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Filamin C dimerisation is regulated by HSPB7 (2025)
Journal Article
Wang, Z., Cao, G., Collier, M. P., Qiu, X., Broadway-Stringer, S., Šaman, D., Ng, J. Z. Y., Sen, N., Azad, A. J., Hooper, C., Zimmermann, J., McDonough, M. A., Brem, J., Rabe, P., Song, H., Alderson, T. R., Schofield, C. J., Bolla, J. R., Djinovic-Carugo, K., Fürst, D. O., …Benesch, J. L. P. (2025). Filamin C dimerisation is regulated by HSPB7. Nature Communications, 16, Article 4090. https://doi.org/10.1038/s41467-025-58889-x

The biomechanical properties and responses of tissues underpin a variety important of physiological functions and pathologies. In striated muscle, the actin-binding protein filamin C (FLNC) is a key protein whose variants causative for a wide range o... Read More about Filamin C dimerisation is regulated by HSPB7.

Modeling Realistic Clay Systems with ClayCode (2024)
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

Clays are a broad class of ubiquitous layered materials. Their specific chemophysical properties are intimately connected to their molecular structure, featuring repeating patterns broken by substitutions. Molecular dynamics simulations can provide i... Read More about Modeling Realistic Clay Systems with ClayCode.

Oligomerization-driven avidity correlates with SARS-CoV-2 cellular binding and inhibition. (2024)
Journal Article
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

Cellular processes are controlled by the thermodynamics of the underlying biomolecular interactions. Frequently, structural investigations use one monomeric binding partner, while ensemble measurements of binding affinities generally yield one affini... Read More about Oligomerization-driven avidity correlates with SARS-CoV-2 cellular binding and inhibition..

Ca2+-dependent lipid preferences shape synaptotagmin-1 C2A and C2B dynamics: Insights from experiments and simulations (2024)
Journal Article
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

Signal transmission between neurons requires exocytosis of neurotransmitters from the lumen of synaptic vesicles into the synaptic cleft. Following an influx of Ca , this process is facilitated by the Ca sensor synaptotagmin-1. The underlying mechan... Read More about Ca2+-dependent lipid preferences shape synaptotagmin-1 C2A and C2B dynamics: Insights from experiments and simulations.

Identification of Graphene Dispersion Agents through Molecular Fingerprints (2022)
Journal Article
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

The scalable production and dispersion of 2D materials, like graphene, is critical to enable their use in commercial applications. While liquid exfoliation is commonly used, solvents such as N-methyl-pyrrolidone (NMP) are toxic and difficult to scale... Read More about Identification of Graphene Dispersion Agents through Molecular Fingerprints.

Allophycocyanin A is a carbon dioxide receptor in the cyanobacterial phycobilisome (2022)
Journal Article
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

Light harvesting is fundamental for production of ATP and reducing equivalents for CO2 fixation during photosynthesis. However, electronic energy transfer (EET) through a photosystem can harm the photosynthetic apparatus when not balanced with CO2. H... Read More about Allophycocyanin A is a carbon dioxide receptor in the cyanobacterial phycobilisome.

Complementing machine learning‐based structure predictions with native mass spectrometry (2022)
Journal Article
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

The advent of machine learning-based structure prediction algorithms such as AlphaFold2 (AF2) and RoseTTa Fold have moved the generation of accurate structural models for the entire cellular protein machinery into the reach of the scientific communit... Read More about Complementing machine learning‐based structure predictions with native mass spectrometry.

Electrospray ionization of native membrane proteins proceeds via a charge equilibration step (2022)
Journal Article
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

Electrospray ionization mass spectrometry is increasingly applied to study the structures and interactions of membrane protein complexes. However, the charging mechanism is complicated by the presence of detergent micelles during ionization. Here, we... Read More about Electrospray ionization of native membrane proteins proceeds via a charge equilibration step.

Biobox: a toolbox for biomolecular modelling (2021)
Journal Article
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

Motivation The implementation of biomolecular modelling methods and analyses can be cumbersome, often carried out with in-house software re-implementing common tasks, and requiring the integration of diverse software libraries. Results We present Bio... Read More about Biobox: a toolbox for biomolecular modelling.

DynDen: Assessing convergence of molecular dynamics simulations of interfaces (2021)
Journal Article
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

Molecular dynamics is a simulation technique used to predict the physical properties of systems based on their chemical structure and evolution of their atomic constituents. For these predictions to be reliable, it is critical that the simulation has... Read More about DynDen: Assessing convergence of molecular dynamics simulations of interfaces.

Deep Learning Protein Conformational Space with Convolutions and Latent Interpolations (2021)
Journal Article
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

Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein conformational... Read More about Deep Learning Protein Conformational Space with Convolutions and Latent Interpolations.

Transmembrane Protein Docking with JabberDock (2021)
Journal Article
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

Transmembrane proteins act as an intermediary for a broad range of biological process. Making up 20% to 30% of the proteome, their ubiquitous nature has resulted in them comprising 50% of all targets in drug design. Despite their importance, they mak... Read More about Transmembrane Protein Docking with JabberDock.

Mass Photometry of Membrane Proteins (2020)
Journal Article
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

Integral membrane proteins (IMPs) are biologically highly significant but challenging to study because they require maintaining a cellular lipid-like environment. Here, we explore the application of mass photometry (MP) to IMPs and membrane-mimetic s... Read More about Mass Photometry of Membrane Proteins.

Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology (2020)
Journal Article
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

Native mass spectrometry (MS) allows the interrogation of structural aspects of macromolecules in the gas phase, under the premise of having initially maintained their solution-phase noncovalent interactions intact. In the more than 25 years since th... Read More about Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology.

Predicting the shapes of protein complexes through collision cross section measurements and database searches (2020)
Journal Article
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

In structural biology, collision cross sections (CCSs) from ion mobility mass spectrometry (IM-MS) measurements are routinely compared to computationally or experimentally derived protein structures. Here, we investigate whether CCS data can inform a... Read More about Predicting the shapes of protein complexes through collision cross section measurements and database searches.

Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data (2020)
Journal Article
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

The past few years have seen a dramatic increase in applications of native mass and ion mobility spectrometry, especially for the study of proteins and protein complexes. This increase has been catalyzed by the availability of commercial instrumentat... Read More about Software Requirements for the Analysis and Interpretation of Native Ion Mobility Mass Spectrometry Data.

Protein docking using a single representation for protein surface, electrostatics and local dynamics (2019)
Journal Article
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

Predicting the assembly of multiple proteins into specific complexes is critical to the understanding of their biological function in an organism, and thus the design of drugs to address their malfunction. Proteins are flexible molecules, and this in... Read More about Protein docking using a single representation for protein surface, electrostatics and local dynamics.

HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C (2019)
Journal Article
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

Mechanical force–induced conformational changes in proteins underpin a variety of physiological functions, typified in muscle contractile machinery. Mutations in the actin-binding protein filamin C (FLNC) are linked to musculo- skeletal pathologies c... Read More about HspB1 phosphorylation regulates its intramolecular dynamics and mechanosensitive molecular chaperone interaction with filamin C.

Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space (2019)
Journal Article
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

Flexibility is often a key determinant of protein func- tion. To elucidate the link between their molecular structure and role in an organism, computational techniques such as molecular dynamics can be leveraged to characterize their conformational s... Read More about Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space.