, Pernot, L., Chami, M., Kudryashev, M., Stahlberg, H., Van Der Goot, F.G. & Dal Peraro, M. (2013). Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanismNature Chemical Biology 9(10): 623-629. [News and Views article]

4. Iacovache, I., Degiacomi, M.T. & van der Goot, F.G. (2012). Pore-forming toxins.

3. Iacovache, I. *, Degiacomi, M.T. *, Pernot, L., Ho, S., Schiltz, M., Dal Peraro, M. & van der Goot, F.G. (2011). Dual chaperone role of the c-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysinPLoS Pathogens 7(7).

2. Wagner, S., Sorg, I., Degiacomi, M., Journet, L., Peraro, M.D. & Cornelis, G.R. (2009). The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome. Molecular Microbiology 71(3): 692-701.

1. S.Gowal, M. De Giacomi & J.-Y. Le Boudec (2007). Comment on: A validated mathematical model of cell-mediated immune response to tumor growth [1]Cancer Research 67(17): 8419-8420.

PATENTS

Method for processing nuclear magnetic resonance (NMR) spectroscopic data European patent, US patent

MEDIA

Scientist Next Door, the virtual public engagement initiative we co-funded, featured in the Northern Echo: “Scientists help children learn during lockdown” (2020)

Our proposed model for abiogenesis featured in an interview on RT: ‘How did life form from rocks?’ Protein puzzle reveals secrets of Earth’s evolution (2018)

Research on injectisome highlighted in BBC “Dara O’Briain’s Science Club” episode “Size Matters” and Science Daily (2013)

Research on aerolysin mode of action featured in the international press, such as BBC Mundo, La Voz de Galicia, Wiener ZeitungScience Daily24 HeuresLe Matin and Tages Anzeiger, and a radio interview (in French) at the Swiss National Radio, RTS (2013)