Research group

Biomolecular simulation, Drug Discovery and design, Experimental structure determination, Molecular Interactions/Docking, Mutation Analysis and design, Protein/Nucleic Acid design, Structural bioinformatics, Structure prediction

Catalina-Hernandez, E., Aguilella-Arzo, M., Peralvarez-Marin, A., & Lopez-Martin, M. (2025). Computational Insights into Membrane Disruption by Cell-Penetrating Peptides. Journal of Chemical Information and Modeling, 65(3), 1549–1559. https://doi.org/10.1021/acs.jcim.4c01940

Catalina-Hernandez, E., Lopez-Martin, M., Aguilella-Arzo, M., & Peralvarez-Marin, A. (2025). Membrane disruption potential of endogenous opioid neuropeptide Dynorphin A and related clinical variants. International Journal of Biological Macromolecules, 316, 144567. https://doi.org/10.1016/j.ijbiomac.2025.144567

Munsamy, G., Illanes-Vicioso, R., Funcillo, S., Nakou, I. T., Lindner, S., Ayres, G., Sheehan, L. S., Moss, S., Eckhard, U., Lorenz, P., & Ferruz, N. (2024). Conditional language models enable the efficient design of proficient enzymes. https://doi.org/10.1101/2024.05.03.592223

Mizgalska, D., Rodríguez-Banqueri, A., Veillard, F., Książęk, M., Goulas, T., Guevara, T., Eckhard, U., Potempa, J., & Gomis-Rüth, F. X. (2024). Structural and functional insights into the C-terminal signal domain of the Bacteroidetes type-IX secretion system. Open Biology, 14(6). https://doi.org/10.1098/rsob.230448

Estevan-Morió, E., Ramírez-Larrota, J. S., Bushi, E., & Eckhard, U. (2024). Dissecting Cytophagalysin: Structural and Biochemical Studies of a Bacterial Pappalysin-Family Metallopeptidase. Biomolecules, 14(12), 1604. https://doi.org/10.3390/biom14121604

Habibnia, M., Catalina-Hernandez, E., Lopez-Martin, M., Masnou-Sanchez, D., & Peralvarez-Marin, A. (2024). Decoding the molecular and structural determinants of the neurokinin A and Aβ1-42 peptide cross-interaction in the amyloid cascade pathway. IScience, 27(11), 111187. https://doi.org/10.1016/j.isci.2024.111187

Catalina-Hernández, È., López-Martín, M., Masnou-Sánchez, D., Martins, M., Lorenz-Fonfria, V. A., Jiménez-Altayó, F., Hellmich, U. A., Inada, H., Alcaraz, A., Furutani, Y., Nonell-Canals, A., Vázquez-Ibar, J. L., Domene, C., Gaudet, R., & Perálvarez-Marín, A. (2024). Experimental and computational biophysics to identify vasodilator drugs targeted at TRPV2 using agonists based on the probenecid scaffold. Computational and Structural Biotechnology Journal, 23, 473–482. https://doi.org/10.1016/j.csbj.2023.12.028

Rodríguez-Banqueri, A., Moliner-Culubret, M., Mendes, S. R., Guevara, T., Eckhard, U., & Gomis-Rüth, F. X. (2023). Structural insights into latency of the metallopeptidase ulilysin (lysargiNase) and its unexpected inhibition by a sulfonyl–fluoride inhibitor of serine peptidases. Dalton Transactions, 52(12), 3610–3622. https://doi.org/10.1039/d3dt00458a

Książek, M., Goulas, T., Mizgalska, D., Rodríguez-Banqueri, A., Eckhard, U., Veillard, F., Waligórska, I., Benedyk-Machaczka, M., Sochaj-Gregorczyk, A. M., Madej, M., Thøgersen, I. B., Enghild, J. J., Cuppari, A., Arolas, J. L., de Diego, I., López-Pelegrín, M., Garcia-Ferrer, I., Guevara, T., Dive, V., … Gomis-Rüth, F. X. (2023). A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia. Chemical Science, 14(4), 869–888. https://doi.org/10.1039/d2sc04166a

Godoy-Gallardo, M., Merino-Gómez, M., Mateos-Timoneda, M. A., Eckhard, U., Gil, F. J., & Perez, R. A. (2023). Advanced Binary Guanosine and Guanosine 5’-Monophosphate Cell-Laden Hydrogels for Soft Tissue Reconstruction by 3D Bioprinting. ACS Applied Materials & Interfaces, 15(25), 29729–29742. https://doi.org/10.1021/acsami.2c23277

Jimenez‐Alesanco, A., Eckhard, U., Asencio del Rio, M., Vega, S., Guevara, T., Velazquez‐Campoy, A., Gomis‐Rüth, F. X., & Abian, O. (2022). Repositioning small molecule drugs as allosteric inhibitors of the BFT‐3 toxin from enterotoxigenic Bacteroides fragilis. Protein Science, 31(10). Portico. https://doi.org/10.1002/pro.4427

Mendes, S. R., Eckhard, U., Rodríguez-Banqueri, A., Guevara, T., Czermak, P., Marcos, E., Vilcinskas, A., & Gomis-Rüth, F. X. (2022). An engineered protein-based submicromolar competitive inhibitor of the Staphylococcus aureus virulence factor aureolysin. Computational and Structural Biotechnology Journal, 20, 534–544. https://doi.org/10.1016/j.csbj.2022.01.001

Ramírez-Larrota, J. S., & Eckhard, U. (2022). An Introduction to Bacterial Biofilms and Their Proteases, and Their Roles in Host Infection and Immune Evasion. Biomolecules, 12(2), 306. https://doi.org/10.3390/biom12020306

del Amo-Maestro, L., Mendes, S. R., Rodríguez-Banqueri, A., Garzon-Flores, L., Girbal, M., Rodríguez-Lagunas, M. J., Guevara, T., Franch, À., Pérez-Cano, F. J., Eckhard, U., & Gomis-Rüth, F. X. (2022). Molecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-32215-1

Chidyausiku, T. M., Mendes, S. R., Klima, J. C., Nadal, M., Eckhard, U., Roel-Touris, J., Houliston, S., Guevara, T., Haddox, H. K., Moyer, A., Arrowsmith, C. H., Gomis-Rüth, F. X., Baker, D., & Marcos, E. (2022). De novo design of immunoglobulin-like domains. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-33004-6

López-Martín, M., Renault, P., Giraldo, J., Vázquez-Ibar, J. L., & Perálvarez-Marín, A. (2022). In Silico Assessment of the Lipid Fingerprint Signature of ATP2, the Essential P4-ATPase of Malaria Parasites. Membranes, 12(7), 702. https://doi.org/10.3390/membranes12070702

Mizgalska, D., Goulas, T., Rodríguez-Banqueri, A., Veillard, F., Madej, M., Małecka, E., Szczesniak, K., Ksiazek, M., Widziołek, M., Guevara, T., Eckhard, U., Solà, M., Potempa, J., & Gomis-Rüth, F. X. (2021). Intermolecular latency regulates the essential C-terminal signal peptidase and sortase of the Porphyromonas gingivalis type-IX secretion system. Proceedings of the National Academy of Sciences, 118(40). https://doi.org/10.1073/pnas.2103573118

Eckhard, U., Körschgen, H., von Wiegen, N., Stöcker, W., & Gomis-Rüth, F. X. (2021). The crystal structure of a 250-kDa heterotetrameric particle explains inhibition of sheddase meprin β by endogenous fetuin-B. Proceedings of the National Academy of Sciences, 118(14). https://doi.org/10.1073/pnas.2023839118

Godoy-Gallardo, M., Eckhard, U., Delgado, L. M., de Roo Puente, Y. J. D., Hoyos-Nogués, M., Gil, F. J., & Perez, R. A. (2021). Antibacterial approaches in tissue engineering using metal ions and nanoparticles: From mechanisms to applications. Bioactive Materials, 6(12), 4470–4490. https://doi.org/10.1016/j.bioactmat.2021.04.033

Blöchl, C., Holzner, C., Luciano, M., Bauer, R., Horejs-Hoeck, J., Eckhard, U., Brandstetter, H., & Huber, C. G. (2021). Proteolytic Profiling of Streptococcal Pyrogenic Exotoxin B (SpeB) by Complementary HPLC-MS Approaches. International Journal of Molecular Sciences, 23(1), 412. https://doi.org/10.3390/ijms23010412

López-Martín, M., Dubern, J.-F., Alexander, M. R., & Williams, P. (2021). AbaM Regulates Quorum Sensing, Biofilm Formation, and Virulence in Acinetobacter baumannii. Journal of Bacteriology, 203(8). https://doi.org/10.1128/jb.00635-20

Eckhard, U., Blöchl, C., Jenkins, B. G. L., Mansfield, M. J., Huber, C. G., Doxey, A. C., & Brandstetter, H. (2020). Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis. Scientific Reports, 10(1). https://doi.org/10.1038/s41598-020-76010-8

Guo, X., Söderholm, A., Kanchugal P, S., Isaksen, G. V., Warsi, O., Eckhard, U., Trigüis, S., Gogoll, A., Jerlström-Hultqvist, J., Åqvist, J., Andersson, D. I., & Selmer, M. (2020). Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family. https://doi.org/10.1101/2020.08.16.253161

Gustafsson, R., Eckhard, U., Ye, W., Enbody, E., Pettersson, M., Jemth, P., Andersson, L., & Selmer, M. (2020). Structure and Characterization of Phosphoglucomutase 5 from Atlantic and Baltic Herring—An Inactive Enzyme with Intact Substrate Binding. Biomolecules, 10(12), 1631. https://doi.org/10.3390/biom10121631

Mayer, C., Romero, M., López-Martín, M., Muras, A., & Otero, A. (2020). Quorum Sensing inAcinetobacterVirulence. Quorum Sensing: Microbial Rules of Life, 115–137. https://doi.org/10.1021/bk-2020-1374.ch007

King, S. L., Goth, C. K., Eckhard, U., Joshi, H. J., Haue, A. D., Vakhrushev, S. Y., Schjoldager, K. T., Overall, C. M., & Wandall, H. H. (2018). TAILS N-terminomics and proteomics reveal complex regulation of proteolytic cleavage by O-glycosylation. Journal of Biological Chemistry, 293(20), 7629–7644. https://doi.org/10.1074/jbc.ra118.001978

Jerlström Hultqvist, J., Warsi, O., Söderholm, A., Knopp, M., Eckhard, U., Vorontsov, E., Selmer, M., & Andersson, D. I. (2018). A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function. Nature Ecology & Evolution, 2(8), 1321–1330. https://doi.org/10.1038/s41559-018-0568-5

Dufour, A., Bellac, C. L., Eckhard, U., Solis, N., Klein, T., Kappelhoff, R., Fortelny, N., Jobin, P., Rozmus, J., Mark, J., Pavlidis, P., Dive, V., Barbour, S. J., & Overall, C. M. (2018). C-terminal truncation of IFN-γ inhibits proinflammatory macrophage responses and is deficient in autoimmune disease. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-04717-4

Tharmarajah, G., Eckhard, U., Jain, F., Marino, G., Prudova, A., Urtatiz, O., Fuchs, H., de Angelis, M. H., Overall, C. M., & Van Raamsdonk, C. D. (2018). Melanocyte development in the mouse tail epidermis requires the Adamts9 metalloproteinase. Pigment Cell & Melanoma Research, 31(6), 693–707. Portico. https://doi.org/10.1111/pcmr.12711

Butler, G. S., Connor, A. R., Sounni, N. E., Eckhard, U., Morrison, C. J., Noël, A., & Overall, C. M. (2017). Degradomic and yeast 2-hybrid inactive catalytic domain substrate trapping identifies new membrane-type 1 matrix metalloproteinase (MMP14) substrates: CCN3 (Nov) and CCN5 (WISP2). Matrix Biology, 59, 23–38. https://doi.org/10.1016/j.matbio.2016.07.006

Eckhard, U., Bandukwala, H., Mansfield, M. J., Marino, G., Cheng, J., Wallace, I., Holyoak, T., Charles, T. C., Austin, J., Overall, C. M., & Doxey, A. C. (2017). Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella. Nature Communications, 8(1). https://doi.org/10.1038/s41467-017-00599-0

Abbey, S. R., Eckhard, U., Solis, N., Marino, G., Matthew, I., & Overall, C. M. (2017). The Human Odontoblast Cell Layer and Dental Pulp Proteomes and N-Terminomes. Journal of Dental Research, 97(3), 338–346. https://doi.org/10.1177/0022034517736054

Klein, T., Eckhard, U., Dufour, A., Solis, N., & Overall, C. M. (2017). Proteolytic Cleavage—Mechanisms, Function, and “Omic” Approaches for a Near-Ubiquitous Posttranslational Modification. Chemical Reviews, 118(3), 1137–1168. https://doi.org/10.1021/acs.chemrev.7b00120

Eckhard, U., Marino, G., Butler, G. S., & Overall, C. M. (2016). Positional proteomics in the era of the human proteome project on the doorstep of precision medicine. Biochimie, 122, 110–118. https://doi.org/10.1016/j.biochi.2015.10.018

Prudova, A., Gocheva, V., auf dem Keller, U., Eckhard, U., Olson, O. C., Akkari, L., Butler, G. S., Fortelny, N., Lange, P. F., Mark, J. C., Joyce, J. A., & Overall, C. M. (2016). TAILS N-Terminomics and Proteomics Show Protein Degradation Dominates over Proteolytic Processing by Cathepsins in Pancreatic Tumors. Cell Reports, 16(6), 1762–1773. https://doi.org/10.1016/j.celrep.2016.06.086

Eckhard, U., Huesgen, P. F., Schilling, O., Bellac, C. L., Butler, G. S., Cox, J. H., Dufour, A., Goebeler, V., Kappelhoff, R., Keller, U. auf dem, Klein, T., Lange, P. F., Marino, G., Morrison, C. J., Prudova, A., Rodriguez, D., Starr, A. E., Wang, Y., & Overall, C. M. (2016). Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses. Matrix Biology, 49, 37–60. https://doi.org/10.1016/j.matbio.2015.09.003

Eckhard, U., Huesgen, P. F., Schilling, O., Bellac, C. L., Butler, G. S., Cox, J. H., Dufour, A., Goebeler, V., Kappelhoff, R., auf dem Keller, U., Klein, T., Lange, P. F., Marino, G., Morrison, C. J., Prudova, A., Rodriguez, D., Starr, A. E., Wang, Y., & Overall, C. M. (2016). Active site specificity profiling datasets of matrix metalloproteinases (MMPs) 1, 2, 3, 7, 8, 9, 12, 13 and 14. Data in Brief, 7, 299–310. https://doi.org/10.1016/j.dib.2016.02.036

Eckhard, U., Marino, G., Abbey, S. R., Tharmarajah, G., Matthew, I., & Overall, C. M. (2015). The Human Dental Pulp Proteome and N-Terminome: Levering the Unexplored Potential of Semitryptic Peptides Enriched by TAILS to Identify Missing Proteins in the Human Proteome Project in Underexplored Tissues. Journal of Proteome Research, 14(9), 3568–3582. https://doi.org/10.1021/acs.jproteome.5b00579

Eckhard, U., Marino, G., Abbey, S. R., Matthew, I., & Overall, C. M. (2015). TAILS N-terminomic and proteomic datasets of healthy human dental pulp. Data in Brief, 5, 542–548. https://doi.org/10.1016/j.dib.2015.10.003

Marino, G., Eckhard, U., & Overall, C. M. (2015). Protein Termini and Their Modifications Revealed by Positional Proteomics. ACS Chemical Biology, 10(8), 1754–1764. https://doi.org/10.1021/acschembio.5b00189

Eckhard, U., Huesgen, P. F., Brandstetter, H., & Overall, C. M. (2014). Proteomic protease specificity profiling of clostridial collagenases reveals their intrinsic nature as dedicated degraders of collagen. Journal of Proteomics, 100, 102–114. https://doi.org/10.1016/j.jprot.2013.10.004

Barré, O., Dufour, A., Eckhard, U., Kappelhoff, R., Béliveau, F., Leduc, R., & Overall, C. M. (2014). Cleavage Specificity Analysis of Six Type II Transmembrane Serine Proteases (TTSPs) Using PICS with Proteome-Derived Peptide Libraries. PLoS ONE, 9(9), e105984. https://doi.org/10.1371/journal.pone.0105984

Prudova, A., Serrano, K., Eckhard, U., Fortelny, N., Devine, D. V., & Overall, C. M. (2014). TAILS N-terminomics of human platelets reveals pervasive metalloproteinase-dependent proteolytic processing in storage. Blood, 124(26), e49–e60. https://doi.org/10.1182/blood-2014-04-569640

Huesgen, P. F., Lange, P. F., Rogers, L. D., Solis, N., Eckhard, U., Kleifeld, O., Goulas, T., Gomis-Rüth, F. X., & Overall, C. M. (2014). LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification. Nature Methods, 12(1), 55–58. https://doi.org/10.1038/nmeth.3177

Aranda, J., López, M., Leiva, E., Magán, A., Adler, B., Bou, G., & Barbé, J. (2014). Role of Acinetobacter baumannii UmuD Homologs in Antibiotic Resistance Acquired through DNA Damage-Induced Mutagenesis. Antimicrobial Agents and Chemotherapy, 58(3), 1771–1773. https://doi.org/10.1128/aac.02346-13

auf dem Keller, U., Prudova, A., Eckhard, U., Fingleton, B., & Overall, C. M. (2013). Systems-Level Analysis of Proteolytic Events in Increased Vascular Permeability and Complement Activation in Skin Inflammation. Science Signaling, 6(258). https://doi.org/10.1126/scisignal.2003512

Eckhard, U., Schönauer, E., & Brandstetter, H. (2013). Structural Basis for Activity Regulation and Substrate Preference of Clostridial Collagenases G, H, and T. Journal of Biological Chemistry, 288(28), 20184–20194. https://doi.org/10.1074/jbc.m112.448548

Marino, G., Huesgen, P. F., Eckhard, U., Overall, C. M., Schröder, W. P., & Funk, C. (2013). Family-wide characterization of matrix metalloproteinases from Arabidopsis thaliana reveals their distinct proteolytic activity and cleavage site specificity. Biochemical Journal, 457(2), 335–346. https://doi.org/10.1042/bj20130196

Kofler, S., Asam, C., Eckhard, U., Wallner, M., Ferreira, F., & Brandstetter, H. (2012). Crystallographically Mapped Ligand Binding Differs in High and Low IgE Binding Isoforms of Birch Pollen Allergen Bet v 1. Journal of Molecular Biology, 422(1), 109–123. https://doi.org/10.1016/j.jmb.2012.05.016

Eckhard, U., Schönauer, E., Nüss, D., & Brandstetter, H. (2011). Structure of collagenase G reveals a chew-and-digest mechanism of bacterial collagenolysis. Nature Structural & Molecular Biology, 18(10), 1109–1114. https://doi.org/10.1038/nsmb.2127

Eckhard, U., & Brandstetter, H. (2011). Polycystic kidney disease-like domains of clostridial collagenases and their role in collagen recruitment. Bchm, 392(11), 1039–1045. https://doi.org/10.1515/bc.2011.099

Ducka, P., Eckhard, U., Schönauer, E., Kofler, S., Gottschalk, G., Brandstetter, H., & Nüss, D. (2009). A universal strategy for high-yield production of soluble and functional clostridial collagenases in E. coli. Applied Microbiology and Biotechnology, 83(6), 1055–1065. https://doi.org/10.1007/s00253-009-1953-4

Eckhard, U., Nüss, D., Ducka, P., Schönauer, E., & Brandstetter, H. (2008). Crystallization and preliminary X-ray characterization of the catalytic domain of collagenase G fromClostridium histolyticum. Acta Crystallographica Section F Structural Biology and Crystallization Communications, 64(5), 419–421. https://doi.org/10.1107/s1744309108010476

Eckhard, U., Schönauer, E., Ducka, P., Briza, P., Nüss, D., & Brandstetter, H. (2008). Biochemical characterization of the catalytic domains of three different clostridial collagenases. Bchm, 390(1), 11–18. https://doi.org/10.1515/bc.2009.004