Staff profile

Matteo T. Degiacomi, born in Lugano (Switzerland), obtained an MSc in Computer Science (2008) and a PhD in computational biophysics (2012) in Ecole Polytechnique Fédérale de Lausanne (EPFL). During his PhD supervised by Prof Matteo Dal Peraro he developed of POW, a flexible parallel optimization environment. POW was applied to the prediction of pore-forming toxin Aerolysin heptameric conformation and of type-III secretion system’s basal body. In 2013 he joined the research groups of Prof Justin Benesch and Prof Dame Carol Robinson FRS in the University of Oxford. His research, funded by a Swiss National Science Foundation Early Postdoc Mobility Fellowship, focused on the development of new computational methods for the prediction of protein molecular assembly guided by ion mobility, cross-linking, SAXS and electron microscopy data, as well as their application to the study of small Heat Shock Proteins and protein-lipid interactions. In 2017 he obtained an EPSRC Junior Research Fellowship, allowing him to establish his independent research in Durham University. In 2020 he was promoted to Associate Professor.

Research Interests

Specific interactions of simple molecules produce phenomena of increasing complexity, culminating with the finely tuned biological mechanisms that ultimately make life possible. Understanding the structure and dynamics of these molecules is an important step to shed light on their function in an organism. The overarching goal of my work is the development and application of computational methods to interpret and exploit multiple sources of experimental data for the modelling of biomolecular systems at near-atomistic resolution. In this conext, we focus on the development of protein-protein docking methods, and techniques combining machine learning and molecular dynamics simulations to sample protein conformational spaces.

• Molecular Dynamics
• Machine Learning
• Computational Biophysics

• Bioactive Chemistry and Synthesis
• Centre for Materials Physics
• Computational and Dynamics

Chapter in book

• Marklund, Erik G., Degiacomi, Matteo T., Politis, Argyris & Landreh, Michael (2021). CHAPTER 8. CCS for Modelling 3D Structures. In Ion Mobility-Mass Spectrometry. 183.
• Iacovache, I., Degiacomi, M.T. & van der Goot, F.G. (2012). Pore-forming toxins. In Comprehensive biophysics. Egelman, Edward H. Amsterdam Boston: Elsevier. 5: 164-188.

Conference Paper

• Leach, Adam, Schmon, Sebastian M., Degiacomi, Matteo T. & Willcocks, Chris G. (2022), Denoising Diffusion Probabilistic Models on SO(3) for Rotational Alignment, ICLR 2022 Workshop on Geometrical and Topological Representation Learning. ICLR.
• Leach, Adam, Rudden, Lucas S.P., Bond-Taylor, Sam, Brigham, John C., Degiacomi, Matteo T. & Willcocks, Chris G. (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). 49-52.

Journal Article

• Goldie, Stuart J., Degiacomi, Matteo T., Jiang, Shan, Clark, Stewart J., Erastova, Valentina & Coleman, Karl S. (2022). Identification of Graphene Dispersion Agents through Molecular Fingerprints. ACS Nano 16(10): 16109.
• Guillen-Garcia, A., Gibson, S., Jordan, C., Ramaswamy, V., Linthwaite, V., Bromley, E.H.C., Brown, A.P. Hodgson, D., Blower, T., Verlet, J., Degiacomi, M., Palsson, L-O. & Cann, M.J. (2022). Allophycocyanin A is a carbon dioxide receptor in the cyanobacterial phycobilisome. Nature Communications 13: 5289.
• Allison, Timothy M., Degiacomi, Matteo T., Marklund, Erik G., Jovine, Luca, Elofsson, Arne, Benesch, Justin L. P. & Landreh, Michael (2022). Complementing machine learning‐based structure predictions with native mass spectrometry. Protein Science 31(6): e4333.
• Yen, Hsin-Yung, Abramsson, Mia L., Agasid, Mark T., Lama, Dilraj, Gault, Joseph, Liko, Idlir, Kaldmäe, Margit, Saluri, Mihkel, Qureshi, Abdul Aziz, Suades, Albert, Drew, David, Degiacomi, Matteo T., Marklund, Erik G., Allison, Timothy M., Robinson, Carol V. & Landreh, Michael (2022). Electrospray ionization of native membrane proteins proceeds via a charge equilibration step. RSC Advances 12(16): 9671-9680.
• Rudden, Lucas S. P., Musson, Samuel C., Benesch, Justin L. P. & Degiacomi, Matteo T. (2022). Biobox: a toolbox for biomolecular modelling. Bioinformatics 38(4): 1149-1151.
• Degiacomi, Matteo T., Tian, Shansi, Greenwell, H. Chris & Erastova, Valentina (2021). DynDen: Assessing convergence of molecular dynamics simulations of interfaces. Computer Physics Communications 269: 108126.
• Ramaswamy, Venkata K., Musson, Samuel C., Willcocks, Chris G. & Degiacomi, Matteo T. (2021). Deep Learning Protein Conformational Space with Convolutions and Latent Interpolations. Physical Review X 11(1): 011052.
• Rudden, Lucas S. P. & Degiacomi, Matteo T. (2021). Transmembrane Protein Docking with JabberDock. Journal of Chemical Information and Modeling 61(3): 1493-1499.
• Olerinyova, Anna, Sonn-Segev, Adar, Gault, Joseph, Eichmann, Cédric, Schimpf, Johannes, Kopf, Adrian H., Rudden, Lucas S.P., Ashkinadze, Dzmitry, Bomba, Radoslaw, Frey, Lukas, Greenwald, Jason, Degiacomi, Matteo T., Steinhilper, Ralf, Killian, J. Antoinette, Friedrich, Thorsten, Riek, Roland, Struwe, Weston B. & Kukura, Philipp (2021). Mass Photometry of Membrane Proteins. Chem 7(1): 224-236.
• Allison, Timothy M., Barran, Perdita, Cianférani, Sarah, Degiacomi, Matteo T., Gabelica, Valérie, Grandori, Rita, Marklund, Erik G., Menneteau, Thomas, Migas, Lukasz G., Politis, Argyris, Sharon, Michal, Sobott, Frank, Thalassinos, Konstantinos & Benesch, Justin L. P. (2020). Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology. Analytical Chemistry 92(16): 10872-10880.
• Landreh, Michael, Sahin, Cagla, Gault, Joseph, Sadeghi, Samira, Drum, Chester Lee, Uzdavinys, Povilas, Drew, David, Allison, Timothy M, Degiacomi, Matteo T. & Marklund, Erik G. (2020). Predicting the shapes of protein complexes through collision cross section measurements and database searches. Analytical Chemistry 92(18): 12297-12303.
• Allison, Timothy M., Barran, Perdita, Benesch, Justin L. P., Cianferani, Sarah, Degiacomi, Matteo T., Gabelica, Valerie, Grandori, Rita, Marklund, Erik G., Menneteau, Thomas, Migas, Lukasz G., Politis, Argyris, Sharon, Michal, Sobott, Frank & Thalassinos, Konstantinos (2020). Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data. Analytical Chemistry 92(16): 10881-10890.
• Rudden, Lucas S.P. & Degiacomi, Matteo T. (2019). Protein docking using a single representation for protein surface, electrostatics and local dynamics. Journal of Chemical Theory and Computation 15(9): 5135-5143.
• Collier, Miranda P., Alderson, T. Reid, de Villiers, Carin P., Nicholls, Daisy, Gastall, Heidi Y., Allison, Timothy M., Degiacomi, Matteo T., Jiang, He, Mlynek, Georg, Fürst, Dieter O., van der Ven, Peter F. M., Djinovic-Carugo, Kristina, Baldwin, Andrew J., Watkins, Hugh, Gehmlich, Katja & Benesch, Justin L. P. (2019). HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C. Science Advances 5(5): eaav8421.
• Degiacomi, Matteo T. (2019). Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space. Structure 27(6): 1034-1040.e3.
• Lyon, Yana A., Collier, Miranda P., Riggs, Dylan L., Degiacomi, Matteo T., Benesch, Justin L.P. & Julian, Ryan R. (2019). Structural and functional consequences of age-related isomerization in α-crystallins. Journal of Biological Chemistry 294(19): 7546.
• Degiacomi, Matteo T. (2019). On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies. Journal of The American Society for Mass Spectrometry 30: 113-117.
• Finelli, Mattéa J., Aprile, Davide, Castroflorio, Enrico, Jeans, Alexander, Moschetta, Matteo, Chessum, Lauren, Degiacomi, Matteo T., Grasegger, Julia, Lupien-Meilleur, Alexis, Bassett, Andrew, Rossignol, Elsa, Campeau, Philippe M., Bowl, Michael R., Benfenati, Fabio, Fassio, Anna & Oliver, Peter L. (2019). The epilepsy-associated protein TBC1D24 is required for normal development, survival and vesicle trafficking in mammalian neurons. Human Molecular Genetics 28(4): 584-597.
• Santhanagopalan, Indu, Degiacomi, Matteo T., Shepherd, Dale A., Hochberg, Georg K.A., Benesch, Justin L.P. & Vierling, Elizabeth (2018). It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate. Journal of Biological Chemistry 293(51): 19511-19521.
• Liko, Idlir, Degiacomi, Matteo T., Lee, Sejeong, Newport, Thomas D., Gault, Joseph, Reading, Eamonn, Hopper, Jonathan T. S., Housden, Nicholas G., White, Paul, Colledge, Matthew, Sula, Altin, Wallace, B. A., Kleanthous, Colin, Stansfeld, Phillip J., Bayley, Hagan, Benesch, Justin L. P., Allison, Timothy M. & Robinson, Carol V. (2018). Lipid binding attenuates channel closure of the outer membrane protein OmpF. Proceedings of the National Academy of Sciences 115(26): 6691-6696.
• Hochberg, Georg K. A., Shepherd, Dale A., Marklund, Erik G., Santhanagoplan, Indu, Degiacomi, Matteo T., Laganowsky, Arthur, Allison, Timothy M., Basha, Eman, Marty, Michael T., Galpin, Martin R., Struwe, Weston B., Baldwin, Andrew J., Vierling, Elizabeth & Benesch, Justin L. P. (2018). Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. Science 359(6378): 930-935.
• Erastova, Valentina, Degiacomi, Matteo T., Fraser, Donald & Greenwell, H. Chris (2017). Mineral Surface Chemistry Control for Origin of Prebiotic Peptides. Nature Communications 8(1): 2033.
• Degiacomi, Matteo T., Schmidt, Carla, Baldwin, Andrew J. & Benesch, Justin L.P. (2017). Accommodating protein dynamics in the modeling of chemical crosslinks. Structure 25(11): 1751-1757.e5.
• Pritišanac, 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 Theory. Journal of the American Chemical Society 139(28): 9523-9533.
• 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 Glycans. Structure 25(5): 773-782.e5.
• Tamò, G., Maesani, A., Träger, S., Degiacomi, M.T., Floreano, D. & Dal Peraro, Matteo (2017). Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies. Scientific reports 7(1): 235.
• 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+ antiporters. Nature Communications 8: 13993.
• Erastova, Valentina, Degiacomi, Matteo T., O'Hare, Dermot & Greenwell, H. Chris (2017). Understanding surface interactions in aqueous miscible organic solvent treated layered double hydroxides. RSC Advances 7(9): 5076-5083.
• 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 binding. Proceedings of the National Academy of Sciences of the United States of America 113(29): 8230-8235.
• 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.
• 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 Shigella Spa33 and Thermotoga FliM/N reveals a new model for C-ring assembly in T3SS. Molecular Microbiology 99(4): 749-766.
• Degiacomi, M.T. & Benesch, J.L.P. (2016). EM∩IM: Software for relating ion mobility mass spectrometry and electron microscopy data. Analyst 141(1): 70-75.
• 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 amyloidogenesis. EMBO Molecular Medicine 7(10): 1337-1349.
• Marklund, E.G., Degiacomi, M.T., Robinson, C.V., Baldwin, A.J. & Benesch, J.L.P. (2015). Collision cross sections for structural proteomics. Structure 23(4): 791-799.
• 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 transporter. Nature Chemistry 7(3): 255-262.
• Spiga, E., Degiacomi, M.T. & Dal Peraro, M. (2014). New strategies for integrative dynamic modeling of macromolecular assembly. Advances in Protein Chemistry and Structural Biology 96: 77-111.
• Bovigny, C., Degiacomi, M.T., Lemmin, T., Dal Peraro, M. & Stenta, M. (2014). Reaction mechanism and catalytic fingerprint of allantoin racemase. Journal of Physical Chemistry B 118(27): 7457-7466.
• 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 function. Nature 510(7503): 172-175.
• 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 mechanism. Nature Chemical Biology 9(10): 623-629.
• 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 injectisome. eLife 2013(2): e00792.
• Degiacomi, M.T. & Dal Peraro, M. (2013). Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling. Structure 21(7): 1097-1106.
• Spiga, E., Alemani, D., Degiacomi, M.T., Cascella, M. & Peraro, M.D. (2013). Electrostatic-consistent coarse-grained potentials for molecular simulations of proteins. Journal of Chemical Theory and Computation 9(8): 3515-3526.
• 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 protein. Journal of Molecular Biology 425(8): 1302-1317.
• 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 aerolysin. PLoS Pathogens 7(7): e1002135.
• 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.
• Gowal, S., De Giacomi, M. & Le Boudec, J.-Y. (2007). Comment on: A validated mathematical model of cell-mediated immune response to tumor growth [1]. Cancer Research 67(17): 8419-8420.