For full current publication list, check also here (pubmed). Publications by team members. * corresponding author, # equal contribution.

2022

  1. Demir F*, Huesgen PF. A User Guide to Validation, Annotation, and Evaluation of N-Terminome Datasets with MANTI. Methods Mol Biol. 2022;2447:271-283.
  2. Demir F, Kuppusamy M, Perrar A, Huesgen PF*. Profiling Sequence Specificity of Proteolytic Activities Using Proteome-Derived Peptide Libraries. Methods Mol Biol. 2022;2447:159-174. 
  3. Demir F, Perrar A, Mantz M, Huesgen PF*. Sensitive Plant N-Terminome Profiling with HUNTER. Methods Mol Biol. 2022;2447:139-158. 
  4. Huebbers JW, Büttgen K, Leissing F, Mantz M, Pauly M, Huesgen PF, Panstruga R. An advanced method for the release, enrichment and purification of high-quality Arabidopsis thaliana rosette leaf trichomes enables profound insights into the trichome proteome. Plant Methods. 2022 Jan 28;18(1):12.
  5.  Oberleitner L, Perrar A, Macorano L, Huesgen PF, Nowack ECM. A bipartite chromatophore transit peptide and N-terminal protein processing in the Paulinella chromatophore. Plant Physiol. 2022 May 3;189(1):152-164.

2021

  1. Dall E, Stanojlovic V, Demir F, Briza P, Dahms SO, Huesgen PF, Cabrele C, Brandstetter H. The Peptide Ligase Activity of Human Legumain Depends on Fold Stabilization and Balanced Substrate Affinities. ACS Catal. 2021 Oct 1;11(19):11885-11896.
  2. Höhfeld J, Benzing T, Bloch W, Fürst DO, Gehlert S, Hesse M, Hoffmann B, Hoppe T, Huesgen PF, Köhn M, Kolanus W, Merkel R, Niessen CM, Pokrzywa W, Rinschen MM, Wachten D, Warscheid B. Maintaining proteostasis under mechanical stress.
    EMBO Rep. 2021 Aug 4;22(8):e52507. doi: 10.15252/embr.202152507. Review.
  3. Kimura K, Ooms A, Graf-Riesen K, Kuppusamy M, Unger A, Schuld J, Daerr J, Lother A, Geisen C, Hein L, Takahashi S, Li G, Röll W, Bloch W, van der Ven PFM, Linke WA, Wu SM, Huesgen PF, Höhfeld J, Fürst DO, Fleischmann BK, Hesse M. Overexpression of human BAG3P209L in mice causes restrictive cardiomyopathy. Nat Commun. 2021 Jun 11;12(1):3575. doi: 10.1038/s41467-021-23858-7.
  4. F, Troldborg A, Thiel S, Lassé M, Huesgen PF, Tomas NM, Wiech T, Rinschen MM. Proteolysis and inflammation of the kidney glomerulus. Cell Tissue Res. 2021 Apr 17:1-12. doi: 10.1007/s00441-021-03433-8. Review.
  5. Alcaraz LB, Mallavialle A, David T, Derocq D, Delolme F, Dieryckx C, Mollevi C, Boissière-Michot F, Simony-Lafontaine J, Du Manoir S, Huesgen PF, Overall CM, Tartare-Deckert S, Jacot W, Chardès T, Guiu S, Roger P, Reinheckel T, Moali C, Liaudet-Coopman E. A 9-kDa matricellular SPARC fragment released by cathepsin D exhibits pro-tumor activity in the triple-negative breast cancer microenvironment. Theranostics. 2021 Apr 15;11(13):6173-6192. doi: 10.7150/thno.58254. 
  6. Mooney BC#, Mantz M#, Graciet E*, Huesgen PF*. Cutting the line: manipulation of plant immunity by bacterial type III effector proteases. J Exp Bot. 2021 Apr 13;72(9):3395-3409. doi: 10.1093/jxb/erab095.PMID: 33640987 Review. 
  7. Passarge A, Demir F, Green K, Depotter JRL, Scott B, Huesgen PF, Doehlemann G, Misas Villamil JC. Host apoplastic cysteine protease activity is suppressed during the mutualistic association of Lolium perenne and Epichloë festucae. J Exp Bot. 2021 Apr 13;72(9):3410-3426. doi: 10.1093/jxb/erab088.
  8. Mielke K, Wagner R, Mishra LS, Demir F, Perrar A, Huesgen PF*, Funk C. Abundance of metalloprotease FtsH12 modulates chloroplast development in Arabidopsis thaliana. J Exp Bot. 2021 Apr 13;72(9):3455-3473. doi: 10.1093/jxb/eraa550.
  9. Demir F*, Kizhakkedathu JN, Rinschen MM, Huesgen PF*. MANTI: Automated Annotation of Protein N-Termini for Rapid Interpretation of N-Terminome Data Sets. Anal Chem. 2021 Apr 6;93(13):5596-5605. doi: 10.1021/acs.analchem.1c00310.
  10. Drexelius M, Reinhardt A, Grabeck J, Cronenberg T, Nitsche F, Huesgen PF, Maier B, Neundorf I. Multistep optimization of a cell-penetrating peptide towards its antimicrobial activity. Biochem J. 2021 Jan 15;478(1):63-78. doi: 10.1042/BCJ20200698.
  11. Hofsetz E, Huesgen PF, Trifunovic A. Identification of Putative Mitochondrial Protease Substrates. Methods Mol Biol. 2021;2192:313-329. doi: 10.1007/978-1-0716-0834-0_21.

2020

  1. Dall E, Zauner FB, Soh WT, Demir F, Dahms SO, Cabrele C, Huesgen PF, Brandstetter H. Structural and functional studies of Arabidopsis thaliana legumain beta reveal isoform specific mechanisms of activation and substrate recognition. J Biol Chem. 2020 Sep 11;295(37):13047-13064. doi: 10.1074/jbc.RA120.014478. Epub 2020 Jul 21.
  2. Hofsetz E, Demir F, Szczepanowska K, Kukat A, Kizhakkedathu J, Trifunovic A*, Huesgen PF*. The mouse heart mitochondria N terminome provides insights into ClpXP-mediated proteolysis. Mol Cell Proteomics. 2020 Aug;19(8):1330-1345. doi: 10.1074/mcp.RA120.002082
  3. Niedermaier S, Schneider T, Bahl M-O, Matsubara S*, Huesgen PF*. Photoprotective Acclimation of the Arabidopsis thaliana Leaf Proteome to Fluctuating Light. Front. Genet. 11:154.  
  4. Soh WT#, Demir F#, Dall E, Perrar A, Dahms SO, Kuppusamy M, Brandstetter H, Huesgen PF*. ExteNDing Proteome Coverage with Legumain as a Highly Specific Digestion Protease. Anal Chem. 92(4):2961-2971. 

2019

  1. Weng SSH,# Demir F#, Ergin EK, Dirnberger S, Uzozie A, Tuscher D, Nierves L, Tsui J, Huesgen PF*, Lange PF*. Sensitive Determination of Proteolytic Proteoforms in Limited Microscale Proteome Samples. Mol Cell Proteomics 18(11):2335-2347.
  2. Niedermaier S, Huesgen PF*. Positional proteomics for identification of secreted proteoforms released by site-specific processing of membrane proteins. Biochim Biophys Acta Proteins Proteom 1867(12):140138. Review.
  3. Huber CV, Jakobs BD#, Mishra LS#, Niedermaier S#, Stift M, Winter G, Adamska I, Funk C*, Huesgen PF*, Funck D*. DEG10 contributes to mitochondrial proteostasis, root growth, and seed yield in Arabidopsis. J Exp Bot 70(19):5423-5436.
  4. Misas Villamil JC, Mueller AN, Demir F, Meyer U, Ökmen B, Schulze Hüynck J, Breuer M, Dauben H, Win J, Huesgen PF, Doehlemann G. A fungal substrate mimicking molecule suppresses plant immunity via an inter-kingdom conserved motif. Nat Commun 10(1):1576. 
  5. Krichel C, Möckel C, Schillinger O, Huesgen PF, Sticht H, Strodel B, Weiergräber OH, Willbold D, Neudecker P. Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site. Sci Rep 9(1):14167.
  6. Zelanis A, Oliveira AK, Prudova A, Huesgen PF, Tashima AK, Kizhakkedathu J, Overall CM, Serrano SMT. Deep Profiling of the Cleavage Specificity and Human Substrates of Snake Venom Metalloprotease HF3 by Proteomic Identification of Cleavage Site Specificity (PICS) Using Proteome Derived Peptide Libraries and Terminal Amine Isotopic Labeling of Substrates (TAILS) N-Terminomics. J Proteome Res 18(9):3419-3428. 
  7. Drescher HK, Weiskirchen R, Fülöp A, Hopf C, González de San Román E, Huesgen PF, de Bruin A, Bongiovanni L, Christ A, Tolba R, Trautwein C, Kroy DC. The Influence of Different Fat Sources on Steatohepatitis and Fibrosis Development in the Western Diet Mouse Model of Non-alcoholic Steatohepatitis (NASH). Front Physiol 10:770.
  8. Elfgen A, Hupert M, Bochinsky K, Tusche M, González de San Román Martin E, Gering I, Sacchi S, Pollegioni L, Huesgen PF, Hartmann R, Santiago-Schübel B, Kutzsche J, Willbold D. Metabolic resistance of the D-peptide RD2 developed for direct elimination of amyloid-β oligomers. Sci Rep 9(1):5715. 
  9. Perrar A, Dissmeyer N*, Huesgen PF*. New beginnings and new ends – Methods for large-scale characterization of protein termini and their use in plant biology. J Exp Bot 70(7):2021-2038.
  10. Soares A, Niedermaier S, Faro R, Loos A, Manadas B, Faro C, Huesgen PF*, Cheung AY*, Simões I*. An atypical aspartic protease modulates lateral root development in Arabidopsis thaliana. J Exp Bot 70(7):2157-2171. 
  11. Demir F*, Perrar A*, Huesgen PF*. Das maßgeschneiderte Proteom: Proteinmodifikation durch Proteolyse. BIOspektrum 25:41-44. Review.
  12. Dahms SO, Demir F, Huesgen PF, Thorn K, Brandstetter H. Sirtilins - the new old members of the vitamin K-dependent coagulation factor family. J Thromb Haemost 17:470-481.
  13. Späth MR, Bartram MP, Palacio-Escat N, Hoyer KJR, Debes C, Demir F, Schroeter CB, Mandel AM, Grundmann F, Ciarimboli G, Beyer A, Kizhakkedathu JN, Brodesser S, Göbel H, Becker JU, Benzing T, Schermer B, Höhne M, Burst V, Saez-Rodriguez J, Huesgen PF, Müller RU, Rinschen MM. The proteome microenvironment determines the protective effect of preconditioning in cisplatin-induced acute kidney injury. Kidney Int 95:333-349. 

2018

  1. Lange J, Demir F, Huesgen PF, Baumann U, von Elert E, Pichlo C. Heterologous expression and characterization of a novel serine protease from Daphnia magna: A possible role in susceptibility to toxic cyanobacteria. Aquat Toxicol, 205:140-7.​
  2. Rinschen MR, Huesgen PF, Koch R. The Podocyte Protease Web: Uncovering the Gatekeepers of Glomerular Disease. Am J Physiol Renal Physiol 315:F1812-16. Review.
  3. Ökmen B, Kemmerich B, Hilbig D, Wemhöner R, Aschenbroich J, Perrar A, Huesgen PF, Schipper K, Doehlemann G. Dual function of a secreted fungalysin metalloprotease in Ustilago maydis. New Phytol 220:249-61.
  4. González de San Román E#, Bidmon HJ#, Malisic M, Susnea I, Küppers A, Hübbers R, Wree A, Nischwitz V, Amunts K*, Huesgen PF*. Molecular composition of the human primary visual cortex profiled by multimodal mass spectrometry imaging. Brain Struct Funct 223:2767-2783.
  5. Demir F#, Niedermaier S#, Villamor JG, Huesgen PF*. Quantitative proteomics in plant protease substrate identification. New Phytol 218(3):936-943. Review.

2017

  1. Rinschen MM*, Hoppe AK, Grahammer F, Kann M, Völker LA, Schurek EM, Binz J, Höhne M, Demir F, Malisic M, Huber TB, Kurschat C, Kizhakkedathu JN, Schermer B, Huesgen PF*, Benzing T*. N-Degradomic analysis reveals a proteolytic network processing the podocyte cytoskeleton. J Am Soc Nephrol, 28: 2867-2878. Highlight comment in Nat Rev Nephrol 13(10):596. 
  2. Demir F, Niedermaier S, Kizhakkedathu JN, Huesgen PF*. Profiling of Protein N-Termini and Their Modifications in Complex Samples. Methods Mol Biol, 574:35-50. 

2016

  1. Biniossek ML, Niemer M, Maksimchuk K, Mayer B, Fuchs J, Huesgen PF, McCafferty DG, Turk B, Fritz G, Mayer J, Haecker G, Mach L, Schilling O. Identification of Protease Specificity by Combining Proteome-Derived Peptide Libraries and Quantitative Proteomics. Mol Cell Proteomics, 15:2515-24. 
  2. Leal AR, Cruz R, Bur D, Huesgen PF, Faro R, Manadas B, Wlodawer A, Faro C,  Simões I. Enzymatic properties, evidence for in vivo expression, and intracellular localization of shewasin D, the pepsin homolog from Shewanella denitrificans. Sci Rep 6:23869. 
  3. Eckhard U#, Huesgen PF#, Schilling O#, Bellac CL, Butler GS, Cox JH, Dufour A, Goebeler V, Kappelhoff R, auf dem Keller U, Klein T, Lange PF, Marino G, Morrison CJ, Prudova A, Rodriguez D, Starr AE, Wang Y, Overall CM. Active site specificity profiling datasets of matrix metalloproteinases (MMP) 1, 2, 3, 7, 8, 9, 12, 13, 14. Data Brief 7:299-310. 
  4. Eckhard U#, Huesgen PF#, Schilling O#, Bellac CL, Butler GS, Cox JH, Dufour A, Goebeler V, Kappelhoff R, auf dem Keller U, Klein T, Lange PF, Marino G, Morrison CJ, Prudova A, Rodriguez D, Starr AE, Wang Y, Overall CM. Active Site Specificity of the Matrix Metalloproteinase Family: Proteomic Identification of 4,300 Cleavage Sites by Nine MMPs explored with Structural and Synthetic Peptide Cleavage Analyses. Matrix Biol 49:37-90. 

2015

  1. Zelanis A, Huesgen PF, Oliveira AK, Tashima AK, Serrano SM and Overall CM. Snake venom serine proteinases specificity mapping by proteomic identification of cleavage sites. J Proteomics 113:260-7. 
  2. Huesgen PF, Lange PF, Rogers LD, Solis N, Eckhard U, Kleifeld O, Goulas T, Gomis-Rüth FX and Overall CM. LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification. Nat Methods 12:55-8. 7
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