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 context, our current research focusses on combining machine learning and molecular dynamics simulations to sample protein conformational spaces.

• Computational Biophysics
• Machine Learning
• Molecular Dynamics

Chapter in book

• Marklund, E. G., Degiacomi, M. T., Politis, A., & Landreh, M. (2021). CHAPTER 8. CCS for Modelling 3D Structures. In Ion Mobility-Mass Spectrometry. https://doi.org/10.1039/9781839162886-00183
• Iacovache, I., Degiacomi, M., & van der Goot, F. (2012). Pore-forming toxins. In E. H. Egelman (Ed.), Comprehensive biophysics (164-188). Elsevier. https://doi.org/10.1016/b978-0-12-374920-8.00518-x

Conference Paper

• Leach, A., Schmon, S. M., Degiacomi, M. T., & Willcocks, C. G. (2022, April). Denoising Diffusion Probabilistic Models on SO(3) for Rotational Alignment. Presented at ICLR 2022 Workshop on Geometrical and Topological Representation Learning
• Leach, A., Rudden, L. S., Bond-Taylor, S., Brigham, J. C., Degiacomi, M. T., & Willcocks, C. G. (2020, December). Shape tracing: An extension of sphere tracing for 3D non-convex collision in protein docking. Presented at 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE)

Journal Article

• Pollak, H., Degiacomi, M. T., & Erastova, V. (2024). Modeling Realistic Clay Systems with ClayCode. Journal of Chemical Theory and Computation, 20(21), 9606–9617. https://doi.org/10.1021/acs.jctc.4c00987
• Bender, J., Kundlacz, T., Rudden, L. S. P., Frick, M., Bieber, J., Degiacomi, M. T., & Schmidt, C. (2024). Ca2+-dependent lipid preferences shape synaptotagmin-1 C2A and C2B dynamics: Insights from experiments and simulations. Structure, 32(10), 1691-1704. https://doi.org/10.1016/j.str.2024.07.017
• Asor, R., Olerinyova, A., Burnap, S. A., Kushwah, M. S., Soltermann, F., Rudden, L. S. P., Hensen, M., Vasiljevic, S., Brun, J., Hill, M., Chang, L., Dejnirattisai, W., Supasa, P., Mongkolsapaya, J., Zhou, D., Stuart, D. I., Screaton, G. R., Degiacomi, M. T., Zitzmann, N., Benesch, J. L. P., …Kukura, P. (2024). Oligomerization-driven avidity correlates with SARS-CoV-2 cellular binding and inhibition. Proceedings of the National Academy of Sciences, 121(40), Article e2403260121. https://doi.org/10.1073/pnas.2403260121
• Cumby, J., Degiacomi, M., Erastova, V., Güven, J., Hobday, C., Mey, A., Pollak, H., & Szabla, R. (2023). Course Materials for an Introduction to Data-Driven Chemistry. The journal of open source education, 6(63), https://doi.org/10.21105/jose.00192
• Allison, T. M., Degiacomi, M. T., Marklund, E. G., Jovine, L., Elofsson, A., Benesch, J. L., & Landreh, M. (2022). Complementing machine learning‐based structure predictions with native mass spectrometry. Protein Science, 31(6), Article e4333. https://doi.org/10.1002/pro.4333
• Rudden, L. S., Musson, S. C., Benesch, J. L., & Degiacomi, M. T. (2022). Biobox: a toolbox for biomolecular modelling. Bioinformatics, 38(4), 1149-1151. https://doi.org/10.1093/bioinformatics/btab785
• Yen, H.-Y., Abramsson, M. L., Agasid, M. T., Lama, D., Gault, J., Liko, I., Kaldmäe, M., Saluri, M., Qureshi, A. A., Suades, A., Drew, D., Degiacomi, M. T., Marklund, E. G., Allison, T. M., Robinson, C. V., & Landreh, M. (2022). Electrospray ionization of native membrane proteins proceeds via a charge equilibration step. RSC Advances, 12(16), 9671-9680. https://doi.org/10.1039/d2ra01282k
• Guillen-Garcia, A., Gibson, S., Jordan, C., Ramaswamy, V., Linthwaite, V., Bromley, E., Brown, A., Hodgson, D., Blower, T., Verlet, J., Degiacomi, M., Palsson, L.-O., & Cann, M. (2022). Allophycocyanin A is a carbon dioxide receptor in the cyanobacterial phycobilisome. Nature Communications, 13, Article 5289. https://doi.org/10.1038/s41467-022-32925-6
• Goldie, S. J., Degiacomi, M. T., Jiang, S., Clark, S. J., Erastova, V., & Coleman, K. S. (2022). Identification of Graphene Dispersion Agents through Molecular Fingerprints. ACS Nano, 16(10), https://doi.org/10.1021/acsnano.2c04406
• Degiacomi, M. T., Tian, S., Greenwell, H. C., & Erastova, V. (2021). DynDen: Assessing convergence of molecular dynamics simulations of interfaces. Computer Physics Communications, 269, Article 108126. https://doi.org/10.1016/j.cpc.2021.108126
• Rudden, L. S., & Degiacomi, M. T. (2021). Transmembrane Protein Docking with JabberDock. Journal of Chemical Information and Modeling, 61(3), 1493-1499. https://doi.org/10.1021/acs.jcim.0c01315
• Ramaswamy, V. K., Musson, S. C., Willcocks, C. G., & Degiacomi, M. T. (2021). Deep Learning Protein Conformational Space with Convolutions and Latent Interpolations. Physical Review X, 11(1), Article 011052. https://doi.org/10.1103/physrevx.11.011052
• Olerinyova, A., Sonn-Segev, A., Gault, J., Eichmann, C., Schimpf, J., Kopf, A. H., Rudden, L. S., Ashkinadze, D., Bomba, R., Frey, L., Greenwald, J., Degiacomi, M. T., Steinhilper, R., Killian, J. A., Friedrich, T., Riek, R., Struwe, W. B., & Kukura, P. (2021). Mass Photometry of Membrane Proteins. Chem, 7(1), 224-236. https://doi.org/10.1016/j.chempr.2020.11.011
• Landreh, M., Sahin, C., Gault, J., Sadeghi, S., Drum, C. L., Uzdavinys, P., Drew, D., Allison, T. M., Degiacomi, M. T., & Marklund, E. G. (2020). Predicting the shapes of protein complexes through collision cross section measurements and database searches. Analytical Chemistry, 92(18), 12297-12303. https://doi.org/10.1021/acs.analchem.0c01940
• Allison, T. M., Barran, P., Benesch, J. L., Cianferani, S., Degiacomi, M. T., Gabelica, V., Grandori, R., Marklund, E. G., Menneteau, T., Migas, L. G., Politis, A., Sharon, M., Sobott, F., & Thalassinos, K. (2020). Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data. Analytical Chemistry, 92(16), 10881-10890. https://doi.org/10.1021/acs.analchem.9b05792
• Allison, T. M., Barran, P., Cianférani, S., Degiacomi, M. T., Gabelica, V., Grandori, R., Marklund, E. G., Menneteau, T., Migas, L. G., Politis, A., Sharon, M., Sobott, F., Thalassinos, K., & Benesch, J. L. (2020). Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology. Analytical Chemistry, 92(16), 10872-10880. https://doi.org/10.1021/acs.analchem.9b05791
• Rudden, L. S., & Degiacomi, M. 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. https://doi.org/10.1021/acs.jctc.9b00474
• Degiacomi, M. T. (2019). Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space. Structure, 27(6), 1034-1040.e3. https://doi.org/10.1016/j.str.2019.03.018
• Collier, M. P., Alderson, T. R., de Villiers, C. P., Nicholls, D., Gastall, H. Y., Allison, T. M., Degiacomi, M. T., Jiang, H., Mlynek, G., Fürst, D. O., van der Ven, P. F., Djinovic-Carugo, K., Baldwin, A. J., Watkins, H., Gehmlich, K., & Benesch, J. L. (2019). HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C. Science Advances, 5(5), Article eaav8421. https://doi.org/10.1126/sciadv.aav8421
• Lyon, Y. A., Collier, M. P., Riggs, D. L., Degiacomi, M. T., Benesch, J. L., & Julian, R. R. (2019). Structural and functional consequences of age-related isomerization in α-crystallins. Journal of Biological Chemistry, 294(19), 7546-7555. https://doi.org/10.1074/jbc.ra118.007052
• 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. (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. https://doi.org/10.1093/hmg/ddy370
• Degiacomi, M. 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(1), 113-117. https://doi.org/10.1007/s13361-018-1974-2
• Santhanagopalan, I., Degiacomi, M. T., Shepherd, D. A., Hochberg, G. K., Benesch, J. L., & Vierling, E. (2018). It takes a dimer to tango: Oligomeric small heat shock proteins dissociate to capture substrate. Journal of Biological Chemistry, 293(51), 19511-19521. https://doi.org/10.1074/jbc.ra118.005421
• Liko, I., Degiacomi, M. T., Lee, S., Newport, T. D., Gault, J., Reading, E., Hopper, J. T., Housden, N. G., White, P., Colledge, M., Sula, A., Wallace, B., Kleanthous, C., Stansfeld, P. J., Bayley, H., Benesch, J. L., Allison, T. M., & Robinson, C. V. (2018). Lipid binding attenuates channel closure of the outer membrane protein OmpF. Proceedings of the National Academy of Sciences, 115(26), 6691-6696. https://doi.org/10.1073/pnas.1721152115
• Hochberg, G. K., 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. (2018). Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. Science, 359(6378), 930-935. https://doi.org/10.1126/science.aam7229
• Erastova, V., Degiacomi, M. T., Fraser, D., & Greenwell, H. C. (2017). Mineral Surface Chemistry Control for Origin of Prebiotic Peptides. Nature Communications, 8, Article 2033. https://doi.org/10.1038/s41467-017-02248-y
• Degiacomi, M. T., Schmidt, C., Baldwin, A. J., & Benesch, J. L. (2017). Accommodating protein dynamics in the modeling of chemical crosslinks. Structure, 25(11), 1751-1757.e5. https://doi.org/10.1016/j.str.2017.08.015
• Pritišanac, I., Degiacomi, M., Alderson, T., Carneiro, M., Ab, E., Siegal, G., & Baldwin, A. J. (2017). Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory. Journal of the American Chemical Society, 139(28), 9523-9533. https://doi.org/10.1021/jacs.6b11358
• Hopper, J., Ambrose, S., Grant, O., Krumm, S., Allison, T., Degiacomi, M., Tully, M., Pritchard, L., Ozorowski, G., Ward, A., Crispin, M., Doores, K., Woods, R., Benesch, J., Robinson, C., & Struwe, W. (2017). The Tetrameric Plant Lectin BanLec Neutralizes HIV through Bidentate Binding to Specific Viral Glycans. Structure, 25(5), 773-782.e5. https://doi.org/10.1016/j.str.2017.03.015
• Tamò, G., Maesani, A., Träger, S., Degiacomi, M., Floreano, D., & Dal Peraro, M. (2017). Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies. Scientific Reports, 7(1), Article 235. https://doi.org/10.1038/s41598-017-00266-w
• Landreh, M., Marklund, E., Uzdavinys, P., Degiacomi, M., Coincon, M., Gault, J., Gupta, K., Liko, I., Benesch, J., Drew, D., & Robinson, C. (2017). Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters. Nature Communications, 8, Article 13993. https://doi.org/10.1038/ncomms13993
• Erastova, V., Degiacomi, M. T., O'Hare, D., & Greenwell, H. C. (2017). Understanding surface interactions in aqueous miscible organic solvent treated layered double hydroxides. RSC Advances, 7(9), 5076-5083. https://doi.org/10.1039/c6ra26834j
• Liko, I., Degiacomi, M., Mohammed, S., Yoshikawa, S., Schmidt, C., & Robinson, C. (2016). Dimer interface of Bovine cytochrome c oxidase is influenced by local posttranslational modifications and lipid binding. Proceedings of the National Academy of Sciences, 113(29), 8230-8235. https://doi.org/10.1073/pnas.1600354113
• Degiacomi, M., Erastova, V., & Wilson, M. (2016). Easy creation of polymeric systems for molecular dynamics with Assemble!. Computer Physics Communications, 202, 304-309. https://doi.org/10.1016/j.cpc.2015.12.026
• Mcdowell, M., Marcoux, J., Mcvicker, G., Johnson, S., Fong, Y., Stevens, R., Bowman, L., Degiacomi, M., Yan, J., Wise, A., Friede, M., Benesch, J., Deane, J., Tang, C., Robinson, C., & Lea, S. (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. https://doi.org/10.1111/mmi.13267
• Degiacomi, M., & Benesch, J. (2016). EM∩IM: Software for relating ion mobility mass spectrometry and electron microscopy data. Analyst, 141(1), 70-75. https://doi.org/10.1039/c5an01636c
• Marcoux, J., Mangione, P., Porcari, R., Degiacomi, M., Verona, G., Taylor, G., Giorgetti, S., Raimondi, S., Sanglier-Cianférani, S., Benesch, J., Cecconi, C., Naqvi, M., Gillmore, J., Hawkins, P., Stoppini, M., Robinson, C., Pepys, M., & Bellotti, V. (2015). A novel mechano-enzymatic cleavage mechanism underlies transthyretin amyloidogenesis. EMBO Molecular Medicine, 7(10), 1337-1349. https://doi.org/10.15252/emmm.201505357
• Marklund, E., Degiacomi, M., Robinson, C., Baldwin, A., & Benesch, J. (2015). Collision cross sections for structural proteomics. Structure, 23(4), 791-799. https://doi.org/10.1016/j.str.2015.02.010
• Bechara, C., Nöll, A., Morgner, N., Degiacomi, M., Tampé, R., & Robinson, C. (2015). A subset of annular lipids is linked to the flippase activity of an ABC transporter. Nature Chemistry, 7(3), 255-262. https://doi.org/10.1038/nchem.2172
• Bovigny, C., Degiacomi, M., Lemmin, T., Dal Peraro, M., & Stenta, M. (2014). Reaction mechanism and catalytic fingerprint of allantoin racemase. Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry), 118(27), 7457-7466. https://doi.org/10.1021/jp411786z
• Laganowsky, A., Reading, E., Allison, T., Ulmschneider, M., Degiacomi, M., Baldwin, A., & Robinson, C. (2014). Membrane proteins bind lipids selectively to modulate their structure and function. Nature, 510(7503), 172-175. https://doi.org/10.1038/nature13419
• Spiga, E., Degiacomi, M., & Dal Peraro, M. (2014). New strategies for integrative dynamic modeling of macromolecular assembly. Advances in protein chemistry and structural biology, 96, 77-111. https://doi.org/10.1016/bs.apcsb.2014.06.008
• Degiacomi, M., Iacovache, I., Pernot, L., Chami, M., Kudryashev, M., Stahlberg, H., Van Der Goot, F., & Dal Peraro, M. (2013). Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Nature Chemical Biology, 9(10), 623-629. https://doi.org/10.1038/nchembio.1312
• Spiga, E., Alemani, D., Degiacomi, M., Cascella, M., & Peraro, M. (2013). Electrostatic-consistent coarse-grained potentials for molecular simulations of proteins. Journal of Chemical Theory and Computation, 9(8), 3515-3526. https://doi.org/10.1021/ct400137q
• Kudryashev, M., Stenta, M., Schmelz, S., Amstutz, M., Wiesand, U., Castaño-Díez, D., Degiacomi, M., Münnich, S., Bleck, C., Kowal, J., Diepold, A., Heinz, D., Dal Peraro, M., Cornelis, G., & Stahlberg, H. (2013). In situ structural analysis of the Yersinia enterocolitica injectisome. eLife, 2013(2), Article e00792. https://doi.org/10.7554/elife.00792
• Degiacomi, M., & Dal Peraro, M. (2013). Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling. Structure, 21(7), 1097-1106. https://doi.org/10.1016/j.str.2013.05.014
• Hofmeyer, T., Schmelz, S., Degiacomi, M., Dal Peraro, M., Daneschdar, M., Scrima, A., Van Den Heuvel, J., Heinz, D., & 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. https://doi.org/10.1016/j.jmb.2012.12.017
• Iacovache, I., Degiacomi, M., Pernot, L., Ho, S., Schiltz, M., Dal Peraro, M., & van der Goot, F. (2011). Dual chaperone role of the c-terminal propeptide in folding and oligomerization of the pore-forming toxin aerolysin. PLoS Pathogens, 7(7), Article e1002135. https://doi.org/10.1371/journal.ppat.1002135
• Wagner, S., Sorg, I., Degiacomi, M., Journet, L., Peraro, M., & Cornelis, G. (2009). The helical content of the YscP molecular ruler determines the length of the Yersinia injectisome. Molecular Microbiology, 71(3), 692-701. https://doi.org/10.1111/j.1365-2958.2008.06556.x
• 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. https://doi.org/10.1158/0008-5472.can-07-0238