References about methodological
developments of our group, as well as about biological
investigations are given below. A lot of analyses have been performed
using Hydrophobic Cluster Analysis (HCA), often in combination with other
methods of sequence analysis and comparison. Investigations of particular
interest relative to HCA are indicated (
).
Methodological developments
HCA
Methodology / Voronoï tesselations / RUSSIA / Tightened End Fragments
(TEFs)/ topohydrophobic positions/ Loops / other methodological
developments - tools
HCA Methodology
Eudes R, Le Tuan K, Delettre J, Mornon JP, Callebaut I. A generalized analysis
of hydrophobic and loop clusters within globular protein sequences. BMC Struct
Biol. 2007 Jan 8;7(1):2. Pubmed
Hennetin J, Le Tuan K, Canard L, Colloc'h N, Mornon JP, Callebaut I. Non-intertwined
binary patterns of hydrophobic/nonhydrophobic amino acids are considerably better
markers of regular secondary structures than nonconstrained patterns. Proteins.
2003 May 1;51(2):236-44. Pubmed
Mornon JP. Hydrophobic compaction, curvature of
space and deciphering protein sequences. Europhysicsnews. 2003. 34:16-9.
Callebaut I, Labesse G, Durand P, Poupon A, Canard L, Chomilier J,
Henrissat B, Mornon JP. Deciphering protein sequence information
through hydrophobic cluster analysis (HCA): current status and
perspectives. Cell Mol Life Sci. 1997 Aug;53(8):621-45. Review. Pubmed
Semertzidis M., Thoreau E, Tasso A, Henrissat B,
Callebaut I, Mornon JP.Exploitation of protein sequences through the 2D
hydrophobic cluster analysis method (HCA). Does the helical net contain
protein folding information. In Visual display of biological
information, Pickover, C. ed, World Scientific Publishing 1995:
129-44.
Bourat G, Thoreau E, Mornon JP.2D-helical hydrophobic
clusters : statistics and morphology. J Pharm Belg. 19940; 49: 226-35.
Woodcock S, Mornon JP, Henrissat B.Detection of secondary structure
elements in proteins by hydrophobic cluster analysis. Protein Eng. 1992
Oct;5(7):629-35. Pubmed
Lemesle-Varloot L, Henrissat B, Gaboriaud C, Bissery V, Morgat A,
Mornon JP. Hydrophobic cluster analysis: procedures to derive
structural and functional information from 2-D-representation of
protein sequences. Biochimie. 1990 Aug;72(8):555-74. Pubmed
Gaboriaud C, Bissery V, Benchetrit T, Mornon JP. Hydrophobic cluster
analysis: an efficient new way to compare and analyse amino acid
sequences. FEBS Lett. 1987 Nov 16;224(1):149-55. Pubmed
Voronoï
tesselations
Dupuis F, Sadoc JF, Jullien R, Angelov B, Mornon JP.
Voro3D: 3D voronoi tessellations applied to protein
structures.Bioinformatics. 2005 Apr 15;21(8):1715-6.Pubmed
Dupuis F, Sadoc JF, Mornon JP. Secondary structure
assignments through Voronoï tesselation. Proteins. 2004 May
15;55(3):519-28. Pubmed.
Angelov B, Sadoc JF, Jullien R, Soyer A, Mornon JP,
Chomilier J. Nonatomic solvent-driven Voronoi tessellation of proteins:
an open tool to analyze protein folds. Proteins. 2002 Dec
1;49(4):446-56. Pubmed
Soyer A, Chomilier J, Mornon JP, Jullien R, Sadoc
JF.Voronoi tessellation reveals the condensed matter character of
folded proteins. Phys Rev Lett. 2000 Oct 16;85(16):3532-5. Pubmed
RUSSIA
Znamenskiy D, Le Tuan K, Mornon JP, Chomilier J. A
new protein folding algorithm based on hydrophobic compactness: Rigid
Unconnected Secondary Structure Iterative Assembly (RUSSIA). II:
Applications. Protein Eng. 2003 Dec;16(12):937-48. Pubmed
Znamenskiy D, Chomilier J, Le Tuan K, Mornon JP. A
new protein folding algorithm based on hydrophobic compactness: Rigid
Unconnected Secondary Structure Iterative Assembly (RUSSIA). I:
Methodology. Protein Eng. 2003 Dec;16(12):925-35. Pubmed
Znamenskiy D, Le Tuan K, Poupon A, Chomilier J,
Mornon JP. Beta-sheet modeling by helical surfaces. Protein Eng. 2000
Jun;13(6):407-12. Pubmed
Tightened
End Fragments (TEFs)
Lamarine M, Mornon JP, Berezovsky N, Chomilier J.
Distribution of tightened end fragments of globular proteins
statistically matches that of topohydrophobic positions: towards an
efficient punctuation of protein folding? Cell Mol Life Sci. 2001
Mar;58(3):492-8. Pubmed
Topohydrophobic positions
Lamarine M, Mornon JP, Berezovsky N, Chomilier J.
Distribution of tightened end fragments of globular proteins
statistically matches that of topohydrophobic positions: towards an
efficient punctuation of protein folding? Cell Mol Life Sci. 2001
Mar;58(3):492-8. Pubmed
Poupon A, Mornon JP. Predicting the protein folding
nucleus from a sequence FEBS Lett. 1999 Jun 11;452(3):283-9. Pubmed
Poupon A, Mornon JP. Populations of hydrophobic
amino acids within protein globular domains: identification of
conserved "topohydrophobic" positions. Proteins. 1998 Nov
15;33(3):329-42. Pubmed
Loops
Wojcik J, Mornon JP, Chomilier J. New efficient
statistical sequence-dependent structure prediction of short to
medium-sized protein loops based on an exhaustive loop classification.
J Mol Biol. 1999 Jun 25;289(5):1469-90.
Pubmed
Kwasigroch JM, Chomilier J, Mornon JP. A global
taxonomy of loops in globular proteins. J Mol Biol. 1996 Jun
21;259(4):855-72. Pubmed
Other methodological
developments / tools
Chomilier J, Lamarine M, Mornon JP, Hernandez Torres J, Eliopoulos
E, Papandreou N. Analysis of fragments induced by simulated lattice
protein folding. C R Biol. 2004 May;327(5):431-43. Pubmed
Labesse G, Mornon J. Incremental threading optimization (TITO) to
help alignment and modelling of remote homologues.Bioinformatics.
1998;14(2):206-11. Pubmed
Durand P, Canard L, Mornon JP. Visual BLAST and visual FASTA:
graphic workbenches for interactive analysis of full BLAST and FASTA
outputs under MICROSOFT WINDOWS 95/NT. Comput Appl Biosci. 1997
Aug;13(4):407-13. Pubmed
Labesse G, Colloc'h N, Pothier J, Mornon JP. P-SEA: a new efficient
assignment of secondary structure from C alpha trace of proteins.
Comput Appl Biosci. 1997 Jun;13(3):291-5. Pubmed
Semertzidis MT, Hazout S, Etchebest C, Mornon JP. Hydrophobic
neighboring homology (HNH) dotplot: an approach for assessing
structurally similar motifs in proteins. Comput Methods Programs
Biomed. 1994 Dec;45(4):265-82. Pubmed
Semertzidis MT, Deplanque S, Mornon JP. OMEGA: a three-dimensional
databank for protein structures (a complement to PDB). Comput Appl
Biosci. 1993 Dec;9(6):667-70. Pubmed
Colloc'h N, Etchebest C, Thoreau E, Henrissat B, Mornon JP.
Comparison of three algorithms for the assignment of secondary
structure in proteins: the advantages of a consensus assignment.
Protein Eng. 1993 Jun;6(4):377-82. Pubmed
Biological investigations
(since 1997)
Dulin F, Callebaut I, Colloc'h N, Mornon JP. Sequence-based
modeling of Abeta42 soluble oligomers. Biopolymers. 2007 In press. Pubmed
Paillisson A, Levasseur A, Gouret P, Callebaut I, Bontoux M,
Pontarotti P, Monget P. Bromodomain testis-specific protein is expressed in
mouse oocyte and evolves faster than its ubiquitously expressed paralogs BRD2,
-3, and -4. Genomics. 2006 In press. Pubmed
Letzelter M, Sorg I, Mota LJ, Meyer S, Stalder J, Feldman M,
Kuhn M, Callebaut I, Cornelis GR. The discovery of SycO highlights a new function
for type III secretion effector chaperones. EMBO J. 2006 Jul 12;25(13):3223-33.
Pubmed
Carre-Mlouka A, Mejean A, Quillardet P, Ashida H, Saito Y,
Yokota A, Callebaut I, Sekowska A, Dittmann E, Bouchier C, de Marsac NT. A new
rubisco-like protein coexists with a photosynthetic rubisco in the planktonic
cyanobacteria Microcystis. J Biol Chem. 2006 Aug 25;281(34):24462-71. Pubmed
Ray H, Moreau K, Dizin E, Callebaut I, Venezia ND. ACCA phosphopeptide
recognition by the BRCT repeats of BRCA1. J Mol Biol. 2006 Jun 16;359(4):973-82.Pubmed
Frenal K, Callebaut I, Wecker K, Prochnicka-Chalufour A, Dendouga
N, Zinn-Justin S, Delepierre M, Tomavo S, Wolff N. Structural and functional
characterization of the TgDRE multidomain protein, a DNA repair enzyme from
Toxoplasma gondii. Biochemistry. 2006 Apr 18;45(15):4867-74.Pubmed
Melin P, Norez C, Callebaut I, Becq F. The glycine residues
G551 and G1349 within the ATP-binding cassette signature motifs play critical
roles in the activation and inhibition of cystic fibrosis transmembrane conductance
regulator channels by phloxine B. J Membr Biol. 2005 Dec;208(3):203-12. Pubmed
Callebaut I, Dulin F, Bertrand O, Ripoche P, Mouro I, Colin
Y, Mornon JP, Cartron JP. Hydrophobic cluster analysis and modeling of the human
Rh protein three-dimensional structures. Transfus Clin Biol. 2006 Mar-Apr;13(1-2):70-84.
Pubmed
Callebaut I, Malivert L, Fischer A, Mornon JP, Revy P, de Villartay
JP. Cernunnos interacts with the XRCC4 x DNA-ligase IV complex and is homologous
to the yeast nonhomologous end-joining factor Nej1. J Biol Chem. 2006 May 19;281(20):13857-60.
Pubmed
Haren L, Remy MH, Bazin I, Callebaut I, Wright M, Merdes A.NEDD1-dependent
recruitment of the gamma-tubulin ring complex to the centrosome is necessary
for centriole duplication and spindle assembly. J Cell Biol. 2006 Feb 13;172(4):505-15.
Pubmed
Murat D, Bance P, Callebaut I, Dassa E. ATP hydrolysis is
essential for the function of the Uup ATP-binding cassette ATPase in precise
excision of transposons. J Biol Chem. 2006 Mar 10;281(10):6850-9. Pubmed
Kakavanos R, Lehn P, Callebaut I, Meikle PJ, Parkinson-Lawrence
EJ, Hopwood JJ, Brooks DA. Common antigenicity for two glycosidases. FEBS Lett.
2006 Jan 9;580(1):87-92.
Pubmed
Eudes R, Lehn P, Ferec C, Mornon JP, Callebaut I. Nucleotide binding domains
of human CFTR: a structural classification of critical residues and disease-causing
mutations. Cell Mol Life Sci. 2005 Sep;62(18):2112-23. Pubmed
Callebaut I, Prat K, Meurice E, Mornon JP, Tomavo S. Prediction
of the general transcription factors associated with RNA polymerase II in Plasmodium
falciparum: conserved features and differences relative to other eukaryotes.
BMC Genomics. 2005 Jul 23;6(1):100. Pubmed
Dentice M, Bandyopadhyay A, Gereben B, Callebaut I,
Christoffolete MA, Kim BW, Nissim S, Mornon JP, Zavacki AM, Zeold A,
Capelo LP, Curcio-Morelli C, Ribeiro R, Harney JW, Tabin CJ, Bianco AC.
The Hedgehog-inducible ubiquitin ligase subunit WSB-1 modulates thyroid
hormone activation and PTHrP secretion in the developing growth plate.
Nat Cell Biol. 2005 Jul;7(7):698-705. Pubmed
Niv-Spector L, Gonen-Berger D, Gourdou I, Biener E,
Gussakowsky EE, Benomar Y, Ramanujan KV, Taouis M, Herman B, Callebaut
I, Djiane J, Gertler A. Identification of the hydrophobic strand in the
A-B loop of leptin as major binding site III: implications for
large-scale preparation of potent recombinant human and ovine leptin
antagonists. Biochem J. 2005 In press Pubmed
Paillisson A, Dade S, Callebaut I, Bontoux M,
Dalbies-Tran R, Vaiman D, Monget P. Identification, characterization
and metagenome analysis of oocyte-specific genes organized in clusters
in the mouse genome. BMC Genomics. 2005 May 20;6(1):76. Pubmed
Callebaut I, Schoentgen F, Prat K, Mornon JP, Jolles P.
Characterization and study of a kappa-casein-like chymosin-sensitive
linkage. Biochim Biophys Acta. 2005 Jun 15;1749(1):75-80. Pubmed
Agrain C*, Callebaut I*, Journet L, Sorg I, Paroz
C, Mota LJ, Cornelis GR. Characterization of a Type III secretion
substrate specificity switch (T3S4) domain in YscP from Yersinia
enterocolitica. Mol Microbiol. 2005 Apr;56(1):54-67 (*equal
participation). Pubmed
Acquaviva C, Benoist JF, Pereira S, Callebaut I, Koskas T, Porquet D,
Elion J. Molecular basis of methylmalonyl-CoA mutase apoenzyme defect
in 40 European patients affected by mut(o) and mut- forms of
methylmalonic acidemia: identification of 29 novel mutations in the MUT
gene. Hum Mutat. 2005 Feb;25(2):167-76. Pubmed
Callebaut I, Mornon JP. OCRE: a novel domain made of
imperfect, aromatic-rich octamer repeats. Bioinformatics. 2005
Mar;21(6):699-702. Pubmed
Feldmann J, Menasche G, Callebaut I, Minard-Colin V,
Bader-Meunier B, Le Clainche L, Fischer A, Le Deist F, Tardieu M, de
Saint Basile G. Severe and progressive encephalitis as a presenting
manifestation of a novel missense perforin mutation and impaired
cytolytic activity. Blood. 2005 Apr 1;105(7):2658-63. Pubmed
Dade S, Callebaut I, Paillisson A, Bontoux M,
Dalbies-Tran R, Monget P. In silico identification and structural
features of six new genes similar to MATER specifically expressed in
the oocyte. Biochem Biophys Res Commun. 2004 Nov 12;324(2):547-53. Pubmed
Hermand P, Gane P, Callebaut I, Kieffer N, Cartron JP, Bailly P.
Integrin receptor specificity for human red cell ICAM-4 ligand.
Critical residues for alphaIIbeta3 binding. Eur J Biochem. 2004
Sep;271(18):3729-40. Pubmed
Charier G, Couprie J, Alpha-Bazin B, Meyer V, Quemeneur E, Guerois R,
Callebaut I, Gilquin B, Zinn-Justin S. The Tudor tandem of 53BP1: a new
structural motif involved in DNA and RG-rich peptide binding. Structure
(Camb). 2004 Sep;12(9):1551-62. Pubmed
Mazerbourg S, Callebaut I, Zapf J, Mohan S, Overgaard M, Monget P. Up
date on IGFBP-4: regulation of IGFBP-4 levels and functions, in vitro
and in vivo. Growth Horm IGF Res. 2004 Apr;14(2):71-84. Pubmed
Charier
G, Alpha-Bazin B, Couprie J, Callebaut I, Berenguer F, Quemeneur E,
Gilquin B, Zinn-Justin S. 1H, 13C and 15N resonance assignments of the
region 1463-1617 of the mouse p53 binding protein 1 (53BP1). J Biomol
NMR. 2004 Mar;28(3):303-4. Pubmed
Callebaut I, Eudes R, Mornon JP, Lehn P. Nucleotide-binding domains of
human cystic fibrosis transmembrane conductance regulator: detailed
sequence analysis and three-dimensional modeling of the heterodimer.
Cell Mol Life Sci. 2004 Jan;61(2):230-42. Pubmed
Poinsignon C, Moshous D, Callebaut I, De Chasseval R, Villey I, De Villartay
JP. The Metallo-{beta}-Lactamase/{beta}-CASP Domain of Artemis Constitutes the
Catalytic Core for V(D)J Recombination. J Exp Med. 2004 Feb 2;199(3):315-321.
Pubmed
Dade S, Callebaut I, Mermillod P, Monget P. Identification of a new
expanding family of genes characterized by atypical LRR domains.
Localization of a cluster preferentially expressed in oocyte. FEBS
Lett. 2003 Dec 18;555(3):533-8. Pubmed
Neven B, Callebaut
I, Prieur AM, Feldmann J, Bodemer C, Lepore L, Derfalvi B,
Benjaponpitak S, Vesely R, Sauvain MJ, Oertle S, Allen R, Morgan G,
Borkhardt A, Hill C, Gardner-Medwin J, Fischer A, de Saint Basile G.
Molecular basis of the spectral expression of CIAS1 mutations
associated with phagocytic cell-mediated autoinflammatory disorders
CINCA/NOMID, MWS, and FCU. Blood. 2004 Apr 1;103(7):2809-15. Pubmed
Gregoire S, Logre C, Metharom P, Loing E, Chomilier
J, Rosset MB, Aucouturier P, Carnaud C. Identification of two
immunogenic domains of the prion protein--PrP--which activate class
II-restricted T cells and elicit antibody responses against the native
molecule. J Leukoc Biol. 2004 Apr 1 Pubmed
Feldmann J, Callebaut
I, Raposo G, Certain S, Bacq D, Dumont C, Lambert N, Ouachee-Chardin M, Chedeville
G, Tamary H, Minard-Colin V, Vilmer E, Blanche S, Le Deist F, Fischer A, de
Saint Basile G. Munc13-4 is essential for cytolytic granules fusion and is mutated
in a form of familial hemophagocytic lymphohistiocytosis (FHL3). Cell. 2003
Nov 14;115(4):461-73. Pubmed
Renault F, Formstecher E, Callebaut I, Junier MP, Chneiweiss H. The
multifunctional protein PEA-15 is involved in the control of apoptosis
and cell cycle in astrocytes. Biochem Pharmacol. 2003 Oct
15;66(8):1581-8. Review. Pubmed
Callebaut I, Curcio-Morelli C, Mornon JP, Gereben B, Buettner C, Huang S, Castro
B, Fonseca TL, Harney JW, Larsen PR, Bianco AC. The iodothyronine selenodeiodinases
are thioredoxin-fold family proteins containing a glycoside hydrolase clan GH-A-like
structure. J Biol Chem. 2003 Sep 19;278(38):36887-96. Pubmed
Moshous
D, Callebaut I, de Chasseval R, Poinsignon C, Villey I, Fischer A, de
Villartay JP. The V(D)J recombination/DNA repair factor artemis belongs
to the metallo-beta-lactamase family and constitutes a critical
developmental checkpoint of the lymphoid system. Ann N Y Acad Sci. 2003
Apr;987:150-7. Review. Pubmed
Mornon
JP, Prat K, Dupuis F, Boisset N, Callebaut I. Structural features of
prions explored by sequence analysis. II. A PrP(Sc) model. Cell Mol
Life Sci. 2002 Dec;59(12):2144-54. Pubmed
Mornon
JP, Prat K, Dupuis F, Callebaut I. Structural features of prions
explored by sequence analysis I. Sequence data. Cell Mol Life Sci. 2002
Aug;59(8):1366-76.Pubmed
Callebaut I, Mignotte V, Souchet M, Mornon JP. EMI domains are
widespread and reveal the probable orthologs of the Caenorhabditis
elegans CED-1 protein. Biochem Biophys Res Commun. 2003 Jan
17;300(3):619-23. Pubmed
Siaut M, Zaros C, Levivier E, Ferri ML, Court M, Werner M, Callebaut I,
Thuriaux P, Sentenac A, Conesa C. An Rpb4/Rpb7-like complex in yeast
RNA polymerase III contains the orthologue of mammalian CGRP-RCP. Mol
Cell Biol. 2003 Jan;23(1):195-205. Pubmed
Peyroche G, Levillain E, Siaut M, Callebaut I, Schultz P, Sentenac A,
Riva M, Carles C. The A14-A43 heterodimer subunit in yeast RNA pol I
and their relationship to Rpb4-Rpb7 pol II subunits. Proc Natl Acad Sci
U S A. 2002 Nov 12;99(23):14670-5. Pubmed
Proux-Gillardeaux V, Galli T, Callebaut I, Mikhailik A, Calothy G, Marx
M. D53 is a novel endosomal SNARE-binding protein that enhances
interaction of syntaxin 1 with the synaptobrevin 2 complex in vitro.
Biochem J. 2003 Feb 15;370(Pt 1):213-21. Pubmed
Fabrega S, Durand P, Mornon JP, Lehn P. [The active
site of human glucocerebrosidase: structural predictions and
experimental validations] J Soc Biol. 2002;196(2):151-60. Review.
French. Pubmed
Colloc'h N, Mornon JP, Camadro JM. Towards a new
T-fold protein?: the coproporphyrinogen III oxidase sequence matches
many structural features from urate oxidase. FEBS Lett. 2002 Aug
28;526(1-3):5-10. Pubmed
Krimm I, Ostlund C, Gilquin B, Couprie J, Hossenlopp
P, Mornon JP, Bonne G, Courvalin JC, Worman HJ, Zinn-Justin S. The
Ig-like structure of the C-terminal domain of lamin A/C, mutated in
muscular dystrophies, cardiomyopathy, and partial lipodystrophy.
Structure (Camb). 2002 Jun;10(6):811-23. Pubmed
Callebaut I, Moshous
D, Mornon JP, de Villartay JP. Metallo-beta-lactamase fold within nucleic acids
processing enzymes: the beta-CASP family.Nucleic Acids Res. 2002 Aug 15;30(16):3592-601.
Pubmed
Chardin P, Callebaut I. The yeast Sar exchange factor Sec12, and its
higher organism orthologs, fold as beta-propellers. FEBS Lett. 2002 Aug
14;525(1-3):171-3. Pubmed
Cavarec L, Kamphausen T, Dubourg B, Callebaut I, Lemeunier F, Metivier
D, Feunteun J, Fischer G, Modjtahedi N. Identification and
characterization of Moca-cyp. A Drosophila melanogaster nuclear
cyclophilin. J Biol Chem. 2002 Oct 25;277(43):41171-82. Pubmed
Dendouga N, Callebaut I, Tomavo S. A novel DNA repair enzyme containing
RNA recognition, G-patch and specific splicing factor 45-like motifs in
the protozoan parasite Toxoplasma gondii. Eur J Biochem. 2002
Jul;269(14):3393-401. Pubmed
Gatot JS, Callebaut I, Van Lint C, Demonte D, Kerkhofs P, Portetelle D,
Burny A, Willems L, Kettmann R. Bovine leukemia virus SU protein
interacts with zinc, and mutations within two interacting regions
differently affect viral fusion and infectivity in vivo. J Virol. 2002
Aug;76(16):7956-67. Pubmed
Del Angel
VD, Dupuis F, Mornon JP, Callebaut I. Viral fusion peptides and
identification of membrane-interacting segments. Biochem Biophys Res
Commun. 2002 May 17;293(4):1153-60. Pubmed
Callebaut
I. An EVH1/WH1 domain as a key actor in TGFbeta signalling. FEBS Lett.
2002 May 22;519(1-3):178-80.Pubmed
Nancy V,
Callebaut I, El Marjou A, de Gunzburg J. The delta subunit of retinal
rod cGMP phosphodiesterase regulates the membrane association of Ras
and Rap GTPases. J Biol Chem. 2002 Apr 26;277(17):15076-84. Pubmed
Mouche F, Gontero B, Callebaut I, Mornon JP, Boisset N. Striking
conformational change suspected within the phosphoribulokinase dimer
induced by interaction with GAPDH. J Biol Chem. 2002 Feb
22;277(8):6743-9.Pubmed
Brooks DA, Fabrega S, Hein LK, Parkinson EJ, Durand
P, Yogalingam G, Matte U, Giugliani R, Dasvarma A, Eslahpazire J,
Henrissat B, Mornon JP, Hopwood JJ, Lehn P. Glycosidase active site
mutations in human alpha-L-iduronidase. Glycobiology. 2001
Sep;11(9):741-50.Pubmed
Bouchard
P, Chomilier J, Ravet V, Mornon JP, Vigues B. Molecular
characterization of the major membrane skeletal protein in the ciliate
Tetrahymena pyriformis suggests n-plication of an early evolutionary
intermediate filament protein subdomain. J Cell Sci. 2001 Jan;114(Pt
1):101-110. Pubmed
Levivier
E, Goud B, Souchet M, Calmels TP, Mornon JP, Callebaut I. uDENN, DENN,
and dDENN: indissociable domains in Rab and MAP kinases signaling
pathways. Biochem Biophys Res Commun. 2001 Sep 28;287(3):688-95.Pubmed
Acquaviva
C, Benoist JF, Callebaut I, Guffon N, Ogier de Baulny H, Touati G,
Aydin A, Porquet D, Elion J. N219Y, a new frequent mutation among
mut(degree) forms of methylmalonic acidemia in Caucasian patients. Eur
J Hum Genet. 2001 Aug;9(8):577-82. Pubmed
Wolff N, Gilquin B, Courchay K, Callebaut I, Worman HJ, Zinn-Justin S.
Structural analysis of emerin, an inner nuclear membrane protein
mutated in X-linked Emery-Dreifuss muscular dystrophy. FEBS Lett. 2001
Jul 20;501(2-3):171-6. Pubmed
Laguri C,
Gilquin B, Wolff N, Romi-Lebrun R, Courchay K, Callebaut I, Worman HJ,
Zinn-Justin S. Structural characterization of the LEM motif common to
three human inner nuclear membrane proteins.Structure (Camb). 2001
Jun;9(6):503-11.Pubmed
Moshous D, Callebaut I, de Chasseval R, Corneo B, Cavazzana-Calvo M, Le Deist
F, Tezcan I, Sanal O, Bertrand Y, Philippe N, Fischer A, de Villartay JP. Artemis,
a novel DNA double-strand break repair/V(D)J recombination protein, is mutated
in human severe combined immune deficiency. Cell. 2001 Apr 20;105(2):177-86.Pubmed
Brault E,
Gautreau A, Lamarine M, Callebaut I, Thomas G, Goutebroze L. Normal
membrane localization and actin association of the NF2 tumor suppressor
protein are dependent on folding of its N-terminal domain.J Cell Sci.
2001 May;114(Pt 10):1901-12. Pubmed
Eyries M, Michaud A, Deinum J, Agrapart M, Chomilier
J, Kramers C, Soubrier F. Increased shedding of angiotensin-converting
enzyme by a mutation identified in the stalk region. J Biol Chem. 2001
Feb 23;276(8):5525-32. Pubmed
Mulsant
P, Lecerf F, Fabre S, Schibler L, Monget P, Lanneluc I, Pisselet C,
Riquet J, Monniaux D, Callebaut I, Cribiu E, Thimonier J, Teyssier J,
Bodin L, Cognie Y, Chitour N, Elsen JM. Mutation in bone morphogenetic
protein receptor-IB is associated with increased ovulation rate in
Booroola Merino ewes. Proc Natl Acad Sci U S A. 2001 Apr
24;98(9):5104-9. Pubmed
El Nemer
W, Gane P, Colin Y, D'Ambrosio AM, Callebaut I, Cartron JP, Van Kim CL.
Characterization of the laminin binding domains of the Lutheran blood
group glycoprotein.J Biol Chem. 2001 Jun 29;276(26):23757-62. Pubmed
Callebaut
I, Poupon A, Bally R, Demaret JP, Housset D, Delettre J, Hossenlopp P,
Mornon JP. The uteroglobin fold. Ann N Y Acad Sci. 2000;923:90-112. Pubmed
Lemaitre
N, Callebaut I, Frenois F, Jarlier V, Sougakoff W.Study of the
structure-activity relationships for the pyrazinamidase (PncA) from
Mycobacterium tuberculosis. Biochem J. 2001 Feb 1;353(Pt 3):453-8. Pubmed
Callebaut I, de Gunzburg J, Goud B, Mornon JP. RUN domains: a new
family of domains involved in Ras-like GTPase signaling. Trends Biochem
Sci. 2001 Feb;26(2):79-83. Pubmed
Benoist
JF, Acquaviva C, Callebaut I, Guffon N, Ogier de Baulny H, Mornon JP,
Porquet D, Elion J. Molecular and structural analysis of two novel
mutations in a patient with mut(-) methylmalonyl-CoA deficiency. Mol
Genet Metab. 2001 Feb;72(2):181-4. Pubmed
Fabrega
S, Durand P, Codogno P, Bauvy C, Delomenie C, Henrissat B, Martin BM,
McKinney C, Ginns EI, Mornon JP, Lehn P. Human glucocerebrosidase:
heterologous expression of active site mutants in murine null
cells.Glycobiology. 2000 Nov;10(11):1217-24. Pubmed
Durand P,
Fabrega S, Henrissat B, Mornon JP, Lehn P. Structural features of
normal and mutant human lysosomal glycoside hydrolases deduced from
bioinformatics analysis. Hum Mol Genet. 2000 Apr 12;9(6):967-77.
Review. Pubmed
Colloc'h
N, Poupon A, Mornon JP. Sequence and structural features of the T-fold,
an original tunnelling building unit. Proteins. 2000 May
1;39(2):142-54. Pubmed
Paoletti
P, Perin-Dureau F, Fayyazuddin A, Le Goff A, Callebaut I, Neyton J.
Molecular organization of a zinc binding n-terminal modulatory domain
in a NMDA receptor subunit. Neuron. 2000 Dec;28(3):911-25. Pubmed
Marques
F, Moreau JL, Peaucellier G, Lozano JC, Schatt P, Picard A, Callebaut
I, Perret E, Geneviere AM. A new subfamily of high molecular mass
CDC2-related kinases with PITAI/VRE motifs. Biochem Biophys Res Commun.
2000 Dec 29;279(3):832-7. Pubmed
Gilges D,
Vinit MA, Callebaut I, Coulombel L, Cacheux V, Romeo PH, Vigon I.
Polydom: a secreted protein with pentraxin, complement control protein,
epidermal growth factor and von Willebrand factor A domains. Biochem J.
2000 Nov 15;352 Pt 1:49-59. Pubmed
Callebaut
I, Gilges D, Vigon I, Mornon JP. HYR, an extracellular module involved
in cellular adhesion and related to the immunoglobulin-like fold.
Protein Sci. 2000 Jul;9(7):1382-90. Pubmed
Souchet
M, Poupon A, Callebaut I, Leger I, Mornon J, Bril A, Calmels TP.
Functional specificity conferred by the unique plasticity of fully
alpha-helical Ras and Rho GAPs. FEBS Lett. 2000 Jul 14;477(1-2):99-105.
Pubmed
Hermand
P, Huet M, Callebaut I, Gane P, Ihanus E, Gahmberg CG, Cartron JP,
Bailly P. Binding sites of leukocyte beta 2 integrins (LFA-1, Mac-1) on
the human ICAM-4/LW blood group protein. J Biol Chem. 2000 Aug
25;275(34):26002-10. Pubmed
Girardeau
JP, Bertin Y, Callebaut I. Conserved structural features in class I
major fimbrial subunits (Pilin) in gram-negative bacteria. Molecular
basis of classification in seven subfamilies and identification of
intrasubfamily sequence signature motifs which might Be implicated in
quaternary structure. J Mol Evol. 2000 May;50(5):424-42. Pubmed
Corneo
B, Moshous D, Callebaut I, de Chasseval R, Fischer A, de Villartay JP.
Three-dimensional clustering of human RAG2 gene mutations in severe
combined immune deficiency. J Biol Chem. 2000 Apr 28;275(17):12672-5. Pubmed
Lin F,
Blake DL, Callebaut I, Skerjanc IS, Holmer L, McBurney MW,
Paulin-Levasseur M, Worman HJ. MAN1, an inner nuclear membrane protein
that shares the LEM domain with lamina-associated polypeptide 2 and
emerin. J Biol Chem. 2000 Feb 18;275(7):4840-7.Pubmed
Poupon A, Jebai F, Labesse G, Gros F, Thibault J,
Mornon JP, Krieger M. Structure modelling and site-directed mutagenesis
of the rat aromatic L-amino acid pyridoxal 5'-phosphate-dependent
decarboxylase: a functional study. Proteins. 1999 Nov 1;37(2):191-203. Pubmed
Talfournier F, Colloc'h N, Mornon JP, Branlant G.
Functional characterization of the phosphorylating D-glyceraldehyde
3-phosphate dehydrogenase from the archaeon Methanothermus fervidus by
comparative molecular modelling and site-directed mutagenesis. Eur J
Biochem. 1999 Oct 1;265(1):93-104. Pubmed
Halaby DM, Poupon A, Mornon J. The immunoglobulin
fold family: sequence analysis and 3D structure comparisons. Protein
Eng. 1999 Jul;12(7):563-71. Pubmed
Wojcik J,
Girault JA, Labesse G, Chomilier J, Mornon JP, Callebaut I. Sequence
analysis identifies a ras-associating (RA)-like domain in the N-termini
of band 4.1/JEF domains and in the Grb7/10/14 adapter family. Biochem
Biophys Res Commun. 1999 May 27;259(1):113-20. Pubmed
Thoreau
V, Berges T, Callebaut I, Guillier-Gencik Z, Gressin L, Bernheim A,
Karst F, Mornon JP, Kitzis A, Chomel JC. Molecular cloning, expression
analysis, and chromosomal localization of human syntaxin 8 (STX8).
Biochem Biophys Res Commun. 1999 Apr 13;257(2):577-83. Pubmed
Callebaut
I, Courvalin JC, Mornon JP. The BAH (bromo-adjacent homology) domain: a
link between DNA methylation, replication and transcriptional
regulation. FEBS Lett. 1999 Mar 5;446(1):189-93.Pubmed
Girault JA, Labesse G, Mornon JP, Callebaut I. The N-termini of FAK and
JAKs contain divergent band 4.1 domains. Trends Biochem Sci. 1999
Feb;24(2):54-7.Pubmed
Girault
JA, Labesse G, Mornon JP, Callebaut I. Janus kinases and focal adhesion
kinases play in the 4.1 band: a superfamily of band 4.1 domains
important for cell structure and signal transduction. Mol Med. 1998
Dec;4(12):751-69. Review. Pubmed
Labesse G, Craescu CT, Mispelter J, Chottard G,
Marden MC, Pin S, Forest E, Mornon JP, Boccara M. Engineering,
expression and biochemical characterization of the hemoglobin domain of
a Erwinia chrysanthemi flavohemoprotein. Eur J Biochem. 1998 May
1;253(3):751-9. Pubmed
The immunoglobulin superfamily: an insight on its
tissular, species, and functional diversity. J Mol Evol. 1998
Apr;46(4):389-400. Pubmed
Talfournier F, Colloc'h N, Mornon JP, Branlant G.
Comparative study of the catalytic domain of phosphorylating
glyceraldehyde-3-phosphate dehydrogenases from bacteria and archaea via
essential cysteine probes and site-directed mutagenesis. Eur J Biochem.
1998 Mar 15;252(3):447-57. Pubmed
Porta A,
Colonna-Romano S, Callebaut I, Franco A, Marzullo L, Kobayashi GS,
Maresca B. An homologue of the human 100-kDa protein (p100) is
differentially expressed by Histoplasma capsulatum during infection of
murine macrophages. Biochem Biophys Res Commun. 1999 Jan
27;254(3):605-13. Pubmed
Callebaut
I, Cossart P, Dehoux P. EVH1/WH1 domains of VASP and WASP proteins
belong to a large family including Ran-binding domains of the RanBP1
family. FEBS Lett. 1998 Dec 18;441(2):181-5. Pubmed
Madry C,
Laabi Y, Callebaut I, Roussel J, Hatzoglou A, Le Coniat M, Mornon JP,
Berger R, Tsapis A. The characterization of murine BCMA gene defines it
as a new member of the tumor necrosis factor receptor superfamily. Int
Immunol. 1998 Nov;10(11):1693-702.
Pubmed
Ayadi L,
Callebaut I, Saguez C, Villa T, Mornon JP, Banroques J. Functional and
structural characterization of the prp3 binding domain of the yeast
prp4 splicing factor. J Mol Biol. 1998 Dec 4;284(3):673-87. Pubmed
Carbonnet
F, Hattab C, Callebaut I, Cochet S, Blancher A, Cartron JP, Bertrand O.
Kx, a quantitatively minor protein from human erythrocytes, is
palmitoylated in vivo. Biochem Biophys Res Commun. 1998 Sep
29;250(3):569-74. Pubmed
Callebaut
I, Mornon JP. The V(D)J recombination activating protein RAG2 consists
of a six-bladed propeller and a PHD fingerlike domain, as revealed by
sequence analysis.Cell Mol Life Sci. 1998 Aug;54(8):880-91. Pubmed
Mornon
JP, Halaby D, Malfois M, Durand P, Callebaut I, Tardieu A.
alpha-Crystallin C-terminal domain: on the track of an Ig fold. Int J
Biol Macromol. 1998 May-Jun;22(3-4):219-27. Pubmed
Gatot JS,
Callebaut I, Mornon JP, Portetelle D, Burny A, Kerkhofs P, Kettmann R,
Willems L. Conservative mutations in the immunosuppressive region of
the bovine leukemia virus transmembrane protein affect fusion but not
infectivity in vivo. J Biol Chem. 1998 May 22;273(21):12870-80. Pubmed
Calmels TP, Callebaut I, Leger I, Durand P, Bril A, Mornon JP, Souchet
M. Sequence and 3D structural relationships between mammalian Ras- and
Rho-specific GTPase-activating proteins (GAPs): the cradle fold. FEBS
Lett. 1998 Apr 17;426(2):205-11. Pubmed
Vincent V, Goffin V, Rozakis-Adcock M, Mornon JP,
Kelly PA. Identification of cytoplasmic motifs required for short
prolactin receptor internalization. J Biol Chem. 1997 Mar
14;272(11):7062-8. Pubmed
Halaby D, Thoreau E, Djiane J, Mornon JP. Homology
modeling of rabbit prolactin hormone complexed with its receptor.
Proteins. 1997 Mar;27(3):459-68. Pubmed
Benit L,
De Parseval N, Casella JF, Callebaut I, Cordonnier A, Heidmann T.
Cloning of a new murine endogenous retrovirus, MuERV-L, with strong
similarity to the human HERV-L element and with a gag coding sequence
closely related to the Fv1 restriction gene. J Virol. 1997
Jul;71(7):5652-7. Pubmed
Callebaut
I, Courvalin JC, Worman HJ, Mornon JP. Hydrophobic cluster analysis
reveals a third chromodomain in the Tetrahymena Pdd1p protein of the
chromo superfamily. Biochem Biophys Res Commun. 1997 Jun
9;235(1):103-7. Pubmed
Ye Q,
Callebaut I, Pezhman A, Courvalin JC, Worman HJ. Domain-specific
interactions of human HP1-type chromodomain proteins and inner nuclear
membrane protein LBR.J Biol Chem. 1997 Jun 6;272(23):14983-9. Pubmed
Durand P, Lehn P, Callebaut I, Fabrega S, Henrissat B, Mornon JP.
Active-site motifs of lysosomal acid hydrolases: invariant features of
clan GH-A glycosyl hydrolases deduced from hydrophobic cluster
analysis. Glycobiology. 1997 Mar;7(2):277-84.
Pubmed
Callebaut I, Mornon JP. From BRCA1 to RAP1: a widespread BRCT module
closely associated with DNA repair. FEBS Lett. 1997 Jan 2;400(1):25-30.
Pubmed
Callebaut I, Mornon JP. The human EBNA-2 coactivator p100: multidomain
organization and relationship to the staphylococcal nuclease fold and
to the tudor protein involved in Drosophila melanogaster development.
Biochem J. 1997 Jan 1;321 ( Pt 1):125-32.Pubmed
Crystal structures
(and
associated publications)
Retailleau P, Colloc'h N, Vivares D, Bonnete F,
Castro B, El-Hajji M, Mornon JP, Monard G, Prange T. Complexed and
ligand-free high-resolution structures of urate oxidase (Uox) from
Aspergillus flavus: a reassignment of the active-site binding mode.
Acta Crystallogr D Biol Crystallogr. 2004 Mar;60(Pt 3):453-62. Pubmed
PDB:1R54
PDB:1R51
PDB:1R4U
PDB:1R4S
Bayol A, Capdevielle J, Malazzi P, Buzy A, Claude
Bonnet M, Colloc'h N, Mornon JP, Loyaux D, Ferrara P. Modification of a
reactive cysteine explains differences between rasburicase and
Uricozyme, a natural Aspergillus flavus uricase. Biotechnol Appl
Biochem. 2002 Aug;36(Pt 1):21-31. Pubmed
Colloc'h N, el Hajji M, Bachet B, L'Hermite G,
Schiltz M, Prange T, Castro B, Mornon JP. Crystal structure of the
protein drug urate oxidase-inhibitor complex at 2.05 A resolution. Nat
Struct Biol. 1997 Nov;4(11):947-52. Pubmed