Publications 2020

*co-first author *co-corresponding author

Barth M, Bender J, Kundlacz T, Schmidt C. (2020) Evaluation of NHS-Acetate and DEPC labelling for determination of solvent accessible amino acid residues in protein complexes. J Proteomics. Accepted.

Wittig S, Songailiene I, Schmidt C. (2020) Stoichiometries and stability of CRISPR-Cascade complexes with varying spacer length revealed by native mass spectrometry. J Am Soc Mass Spectrom 31(3):538-546. doi: 10.1021/jasms.9b00011

Publications 2019

*co-first author *co-corresponding author

Volland C, Schott P, Didié M, Männer J, Unsöld B, Toischer K, Schmidt C, Urlaub H, Nickels K, Knöll R, Schmidt A, Guan K, Hasenfuß G, Seidler T. (2019) Control of p21Cip by BRAP is Critical for Cardiomyocyte Cell Cycle Progression and Survival. Cardiovasc Res. 116(3):592-604. doi: 10.1093/cvr/cvz177.

Pyle E, Guo C, Hofmann T, Schmidt C, Ribeiro O, Politis A, Byrne B. (2019) Protein-lipid interactions stabilise the oligomeric state of Bor1p from Saccharomyces cerevisiae. Anal Chem. 91(20):13071-13079. doi: 10.1021/acs.analchem.9b03271.

Faull SV, Lau AMC, Martens C, Ahdash Z, Hansen K, Yebenes H, Schmidt C, Beuron F, Cronin NB, Morris EP, Politis A. (2019) Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome. Nat Commun. 10(1):3814. doi: 10.1038/s41467-019-11772-y.

Inga Songailiene, Marius Rutkauskas, Tomas Sinkunas, Elena Manakova, Sabine Wittig, Carla Schmidt, Virginijus Siksnys*and Ralf Seidel* (2019) Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length Cell Rep 28(12), 3157-3166

Bender J, Schmidt C. (2019) The CroCo cross-link converter: a user-centred tool to convert results from crosslinking mass spectrometry experiments. Bioinformatics. 36(4):1296-1297. doi: 10.1093/bioinformatics/btz732.

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O’Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. (2019) First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem. 91(11):6953-6961.  doi: 10.1021/acs.analchem.9b00658.

Prajapati S, Haselbach D, Wittig S, Patel MS, Chari A, Schmidt C, Stark H, Tittmann K (2019) Structural and Functional Analyses of the Human PDH Complex Suggest a “Division-of-Labor” Mechanism by Local E1 and E3 Clusters. Structure 27(7):1124-1136. doi: 10.1016/j.str.2019.04.009.

Hofmann T, Schmidt C (2019) Instrument response of phosphatidylglycerol lipids with varying fatty acyl chain length in nano-ESI shotgun experiments. Chem Phys Lipids. 223:104782. doi: 10.1016/j.chemphyslip.2019.05.007.

Bender J, Schmidt C (2019) Mass spectrometry of membrane protein complexes. Biol Chem. 400(7):813-829. doi: 10.1515/hsz-2018-0443.

Frick M, Schmidt C (2019) Mass spectrometry – a Versatile Tool for Characterizing the Lipid Environment of Membrane Protein Assemblies. Chem Phys Lipids. 221:145-157. doi: 10.1016/j.chemphyslip.2019.04.001

Frick M, Schmidt C (2019) Massenspektrometrie von Phospholipiden aus Liposomen. Biospektrum 25(2):167-169

Wittig S, Haupt C, Hoffmann W, Kostmann S, Pagel K, Schmidt C (2019) Oligomerisation of Synaptobrevin-2 Studied by Native Mass Spectrometry and Chemical Cross-Linking. J Am Soc Mass Spectrom. 30(1):149-160. doi: 10.1007/s13361-018-2000-4

Publications 2018

*co-first author *co-corresponding author

Nagarathinam K, Nakada-Nakura Y, Parthier C, Terada T, Juge N, Jaenecke F, Liu K, Hotta Y, Mivaji T, Omote H, Iwata S, Nomura N, Stubbs MT, Tanabe M (2018) Outward open conformation of a Major Facilitator Superfamily multidrug/H+ antiporter provides insights into switching mechanism. Nat commun 9(1):4005.

Bonvin AMJJ, Karaca E, Kastritis PL, Rodrigues JPGLM (2018) Defining distance restraints in HADDOCK. Nat Protoc. 13(7):1503, doi: 10.1038/s41596-018-0017-6

Frick M, Hofmann T, Haupt C, Schmidt C (2018) A novel sample preparation strategy for shotgun lipidomics of phospholipids employing multilamellar vesicles. Anal Bioanal Chem. 410(18):4253-4258, doi: 10.1007/s00216-018-1113-8

Prochaska H, Thieme S, Daum S, Grau J, Schmidtke C, Hallensleben M, John P, Bacia K, Bonas U (2018) A conserved motif promotes HpaB-regulated export of type III effectors from Xanthomonas. Mol Plant Pathol. doi: 10.1111/mpp.12725

Publications 2017

*involved in equal shares, *co-corresponding author

Nagarathinam K, Jaenecke F, Nakada-Nakura Y, Hotta Y, Liu K, Iwata S, Stubbs MT, Nomura N, Tanabe M. (2017) The multidrug-resistance transporter MdfA from Escherichia coli: crystallization and X-ray diffraction analysis. Act Crystallogr F Struct Biol Commun 73(Pt 7):423-430.

Blees A, Januliene D, Hofmann T, Koller N, Schmidt C, Trowitzsch S, Moeller A, Tampé R (2017) Structure of the human MHC-I peptide-loading complex. Nature 551(7681):525-528, doi: 10.1038/nature24627

Cotrim CA, Weidner A, Strehmel N, Bisol TB, Meyer D, Brandt W, Wessjohann LA, Stubbs, MT (2017) A Distinct Arimatic Prenyltransferase Associated with the Futalosine Pathway. ChemistrySelect 2:9319-9325, doi: 10.1002/slct.201702151

Degiacomi M, Schmidt C, Baldwin AJ, Benesch JLP (2017) Accommodating protein dynamics in the modelling of che-mical cross-links. Structure 25:1751-1757.e5, doi: 10.1016/j.str.2017.08.015

Fonseca-Ornelas L, Schmidt C, Camacho-Zarco AR, Fernandez CO, Becker S, Zweckstetter M (2017) Small-Molecule-Induced Soluble Oligomers of α-Synuclein with Helical Structure. Chemistry 23(53):13010-13014, doi: 10.1002/chem.201703001

Haupt C*, Hofmann T*, Wittig S*, Politis A, Schmidt C (2017) Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies. J Vis Exp. 129, doi: 10.3791/56747

Ichikawa M, Liu D, Kastritis PL, Basu K, Hsu TC, Yang S, Bui KH (2017) Subnanometre-resolution structure of the doublet microtubule reveals new classes of microtubule-associated proteins. Nat Commun. 8:15035, doi: 10.1038/ncomms15035

Kastritis PL*, O’Reilly FJ*, Bock T*, Li Y, Rogon MZ, Buczak K, Romanov N, Betts MJ, Bui KH, Hagen WJ, Hennrich ML, Mackmull MT, Rappsilber J, Russell RB, Bork P, Beck M, Gavin AC (2017) Capturing protein communities by structural proteomics in a thermophilic eukaryote. Mol Syst Biol. 13(7):936,
doi: 10.15252/msb.20167412

Krüger D, Ebenhan J, Werner S, Bacia K (2017) Measuring Protein Binding to Lipid Vesicles by Fluorescence Cross-Corre-lation Spectroscopy. Biophys Journal. 113(6): 1311–1320, doi: 10.1016/j.bpj.2017.06.023

Kumar A, Balbach J (2017) Targeting the molecular chaperone SlyD to inhibit bacterial growth with a small molecule. Sci Rep. 7:42141, doi: 10.1038/srep42141

Nagarathinam K, Jaenecke F, Nakada-Nakura Y, Hotta Y, Liu K, Iwata S, Stubbs MT, Nomura N, Tanabe M (2017) The mul-tidrug-resistance transporter MdfA from Escherichia coli: crystallization and X-ray diffraction analysis. Acta Crystallogr F Struct Biol Commun. 73(Pt 7):423-430,
doi: 10.1107/S2053230X17008500

Piechotta A, Parthier C, Kleinschmidt M, Gnoth K, Pillot T, Lues I, Demuth HU, Schilling S, Rahfeld JU, Stubbs MT (2017) Structural and functional analyses of pyroglutamate-amyloid-β-specific antibodies as a basis for Alzheimer immunothe-rapy. J Biol Chem. 292(30):12713-12724, doi: 10.1074/jbc.M117.777839

Politis A#, Schmidt C# (2017) Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling. J Proteomics pii: S1874-3919(17)30146-X, doi: 10.1016/j.jprot.2017.04.019

Scacioc A, Schmidt C*, Hofmann T, Urlaub H, Kühnel K*, Pérez-Lara Á* (2017) Structure based biophysical characterizati-on of the PROPPIN Atg18 shows Atg18 oligomerization upon membrane binding. Sci Rep. 7(1):14008, doi: 10.1038/s41598-017-14337-5

Schaller-Laudel S, Latowski D, Jemioła-Rzemińska M, Strzałka K, Daum S, Bacia K, Wilhelm C, Goss R (2017) Influence of thylakoid membrane lipids on the structure of aggregated light-harvesting complexes of the diatom Thalassiosira pseu-donana and the green alga Mantoniella squamata. Physiol Plant. 160(3):339-358, doi: 10.1111/ppl.12565

Schmidt C, Urlaub H (2017) Combining Cross-linking Mass Spectrometry (CX-MS) and Cryo-electron Microscopy (cryo-EM) for Structural Elucidations of Large Protein Complexes. Curr Opin Struct Biol. 46:157-168, doi: 10.1016/j.sbi.2017.10.005

Schmidt C, Robinson CV (2017) Biophysical methods: behind the scenes of the cryo-EM revolution. Curr Opin Struct Biol. Editorial. 46:ix-xi, doi: 10.1016/j.sbi.2017.10.018

Scacioc A, Schmidt C*, Hofmann T, Urlaub H, Kühnel K*, Pérez-Lara Á* (2017) Structure based biophysical characterizati-on of the PROPPIN Atg18 shows Atg18 oligomerization upon membrane binding

Vangone A, Rodrigues JP, Xue LC, van Zundert GC, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond AS, Visscher KM, Trellet M, Kastritis PL, Bonvin AM (2017) Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1. Proteins. 85(3):417-423, doi: 10.1002/prot.25198

Publications 2016

*involved in equal shares, *co-corresponding author

Adler J, Baumann M, Voigt B, Scheidt HA, Bhowmik D, Häupl T, Abel B, Madhu PK, Balbach J, Maiti S, Huster D (2016) A Detailed Analysis of the Morphology of Fibrils of Selectively Mutated Amyloid ß (1-40). Chemphyschem. 17(17):2744-53, doi: 10.1002/cphc.201600413

Achilles A, Baerenwald R, Lechner BD, Werner S, Ebert H, Tschierske C, Blume A, Bacia K, Saalwaechter K (2016) Self-Assembly of X-Shaped Bolapolyphiles in Lipid Membranes: Solid-State NMR Investigations. Langmuir, 32(3): 673-682, doi: 10.1021/acs

Daum B, Auerswald A, Gruber T, Hause G, Balbach J, Kühlbrandt W, Meister A (2016) Supramolecular organization of the human N-BAR domain in shaping the sarcolemma membrane. J Struct Biol. 194(3):375-82, doi: 10.1016/j. jsb.2016.03.017

Garvey M, Baumann M, Wulff M, Kumar ST, Markx D, Morgado I, Knüpfer U, Horn U, Mawrin C, Fändrich M, Balbach J (2016) Molecular architecture of Aß fibrils grown in cerebrospinal fluid solution and in a cell culture model of Aß plaque formation. Amyloids 23(2):76-85, doi: 10.3109/13506129.2016.1146989

Krüger M, Kalbacher H, Kastritis PL, Bischof J, Barth H, Henne-Bruns D, Vorgias C, Sarno S, Pinna LA, Knippschild U (2016) New potential peptide therapeutics perturbing CK1d/a-tubulin interaction. Cancer Lett. Jun 1;375(2):375-383, doi: 10.1016/j.canlet.2016.03.021

Kumar A, Baumann M, Balbach J (2016) Small Molecule Inhibited Parathyroid Hormone Mediated cAMP Response by N-Terminal Peptide Binding. Sci Rep. 6:22533, doi: 10.1038/srep22533

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ. (2016) Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins. 84 Suppl 1:323-48, doi: 10.1002/prot.25007

Liko I, Degiacomi MT, Mohammed S, Yoshikawa S, Schmidt C#, Robinson CV# (2016) Dimer interface of bovine cytochrome c oxidase is influenced by local posttranslational modifications and lipid binding. Proc Natl Acad Sci U S A. 113(29):8230-5, doi: 10.1073/pnas.1600354113

Mazhab-Jafari MT, Rohou A, Schmidt C, Bueler SA, Benlekbir S, Robinson CV, Rubinstein JL (2016) Atomic model for the membrane-embedded V0 motor of a eukaryotic V-ATPase. Nature 539(7627):118-122,
doi: 10.1038/nature19828

Ori A, Iskar M, Buczak K, Kastritis PL, Parca L, Andrés-Pons A, Singer S, Bork P, Beck M.
Spatiotemporal variation of mammalian protein complex stoichiometries. (2016) Genome Biol. 17:47,
doi: 10.1186/s13059-016-0912-5

Roos M, Ott M, Hofmann M, Link S, Rössler E, Balbach J, Krushelnitsky A, Saalwächter K. (2016) Coupling and Decoupling of Rotational and Translational Diffusion of Proteins under Crowding Conditions. J Am Chem Soc. 138(32):10365-72, doi: 10.1021/jacs.6b06615

Rothe M, Gruber T, Gröger S, Balbach J, Saalwächter K, Roos M (2017) Transient binding accounts for apparent violation of the generalized Stokes-Einstein relation in crowded protein solutions. Phys Chem Chem Phys. 18(27):18006-14, doi: 10.1039/c6cp01056c

Silva-Martin N, Daudén MI, Glatt S, Hoffmann NA, Kastritis PL, Bork P, Beck M, Müller CW.
The Combination of X-Ray Crystallography and Cryo-Electron Microscopy Provides Insight into the Overall Architecture of the Dodecameric Rvb1/Rvb2 Complex. (2016) PLoS One. 11(1):e0146457,
doi: 10.1371/journal.pone.0146457

Spiliotopoulos D, Kastritis PL, Melquiond AS, Bonvin AM, Musco G, Rocchia W, Spitaleri A.
dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking. (2016) Front Mol Biosci. 3:46, doi: 10.3389/fmolb.2016.00046

Villmow M, Baumann M, Malesevic M, Sachs R, Hause G, Fändrich M, Balbach J, Schiene-Fischer C (2016) Inhibition of Aß(1-40) fibril formation by cyclophilins. Biochem J. 473(10):1355-68,
doi: 10.1042/BCJ20160098

Wulff M, Baumann M, Thümmler A, Yadav JK, Heinrich L, Knüpfer U, Schlenzig D, Schierhorn A, Rahfeld JU, Horn U, Balbach J, Demuth HU, Fändrich M. (2016) Enhanced Fibril Fragmentation of N-Terminally Truncated and Pyroglutamyl-Modified Aß Peptides. Angew Chem Int Ed Engl. 55(16):5081-4,
doi: 10.1002/anie.201511099

Xue LC, Rodrigues JP, Kastritis PL, Bonvin AM, Vangone A. (2016)
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. Bioinformatics. 32(23):3676-3678, doi: 10.1093/bioinformatics/btw514