Research Groups


Publications of Achilleas Frangakis (Results: 67)


Cryo-electron tomography reveals the binding and release states of the major adhesion complex from Mycoplasma genitalium.
PLoS pathogens
Sprankel L, Scheffer MP, Manger S, Ermel UH, Frangakis AS PubMed
Nov 2023 Volume: 19 Issue: 11 Pages: e1011761

Essential protein P116 extracts cholesterol and other indispensable lipids for Mycoplasmas.
Nature structural & molecular biology
Sprankel L, Vizarraga D, Martín J, Manger S, Meier-Credo J, Marcos M, Julve J, Rotllan N, Scheffer MP, Escolà-Gil JC, Langer JD, Piñol J, Fita I, Frangakis AS PubMed
Mar 2023 Volume: 30 Issue: 3 Pages: 321-329

ArtiaX: An electron tomography toolbox for the interactive handling of sub-tomograms in UCSF ChimeraX.
Protein science : a publication of the Protein Society
Ermel UH, Arghittu SM, Frangakis AS PubMed
Dec 2022 Volume: 31 Issue: 12 Pages: e4472

Biochemical Characterization of Cell-free Synthesized Human β Adrenergic Receptor Cotranslationally Inserted into Nanodiscs.
Journal of molecular biology
Köck Z, Ermel U, Martin J, Morgner N, Frangakis AS, Dötsch V, Hilger D, Bernhard F PubMed
Aug 2022 Volume: 434 Issue: 16 Pages: 167687

Mean curvature motion facilitates the segmentation and surface visualization of electron tomograms.
Journal of structural biology
Frangakis AS PubMed
Mar 2022 Volume: 214 Issue: 1 Pages: 107833

Structural and functional analysis of the promiscuous AcrB and AdeB efflux pumps suggests different drug binding mechanisms.
Nature communications
Ornik-Cha A, Wilhelm J, Kobylka J, Sjuts H, Vargiu AV, Malloci G, Reitz J, Seybert A, Frangakis AS, Pos KM PubMed
Nov 2021 Volume: 12 Issue: 1 Pages: 6919

It's noisy out there! A review of denoising techniques in cryo-electron tomography.
Journal of structural biology
Frangakis AS PubMed
Dec 2021 Volume: 213 Issue: 4 Pages: 107804

Ex vivo visualization of RNA polymerase III-specific gene activity with electron microscopy.
Communications biology
Manger S, Ermel UH, Frangakis AS PubMed
Feb 2021 Volume: 4 Issue: 1 Pages: 234

Cysteine oxidation and disulfide formation in the ribosomal exit tunnel.
Nature communications
Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer JD, Blackledge M, Frangakis AS, Glaubitz C, Schwalbe H PubMed
Nov 2020 Volume: 11 Issue: 1 Pages: 5569

Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography.
Proceedings of the National Academy of Sciences of the United States of America
Sikora M, Ermel UH, Seybold A, Kunz M, Calloni G, Reitz J, Vabulas RM, Hummer G, Frangakis AS PubMed
Nov 2020 Volume: 117 Issue: 44 Pages: 27132-27140

Immunodominant proteins P1 and P40/P90 from human pathogen Mycoplasma pneumoniae.
Nature communications
Vizarraga D, Kawamoto A, Matsumoto U, Illanes R, Pérez-Luque R, Martín J, Mazzolini R, Bierge P, Pich OQ, Espasa M, Sanfeliu I, Esperalba J, Fernández-Huerta M, Scheffer MP, Pinyol J, Frangakis AS, Lluch-Senar M, Mori S, Shibayama K, Kenri T, Kato T, Namba K, Fita I, Miyata M, Aparicio D PubMed
Oct 2020 Volume: 11 Issue: 1 Pages: 5188

SARS-CoV-2 infects and induces cytotoxic effects in human cardiomyocytes.
Cardiovascular research
Bojkova D, Wagner JUG, Shumliakivska M, Aslan GS, Saleem U, Hansen A, Luxán G, Günther S, Pham MD, Krishnan J, Harter PN, Ermel UH, Frangakis AS, Milting H, Zeiher AM, Klingel K, Cinatl J, Dendorfer A, Eschenhagen T, Tschöpe C, Ciesek S, Dimmeler S PubMed
Dec 2020 Volume: 116 Issue: 14 Pages: 2207-2215

Structure and mechanism of the Nap adhesion complex from the human pathogen Mycoplasma genitalium.
Nature communications
Aparicio D, Scheffer MP, Marcos-Silva M, Vizarraga D, Sprankel L, Ratera M, Weber MS, Seybert A, Torres-Puig S, Gonzalez-Gonzalez L, Reitz J, Querol E, Piñol J, Pich OQ, Fita I, Frangakis AS PubMed
Jun 2020 Volume: 11 Issue: 1 Pages: 2877

Crystalline Niobium Carbide Superconducting Nanowires Prepared by Focused Ion Beam Direct Writing.
ACS nano
Porrati F, Barth S, Sachser R, Dobrovolskiy OV, Seybert A, Frangakis AS, Huth M PubMed
Jun 2019 Volume: 13 Issue: 6 Pages: 6287-6296

The desmosome is a mesoscale lipid raft-like membrane domain.
Molecular biology of the cell
Lewis JD, Caldara AL, Zimmer SE, Stahley SN, Seybold A, Strong NL, Frangakis AS, Levental I, Wahl JK, Mattheyses AL, Sasaki T, Nakabayashi K, Hata K, Matsubara Y, Ishida-Yamamoto A, Amagai M, Kubo A, Kowalczyk AP PubMed
Jun 2019 Volume: 30 Issue: 12 Pages: 1390-1405

Nucleosome conformational variability in solution and in interphase nuclei evidenced by cryo-electron microscopy of vitreous sections.
Nucleic acids research
Eltsov M, Grewe D, Lemercier N, Frangakis A, Livolant F, Leforestier A PubMed
Sep 2018 Volume: 46 Issue: 17 Pages: 9189-9200

The molecular recognition of phosphatidic acid by an amphipathic helix in Opi1.
The Journal of cell biology
Hofbauer HF, Gecht M, Fischer SC, Seybert A, Frangakis AS, Stelzer EHK, Covino R, Hummer G, Ernst R PubMed
Sep 2018 Volume: 217 Issue: 9 Pages: 3109-3126

Cryo-electron tomography analyses of terminal organelle mutants suggest the motility mechanism of Mycoplasma genitalium.
Molecular microbiology
Seybert A, Gonzalez-Gonzalez L, Scheffer MP, Lluch-Senar M, Mariscal AM, Querol E, Matthaeus F, Piñol J, Frangakis AS PubMed
May 2018 Volume: 108 Issue: 3 Pages: 319-329

Structural characterization of the NAP; the major adhesion complex of the human pathogen Mycoplasma genitalium.
Molecular microbiology
Scheffer MP, Gonzalez-Gonzalez L, Seybert A, Ratera M, Kunz M, Valpuesta JM, Fita I, Querol E, Piñol J, Martín-Benito J, Frangakis AS PubMed
Sep 2017 Volume: 105 Issue: 6 Pages: 869-879

Blood RNA biomarkers in prodromal PARK4 and rapid eye movement sleep behavior disorder show role of complexin 1 loss for risk of Parkinson's disease.
Disease models & mechanisms
Lahut S, Gispert S, Ömür Ö, Depboylu C, Seidel K, Domínguez-Bautista JA, Brehm N, Tireli H, Hackmann K, Pirkevi C, Leube B, Ries V, Reim K, Brose N, den Dunnen WF, Johnson M, Wolf Z, Schindewolf M, Schrempf W, Reetz K, Young P, Vadasz D, Frangakis AS, Schröck E, Steinmetz H, Jendrach M, Rüb U, Başak AN, Oertel W, Auburger G PubMed
May 2017 Volume: 10 Issue: 5 Pages: 619-631

Structure of RNA polymerase I transcribing ribosomal DNA genes.
Neyer S, Kunz M, Geiss C, Hantsche M, Hodirnau VV, Seybert A, Engel C, Scheffer MP, Cramer P, Frangakis AS PubMed
Dec 2016 Volume: 540 Issue: 7634 Pages: 607-610

A flexible, multilayered protein scaffold maintains the slit in between glomerular podocytes.
JCI insight
Grahammer F, Wigge C, Schell C, Kretz O, Patrakka J, Schneider S, Klose M, Kind J, Arnold SJ, Habermann A, Bräuniger R, Rinschen MM, Völker L, Bregenzer A, Rubbenstroth D, Boerries M, Kerjaschki D, Miner JH, Walz G, Benzing T, Fornoni A, Frangakis AS, Huber TB PubMed
Jun 2016 Volume: 1 Issue: 9 Pages:

Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria.
Proceedings of the National Academy of Sciences of the United States of America
Mühleip AW, Joos F, Wigge C, Frangakis AS, Kühlbrandt W, Davies KM PubMed
Jul 2016 Volume: 113 Issue: 30 Pages: 8442-7

Three-dimensional CTF correction improves the resolution of electron tomograms.
Journal of structural biology
Kunz M, Frangakis AS PubMed
Feb 2017 Volume: 197 Issue: 2 Pages: 114-122

M-free: Mask-independent scoring of the reference bias.
Journal of structural biology
Kunz M, Yu Z, Frangakis AS PubMed
Nov 2015 Volume: 192 Issue: 2 Pages: 307-11

Quantitative analysis of cytoskeletal reorganization during epithelial tissue sealing by large-volume electron tomography.
Nature cell biology
Eltsov M, Dubé N, Yu Z, Pasakarnis L, Haselmann-Weiss U, Brunner D, Frangakis AS PubMed
May 2015 Volume: 17 Issue: 5 Pages: 605-14

PLEKHM1 regulates Salmonella-containing vacuole biogenesis and infection.
Cell host & microbe
McEwan DG, Richter B, Claudi B, Wigge C, Wild P, Farhan H, McGourty K, Coxon FP, Franz-Wachtel M, Perdu B, Akutsu M, Habermann A, Kirchof A, Helfrich MH, Odgren PR, Van Hul W, Frangakis AS, Rajalingam K, Macek B, Holden DW, Bumann D, Dikic I PubMed
Jan 2015 Volume: 17 Issue: 1 Pages: 58-71

Super-sampling SART with ordered subsets.
Journal of structural biology
Kunz M, Frangakis AS PubMed
Nov 2014 Volume: 188 Issue: 2 Pages: 107-15

M-free: scoring the reference bias in sub-tomogram averaging and template matching.
Journal of structural biology
Yu Z, Frangakis AS PubMed
Jul 2014 Volume: 187 Issue: 1 Pages: 10-19

Correlative light- and electron microscopy with chemical tags.
Journal of structural biology
Perkovic M, Kunz M, Endesfelder U, Bunse S, Wigge C, Yu Z, Hodirnau VV, Scheffer MP, Seybert A, Malkusch S, Schuman EM, Heilemann M, Frangakis AS PubMed
May 2014 Volume: 186 Issue: 2 Pages: 205-13

CENP-A arrays are more condensed than canonical arrays at low ionic strength.
Biophysical journal
Geiss CP, Keramisanou D, Sekulic N, Scheffer MP, Black BE, Frangakis AS PubMed
Feb 2014 Volume: 106 Issue: 4 Pages: 875-82

Three-dimensional visualization of the molecular architecture of cell-cell junctions in situ by cryo-electron tomography of vitreous sections.
Methods in molecular biology (Clifton, N.J.)
Al-Amoudi A, Frangakis AS PubMed
2013 Volume: 961 Issue: Pages: 97-117

3D Ultrastructural organization of whole Chlamydomonas reinhardtii cells studied by nanoscale soft x-ray tomography.
PloS one
Hummel E, Guttmann P, Werner S, Tarek B, Schneider G, Kunz M, Frangakis AS, Westermann B PubMed
2012 Volume: 7 Issue: 12 Pages: e53293

Heritable yeast prions have a highly organized three-dimensional architecture with interfiber structures.
Proceedings of the National Academy of Sciences of the United States of America
Saibil HR, Seybert A, Habermann A, Winkler J, Eltsov M, Perkovic M, Castaño-Diez D, Scheffer MP, Haselmann U, Chlanda P, Lindquist S, Tyedmers J, Frangakis AS PubMed
Sep 2012 Volume: 109 Issue: 37 Pages: 14906-11

Special issue on electron tomography.
Journal of structural biology
Medalia O, Frangakis A PubMed
May 2012 Volume: 178 Issue: 2 Pages: 75

Human mitotic chromosomes consist predominantly of irregularly folded nucleosome fibres without a 30-nm chromatin structure.
The EMBO journal
Nishino Y, Eltsov M, Joti Y, Ito K, Takata H, Takahashi Y, Hihara S, Frangakis AS, Imamoto N, Ishikawa T, Maeshima K PubMed
Apr 2012 Volume: 31 Issue: 7 Pages: 1644-53

Atheroprotective communication between endothelial cells and smooth muscle cells through miRNAs.
Nature cell biology
Hergenreider E, Heydt S, Tréguer K, Boettger T, Horrevoets AJ, Zeiher AM, Scheffer MP, Frangakis AS, Yin X, Mayr M, Braun T, Urbich C, Boon RA, Dimmeler S PubMed
Feb 2012 Volume: 14 Issue: 3 Pages: 249-56

Nucleosomes stacked with aligned dyad axes are found in native compact chromatin in vitro.
Journal of structural biology
Scheffer MP, Eltsov M, Bednar J, Frangakis AS PubMed
May 2012 Volume: 178 Issue: 2 Pages: 207-14

Binary Pt-Si nanostructures prepared by focused electron-beam-induced deposition.
ACS nano
Winhold M, Schwalb CH, Porrati F, Sachser R, Frangakis AS, Kämpken B, Terfort A, Auner N, Huth M PubMed
Dec 2011 Volume: 5 Issue: 12 Pages: 9675-81

Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei.
Proceedings of the National Academy of Sciences of the United States of America
Scheffer MP, Eltsov M, Frangakis AS PubMed
Oct 2011 Volume: 108 Issue: 41 Pages: 16992-7

The three-dimensional molecular structure of the desmosomal plaque.
Proceedings of the National Academy of Sciences of the United States of America
Al-Amoudi A, Castaño-Diez D, Devos DP, Russell RB, Johnson GT, Frangakis AS PubMed
Apr 2011 Volume: 108 Issue: 16 Pages: 6480-5

Classification of electron sub-tomograms with neural networks and its application to template-matching.
Journal of structural biology
Yu Z, Frangakis AS PubMed
Jun 2011 Volume: 174 Issue: 3 Pages: 494-504

Structure of reconstituted bacterial membrane efflux pump by cryo-electron tomography.
Biochimica et biophysica acta
Trépout S, Taveau JC, Benabdelhak H, Granier T, Ducruix A, Frangakis AS, Lambert O PubMed
Oct 2010 Volume: 1798 Issue: 10 Pages: 1953-60

Visualization of macromolecular structures.
Nature methods
O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ PubMed
Mar 2010 Volume: 7 Issue: 3 Suppl Pages: S42-55

Alignator: a GPU powered software package for robust fiducial-less alignment of cryo tilt-series.
Journal of structural biology
Castaño-Díez D, Scheffer M, Al-Amoudi A, Frangakis AS PubMed
Apr 2010 Volume: 170 Issue: 1 Pages: 117-26

Quantitative and spatio-temporal features of protein aggregation in Escherichia coli and consequences on protein quality control and cellular ageing.
The EMBO journal
Winkler J, Seybert A, König L, Pruggnaller S, Haselmann U, Sourjik V, Weiss M, Frangakis AS, Mogk A, Bukau B PubMed
Mar 2010 Volume: 29 Issue: 5 Pages: 910-23

Proteome organization in a genome-reduced bacterium.
Science (New York, N.Y.)
Kühner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P, Castaño-Diez D, Chen WH, Devos D, Güell M, Norambuena T, Racke I, Rybin V, Schmidt A, Yus E, Aebersold R, Herrmann R, Böttcher B, Frangakis AS, Russell RB, Serrano L, Bork P, Gavin AC PubMed
Nov 2009 Volume: 326 Issue: 5957 Pages: 1235-40

Cytoplasmic relaxation of active Eph controls ephrin shedding by ADAM10.
PLoS biology
Janes PW, Wimmer-Kleikamp SH, Frangakis AS, Treble K, Griesshaber B, Sabet O, Grabenbauer M, Ting AY, Saftig P, Bastiaens PI, Lackmann M PubMed
Oct 2009 Volume: 7 Issue: 10 Pages: e1000215

Analysis of cryo-electron microscopy images does not support the existence of 30-nm chromatin fibers in mitotic chromosomes in situ.
Proceedings of the National Academy of Sciences of the United States of America
Eltsov M, Maclellan KM, Maeshima K, Frangakis AS, Dubochet J PubMed
Dec 2008 Volume: 105 Issue: 50 Pages: 19732-7

Performance evaluation of image processing algorithms on the GPU.
Journal of structural biology
Castaño-Díez D, Moser D, Schoenegger A, Pruggnaller S, Frangakis AS PubMed
Oct 2008 Volume: 164 Issue: 1 Pages: 153-60

A visualization and segmentation toolbox for electron microscopy.
Journal of structural biology
Pruggnaller S, Mayr M, Frangakis AS PubMed
Oct 2008 Volume: 164 Issue: 1 Pages: 161-5

Structural studies on desmosomes.
Biochemical Society transactions
Al-Amoudi A, Frangakis AS PubMed
Apr 2008 Volume: 36 Issue: Pt 2 Pages: 181-7

Reprint of "Fiducial-less alignment of cryo-sections" [J. Struct. Biol. 159 (2007) 413-423].
Journal of structural biology
Castaño-Díez D, Al-Amoudi A, Glynn AM, Seybert A, Frangakis AS PubMed
Mar 2008 Volume: 161 Issue: 3 Pages: 249-59

The molecular architecture of cadherins in native epidermal desmosomes.
Al-Amoudi A, Díez DC, Betts MJ, Frangakis AS PubMed
Dec 2007 Volume: 450 Issue: 7171 Pages: 832-7

Classification of cryo-electron sub-tomograms using constrained correlation.
Journal of structural biology
Förster F, Pruggnaller S, Seybert A, Frangakis AS PubMed
Mar 2008 Volume: 161 Issue: 3 Pages: 276-86

Fiducial-less alignment of cryo-sections.
Journal of structural biology
Castaño-Díez D, Al-Amoudi A, Glynn AM, Seybert A, Frangakis AS PubMed
Sep 2007 Volume: 159 Issue: 3 Pages: 413-23

Plastic-embedded protein crystals.
Journal of synchrotron radiation
Ravelli RB, Haselmann-Weiss U, McGeehan JE, McCarthy AA, Marquez JA, Antony C, Frangakis AS, Stranzl G PubMed
Jan 2007 Volume: 14 Issue: Pt 1 Pages: 128-32

Visualization of cell microtubules in their native state.
Biology of the cell
Bouchet-Marquis C, Zuber B, Glynn AM, Eltsov M, Grabenbauer M, Goldie KN, Thomas D, Frangakis AS, Dubochet J, Chrétien D PubMed
Jan 2007 Volume: 99 Issue: 1 Pages: 45-53

Implementation and performance evaluation of reconstruction algorithms on graphics processors.
Journal of structural biology
Castaño Díez D, Mueller H, Frangakis AS PubMed
Jan 2007 Volume: 157 Issue: 1 Pages: 288-95

Multiple large filament bundles observed in Caulobacter crescentus by electron cryotomography.
Molecular microbiology
Briegel A, Dias DP, Li Z, Jensen RB, Frangakis AS, Jensen GJ PubMed
Oct 2006 Volume: 62 Issue: 1 Pages: 5-14

Structural analysis of Mycoplasma pneumoniae by cryo-electron tomography.
Journal of structural biology
Seybert A, Herrmann R, Frangakis AS PubMed
Nov 2006 Volume: 156 Issue: 2 Pages: 342-54

Tilt-series and electron microscope alignment for the correction of the non-perpendicularity of beam and tilt-axis.
Journal of structural biology
Díez DC, Seybert A, Frangakis AS PubMed
May 2006 Volume: 154 Issue: 2 Pages: 195-205

Cryo-electron tomography reveals the cytoskeletal structure of Spiroplasma melliferum.
Science (New York, N.Y.)
Kürner J, Frangakis AS, Baumeister W PubMed
Jan 2005 Volume: 307 Issue: 5708 Pages: 436-8

Computational exploration of structural information from cryo-electron tomograms.
Current opinion in structural biology
Frangakis AS, Förster F PubMed
Jun 2004 Volume: 14 Issue: 3 Pages: 325-31

Macromolecular architecture in eukaryotic cells visualized by cryoelectron tomography.
Science (New York, N.Y.)
Medalia O, Weber I, Frangakis AS, Nicastro D, Gerisch G, Baumeister W PubMed
Nov 2002 Volume: 298 Issue: 5596 Pages: 1209-13

Identification of macromolecular complexes in cryoelectron tomograms of phantom cells.
Proceedings of the National Academy of Sciences of the United States of America
Frangakis AS, Böhm J, Förster F, Nickell S, Nicastro D, Typke D, Hegerl R, Baumeister W PubMed
Oct 2002 Volume: 99 Issue: 22 Pages: 14153-8

Segmentation of two- and three-dimensional data from electron microscopy using eigenvector analysis.
Journal of structural biology
Frangakis AS, Hegerl R PubMed
2002 Volume: 138 Issue: 1-2 Pages: 105-13