Publications

Selected Publications

2024

Morgan JAM, Singh A, Kurz L, Nadler-Holly M, Ruwolt M, Ganguli S, Sharma S, Penkert M, Krause E, Liu F, Bhandari R, Fiedler D. Extensive protein pyrophosphorylation revealed in human cell lines. Nat Chem Biol. (DOI: 10.1038/s41589-024-01613-5)

Zhu Y., Akkaya KC., Ruta J., Yokoyama N., Wang C., Ruwolt M., Lima DB., Lehmann M., Liu F. Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies. Nat Commun. (DOI: 10.1038/s41467-024-47569-x)

Klössel S, Zhu Y, Amado L, Bisinski DD, Ruta J, Liu F, González Montoro A. Yeast TLDc domain proteins regulate assembly state and subcellular localization of the V-ATPase. EMBO J. (DOI: 10.1038/s44318-024-00097-2)

Kurt LU, Clasen MA, Biembengut ÍV, Ruwolt M, Liu F, Gozzo FC, Lima DB, Carvalho PC. RawVegetable 2.0: Refining XL-MS Data Acquisition through Enhanced Quality Control. J Proteome Res. (DOI: 10.1021/acs.jproteome.3c00791)

2023

Bogdanow B.#*, Mühlberg L.*, Gruska I., Vetter B., Ruta J., Elofsson A., Wiebusch L.#, Liu F.# Structural Host-Virus Interactome Profiling of Intact Infected Cells. bioRxiv. (DOI: 10.1101/2023.12.03.569778)

Clasen MA.*, Ruwolt M.*, Kurt LU., Gozzo FC., Wang S., Chen T., Carvalho PC.#, Lima DB.#, Liu F.# Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics. bioRxiv. (DOI: 10.1101/2023.11.30.569448)

Bogdanow B.#, Gruska I., Mühlberg L., Protze J., Hohensee S., Vetter B., Bosse JB., Lehmann M., Sadeghi M.#, Wiebusch L.#, Liu F#. Spatially resolved protein map of intact human cytomegalovirus virions. Nat Microbiol. (DOI: 10.1038/s41564-023-01433-8)

Ramesh N, Escher M, Turrel O, Lützkendorf J, Matkovic T, Liu F, Sigrist SJ. An antagonism between Spinophilin and Syd-1 operates upstream of memory-promoting presynaptic long-term plasticity. Elife. (DOI: 10.7554/eLife.86084)

Lučić I, Héluin L, Jiang PL, Castro Scalise AG, Wang C, Franz A, Heyd F, Wahl M, Liu F, Plested AJR. CaMKII autophosphorylation can occur between holoenzymes without subunit exchange. Elife. (DOI: 10.7554/eLife.86090)

Bogdanow B., Wang C., Ruwolt M., Ruta J., Mühlberg L., Zeng W., Elofsson A., Liu F. Enhancing Inter-link Coverage in Cross-Linking Mass Spectrometry through Context-Sensitive Subgrouping and Decoy Fusion. bioRxiv. (DOI: 10.1101/2023.07.19.549678)

Ruwolt M., Piazza I.#, Liu F.# The potential of cross-linking mass spectrometry in the development of protein-protein interaction modulators. Curr Opin Struct Biol. (DOI: 10.1016/j.sbi.2023.102648)

Ruwolt M., He Y, Lima D.B., Barshop W., Broichhagen J., Huguet R., Viner R., Liu F. Real-time library search increases cross-link identification depth across all levels of sample complexity. Anal Chem. (DOI: 10.1021/acs.analchem.2c05141)

2022

Jang W., Puchkov D., Samsó P., Liang Y., Nadler-Holly M., Sigrist S.J., Kintscher U., Liu F., Mamchaoui K., Mouly V., Haucke V., Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function. Science. (DOI: 10.1126/science.abq5209)

Ayala Mariscal S.M., Pigazzini M.L., Richter Y., Özel M., Grothaus I.L., Protze J., Ziege K., Kulke M., ElBediwi M., Vermaas J.V., Colombi Ciacchi L., Köppen S., Liu F. & Kirstein J., Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT. Nat Commun. (DOI: s41467-022-32370-5)

Ruwolt M, Schnirch L, Lima DB, Nadler-Holly M, Viner R, Liu F.  Optimized TMT-Based Quantitative Cross-Linking Mass Spectrometry Strategy for Large-Scale Interactomic Studies. Anal. Chem. (DOI: 10.1021/acs.analchem.1c04812)

Lo WT, Zhang Y, Vadas O, Roske Y, Gulluni F, De Santis MC, Zagar AV, Stephanowitz H, Hirsch E, Liu F, Daumke O, Kudryashev M, Haucke V. Structural basis of phosphatidylinositol 3-kinase C2α function. Nature Structural & Molecular Biology (DOI: 10.1038/s41594-022-00730-w)

Ashok Y., Vela-Rodríguez C., Yang C., Alanen H.I., Liu F., Paschal B.M., Lehtiö L. Reconstitution of the DTX3L-PARP9 complex reveals determinants for high-affinity heterodimerization and multimeric assembly. Biochem J. (DOI: 10.1042/BCJ20210722)

2021

Jiang PL, Wang C, Diehl A, Viner R, Etienne C, Nandhikonda P, Foster L, Bomgarden R, Liu F. A Membrane-Permeable and Immobilized Metal Affinity Chromatography (IMAC)-Enrichable Cross-Linking Reagent to Advance In Vivo Cross-Linking Mass Spectrometry. Angew Chem Int Ed Engl. (DOI: 10.1002/anie.202113937)

Schoppe J, Schubert E, Apelbaum A, Yavavli E, Birkholz O, Stephanowitz H, Han Y, Perz A, Hofnagel O, Liu F, Piehler J, Raunser S, Ungermann C. Flexible open conformation of the AP-3 complex explains its role in cargo recruitment at the Golgi. J Biol Chem. (DOI: 10.1016/j.jbc.2021.101334)

Liang Y, Piao C, Beuschel CB, Toppe D, Kollipara L, Bogdanow B, Maglione M, Lützkendorf J, See JCK, Huang S, Conrad TOF, Kintscher U, Madeo F, Liu F, Sickmann A, Sigrist SJ. eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction. Cell Rep. (DOI: 10.1016/j.celrep.2021.108941)

Gallrein C, Iburg M, Michelberger T, Koçak A, Puchkov D, Liu F, Ayala Mariscal SM, Nayak T, Kaminski Schierle GS, Kirstein J. Novel amyloid-beta pathology C. elegans model reveals distinct neurons as seeds of pathogenicity. Prog Neurobiol. (DOI: 10.1016/j.pneurobio.2020.101907)

2020

Schnirch L, Nadler-Holly M, Siao S, Frese CK, Viner R, and Liu F. Expanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS. Anal Chem (DOI: 10.1101/2020.04.23.057091)

Petzoldt A, Götz T, Driller J, Lützkendorf J, Reddy-Alla S, Matkovic-Rachid T, Liu S, Knoche E, Mertel S, Ugorets V, Lehmann M, Ramesh N, Beuschel C, Kuropka B, Freund C, Stelzl U, Loll B, Liu F, Wahl M, and Sigrist S. RIM-Binding protein couples synaptic vesicle recruitment to release sites. JCB (DOI:10.1083/jcb.201902059)

Gonzalez-Lozano MA, Koopmans F, Sullivan PF, Protze J, Krause G, Verhage M, Li KW#, Liu F#, Smit AB#. Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions. Sci Adv (DOI: 10.1126/sciadv.aax5783)

Furkert D, Hostachy S, Nadler-Holly M, Fiedler D. Triplexed Affinity Reagents to Sample the Mammalian Inositol Pyrophosphate Interactome. Cell Chemical Biology (DOI: 10.1016/j.chembiol.2020.07.017)

2019

Laezer I, Palma-Vera SE, Liu F, Frank M, Trakooljul N, Vernunft A, Schoen J, ChenS. Dynamic profile of EVs in porcine oviductal fluid during the periovulatory period. Reproduction (DOI: 10.1530/REP-19-0219)

Pavulraj S, Kamel M, Stephanowitz H, Liu F, Plendl J, Osterrieder N, Azab W. Equine Herpesvirus Type 1 Modulates Cytokine and Chemokine Profiles of Mononuclear Cells for Efficient Dissemination to Target Organs. Viruses (DOI: 10.3390/v12090999)

2017

Juling S, Niedzwiecka A, Böhmert L, Lichtenstein D, Selve S, Braeuning A, Thünemann AF, Krause E, Lampen A (2017) Protein corona analysis of silver nanoparticles links to their cellular effects
J. Proteome Res. 16: 4020-4034.

Penkert M, Yates LM, Schümann M, Perlman D, Fiedler D, Krause E (2017) Unambiguous identification of serine and threonine pyrophosphorylation using neutral-loss-triggered electron-transfer/higher-energy collision dissociation
Anal. Chem. 89: 3672-3680.

Herce HD, Schumacher D, Schneider AFL, Ludwig AK, Mann FA, Fillies M, Kasper MA, Reinke S, Krause E, Leonhardt H, M. Cardoso MC, Hackenberger CPR (2017) Cell-permeable nanobodies for targeted immunolabeling and antigen manipulation in living cells
Nature Chem. 9: 762-771.

Chen S, Palma-Vera SE, Langhammer M, Galuska SP, Braun BC, Krause E, Lucas-Hahn A, Schoen J (2017) An air-liquid interphase approach for modeling the early embryo-maternal contact zone
Sci. Rep. 7: 42298.

Berger TK, Fußhöller DM, Goodwin N, Bönigk W, Müller A, Khesroshahi ND, Brenker C, Wachten D, Krause E, Kaupp UB, Strünker T (2017) Posttranslational cleavage of Hv1 in human sperm tunes pH- and voltage-dependent gating
J. Physiol. 595.5: 1533-1546.

Schröter F, Müller K, Müller P, Krause E, Braun BC (2017) Recombinant expression of porcine spermadhesin AWN and its phospholipid interaction: indication for a novel lipid binding property
Reprod. Dom. Anim. 52: 585-595.

Buhrke T, Voß L, Briese A, Stephanowitz H, Krause E, Braeuning A, Lampen A (2017) Oxidative inactivation of the endogenous antioxidant protein DJ-1 by the food contaminants 3-MCPD and 2-MCPD
Arch. Toxicol.  DOI 10.1007/s00204-017-2027-5. [Epub ahead of print]

Thaa B, Kaufer S, Neumann SA, Peibst B, Nauwynck H, Krause E, Veit M (2017) The complex co-translational processing of glycoprotein GP5 of type 1 porcine reproductive and respiratory syndrome virus
Virus Res. 240: 112-120.

Hauser A, Penkert M, Hackenberger CPR (2017) Chemical approaches to investigate labile peptide and protein phosphorylation
Acc. Chem. Res. 50: 1883-1893.

2016

Bertran-Vicente J, Penkert M, Nieto-Garcia O, Jeckelmann JM, Schmieder P, Krause E, Hackenberger CPR (2016) Chemoselective synthesis and analysis of naturally occurring phosphorylated cysteine peptides
Nature Commun. 7: 12703.

Kuropka B, Schraven B, Kliche S, Krause E, Freund C (2016) Tyrosine-phosphorylation of the scaffold protein ADAP and its role in T cell signaling
Exp. Rev. Proteomics 13: 545-554.

Gabriel CH, Gross F, Karl M, Stephanowitz H, Hennig AF, Weber M, Gryzik S, Bachmann I, Hecklau K, Wienands J, Schuchhardt J, Herzel H, Radbruch A, Krause E, Baumgrass R (2016) Identification of novel nuclear factor of activated T cells (NFAT)-associated proteins in T cells
J. Biol. Chem. 291: 24172-24187.

Amelkina O, Zschockelt L, Painer J, Serra R, Villaespesa F, Krause E, Jewgenow K, Braun BC (2016) Progesterone, estrogen, and androgen receptors in the corpus luteum of the domestic cat, Iberian lynx (Lynx pardinus) and Eurasian lynx (Lynx lynx)
Theriogenology 86: 2107-2118.

Fritsch J, Fickers R, Klawitter J, Särchen V, Zingler P, Adam D, Janssen O, Krause E, Schütze S (2016) TNF induced cleavage of HSP90 by cathepsin D potentiates apoptotic cell death
Oncotarget  7: 75774-75789.

Pfeiffer A, Stephanowitz H, Krause E, Volkwein C, Hirsch C, Jarosch E, Sommer T. (2016) A complex of Htm1 and the oxidoreductase Pdi1 accelerates degradation of misfolded glycoproteins
J. Biol. Chem. 291: 12195-12207.

Hartl D, Nebrich G, Klein O, Stephanowitz H, Krause E, Rohe M (2016) SORLA regulates calpain-dependent degradation of synapsin
Alzheimer’s Dement. 12: 952-963.

Spiesschaert B, Stephanowitz H, Krause E, Osterrieder N, Azab W (2016) Glycoprotein B of equine herpesvirus type 1 (EHV-1) has two recognition sites for subtilisin-like proteases that are cleaved by furin
J. Gen. Virol. 97: 1218-1228.

2015

Feutlinske F, Browarski M, Ku MC, Trnka P, Waiczies S, Niendorf T, Stallcup WB, Glass R, Krause E, Maritzen T (2015) Stonin1 mediates endocytosis of the proteoglycan NG2 and regulates focal adhesion dynamics and cell motility
Nature Commun. 6: 8535.

Bertran-Vicente J, Schümann M, Hackenberger CP, Krause E (2015) Gas-phase rearrangement in lysine phosphorylated peptides during electron-transfer dissociation tandem mass spectrometry
Anal. Chem. 87: 6990-6994.

Kuropka B, Royla N, Freund C, Krause E (2015) Sortase A-mediated site-specific immobilization for identification of protein interactions in affinity purification-mass spectrometry experiments
Proteomics 15: 1230-1234.

Hecht AM, Braun BC, Krause E, Voigt CC, Greenwood AD, Czirjak GA (2015) Plasma proteomic analysis of active and torpid greater mouse-eared bats (Myotis myotis)
Sci. Rep. 5: 16604.

Günther R, Krause E, Schümann M, Blasig IE, Haseloff RF (2015) Depletion of highly abundant proteins from human cerebrospinal fluid: a cautionary note
Mol. Neurodegener. 10: 53.

Schumacher D, Helma J, Mann F, Pichler G, Natale F, Krause E, Cardoso C, Hackenberger CPR, Leonhardt H (2015) Versatile and efficient site-specific protein functionalization by tubulin tyrosine ligase
Angew. Chem. Int. Ed. 54: 13787-13791.

Kuropka B, Witte A, Sticht J, Waldt N, Majkut P, Hackenberger CPR, Schraven B, Krause E, Kliche S, Freund C (2015) Analysis of phosphorylation-dependent protein interactions of ADAP reveals novel interaction partners required for chemokine-directed T cell migration
Mol. Cell. Proteomics 14: 2961-2972.

Serwa RA, Abaitua F, Krause E, Tate EW, O’Hare P (2015) Systems analysis of protein fatty acylation in herpes simplex virus-infected cells using chemical proteomics
Chemistry & Biology 22: 1008-1017.

Morrison E, Kuropka B, Kliche S, Brügger B, Krause E, Freund C (2015) Quantitative analysis of the human T cell palmitome
Sci. Rep. 5: 11598.

Schmohl L, Wagner FR, Schümann M, Krause E, Schwarzer D (2015) Semisynthesis and initial characterization of sortase A mutants containing selenocysteine and homocysteine
Bioorg. Med. Chem. 23: 2883-2889.

Bertran-Vicente J, Schümann M, Schmieder P, Krause E, Hackenberger CPR (2015) Direct access of site-specifically phosphorylated-lysine peptides from solid-support
Org. Biomol. Chem. 13: 6839-6843.

Broncel M, Serwa RA, Ciepla P, Krause E, Dallman MJ, Magee AI, Tate EW (2015) Multifunctional reagents for quantitative proteome-wide analysis of protein modification in human cells and dynamic profiling of protein lipidation during vertebrate development
Angew. Chem. Int. Ed. 54: 5948-5951.

Broncel M, Serwa RA, Ciepla P, Krause E, Dallman MJ, Magee AI, Tate EW (2015) Myristoylation profiling in human cells and zebrafish
Data Brief 4: 379-383.

Klingberg R, Jost JO, Schümann M, Gelato KA, Fischle W, Krause E, Schwarzer D (2015) Analysis of phosphorylation-dependent protein-protein interactions of histone H3
ACS Chem. Biol. 10: 138-145.

Dabrowski S, Staat C, Zwanziger D, Sauer RS, Bellmann C, Günther R, Krause E, Haseloff RF, Rittner H, Blasig IE (2015) Redox-sensitive structure and function of the first extracellular loop of the cell-cell contact protein claudin-1: Lessons from molecular structure to animals
Antioxid. Redox Signal. 22: 1-14.

Klein W, Westendorf C, Schmidt A, Conill-Cortes M, Rutz C, Blohs M, Beyermann M, Protze J, Krause G, Krause E, Schülein R (2015) Defining a conformational consensus motif in cotransin-sensitive signal sequences: a proteomic and site-directed mutagenesis study
PLoS One 10(3): e0120886.

Albert GI, Schell C, Kirschner KM, Schaefer S, Naumann R, Mueller A, Kretz O, Kuropka B, Girbig M, Huebner N, Krause E, Scholz H, Huber TB, Knobeloch KP, Freund C (2015) The GYF domain protein CD2BP2 is critical for embryogenesis and podocyte function
J. Mol. Cell Biol. 7: 402-414.

Shymanets A, Prajwal, Vadas O, Czupalla C, LoPiccolo J, Brenowitz M, Ghigo A, Hirsch E, Krause E, Wetzker R, Williams RL, Harteneck C, Nürnberg B (2015) Different inhibition of Gβγ-stimulated class IB phosphoinositide 3-kinase (PI3K) variants by a monoclonal antibody. Specific function of p101 as a Gβγ -dependent regulator of PI3Kγ enzymatic activity
Biochem. J. 469: 59-69.

2014

Bertran-Vicente J, Serwa R, Schümann M, Schmieder P, Krause E, Hackenberger CPR (2014) Site-specifically phosphorylated lysine peptides
J. Am. Chem. Soc. 136: 13622-13628.