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Durham University

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Staff Profile

Dr Matteo T. Degiacomi

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Associate Professor in the Department of Physics
Associate Professor in the Centre for Materials Physics

(email at matteo.t.degiacomi@durham.ac.uk)

Biography

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 promotes 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.

Research Groups

Department of Chemistry

  • Bioactive Chemistry and Synthesis
  • Computational and Dynamics

Research Interests

  • Artificial Intelligence
  • Integrative Modelling
  • Molecular Dynamics

Selected Publications

Journal Article

  • 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.
  • 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 (2020). Mass Photometry of Membrane Proteins. Chem
  • 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.
  • Degiacomi, Matteo T. (2019). Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space. Structure 27(6): 1034-1040.e3.
  • 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). 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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., Fraser, Donald & Greenwell, H. Chris (2017). Mineral Surface Chemistry Control for Origin of Prebiotic Peptides. Nature Communications 8(1): 2033.
  • 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.
  • 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. & Benesch, J.L.P. (2016). EM∩IM: Software for relating ion mobility mass spectrometry and electron microscopy data. Analyst 141(1): 70-75.
  • 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. & Dal Peraro, M. (2013). Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling. Structure 21(7): 1097-1106.
  • 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.

Conference Paper

  • 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.

Show all publications

Supervises