Andrei N Lupas

Summary

Affiliation: Max Planck Institute for Biological Cybernetics
Country: Germany

Publications

  1. pmc Fold recognition without folds
    Kristin K Koretke
    Microbial Bioinformatics Group, GlaxoSmithKline, Collegeville, Pennsylvania 19426 0989, USA
    Protein Sci 11:1575-9. 2002
  2. ncbi request reprint Common evolutionary origin of swapped-hairpin and double-psi beta barrels
    Murray Coles
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 14:1489-98. 2006
  3. ncbi request reprint Evolution of the beta-propeller fold
    Indronil Chaudhuri
    Department for Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
    Proteins 71:795-803. 2008
  4. ncbi request reprint AAA proteins
    Andrei N Lupas
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, D 72076 Tubingen, Germany
    Curr Opin Struct Biol 12:746-53. 2002
  5. ncbi request reprint Bioinformatic analysis of ClpS, a protein module involved in prokaryotic and eukaryotic protein degradation
    Andrei N Lupas
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, D 72076 Tubingen, Germany
    J Struct Biol 141:77-83. 2003
  6. doi request reprint The long coming of computational structural biology
    Andrei N Lupas
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, D 72076 Tubingen, Germany
    J Struct Biol 163:254-7. 2008
  7. doi request reprint Mechanism of regulation of receptor histidine kinases
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 20:56-66. 2012
  8. doi request reprint Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases
    Sergej Djuranovic
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    Mol Cell 34:580-90. 2009
  9. doi request reprint The mechanisms of HAMP-mediated signaling in transmembrane receptors
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 19:378-85. 2011
  10. pmc A coiled-coil motif that sequesters ions to the hydrophobic core
    Marcus D Hartmann
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Proc Natl Acad Sci U S A 106:16950-5. 2009

Collaborators

Detail Information

Publications53

  1. pmc Fold recognition without folds
    Kristin K Koretke
    Microbial Bioinformatics Group, GlaxoSmithKline, Collegeville, Pennsylvania 19426 0989, USA
    Protein Sci 11:1575-9. 2002
    ..Since the method, SENSER, does not require knowledge of the three-dimensional structure, it can be used to infer relationships that are not tractable by methods dependent on structural templates...
  2. ncbi request reprint Common evolutionary origin of swapped-hairpin and double-psi beta barrels
    Murray Coles
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 14:1489-98. 2006
    ..We propose that swapped-hairpin beta barrels arose from an ancestral RIFT barrel by strand invasion and double-psi beta barrels by a strand swap. We group the three barrel types into a metafold, the cradle-loop barrels...
  3. ncbi request reprint Evolution of the beta-propeller fold
    Indronil Chaudhuri
    Department for Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
    Proteins 71:795-803. 2008
    ..The observation of propellers with nearly identical blades in genomic sequences show that these mechanisms are still operating today...
  4. ncbi request reprint AAA proteins
    Andrei N Lupas
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, D 72076 Tubingen, Germany
    Curr Opin Struct Biol 12:746-53. 2002
    ..Structural studies have highlighted the organization of their constituent ATPase domains and indicate that hexamerization in combination with unfoldase activity is a common underlying feature of this ubiquitous protein family...
  5. ncbi request reprint Bioinformatic analysis of ClpS, a protein module involved in prokaryotic and eukaryotic protein degradation
    Andrei N Lupas
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, D 72076 Tubingen, Germany
    J Struct Biol 141:77-83. 2003
    ..Despite very low levels of sequence similarity to proteins of known structure, there appears to be substantial structural similarity between ClpS and the C-terminal domain of ribosomal protein L7/12 (1CTF)...
  6. doi request reprint The long coming of computational structural biology
    Andrei N Lupas
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, D 72076 Tubingen, Germany
    J Struct Biol 163:254-7. 2008
    ..Computational structural biology, whose influence is already pervasive, will come to dominate structural approaches in the next decades...
  7. doi request reprint Mechanism of regulation of receptor histidine kinases
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 20:56-66. 2012
    ..We propose that altered recognition of the catalytic domain by DHp, rather than a shift in position of the phospho-accepting histidine, forms the basis for regulation of kinase activity...
  8. doi request reprint Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases
    Sergej Djuranovic
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    Mol Cell 34:580-90. 2009
    ..The structures suggest a molecular mechanism for substrate processing based on concerted radial motions of the coiled coils relative to the OB rings...
  9. doi request reprint The mechanisms of HAMP-mediated signaling in transmembrane receptors
    Hedda U Ferris
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 19:378-85. 2011
    ..These are correlated with activity and ligand response in vitro and in vivo by incorporating Af1503 HAMP into mycobacterial adenylyl cyclase assay systems...
  10. pmc A coiled-coil motif that sequesters ions to the hydrophobic core
    Marcus D Hartmann
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Proc Natl Acad Sci U S A 106:16950-5. 2009
    ..More generally, we think that polar motifs that are both periodic and conserved may often reflect special folding requirements, rather than an unstructured state of the mature proteins...
  11. pmc The archaeal proteasome is regulated by a network of AAA ATPases
    Dara Forouzan
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    J Biol Chem 287:39254-62. 2012
    ..The prevalent presence of multiple, distinct proteasomal ATPases in archaea thus results in a network of regulatory ATPases that may widen the substrate spectrum of proteasomal protein degradation...
  12. pmc Complete fiber structures of complex trimeric autotransporter adhesins conserved in enterobacteria
    Marcus D Hartmann
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Proc Natl Acad Sci U S A 109:20907-12. 2012
    ....
  13. ncbi request reprint AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels
    Murray Coles
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 13:919-28. 2005
    ....
  14. pmc HHomp--prediction and classification of outer membrane proteins
    Michael Remmert
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 37:W446-51. 2009
    ..In Escherichia coli, HHomp identifies 57 out of 59 known OMPs and correctly assigns them to their functional subgroups. HHomp can be accessed at http://toolkit.tuebingen.mpg.de/hhomp...
  15. ncbi request reprint A new expression system for protein crystallization using trimeric coiled-coil adaptors
    Birte Hernandez Alvarez
    Department Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, 72076 Tubingen, Germany
    Protein Eng Des Sel 21:11-8. 2008
    ..The system can be adapted for constructs with dimeric or tetrameric coiled coils, using the corresponding GCN4 variants...
  16. ncbi request reprint The HAMP domain structure implies helix rotation in transmembrane signaling
    Michael Hulko
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Cell 126:929-40. 2006
    ..coli chemotaxis receptor. Structural and functional studies show that the equilibrium between the two forms is dependent on the side-chain size of residue 291, which is alanine in the wild-type protein...
  17. pmc A galaxy of folds
    Vikram Alva
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen 72076, Germany
    Protein Sci 19:124-30. 2010
    ..Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains...
  18. pmc HHsenser: exhaustive transitive profile search using HMM-HMM comparison
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 34:W374-8. 2006
    ..HHsenser can be accessed at http://hhsenser.tuebingen.mpg.de/. It has also been integrated into our structure and function prediction server HHpred (http://hhpred.tuebingen.mpg.de/) to improve predictions for near-singleton sequences...
  19. pmc The MPI Bioinformatics Toolkit for protein sequence analysis
    Andreas Biegert
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 34:W335-9. 2006
    ..The Toolkit framework and the tools developed in-house will be packaged and freely available under the GNU Lesser General Public Licence (LGPL). The Toolkit can be accessed at http://toolkit.tuebingen.mpg.de...
  20. doi request reprint Measuring the conformational space of square four-helical bundles with the program samCC
    Stanislaw Dunin-Horkawicz
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, 72076 Tubingen, Germany
    J Struct Biol 170:226-35. 2010
    ..We also find that one of the originally proposed Alacoil proteins, Rop, in fact has canonical packing. SamCC is freely available as a web service athttp://toolkit.tuebingen.mpg.de/samcc...
  21. doi request reprint A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins
    Birte Hernandez Alvarez
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    J Struct Biol 170:236-45. 2010
    ..Here we present the first detailed analysis of two fundamentally different coiled-coil periodicities being accommodated in the same structure...
  22. ncbi request reprint A CTP-dependent archaeal riboflavin kinase forms a bridge in the evolution of cradle-loop barrels
    Moritz Ammelburg
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Structure 15:1577-90. 2007
    ..Mj0056 is unusual in utilizing CTP rather than ATP as the donor nucleotide, and sequence conservation in the relevant residues suggests that this is a general feature of archaeal riboflavin kinases...
  23. pmc On the origin of the histone fold
    Vikram Alva
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen, Germany
    BMC Struct Biol 7:17. 2007
    ..We have searched for the evolutionary origin of this fold using sequence and structure comparisons, based on the hypothesis that folded proteins evolved by combination of an ancestral set of peptides, the antecedent domain segments...
  24. ncbi request reprint Characterization of AMA, a new AAA protein from Archaeoglobus and methanogenic archaea
    Sergej Djuranovic
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, D 72076 Tubingen, Germany
    J Struct Biol 156:130-8. 2006
    ..The ability to interact with non-native proteins resides in the N-domain and is energy-independent...
  25. pmc Structure of the head of the Bartonella adhesin BadA
    Pawel Szczesny
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen, Germany
    PLoS Pathog 4:e1000119. 2008
    ..Thus, the BadA head appears to be a chimera of domains seen in two other TAAs, YadA and Hia, highlighting the combinatorial evolutionary strategy taken by pathogens...
  26. ncbi request reprint Modeling AAA+ ring complexes from monomeric structures
    Alexander V Diemand
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    J Struct Biol 156:230-43. 2006
    ....
  27. pmc TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences
    Manjunatha R Karpenahalli
    Department of Protein Evolution, Max Planck lnstitute for Developmental Biology, Spemannstrasse 35, D 72076 Tubingen, Germany
    BMC Bioinformatics 8:2. 2007
    ..Several resources are available for the prediction of TPRs, however, they often fail to detect divergent repeat units...
  28. pmc The HHpred interactive server for protein homology detection and structure prediction
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology Spemannstrasse 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W244-8. 2005
    ..A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred...
  29. pmc The GD box: a widespread noncontiguous supersecondary structural element
    Vikram Alva
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Protein Sci 18:1961-6. 2009
    ....
  30. doi request reprint Two unique membrane-bound AAA proteins from Sulfolobus solfataricus
    Justyna Serek-Heuberger
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Biochem Soc Trans 37:118-22. 2009
    ..They form ring complexes, which are stable after solubilization in a mild detergent and whose formation is dependent on the presence of the N-terminal extensions...
  31. doi request reprint Comprehensive analysis of HAMP domains: implications for transmembrane signal transduction
    Stanislaw Dunin-Horkawicz
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, D 72076 Tuebingen, Germany
    J Mol Biol 397:1156-74. 2010
    ....
  32. doi request reprint The Sulfolobus solfataricus AAA protein Sso0909, a homologue of the eukaryotic ESCRT Vps4 ATPase
    Cedric F V Hobel
    Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstrasse 35, 72076 Tubingen, Germany
    Biochem Soc Trans 36:94-8. 2008
    ..We expressed Sso0909 in Escherichia coli and S. solfataricus, but have not obtained preparations with ATPase activity so far...
  33. doi request reprint Cradle-loop barrels and the concept of metafolds in protein classification by natural descent
    Vikram Alva
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, D 72076 Tubingen, Germany
    Curr Opin Struct Biol 18:358-65. 2008
    ..We see this as an important step on the way to a classification of proteins by natural descent...
  34. doi request reprint Crystal structure of a dimeric archaeal cleavage and polyadenylation specificity factor
    Bijàn Mir-Montazeri
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    J Struct Biol 173:191-5. 2011
    ..It reveals a dimerization mode of the MβL domain that has not been observed before and suggests that RNA is bound across the dimer interface, recognized by the KH domains of one monomer, and cleaved at the active site of the other...
  35. pmc prlF and yhaV encode a new toxin-antitoxin system in Escherichia coli
    Oliver Schmidt
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076, Tubingen, Germany
    J Mol Biol 372:894-905. 2007
    ..As homologs of MazE and RelE, respectively, PrlF and YhaV provide an evolutionary connection between the two best-characterized toxin-antitoxin systems in E. coli, mazEF and relEB...
  36. doi request reprint Bioinformatics of the TULIP domain superfamily
    Klaus O Kopec
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tubingen, Germany
    Biochem Soc Trans 39:1033-8. 2011
    ..We propose to group these families together into one superfamily that we term as the TULIP (tubular lipid-binding) domain superfamily...
  37. pmc Homology of SMP domains to the TULIP superfamily of lipid-binding proteins provides a structural basis for lipid exchange between ER and mitochondria
    Klaus O Kopec
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen, Germany
    Bioinformatics 26:1927-31. 2010
    ..This relationship suggests that the SMP domains of the ERMES complex mediate lipid exchange between ER and mitochondria...
  38. ncbi request reprint Classification of AAA+ proteins
    Moritz Ammelburg
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    J Struct Biol 156:2-11. 2006
    ..We also present a new and more comprehensive cluster map, which assigns a central position to RuvB and clarifies the relationships between the clades of the AAA+ superfamily...
  39. ncbi request reprint Gene duplication of the eight-stranded beta-barrel OmpX produces a functional pore: a scenario for the evolution of transmembrane beta-barrels
    Thomas Arnold
    Max Planck Institute for Developmental Biology, Department Protein Evolution, Spemannstr 35, 72076 Tubingen, Germany
    J Mol Biol 366:1174-84. 2007
    ..Fusions of the homologous proteins OmpX, OmpA and OmpW were able to fold in vitro in all combinations tested, revealing that the general propensity to form a beta-barrel is sufficient to evolve larger barrels by simple genetic events...
  40. pmc Inherent chaperone-like activity of aspartic proteases reveals a distant evolutionary relation to double-psi barrel domains of AAA-ATPases
    Michael Hulko
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    Protein Sci 16:644-53. 2007
    ..The latent chaperone-like activity in aspartic proteases can be seen as a relic that has further evolved to serve substrate binding in the context of proteolytic activity...
  41. pmc REPPER--repeats and their periodicities in fibrous proteins
    Markus Gruber
    Max Planck Institute for Developmental Biology Spemannstr 35, 72076 Tubingen, Germany
    Nucleic Acids Res 33:W239-43. 2005
    ..REPPER is available at http://protevo.eb.tuebingen.mpg.de/repper...
  42. pmc SMG6 interacts with the exon junction complex via two conserved EJC-binding motifs (EBMs) required for nonsense-mediated mRNA decay
    Isao Kashima
    Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    Genes Dev 24:2440-50. 2010
    ....
  43. ncbi request reprint Coiled coils meet the chaperone world
    JORG MARTIN
    Max Planck Institute for Developmental Biology, Spemannstrasse 35, D 72076 Tubingen, Germany
    Trends Biochem Sci 29:455-8. 2004
    ..The use of coiled coils to mediate the binding of non-native proteins represents a novel strategy in chaperone design and a new function for coiled coils...
  44. pmc PhyloGenie: automated phylome generation and analysis
    Tancred Frickey
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, D 72076 Tuebingen, Germany
    Nucleic Acids Res 32:5231-8. 2004
    ..The generation and analysis of the Danio rerio phylome provided more than twice as many proteins as described previously, supporting the hypothesis of an additional round of genome duplication in the actinopterygian lineage...
  45. ncbi request reprint Phylogenetic analysis of AAA proteins
    Tancred Frickey
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstr 35, Tubingen D 72076, Germany
    J Struct Biol 146:2-10. 2004
    ..It also revealed highly degenerate D1 domains in plant MSP1 sequences and in at least one deeply branching group of hypothetical proteins (YC46), showing that AAA proteins with two ATPase domains arose at least three times independently...
  46. ncbi request reprint More than the sum of their parts: on the evolution of proteins from peptides
    Johannes Söding
    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tubingen, Germany
    Bioessays 25:837-46. 2003
    ..Their association into larger structures and eventual fusion into polypeptide chains would have allowed them to become independent of their RNA scaffold, leading to the evolution of a novel type of macromolecule: the folded protein...
  47. pmc A conserved glycine residue of trimeric autotransporter domains plays a key role in Yersinia adhesin A autotransport
    Ulrike Grosskinsky
    Institut fur Medizinische Mikrobiologie und Hygiene, Universitatsklinikum Tubingen, Tubingen, Germany
    J Bacteriol 189:9011-9. 2007
    ..We conclude that the conserved glycine residue affects both the export and the stability of YadA and consequently some of its putative functions in pathogenesis...
  48. ncbi request reprint Comparative analysis of coiled-coil prediction methods
    Markus Gruber
    Max Planck Institute for Developmental Biology, Spemannstr 35, 72076 Tubingen, Germany
    J Struct Biol 155:140-5. 2006
    ....
  49. ncbi request reprint Historical review: another 50th anniversary--new periodicities in coiled coils
    Markus Gruber
    Max Planck Institute for Developmental Biology, Spemannstr 35 D 72076, Tubingen, Germany
    Trends Biochem Sci 28:679-85. 2003
    ..Pauling's laboratory notebooks suggest that he searched unsuccessfully for this packing mode in 1953...
  50. ncbi request reprint Model structure of the prototypical non-fimbrial adhesin YadA of Yersinia enterocolitica
    Kristin K Koretke
    Protein Bioinformatics Group, GlaxoSmithKline, Collegeville, PA 19426 0989, USA
    J Struct Biol 155:154-61. 2006
    ..After export is completed, the fiber folds and the pore is occluded by the coiled coil. Our model explains how these proteins can act as autotransporters in the absence of any homology to classical, single-chain autotransporters...
  51. ncbi request reprint The structure of alpha-helical coiled coils
    Andrei N Lupas
    Max Planck Institute for Developmental Biology, D 72076 Tubingen, Germany
    Adv Protein Chem 70:37-78. 2005
    ..Here, we review the principles of coiled-coil structure, the determinants of their folding and stability, and the diversity of structural forms they assume...
  52. ncbi request reprint Purification of the YadA membrane anchor for secondary structure analysis and crystallization
    Petra Wollmann
    Max Planck Institute for Biochemistry, Department Membrane Biochemistry, Am Klopferspitz 18a, 82152 Martinsried, Germany
    Int J Biol Macromol 39:3-9. 2006
    ..We have crystallized the protein under various conditions and present X-ray data to 3.8 A resolution...
  53. pmc Functional mapping of YadA- and Ail-mediated binding of human factor H to Yersinia enterocolitica serotype O:3
    Marta Biedzka-Sarek
    Department of Bacteriology and Immunology, Haartman Institute, P O Box 21, 00014 University of Helsinki, Helsinki, Finland
    Infect Immun 76:5016-27. 2008
    ..On the other hand, the complement-sensitive Ail mutants were not affected in FH binding. Our results also suggested that Ail- and YadA-mediated CR does not depend solely on FH binding...