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Publications

 
 

2017

 
 
 
Ziegler M., Bassler J., Beltz S., Schultz A., Lupas AN., Schultz JE. (2017) Characterization of a Novel Signal Transducer Element Intrinsic
to Class IIIa/b Adenylate Cyclases and Guanylate Cyclases.
FEBS J. doi: 10.1111/febs.14047. [Epub ahead of print].
PMID: 
28222489
 
Lupas AN., Bassler J., Dunin-Horkawicz S. (2017) The Structure and Topology of α-Helical Coiled Coils. Subcell Biochem. 82:95-129.
doi: 10.1007/978-3-319-49674-0_4.
PMID: 
28101860
 
McCarthy N. L. C., Brooks N.J., Tyler A. I. I., ElGamacy M., Welche P. R. L., Payne M. C., Chau P.-L. (2017) A combined X-ray scattering
and simulation study of halothane in membranes at raised pressures.
Chem Phys Lett. 671:21-27. doi: 10.1016/j.cplett.2016.12.041
 
 
 

2016

 
 
Lupas AN., Bassler J. (2016) Coiled Coils – A Model System for the 21st Century. Trends in Biochem Sci.
pii: S0968-0004(16)30185-2. doi: 10.1016/j.tibs.2016.10.007. [Epub ahead of print].
PMID: 
27884598
 
Murray DH., Jahnel M., Lauer J., Avellaneda MJ., Brouilly N., Cezanne A., Morales-Navarrete H., Perini ED., Ferguson C., Lupas AN.,
Kalaidzidis Y., Parton RG., Grill SW., Zerial M. (2016) An endosomal tether undergoes an entropic collapse to bring vesicles together.
Nature 537(7618):107-111. doi: 10.1038/nature19326. [Epub ahead of print].
PMID: 
27556945
 
Alva V., Nam SZ., Söding J., Lupas AN. (2016) The MPI bioinformatics Toolkit as an integrative platform for advanced protein
sequence and structure analysis.
Nucleic Acids Res 29. pii: gkw348. [Epub ahead of print].
PMID: 
27131380
 
Eipper S., Steiner R., Lesner A., Sienczyk M., Palesch D., Halatsch ME., Zaczynska E., Heim C., Hartmann MD., Zimecki M., Wirtz CR.,
Burster T. (2016) Lactoferrin Is an Allosteric Enhancer of the Proteolytic Activity of Cathepsin G.
PLoS One doi: 10.1371/journal.pone.0151509.
PMCID: 
PMC4795699
 
Beltz S., Bassler J., Schultz JE. (2016) Regulation by the quorum sensor from Vibrio indicates a receptor function for the
membrane anchors of adenylate cyclases.
Elife pii: e13098. doi: 10.7554/eLife.13098. [Epub ahead of print]
PMID: 
26920221
 
Alva V., Lupas AN. (2016) The TULIP superfamily of eukaryotic lipid-binding proteins as a mediator of lipid sensing and transport.
Biochim Biophys Acta doi: 10.1016/j.bbalip.2016.01.016.
PMID: 
26825693
 
Hartmann MD., Mendler CT., Bassler J., Karamichali I., Ridderbusch O., Lupas AN., Hernandez Alvarez B. (2016) α/β coiled coils.
ELife pii: e11861. doi: 10.7554/eLife.11861. [Epub ahead of print].
PMID: 
26771248
 
Boichenko I., Deiss S., Bär K., Hartmann MD., Hernandez Alvarez B. (2016) A FRET-based assay for the identification and
characterization of cereblon ligands.
J Med Chem [Epub ahead of print].
PMID: 
26730808
 
 
 

2015

 
Koiwai K., Hartmann MD., Linke D., Lupas AN., Hori K. (2015) Structural Basis for Toughness and Flexibility in the C-terminal
Passenger Domain of an Acinetobacter Trimeric Autotransporter Adhesin.
J Biol Chem 291(8):3705-24.
PMID: 
26698633
 
Alva V., Söding J., Lupas AN. (2015) A vocabulary of ancient peptides at the origin of folded proteins. eLife pii: e09410.
doi: 10.7554/eLife.09410.
PMID: 
26653858
 
Kryshtafovych A., Moult J., Baslé A., Burgin A., Craig TK., Edwards RA., Fass D., Hartmann MD., Korycinski M., Lewis RJ.,
Lorimer D., Lupas AN., Newman J., Peat TS., Piepenbrink KH., Prahlad J., an Raaij MJ., Rohwer F., Segall AM., Seguritan V.,
Sundberg EJ., Singh AK., Wilson MA., Schwede T. (2015) Some of the most interesting CASP11 targets through the
eyes of their authors.
Proteins doi: 10.1002/prot.24942.
PMID: 26473983
 
Wieteska JR., Welche PRL., Tu KM., ElGamacy M., Csanyi G., Payne MC., Chau PL. (2015) Isoflurane does not aggregate inside
POPC bilayers at high pressure: Implications for pressure reversal of general anaesthesia.
Chem Phys Lett 638:116
 
Korycinski M., Albrecht R., Ursinus A., Hartmann MD., Coles M., Martin J., Dunin-Horkawicz S., Lupas AN. (2015) STAC - a new
domain associated with transmembrane solute transport and two-component signal transduction systems.
J Mol
Biol pii: S0022-2836(15)00482-9. doi: 10.1016/j.jmb.2015.08.017.
PMID: 26321252
 
ElGamacy M., Van Meervelt L. (2015) A fast topological analysis algorithm for large-scale similarity evaluations of ligands and
binding pockets.
J Cheminform 7:42
PMID: 26561508
 
Hartmann MD., Boichenko I., Coles M., Lupas AN., Hernandez Alvarez B. (2015) Structural dynamics of the
cereblon ligand binding domain.
PLoS One 10(5):e0128342
PMID: 26024445
 
Thoma L., Dobrowinski H., Finger C., Guezquez J., Linke D., Sepulveda E., Muth G. (2015) A Multiprotein DNA Translocation
Complex Directs Intramycelial Plasmid Spreading during Streptomyces Conjugation.
MBio. 6(3):e02559-14
PMID: 26015502
 
Wuertenberger S., Groemping Y. (2015) A single PXXP motif in the C-terminal region of srGAP3 mediates
binding to multiple SH3 domains.
FEBS Lett 589(10):1156-63
PMID: 25819436
 
Pozzi R., Coles M., Linke D., Kulik A., Nega M., Wohlleben W., Stegmann E. (2015) Distinct mechanisms contribute to immunity
in the lantibiotic NAI-107 producer strain Microbispora ATCC PTA-5024. 
Environ Microbiol
PMID: 25923468
 
Kretschmer D., Rautenberg M., Linke D., Peschel A. (2015) Peptide length and folding state govern the capacity
of staphylococcal β-type phenol-soluble modulins to activate human formyl-peptide receptors 1 or 2.

J Leukoc Biol 97(4):689-97
PMID: 25724390
 
Yin J., Zhu H., Xia L., Ding X., Hoffmann T., Hoffmann M., Bian X., Müller R., Fu J., Stewart AF., Zhang Y. (2015)
A new recombineering system for Photorhabdus and Xenorhabdus.
43(6):e36
PMID: 25539914
 
Scharfenberg F., Serek-Heuberger J., Coles M., Hartmann MD., Habeck M., Martin J., Lupas AN., Alva V. (2015)
Structure and evolution of N-domains in AAA metalloproteases.
J Mol Biol 427(4):910-23 
PMID: 25576874
 
Leo JC., Oberhettinger P., Schütz M., Linke D. (2015) The inverse autotransporter family: intimin, invasin and
related proteins.
Int J Med Microbiol 305(2):276-82 
PMID: 25596886
 
Bassler J., Hernandez Alvarez B., Hartmann MD., Lupas AN. (2015) A domain dictionary of trimeric autotransporter
adhesins.
Int J Med Microbiol 305(2):265-75 
PMID: 25583454
 
Braun V., Helbig S., Patzer SI., Pramanik A., Römer C. (2015) Import and export of bacterial protein toxins.
Int J Med Microbiol 305(2):238-42 
PMID: 25620353
 
Braun V. (2015) Bacterial cell wall research in Tübingen: a brief historical account. Int J Med Microbiol 305(2):
178-82 
PMID: 25583455
 
Braun V., Götz F., Schultz JE., Wohlleben W. (2015) The bacterial cell envelope: structure, function, and infection
interface.
Int J Med Microbiol 305(2):175-7 
PMID: 25660413
 
Lupas AN., Zhu H., Korycinski M. (2015) The thalidomide-binding domain of cereblon defines the CULT domain
family and is a new member of the β-tent fold.
PLoS Comput Biol 11(1) 
PMID: 25569776
 
Leo JC., Oberhettinger P., Chaubey M., Schütz M., Kühner D., Bertsche U., Schwarz H., Götz F., Autenrieth IB.,
Coles M., Linke D. (2015) The Intimin periplasmic domain mediates dimerisation and binding to
peptidoglycan.
Mol Microbiol 95(1):80-100 
PMID: 25353290
 
 
 

2014

 
Lupas AN. (2014) Protein Design. What I cannot create, I do not understand. Science 346(6216):1455-56
PMID: 25525230
 
Hartmann MD., Boichenko I., Coles M., Zanini F.,  Lupas AN., Hernandez Alvarez B. (2014) Thalidomide mimics uridine
binding to an aromatic cage in cereblon.
J Struct Biol 188(3):225-32
PMID: 25448889
 
Kumar A., Pate KM., Moss MA., Dean DN., Rangachari V. (2014) 
Self-propagative replication of Aβ oligomers suggests potential transmissibility in Alzheimer disease.
PLoS One 9(11):e111492. doi: 10.1371/journal.pone.0111492
PMID: 25365422
 
Chellamuthu VR. , Ermilova E., Lapina T., Lüddecke J., Minaeva E., Herrmann C.,  Hartmann MD., Forchammer K. (2014) 
A widespread glutamine-sensing mechanism in the plant kingdom.Cell 159(5):1188-99
PMID: 25416954
 
Thoma L. , Sepulveda E., Latus A., Muth G. (2014) 
The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly
conserved short palindromic sequence motif.
Front. Microbiol. 5(499)
PMCID: PMC4170104
 
Linke D. (2014) Explanatory chapter: choosing the right detergent. Methods Enzymol 541:141-8
PMID: 24674068
 
Dunin-Horkawicz S., Kopec KO., Lupas AN. (2014) Prokaryotic ancestry of eukaryotic protein networks
mediating innate immunity and apoptosis.
J Mol Biol 426(7):1568-82 
PMID: 24333018
 
Albrecht R., Schütz M., Oberhettinger P., Faulstich M., Bermejo I., Rudel T., Diederichs K., Zeth K. (2014)
Structure of BamA, an essential factor in outer membrane protein biogenesis.

Acta Crystallogr D Biol Crystallogr 70(Pt 6):1779-89 
PMID: 24914988
 
Ferris HU., Zeth K., Hulko M., Dunin-Horkawicz S., Lupas AN. (2014) Axial helix rotation as a mechanism for
signal regulation inferred from the crystallographic analysis of the E. coli serine chemoreceptor.

J Struct Biol 186(3):349-56 
PMID: 24680785
 
Ferris HU., Coles M., Lupas AN., Hartmann MD. (2014) Crystallographic snapshot of the Escherichia coli
EnvZ histidine kinase in an active conformation.
J Struct Biol 186(3):376-9 
PMID: 24681325
 
Hartmann MD., Dunin-Horkawicz S., Hulko M., Martin J., Coles M., Lupas AN. (2014) A soluble mutant
of the transmembrane receptor Af1503 features strong changes in coiled-coil periodicity.

J Struct Biol 186(3):357-66 
PMID: 24568954
 
Deiss S., Hernandez Alvarez B., Bär K., Ewers CP., Coles M., Albrecht R., Hartmann MD. (2014) Your personalized
protein structure: Andrei N. Lupas fused to GCN4 adaptors.
J Struct Biol 186(3) 
PMID: 24486584
 
Mechelke M., Habeck M. (2014) Bayesian weighting of statistical potentials in NMR structure calculation.
PLoS One 9(6) 
PMID: 24956116
 
Pramanik A., Könninger U., Selvam A., Braun V. (2014) Secretion and activation of the Serratia marcescens
hemolysin by structurally defined ShlB mutants.
Int J Med Microbiol 304 (3-4):351-9 
PMID: 24462008
 
Zeth K., Fokina O., Forchhammer K. (2014) Structural basis and target-specific modulation of ADP sensing
by the Synechococcus elongatus PII signaling protein.
J Biol Chem 289(13):8960-72 
PMID: 24519945
 
Grin I., Hartmann MD., Sauer G., Hernandez Alvarez B., Schütz M., Wagner S., Madlung J., Macek B., Felipe-Lopez A.,
Hensel M., Lupas A., Linke D. (2014) A trimeric lipoprotein assists in trimeric autotransporter biogenesis in
enterobacteria.
J Biol Chem 289(11):7388-98 
PMID: 24369174
 
 
 

2013

 
Kalev I., Habeck M. (2013) Confidence-guided local structure prediction with HHfrag. PLoS One 8(10) 
PMID: 24146881
 
Braun V., Patzer SI. (2013) Intercellular communication by related bacterial protein toxins: colicins,
contact-dependent inhibitors, and proteins exported by the type VI secretion system.

FEMS Microbiol Lett 345(1):13-21 
PMID: 23701660
 
Mechelke M., Habeck M. (2013) A probabilistic model for secondary structure prediction from protein
chemical shifts.
Proteins 81(6):984-93 
PMID: 23292699
 
Zaparty M., Hagemann A., Bräsen C., Hensel R., Lupas AN., Brinkmann H., Siebers B. (2013) The first prokaryotic
trehalose synthase complex identified in the hyperthermophilic crenarchaeon Thermoproteus tenax.

PLoS One 8(4) 
PMID: 23626675
 
Chellamuthu VR., Alva V. , Forchhammer K. (2013) From cyanobacteria to plants: conservation of PII functions
during plastid evolution.
Planta 237(2):451-62 
PMID: 23192387
 
 
 

2012

 
Forouzan D., Ammelburg M., Hobel CF., Ströh LJ., Sessler N., Martin J., Lupas AN. (2012) The archaeal
proteasome is regulated by a network of AAA ATPases.
J Biol Chem. 287(46):39254-62 
PMID: 22992741
 
Hartmann MD., Grin I., Dunin-Horkawicz S., Deiss S., Linke D., Lupas AN., Hernandez Alvarez B. (2012)
Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria.

Proc Natl Acad Sci U S A. 109(51):20907-12 
PMID: 23213248
 
Braun V., Helbig S., Patzer SI. (2012) Import of periplasmic bacteriocins targeting the murein.
Biochem Soc Trans. 40(6):1449-55 
PMID: 23176497
 
Kalev I., Mechelke M., Kopec KO., Holder T., Carstens S., Habeck M. (2012) CSB: a Python framework for
structural bioinformatics.
Bioinformatics 28(22):2996-7 
PMID: 22942023
 
Helbig S., Hantke K., Ammelburg M., Braun V. (2012) CbrA is a flavin adenine dinucleotide protein that modifies
the Escherichia coli outer membrane and confers specific resistance to Colicin M.
J Bacteriol 194(18):4894-903 
PMID: 22773789
 
Poleszak K., Kaminska KH., Dunin-Horkawicz S., Lupas A., Skowronek KJ., Bujnicki JM. (2012) Delineation of
structural domains and identification of functionally important residues in DNA repair enzyme
exonuclease VII. 
Nucleic Acids Res 40(16):8163-74 
PMID: 22718974
 
Lupas AN., Russell RB. (2012) The structure of proteins. J Struct Biol 179(3):251 
PMID: 22641090
 
Zeth K., Fokina O., Forchhammer K. (2012) An engineered PII protein variant that senses a novel ligand:
atomic resolution structure of the complex with citrate.
Acta Crystallogr D Biol Crystallogr 68(Pt 8) 
PMID: 22868755
 
Patzer SI., Albrecht R., Braun V., Zeth K. (2012) Structural and mechanistic studies of pesticin, a bacterial
homolog of phage lysozymes.
J Biol Chem 287(28):23381-96 
PMID: 22593569
 
Leo JC., Grin I., Linke D. (2012) Type V secretion: mechanism(s) of autotransport through the bacterial
outer membrane.
Philos Trans R Soc Lond B Biol Sci 367(1592):1088-101 
PMID: 22411980
 
Rockel B., Kopec KO., Lupas AN., Baumeister W. (2012) Structure and function of tripeptidyl peptidase II,
a giant cytosolic protease.
Biochim Biophys Acta 1824(1):237-45 
PMID: 21771670
 
Usón I., Patzer SI., Rodríguez DD., Braun V., Zeth K. (2012) The crystal structure of the dimeric colicin M
immunity protein displays a 3D domain swap.
J Struct Biol 178:45-53 
PMID: 22366279
 
Paulmann M., Arnold T., Linke D., Özdirekcan S., Kopp A., Gutsmann T., Kalbacher H., Wanke I., Schuenemann VJ.,
Habeck M., Bürck J., Ulrich AS., Schittek B. (2012) Structure-activity analysis of the dermcidin-derived
peptide DCD-1L, an anionic antimicrobial peptide present in human sweat.
J Biol Chem 287:8434-43 
PMID: 22262861
 
Mondéjar LG., Lupas A., Schultz A., Schultz JE. (2012) HAMP domain-mediated signal transduction probed with a
mycobacterial adenylyl cyclase as a reporter.
J Biol Chem 287:1022-31 
PMID: 22094466
 
Kaiser PO., Linke D., Schwarz H., Leo JC., Kempf VA. (2012) Analysis of the BadA stalk from Bartonella henselae
reveals domain-specific and domain-overlapping functions in the host cell infection process.
Cell Microbiol 14:
198-209 
PMID: 21981119
 
Eisenbeis S., Proffitt W., Coles M., Truffault V., Shanmugaratnam S., Meiler J., Höcker B. (2012) Potential of fragment
recombination for rational design of proteins.
J Am Chem Soc 134:4019-22 
PMID: 22329686
 
Ferris HU., Dunin-Horkawicz S., Hornig N., Hulko M., Martin J., Schultz JE., Zeth K., Lupas AN., Coles M. (2012)
Mechanism of regulation of receptor histidine kinases.
Structure 20:56-66 
PMID: 22244755
 
 
 

2011

 
Zeth K., Pechlivanis M., Samol A., Pleiser S., Vonrhein C., Kerkhoff E. (2011) Molecular basis of actin nucleation
factor cooperativity: crystal structure of the Spir-1 kinase non-catalytic C-lobe domain (KIND)•formin-2
formin SPIR interaction motif (FSI) complex.
J Biol Chem 286:30732-9 
PMID: 21705804
 
Wagner C., Polke M., Gerlach RG., Linke D., Stierhof YD., Schwarz H., Hensel M. (2011) Functional dissection of
SiiE, a giant non-fimbrial adhesin of Salmonella enterica.
Cell Microbiol 13:1286-301 
PMID: 21729227
 
Vogelmann J., Ammelburg M., Finger C., Guezguez J., Linke D., Flötenmeyer M., Stierhof YD., Wohlleben W.,
Muth G. (2011) Conjugal plasmid transfer in Streptomyces resembles bacterial chromosome segregation
by FtsK/SpoIIIE.
EMBO J 30:2246-54 
PMID: 21505418
 
Kopec KO., Alva V., Lupas AN. (2011) Bioinformatics of the TULIP domain superfamily. Biochem Soc Trans
39(4):1033-8
PMID: 21787343
 
Varnay I., Truffault V., Djuranovic S., Ursinus A., Coles M., Kessler H. (2011) Optimized measurement temperature
gives access to the solution structure of a 49 kDa homohexameric b-propeller.
J Am Chem Soc 132:15692-8 
PMID: 20961124
 
Römer C., Patzer SI., Albrecht R., Zeth K., Braun V. (2011) Expression, purification and crystallization of the Cmi
immunity protein from Escherichia coli.
Acta Crystallogr Sect F Struct Biol Cryst Commun 67:517-20 
PMID: 21505256
 
Pesek J., Büchler R., Albrecht R., Boland W., Zeth K. (2011) Structure and mechanism of iron translocation by
a Dps protein from Microbacterium arborescens.
J Biol Chem 286:34872-82 
PMID: 21768097
 
Paramasivam N., Linke D. (2011) ClubSub-P: Cluster-Based Subcellular Localization Prediction for
Gram-Negative Bacteria and Archaea.
Front Microbiol 2:218 
PMID: 22073040
 
Müller JE., Papic D., Ulrich T., Grin I., Schütz M., Oberhettinger P., Tommassen J., Linke D., Dimmer KS., Autenrieth IB.,
Rapaport D. (2011) Mitochondria can recognize and assemble fragments of a beta-barrel structure.
Mol Biol Cell 22:1638-47 
PMID: 21460184
 
Müller NF., Kaiser PO., Linke D ., Schwarz H., Riess T., Schäfer A., Eble JA., Kempf VA. (2011) Trimeric autotransporter
adhesin-dependent adherence of Bartonella henselae, Bartonella quintana, and Yersinia enterocolitica to
matrix components and endothelial cells under static and dynamic flow conditions.
Infect Immun 79:2544-53 
PMID: 21536788
 
Mager F., Gessmann D., Nussberger S., Zeth K. (2011) Functional refolding and characterization of two Tom40
isoforms from human mitochondria.
J Membr Biol 242:11-21 
PMID: 21717124
 
Leo JC., Lyskowski A., Hattula K., Hartmann MD., Schwarz H., Butcher SJ., Linke D., Lupas AN., Goldman A. (2011)
The structure of E. coli IgG-binding protein D suggests a general model for bending and binding in trimeric
autotransporter adhesins.
Structure 19(7):1021-30 
PMID: 21742268
 
Khazina E., Truffault V., Büttner R., Schmidt S., Coles M., Weichenrieder O. (2011) Trimeric structure and flexibility
of the L1ORF1 protein in human L1 retrotransposition.
Nat Struct Mol Biol 18:1006-14 
PMID: 21822284
 
Helbig S., Patzer SI., Schiene-Fischer C., Zeth K., Braun V. (2011) Activation of colicin M by the FkpA prolyl cis-trans
isomerase/chaperone.
J Biol Chem 286:6280-90 
PMID: 21149455
 
Grin I., Linke D. (2011) GCView: the genomic context viewer for protein homology searches. Nucleic Acids Res 39
(Web Server issue):W353-6 
PMID: 21609955
 
Gessmann D., Mager F., Naveed H., Arnold T., Weirich S., Linke D., Liang J., Nussberger S. (2011) Improving the
resistance of a eukaryotic β-barrel protein to thermal and chemical perturbations.
J Mol Biol 413:150-61 
PMID: 21835183
 
Ferris HU., Dunin-Horkawicz S., Mondéjar LG., Hulko M., Hantke K., Martin J., Schultz JE., Zeth K., Lupas AN., Coles M.
(2011) The mechanisms of HAMP-mediated signaling in transmembrane receptors. Structure 19:378-85. 
PMID: 21397188
 
Albrecht R., Zeth K. (2011) Structural basis of outer membrane protein biogenesis in bacteria. J Biol Chem 286:
27792-803 
PMID: 21586578
 
Björnsson H., Marteinsson V., Friðjónsson OH., Linke D., Benediktsdóttir E. (2011) Isolation and characterization
of an antigen from the fish pathogen Moritella viscosa.
J Appl Microbiol 111:17-25 
PMID: 21457415
 
Bonitz T., Alva V., Saleh O., Lupas AN., Heide L. (2011) Evolutionary relationships of microbial aromatic
prenyltransferases.
PLoS One 6:e27336 
PMID: 22140437
 
 

 

2010

 
Thein M., Sauer G., Paramasivam N., Grin I., Linke D. (2010) Efficient subfractionation of gram-negative bacteria
for proteomics studies.
J Proteome Res 9:6135-47 
PMID: 20932056
 
Oberhettinger P., Schütz M., Raddatz G., Keller H., Autenrieth IB., Linke D. (2010) The sequence of the pYV
virulence plasmid from Yersinia enterocolitica strain WA-314 biogroup 1B serotype O:8.
Plasmid 65:20-4 
PMID: 20875451
 
Mir-Montazeri B., Ammelburg M., Forouzan D., Lupas AN., Hartmann MD. (2010) Crystal structure of a dimeric
archaeal cleavage and polyadenylation specificity factor.
J Struct Biol 173:191-5 
PMID: 20851187
 
Lehr U., Schütz M., Oberhettinger P., Ruiz-Perez F., Donald JW., Palmer T., Linke D., Henderson IR., Autenrieth IB.
(2010) C-terminal amino acid residues of the trimeric autotransporter adhesin YadA of Yersinia enterocolitica
are decisive for its recognition and assembly by BamA.
Mol Microbiol 78:932-46 
PMID: 20815824
 
Khrunyk Y., Münch K., Schipper K., Lupas AN., Kahmann R. (2010) The use of FLP-mediated recombination for the
functional analysis of an effector gene family in the biotrophic smut fungus Ustilago maydis.
New Phytol 187:
957-68 
PMID: 20673282
 
Kashima I., Jonas S., Jayachandran U., Buchwald G., Conti E., Lupas AN., Izaurralde E. (2010) SMG6 interacts
with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for
nonsense-mediated mRNA decay.
Genes Dev 24:2440-50 
PMID: 20930030
 
Hiller S., Abramson J., Mannella C., Wagner G., Zeth K.  (2010) The 3D structures of VDAC represent a native
conformation.
Trends Biochem Sci 35:514-21 
PMID: 20708406
 
Hagn F., Eisoldt L., Hardy JG., Vendrely C., Coles M. , Scheibel T., Kessler H. (2010) A conserved spider silk
domain acts as a molecular switch that controls fibre assembly.
Nature 465:239-42 
PMID: 20463741
 
Fokina O., Chellamuthu VR. , Forchhammer K., Zeth K. (2010) Mechanism of 2-oxoglutarate signaling by the
Synechococcus elongatus PII signal transduction protein.
Proc Natl Acad Sci U S A 107:19760-5 
PMID: 21041661
 
Albrecht R., Zeth K. (2010) Crystallization and preliminary X-ray data collection of the Escherichia coli
lipoproteins BamC, BamD and BamE.
Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1586-90 
PMID: 21139201
 
Kintscher C., Wuertenberger S., Eylenstein R., Uhlendorf T., Groemping Y. (2010) Autoinhibition of GEF activity in
Intersectin1L is mediated by the short SH3-DH domain linker.
Protein Sci 19(11):2164-74 
PMID: 20842712
 
Norum M., Tång E., Chavoshi T., Schwarz H., Linke D., Uv A., Moussian B. (2010) Trafficking through
COPII stabilises cell polarity and drives secretion during Drosophila epidermal differentiation.

PLoS One 5(5) 
PMID: 20520821
 
Zeth K. (2010) Structure and evolution of mitochondrial outer membrane proteins of beta-barrel topology.
Biochim Biophys Acta 1797(6-7):1292-1299 
PMID: 20450883
 
Kopec KO., Alva V., Lupas AN. (2010) Homology of SMP domains to the TULIP superfamily of lipid-binding
proteins provides a structural basis for lipid exchange between ER and mitochondria.
Bioinformatics 26(16):
1927-31 
PMID: 20554689
 
Fokina O., Chellamuthu VR., Zeth K., Forchhammer K. (2010) A novel signal transduction protein P(II) variant
from Synechococcus elongatus PCC 7942 indicates a two-step process for NAGK- P(II) complexformation.
J Mol Biol 399(3):410-21 
PMID: 20399792
 
Dougan DA., Truscott KN., Zeth K. (2010) The bacterial N-end rule pathway: expect the unexpected.
Mol Microbiol 76(3):545-58 
PMID: 20374493
 
Arnold T., Zeth K., Linke D. (2010) Omp85 from the thermophilic cyanobacterium thermosynechococcus
elongatus differs from proteobacterial Omp85 in structure and domain composition.

J Biol Chem 285(23):18003-15 
PMID: 20351097
 
Schütz M., Weiss EM., Schindler M., Hallström T., Zipfel PF., Linke D ., Autenrieth IB. (2010) Trimer stability of
YadA is critical for virulence of Yersinia enterocolitica.
Infect Immun 78(6):2677-90 
PMID: 20308293
 
Bleicken S., Classen M., Padmavathi PV., Ishikawa T., Zeth K., Steinhoff HJ., Bordignon E. (2010) Molecular
details of Bax activation, oligomerization, and membraneinsertion.
J Biol Chem 285(9):6636-47 
PMID: 20008353
 
Dunin-Horkawicz S., Lupas AN. (2010) Comprehensive Analysis of HAMP Domains: Implications for
Transmembrane Signal Transduction.
J MolBiol 397(5):1156-74
PMID: 20184894
 
Hernandez Alvarez B., Gruber M., Ursinus A., Dunin-Horkawicz S., Lupas AN., Zeth K. (2010) A transition from strong
right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric
autotransporter adhesins.
J StructBiol 170(2):236-45 
PMID: 20178846
 
Giamarchi A., Feng S., Rodat-Despoix L., Xu Y., Bubenshchikova E., Newby LJ., Hao J., Gaudioso C., Crest M.,
Lupas AN., Honoré E., Williamson MP., Obara T., Ong AC., Delmas P. (2010) A polycystin-2 (TRPP2)
dimerization domain essential for the function of heteromeric polycystin complexes.

EMBO J 29(7):1176-91 
PMID: 20168298
 
Dunin-Horkawicz S., Lupas AN. (2010) Measuring the conformational space of square four-helical bundles
with the program samCC.
J Struct Biol. 170(2):226-35 
PMID: 20139000
 
Diercks T., Truffault V., Coles M., Millet O. (2010) Diagonal-Free 3D/4D HN,HN-TROSY-NOESY-TROSY.
J Am Chem Soc 132(7):2138-9 
PMID: 20121126
 
Remmert M., Biegert A.,  Linke D. Lupas AN., Söding J. (2010) Evolution of outer membrane β-barrels from
an ancestral 
ββ-hairpin. Mol Biol Evo. 22(6):1348-58
PMID: 20106904
 
Alva V., Remmert M., Biegert A., Lupas AN., Söding J. (2010) A galaxy of folds. Protein Sci 19(1):124-30 
PMID: 19937658
 
 

 

2009

 
Linke D. (2009) Detergents: an overview. Methods Enzymol. 463:603-17. Review. 
PMID: 19892194
 
Linke D. (2009) Commentary: never trust your word processor. Biochemistry and Molecular
Biology Education 37: 377 
PMID: 21567776
 
Rohner N., Bercsényi M., Orbán L., Kolanczyk ME., Linke D., Brand M., Nüsslein-Volhard C., Harris MP. (2009)
Duplication of fgfr1 permits Fgf signaling to serve as a target for selection during domestication.

Curr Biol 19(19):1642-7 
PMID: 19733072
 
Hartmann MD., Ridderbusch O., Zeth K., Albrecht R., Testa O., Woolfson DN., Sauer G., Dunin-Horkawicz S.,
Lupas AN., Hernandez Alvarez B. (2009) A coiled-coil motif that sequesters ions to the hydrophobic core.
Proc Natl Acad Sci U S A. 106(40):16950-5 
PMID: 19805097
 
Alva V., Dunin-Horkawicz S., Habeck M., Coles M., Lupas AN. (2009) The GD box: A widespread
non-contiguous supersecondary structural element.
Protein Sci. 18(9):1961-6 
PMID: 19609930
 
Gröbner S., Linke D. , Schütz W., Fladerer C., Madlung J., Autenrieth IB., Witte W., Pfeifer Y. (2009)
Emergence of carbapenem-non-susceptible extended-spectrum beta-lactamase-producing
Klebsiella pneumoniae isolates at the university hospital of Tübingen, Germany.

J Med Microbiol 58(Pt 7): 912-22 
PMID: 19502377
 
Djuranovic S., Hartmann MD., Habeck M., Ursinus A., Zwickl P., Martin J., Lupas AN., Zeth K. (2009)
Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases.

Mol Cell 34(5):580-90 
PMID:19481487
 
Remmert M., Linke D., Lupas AN., Söding J. (2009) HHomp--prediction and classification of
outer membrane proteins.
Nucleic Acids Res 37 (Web Server issue):W446-51 
PMID: 19429691
 
Rufer AC., Rumpf J., von Holleben M., Beer S., Rittinger K., Groemping Y. (2009) Isoform-selective
interaction of the adaptor protein Tks5/FISH with Sos1 and dynamins.
J Mol Biol. 390(5):939-50 
PMID: 19464300
 
Bardiaux B., Bernard A., Rieping W., Habeck M., Malliavin TE., Nilges M. (2009) Influence of different
assignment conditions on the determination of symmetric homodimeric structures with ARIA.

Proteins 75(3):569-85 
PMID: 18951392
 
Schuenemann VJ., Kralik SM., Albrecht R., Spall SK., Truscott KN., Dougan DA., Zeth K. (2009)
Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor
protein ClpS.
Erratum in: EMBO Rep 10(6):662 
PMID: 19373253
 
Ginzinger SW., Coles M. (2009) SimShiftDB; local conformational restraints derived from chemical
shift similarity searches on a large synthetic database.
J Biomol NMR 43(3):179-85 
PMID: 19224375
 
Kintscher C., Groemping Y. (2009) Characterisation of the nucleotide exchange factor ITSN1L:
evidence for a kinetic discrimination of GEF-stimulated nucleotide release from Cdc42.

J Mol Biol 387(2):270-83 
PMID: 19356586
 
Asen I., Djuranovic S., Lupas AN., Zeth K. (2009) Crystal Structure of SpoVT, the Final Modulator
of Gene Expression during Spore Development in Bacillus subtilis.
J Mol Biol 386(4):962-75 
PMID: 18996130
 
Arnold T., Zeth K., Linke D. (2009) Structure and function of colicin S4, acolicin with a duplicated
receptor binding domain.
Journal of Biological Chemistry 284(10):6403-13 
PMID: 19056731
 
Bleicken S., Zeth K. (2009) Conformational changes and protein stability of the pro-apoptotic
protein Bax.
J Bioenerg Biomembr 41(1):29-40 
PMID: 19255832
 
Serek-Heuberger J., Hobel CF., Dunin-Horkawicz S., Rockel B.,  Martin J., Lupas AN. (2009) Two unique
membrane-bound AAA proteins from Sulfolobus solfataricus.
Biochem Soc Trans 37(Pt 1):118-22 
PMID: 19143614
 
 
 

2008

 
Biedzka-Sarek M., Salmenlinna S., Gruber M.,  Lupas AN., Meri S., Skurnik M. (2008) Functional
mapping of YadA- and Ail-mediated binding of human factor H toYersinia enterocolitica
serotype O:3.
Infect Immun 76(11):5016-27 
PMID: 18765735
 
Tritschler F., Eulalio A., Helms S., Schmidt S., Coles M., Weichenrieder O., Izaurralde E., Truffault V. (2008)
Similar modes of interaction enable Trailer Hitch and EDC3 to associate with DCP1 and Me31B in
distinct protein complexes.
Mol Cell Biol 28(21):6695-708 
PMID: 18765641
 
Klages J., Kotzsch A., Coles M., Sebald W., Nickel J., Müller T., Kessler H. (2008) The solution structure of
BMPR-IA reveals a local disorder-to-ordertransition upon BMP-2 binding.
Biochemistry 47(46):
11930-9 
PMID: 18937504
 
Kaiser PO., Riess T., Wagner CL., Linke D., Lupas AN., Schwarz H., Raddatz G., Schäfer A., Kempf VA. (2008)
The head of Bartonella adhesin A is crucial for host cell interaction of Bartonella henselae.

Cell Microbiol 10(11):2223-34 
PMID: 18627378
 
Wagner C., Riess T., Linke D. , Eberhardt C., Schäfer A., Reutter S., Maggi R., Kempf V. (2008) Use of
Bartonella adhesin A (BadA) in serodiagnosis of Bartonella henselae infections.

International Journal of Medical Microbiology 298(7-8):579-90
PMID: 18501673
 
Bayrhuber M., Meins T., Habeck M ., Becker S., Giller K.,Villinger S., Vonrhein C., Griesinger C., Zweckstetter M.,
Zeth K . (2008) Structure of the human voltage-dependent anion channel. Proc Natl Acad Sci U S A
105(40):15370-5 
PMID: 18832158
 
Hirsch M., Habeck M. (2008) Mixture models for protein structure ensembles. Bioinformatics 24(19):
2184-92 
PMID: 18662925
 
Bardiaux B., Bernard A., Rieping W., Habeck M. , Malliavin TE., Nilges M. (2008) Influence of
different assignment conditions on the determination of symmetric homodimeric structures
with ARIA.
Proteins 75(3):569-85 
PMID: 18951392
 
Nilges M., Bernard A., Bardiaux B., Malliavin T., Habeck M., Rieping W. (2008) Accurate NMR structures
through minimization of an extended hybrid energy.
Structure 16(9):1305-12 
PMID: 18786394
 
Szczesny P., Linke D., Ursinus A., Bär K., Schwarz H., Riess TM., Kempf VA., Lupas AN., Martin J.,
Zeth K. (2008) Structure of the head of the Bartonella adhesin BadA. PLoS Pathog 4(8) 
PMID: 18688279
 
Arnold T., Linke D. (2008) The use of detergents to purify membrane proteins. Curr Protoc
Protein Sci Chapter 4:Unit 4.8.1-4.8.30 
PMID: 18729050
 
Lupas AN. (2008) The long coming of computational structural biology. J Struct Biol 163(3):254-7 
PMID: 18406171
 
Alva V., Koretke KK., Coles M., Lupas AN. (2008) Cradle-loop barrels and the concept of metafolds
in protein classification by natural descent.
Curr Opin Struct Biol (3):358-65 
PMID: 18457946
 
Bardiaux B., Bernard A., Rieping W., Habeck M., Malliavin TE., Nilges M. (2008) Graphical analysis of
NMR structural quality and interactive contact map of NOE assignments in ARIA.
BMC Struct Biol 8:
30 
PMID: 18533992
 
Zeth K., Meins T., Vonrhein C. (2008) Approaching the structure of human VDAC1, a key molecule in
mitochondrial cross-talk.
J Bioenerg Biomembr 40(3):127-32 
PMID: 18690523
 
Szczesny P., Lupas A. (2008) Domain annotation of trimeric autotransporter adhesins--daTAA.
Bioinformatics 24(10):1251-6 
PMID: 18397894
 
Rieping W., Nilges M., Habeck M. (2008) ISD: a software package for Bayesian NMR structure
calculation.
Bioinformatics 24(8):1104-5 
PMID: 18310055
 
Biegert A., Söding J. (2008) De novo identification of highly diverged protein repeats by probabilistic
consistency.
Bioinformatics  24(6):807-14 
PMID: 18245125
 
Fischer JD., Mayer CE., Söding J. (2008) Prediction of protein functional residues from sequence by
probability density estimation.
Bioinformatics 24(5):613-20 
PMID: 18174181
 
Hobel CF., Albers SV., Driessen AJ., Lupas AN. (2008) The Sulfolobus solfataricus AAA protein
Sso0909, a homologue of the eukaryotic ESCRT Vps4 ATPase.
Biochem Soc Trans 36(Pt 1):94-8 
PMID: 18208393
 
Habeck M., Nilges M., Rieping W. (2008) A unifyingprobabilistic framework for analyzing residual
dipolar couplings.
J Biomol NMR 40(2):135-44 
PMID: 18095170
 
Wolff N., Izadi-Pruneyre N., Couprie J., Habeck M., Linge J., Rieping W., Wandersman C., Nilges M.,
Delepierre M., Lecroisey A. (2008) Comparative analysis of structural and dynamic properties
of the loaded and unloaded hemophore HasA: functional implications.
J Mol Biol 376(2):517-25 
PMID: 18164722
 
Hernandez Alvarez B., Hartmann MD., Albrecht R., Lupas AN., Zeth K., Linke D. (2008) A new expression
system for protein crystallization using trimeric coiled-coiladaptors.
Protein Eng Des Sel 21(1):11-8 
PMID: 18093992
 
 
 

2007


Tritschler F., Eulalio A., Truffault V., Hartmann MD., Helms S., Schmidt S., Coles M., Izaurralde E.,
Weichenrieder O. (2007) A divergent Sm fold in EDC3 proteins mediates DCP1 binding and
P-body targeting.
Mol Cell Biol 27(24):8600-11 
PMID: 17923697
 
Ammelburg M., Hartmann MD., Djuranovic S., Alva V., Koretke KK., Martin J., Sauer G., Truffault V., Zeth K.,
Lupas AN., Coles M. (2007) A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution
of cradle-loop barrels.
Structure 15(12):1577-90
PMID:18073108
 
 
Grosskinsky U., Schütz M., Fritz M., Schmid Y., Lamparter MC., Szczesny P., Lupas AN., Autenrieth IB.,
Linke D. (2007) A conserved glycine residue of trimeric autotransporter domains plays a key
role in Yersinia adhesin A autotransport.
J Bacteriol 189(24):9011-9 
PMID: 17921300
 
Arnold T., Linke D. (2007) Phase separation in the isolation and purification of membrane proteins.
Biotechniques 43(4):427-30, 432, 434 passim. Review. 
PMID: 18019333
 
Schmidt O., Schuenemann VJ., Hand NJ., Silhavy TJ., Martin J., Lupas AN., Djuranovic S. (2007) prlF and yhaV
encode a new toxin-antitoxin system in Escherichia coli.
J Mol Biol 372(4):894-905 
PMID: 17706670
 
Gerlach RG., Jäckel D., Stecher B., Wagner C., Lupas A., Hardt WD., Hensel M. (2007) Salmonella Pathogenicity
Island 4 encodes a giant non-fimbrial adhesin and the cognate type 1 secretion system.

Cell Microbiol 9(7):1834-50 
PMID: 17388786
 
Krämer J., Fischer JD., Zientz E., Vijayan V., Griesinger C., Lupas A., Unden G. (2007) Citrate sensing by
the C4-dicarboxylate/citrate sensor kinase DcuS of Escherichia coli: binding site and conversion of
DcuS to a C4-dicarboxylate- or citrate-specific sensor.
JBacteriol 189(11):4290-8 
PMID: 17416661
 
Chaudhuri I., Söding J., Lupas AN. (2008) Evolution of the beta-propeller fold. Proteins 71(2):795-803 
PMID:17979191
 
Habeck M. (2007) Bayesian reconstruction of the density of states. Phys Rev Lett 98(20):200601 
PMID: 17677679
 
Hsiao NH., Söding J., Linke D., Lange C., Hertweck C., Wohlleben W., Takano E. (2007) ScbA from
Streptomyces coelicolor A3(2) has homology to fatty acid synthases and is able to synthesize
gamma-butyrolactones.
Microbiology 153(Pt 5):1394-404 
PMID: 17464053
 
Hulko M., Lupas AN., Martin J. (2007) Inherent chaperone-like activity of aspartic proteases reveals a
distant evolutionary relation to double-psi barrel domains of AAA-ATPases.
Protein Sci 16(4):644-53 
PMID: 17384229
 
Alva V., Ammelburg M., Söding J., Lupas AN. (2007) On the origin of the histone fold. BMC Struct Biol 7:17 
PMID: 17391511
 
Arnold T., Poynor M., Nussberger S., Lupas AN., Linke D. (2007) Gene duplication of the eight-stranded
beta-barrel OmpX produces a functional pore: a scenario for the evolution of transmembrane
beta-barrels.
J Mol Biol 366(4):1174-84 
PMID: 17217961
 
Rieping W., Habeck M., Bardiaux B., Bernard A., Malliavin TE., Nilges M. (2007) ARIA2: automated NOE
assignment and data integration in NMR structure calculation.
Bioinformatics 23(3):381-2 
PMID: 17121777
 
Karpenahalli MR., Lupas AN., Söding J. (2007) TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like
repeats from protein sequences.
BMC Bioinformatics 8:2 
PMID: 17199898
 
Riess T., Raddatz G., Linke D., Schäfer A., Kempf V. (2007) Analysis of Bartonella adhesin A expression
reveals differences between various B. henselae strains.
Infection and Immunity 75(1):35-43 
PMID: 17060468
 
 
 

2006

 
Nicastro G., Habeck M., Masino L., Svergun DI., Pastore A. (2006) Structure validation of the Josephin
domain of ataxin-3: conclusive evidence for an open conformation.
J Biomol NMR 36(4):267-77 
PMID: 17096206
 
Ab E., Atkinson AR., Banci L., Bertini I., Ciofi-Baffoni S., Brunner K., Diercks T., Dötsch V., Engelke F.,
Folkers GE., Griesinger C., Gronwald W., Günther U., Habeck M ., de Jong RN., Kalbitzer HR., Kieffer B.,
Leeflang BR., Loss S., Luchinat C., Marquardsen T., Moskau D., Neidig KP., Nilges M., Piccioli M., Pierattelli R.,
Rieping W., Schippmann T., Schwalbe H., Travé G., Trenner J., Wöhnert J.,Zweckstetter M., Kaptein R. (2006)
NMR in the SPINE Structural Proteomics project.
Acta Crystallogr D Biol Crystallogr 62(Pt 10):1150-61 
PMID: 17001092
 
Coles M., Hulko M., Djuranovic S., Truffault V., Koretke K., Martin J., Lupas AN. (2006) Common evolutionary
origin of swapped-hairpin and double-psi beta barrels.
Structure 14(10):1489-98 
PMID: 17027498
 
Hulko M., Berndt F., Gruber M., Linder JU., Truffault V., Schultz A., Martin J., Schultz JE., Lupas AN., Coles M. 
(2006) The HAMP domain structure implies helix rotation in transmembrane signaling.
Cell 126(5):929-40 
PMID: 16959572
 
Schulte B., Linke D., Klumpp S., Schaller M., Riess T., Autenrieth I., Kempf V. (2006) Bartonella quintana
variably expressed outer membrane proteins mediate vascular endothelial growth factor secretion
but not host cell adherence.
Infection and Immunity 74(9):5003-13 
PMID: 16926391
 
Gruber M., Söding J., Lupas AN. (2006) Comparative analysis of coiled-coil prediction methods.
J Struct Biol 155(2):140-5 
PMID: 16870472
 
Nilges M., Habeck M., O'Donoghue SI., Rieping W. (2006) Error distribution derived NOE distance
restraints.
Proteins 64(3):652-64 
PMID: 16729263
 
Söding J., Remmert M., Biegert A., Lupas AN. (2006) HHsenser: exhaustive transitive profile search
using HMM-HMM comparison.
Nucleic Acids Res 34(Web Server issue):W374-8 
PMID: 16845029
 
Söding J., Remmert M., Biegert A. (2006) HHrep: de novo protein repeat detection and the origin of
TIM barrels.
Nucleic Acids Res 34(Web Server issue):W137-42 
PMID: 16844977
 
Biegert A., Mayer C ., Remmert M., Söding J., Lupas AN. (2006) The MPI Bioinformatics Toolkit for protein
sequence analysis.
Nucleic Acids Res 34(Web Server issue):W335-9 
PMID: 16845021
 
Ammelburg M. , Frickey T. , Lupas AN . (2006) Classification of AAA+ proteins. J Struct Biol 156(1):2-11 
PMID: 16828312
 
Diemand AV., Lupas AN. (2006) Modeling AAA+ ring complexes from monomeric structures.
J Struct Biol 156(1):230-43 
PMID: 16765605
 
Djuranovic S., Rockel B., Lupas AN., Martin J. (2006) Characterization of AMA, a new AAA protein from
Archaeoglobus and methanogenic archaea.
J Struct Biol 156(1):130-8 
PMID: 16730457 
 
Linke D., Riess T., Autenrieth IB., Lupas A., Kempf VA. (2006) Trimeric autotransporter adhesins:
variable structure, common function.
Trends Microbiol 14(6):264-70 
PMID: 16678419
 
Koretke KK., Szczesny P., Gruber M., Lupas AN. (2006) Model structure of the prototypical non-fimbrial
adhesin YadA of Yersinia enterocolitica.
J Struct Biol 155(2):154-61 
PMID: 16675268
 
Wollmann P., Zeth K., Lupas AN., Linke D. (2006) Purification of the YadA membrane anchor for secondary
structure analysis and crystallization.
Int J Biol Macromol 39(1-3):3-9 
PMID: 16405993
 
Albrecht R., Zeth K., Söding J., Lupas A., Linke D. (2006) Expression, crystallization and preliminary X-ray
crystallographic studies of the outer membrane protein OmpW from Escherichia coli.

Acta Crystallogr Sect F Struct Biol Cryst Commun 62(Pt 4):415-8 
PMID: 16582500
 
Habeck M., Rieping W., Nilges M. (2006) Weighting of experimental evidence in macromolecular structure
determination.
Proc Natl Acad Sci U S A 103(6):1756-61 
PMID: 16446450



 

2005

 
Söding J., Biegert A., Lupas AN. (2005) The HHpred interactive server for protein homology detection
and structure prediction.
Nucleic Acids Res 33(Web Server issue):W244-8 
PMID: 15980461
 
Gruber M., Söding J., Lupas AN. (2005) REPPER--repeats and their periodicities in fibrous proteins.
Nucleic Acids Res 33(Web Server issue):W239-43 
PMID: 15980460
 
Moussian B., Söding J., Schwarz H., Nüsslein-Volhard C. (2005) Retroactive, a membrane-anchored
extracellular protein related to vertebrate snake neurotoxin-like proteins, is required
for cuticle organization in the larva of Drosophilamelanogaster.
Dev Dyn 233(3):1056-63 
PMID: 15844167
 
Coles M., Djuranovic S., Söding J., Frickey T., Koretke K., Truffault V., Martin J., Lupas AN. (2005) AbrB-like
transcription factors assume a swapped hairpin fold that isevolutionarily related to double-psi beta
barrels.
Structure 13(6):919-28 
PMID: 15939023
 
Söding J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21(7):951-60 
PMID: 15531603
 
Lupas AN., Gruber M. (2005) The structure of alpha-helical coiled coils. Adv Protein Chem 70:37-78. Review. 
PMID: 15837513
 
 
 

2004

 
Proikas-Cezanne T., Waddell S., Gaugel A., Frickey T., Lupas A., Nordheim A. (2004) WIPI-1alpha (WIPI49),
a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is
linked tostarvation-induced autophagy.
Oncogene 23(58):9314-25 
PMID: 15602573
 
Santos L., Frickey T., Peters J., Baumeister W., Lupas A., Zwickl P. (2004) Thermoplasma acidophilum TAA43
is an archaeal member of the eukaryotic meiotic branch of AAA ATPases.
Biol Chem 385(11):1105-11 
PMID: 15576333
 
Riess T., Andersson SG., Lupas A., Schaller M., Schäfer A., Kyme P., Martin J., Wälzlein JH., Ehehalt U., Lindroos H.,
Schirle M., Nordheim A., Autenrieth IB., Kempf VA. (2004) Bartonella adhesin a mediates a proangiogenic host
cell response.
J Exp Med 200(10):1267-78 
PMID: 15534369 
 
Martin J. (2004) Chaperonin function – effects of crowding and confinement. J Mol Recognit 17(5):465-72.
Review. 
PMID: 15362106
 
Frickey T., Lupas AN. (2004) PhyloGenie: automated phylome generation and analysis. Nucleic Acids Res 32(17):
5231-8 
PMID: 15459293
 
Martin J., Gruber M., Lupas AN. (2004) Coiled coils meet the chaperone world. Trends Biochem Sci 29(9):455-8.
Review. 
PMID: 15337117

Rabus R., Ruepp A., Frickey T., Rattei T., Fartmann B., Stark M., Bauer M., Zibat A., Lombardot T., Becker I., Amann J.,
Gellner K., Teeling H., Leuschner WD., Glöckner FO., Lupas AN., Amann R., Klenk HP. (2004) The genome of
Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments.
Environ Microbiol
6(9):887-902 
PMID: 15305914
 
Frickey T., Lupas A. (2004) CLANS: a Java application for visualizing protein families based on pairwise
similarity.
Bioinformatics 20(18):3702-4 
PMID: 15284097
 
Frickey T., Lupas AN. (2004) Phylogenetic analysis of AAA proteins. J Struct Biol 146(1-2):2-10 
PMID: 15037233
 
 
 

2003

 
Gruber M., Lupas AN. (2003) Historical review: another 50th anniversary--new periodicities in coiled coils.
Trends Biochem Sci 28(12):679-85. Review.
PMID: 14659700
 
Söding J., Lupas AN. (2003) More than the sum of their parts: on the evolution of proteins from peptides.
Bioessays 25(9):837-46. Review. 
PMID: 12938173
 
Macchi P., Kroening S., Palacios IM., Baldassa S., Grunewald B., Ambrosino C., Goetze B., Lupas A., St Johnston D.,
Kiebler M. (2003) Barentsz, a new component of the Staufen-containingribonucleoprotein particles in
mammalian cells, interacts with Staufen in an RNA-dependent manner.
J Neurosci 23(13):5778-88  
PMID: 12843282
 
Kusmierczyk AR., Martin J. (2003) Nested cooperativity and salt dependence of the ATPase activity of the
archaeal chaperonin Mm-cpn.
FEBS Lett 547(1-3):201-4 
PMID: 12860414
 
Kusmierczyk AR., Martin J. (2003) Nucleotide-dependant protein foldingin the type II chaperonin from the
mesophilic archaeon Methanococcus maripaludis.
Biochem J 371(Pt 3):669-73 
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Lupas AN., Koretke KK. (2003)  Bioinformatic analysis of ClpS, a protein module involved in prokaryotic and
eukaryotic protein degradation.
J Struct Biol 141(1):77-83 
PMID: 12576022
 
 
 

2002

 
Lupas AN. , Martin J. (2002) AAA proteins. Curr Opin Struct Biol 12(6):746-53. Review. 
PMID: 12504679
 
Martin J. (2002) Requirement for GroEL/GroES-dependent protein folding under non-permissive conditions
of macromolecular crowding.
Biochemistry 41(15):5050-5 
PMID: 11939802