http://publicationslist.org/data/a.thomas/atom.xml Annick Thomashttp://publicationslist.org/a.thomas$basepathfavicon.icoRecent additions to Annick Thomas's PublicationsList.org pagehttp://publicationslist.org/publications.png2009-05-11T11:25:43Z http://publicationslist.org/a.thomas/refid7 2009-05-11T11:17:27Z

Annick Thomas, Sébastien Deshayes, Marc Decaffmeyer, Marie-Hélène Van Eyck, Benoit B Charloteaux, Robert Brasseur (2009) <i>Adv Exp Med Biol</i> <i></i> <i></i> 611: 459-460<br/>

http://publicationslist.org/a.thomas/refid11 2009-05-11T11:17:27Z

Physical properties of membranes, such as fluidity, charge or curvature influence their function. Proteins and peptides can modulate those properties and conversely, the lipids can affect the activity and/or the structure of the former. Tilted peptides are short hydrophobic protein fragments characterized by an asymmetric distribution of their hydrophobic residues when helical. They were detected ...<br/><br/>L Lins, M Decaffmeyer, A Thomas, R Brasseur (2008) <i>Biochim Biophys Acta</i> <i></i> <i></i> 1778: 7-8 1537-1544<br/>

http://publicationslist.org/a.thomas/refid12 2009-05-11T11:17:27Z

Despite numerous investigations, the important structural features of Cell Penetrating Peptides (CPPs) remain unclear as demonstrated by the difficulties encountered in designing new molecules. In this study, we focused our interest on Penetratin and Transportan and several of their variants. Penetratin W48F and Penetratin W48F/W56F exhibit a reduced and a complete lack of cellular uptake, respect...<br/><br/>Sébastien Deshayes, Marc Decaffmeyer, Robert Brasseur, Annick Thomas (2008) <i>Biochim Biophys Acta</i> <i></i> <i></i> 1778: 5 1197-1205<br/>

http://publicationslist.org/a.thomas/refid10 2009-05-11T11:17:27Z

Colipase is a key element in the lipase-catalyzed hydrolysis of dietary lipids. Although devoid of enzymatic activity, colipase promotes the pancreatic lipase activity in physiological intestinal conditions by anchoring the enzyme at the surface of lipid droplets. Analysis of structures of NMR colipase models and simulations of their interactions with various lipid aggregates, lipid droplet, and b...<br/><br/>Brigitte Kerfelec, Maya Allouche, Damien Colin, Marie Hélène Van Eyck, Robert Brasseur, Annick Thomas (2008) <i>Proteins</i> <i></i> <i></i> 73: 4 828-838<br/>

http://publicationslist.org/a.thomas/refid13 2009-05-11T11:17:27Z

We investigated the peptides N-acetyl-AWYIK-amide and N-acetyl-VWYIK-amide corresponding to single amino acid substitutions in LWYIK, a segment found in the gp41 protein of HIV and believed to play a role in sequestering this protein to a cholesterol-rich domain in the membrane. The effects of these peptides on the thermotropic phase transitions of 1-stearoyl-2-oleoylphosphatidylcholine (SOPC) and...<br/><br/>Sundaram A Vishwanathan, Annick Thomas, Robert Brasseur, Raquel F Epand, Eric Hunter, Richard M Epand (2008) <i>Biochemistry</i> <i></i> <i></i> 47: 1 124-130<br/>

http://publicationslist.org/a.thomas/refid9 2009-05-11T11:17:27Z

The epsilon isoform of diacylglycerol kinase (DGKepsilon) is unique among mammalian DGKs in having a segment of hydrophobic amino acids comprising approximately residues 20 to 41. Several algorithms predict this segment to be a transmembrane (TM) helix. Using PepLook, we have performed an in silico analysis of the conformational preference of the segment in a hydrophobic environment comprising res...<br/><br/>Marc Decaffmeyer, Yulia V Shulga, Armela O Dicu, Annick Thomas, Ray Truant, Matthew K Topham, Robert Brasseur, Richard M Epand (2008) <i>J Mol Biol</i> <i></i> <i></i> 383: 4 797-809<br/>

http://publicationslist.org/a.thomas/refid8 2009-05-11T11:17:27Z

The membrane-proximal external region (MPER) of the gp41 fusion protein of HIV is highly conserved among isolates of this virus and is considered a target for vaccine development. This region also appears to play a role in membrane fusion as well as localization of the virus to cholesterol-rich domains in membranes. The carboxyl terminus of MPER has the sequence LWYIK and appears to have an import...<br/><br/>Sundaram A Vishwanathan, Annick Thomas, Robert Brasseur, Raquel F Epand, Eric Hunter, Richard M Epand (2008) <i>Biochemistry</i> <i></i> <i></i> 47: 45 11869-11876<br/>

http://publicationslist.org/a.thomas/refid16 2009-05-11T11:17:27Z

Model peptides composed of alanine and leucine residues are often used to mimic single helical transmembrane domains. Many studies have been carried out to determine how they interact with membranes. However, few studies have investigated their lipid-destabilizing effect. We designed three peptides designated KALRs containing a hydrophobic stretch of 14, 18, or 22 alanines/leucines surrounded by c...<br/><br/>Aurélien Lorin, Benoit Charloteaux, Yael Fridmann-Sirkis, Annick Thomas, Yechiel Shai, Robert Brasseur (2007) <i>J Biol Chem</i> <i></i> <i></i> 282: 25 18388-18396<br/>

http://publicationslist.org/a.thomas/refid15 2009-05-11T11:17:27Z

The TRE2 oncoprotein is structurally related to the RabGAP (GTPase-activating protein) family. However, TRE2 seems enzymatically inactive. Two regions are important for its lack of GAP activity. First, the TBC domain, forming the catalytically active domain of RabGAPs, is non-functional in the oncoprotein. Also involved in TRE2 inactivity is the 93-aa region flanking the TBC domain on the C-termin...<br/><br/>Christelle Bizimungu, Annick Thomas, Robert Brasseur, Micheline Vandenbol (2007) <i>Biotechnol Lett</i> <i></i> <i></i> 29: 12 1927-1937<br/>

http://publicationslist.org/a.thomas/refid14 2009-05-11T11:17:27Z

Colicins are toxic proteins produced by Escherichia coli that must cross the membrane to exert their activity. The lipid insertion of their pf domain is linked to a conformational change which enables the penetration of a hydrophobic hairpin. They provide useful models to more generally study insertion of proteins, channel formation and protein translocation in and across membranes. In this paper,...<br/><br/>L Lins, K El Kirat, B Charloteaux, C Flore, V Stroobant, A Thomas, Y Dufrene, R Brasseur (2007) <i>Mol Membr Biol</i> <i></i> <i></i> 24: 5-6 419-430<br/>

http://publicationslist.org/a.thomas/refid22 2009-05-11T11:18:14Z

The Chameleon peptide (Cham) is a peptide designed from two regions of the GB1 protein, one folded as an alpha-helix and the other as a beta structure. Depending on the environment, the Cham peptide adopts an alpha or a beta conformation when inserted in different locations of GB1. This environment dependence is also observed for tilted peptides. These short protein fragments, able to destabilise ...<br/><br/>A Lorin, A Thomas, V Stroobant, R Brasseur, L Lins (2006) <i>Chem Phys Lipids</i> <i></i> <i></i> 141: 1-2 185-196<br/>

http://publicationslist.org/a.thomas/refid23 2009-05-11T11:18:14Z

Wall-associated kinase 1--WAK1 is a transmembrane protein containing a cytoplasmic Ser/Thr kinase domain and an extracellular domain in contact with the pectin fraction of the plant cell wall in Arabidopsis thaliana (L.) HEYNH. In a previous paper [Decreux, A., Messiaen, J., 2005. Wall-associated kinase WAK1 interacts with cell wall pectins in a calcium-induced conformation. Plant Cell Physiol. 46...<br/><br/>Annabelle Decreux, Annick Thomas, Benoît Spies, Robert Brasseur, Pierre Van Cutsem, Johan Messiaen (2006) <i>Phytochemistry</i> <i></i> <i></i> 67: 11 1068-1079<br/>

http://publicationslist.org/a.thomas/refid25 2009-05-11T11:18:14Z

In this study, we describe an in silico method to design peptides that can be made of non-natural amino acids and elicit specific membrane-interacting properties. The originality of the method holds in the capacities developed to design peptides from any non-natural amino acids as easily as from natural ones, and to test the structure stability by an angular dynamics rather than the currently-used...<br/><br/>L Lins, B Charloteaux, C Heinen, A Thomas, R Brasseur (2006) <i>Biophys J</i> <i></i> <i></i> 90: 2 470-479<br/>

http://publicationslist.org/a.thomas/refid21 2009-05-11T11:18:14Z

Here, we predicted the minimal N-terminal fragment of gp41 required to induce significant membrane destabilization using IMPALA. This algorithm is dedicated to predict peptide interaction with a membrane. We based our prediction of the minimal fusion peptide on the tilted peptide theory. This theory proposes that some protein fragments having a peculiar distribution of hydrophobicity adopt a tilte...<br/><br/>B Charloteaux, A Lorin, J M Crowet, V Stroobant, L Lins, A Thomas, R Brasseur (2006) <i>J Mol Biol</i> <i></i> <i></i> 359: 3 597-609<br/>

http://publicationslist.org/a.thomas/refid24 2009-05-11T11:18:14Z

Peptides in solution currently exist under several conformations; an equilibrium which varies with solvent polarity. Despite or because of this structure versatility, peptides can be selective biological tools: they can adapt to a target, vary conformation with solvents and so on. These capacities are crucial for cargo carriers. One promising way of using peptides in biotechnologies is to decipher...<br/><br/>Marc Decaffmeyer, Laurence Lins, Benoit Charloteaux, Marie Hélène VanEyck, Annick Thomas, Robert Brasseur (2006) <i>Biochim Biophys Acta</i> <i></i> <i></i> 1758: 3 320-327<br/>

http://publicationslist.org/a.thomas/refid18 2009-05-11T11:18:14Z

N-terminal mutations in the KCNQ1 channel are frequently linked to fatal arrhythmias in newborn children and adolescents but the cellular mechanisms involved in this dramatic issue remain, however, to be discovered. Here, we analyzed the trafficking of a series of N-terminal truncation mutants and identified a critical trafficking motif of KCNQ1. This determinant is located in the juxtamembranous ...<br/><br/>Shehrazade Dahimène, Sébastien Alcoléa, Patrice Naud, Philippe Jourdon, Denis Escande, Robert Brasseur, Annick Thomas, Isabelle Baró, Jean Mérot (2006) <i>Circ Res</i> <i></i> <i></i> 99: 10 1076-1083<br/>

http://publicationslist.org/a.thomas/refid20 2009-05-11T11:18:14Z

We investigated the properties of several peptides with sequences related to LWYIK, a segment found in the gp41 protein of HIV and believed to play a role in sequestering this protein to a cholesterol-rich domain in the membrane. This segment fulfills the requirements to be classified as a CRAC motif that has been suggested to predict those proteins that will partition into cholesterol-rich region...<br/><br/>Raquel F Epand, Annick Thomas, Robert Brasseur, Sundaram A Vishwanathan, Eric Hunter, Richard M Epand (2006) <i>Biochemistry</i> <i></i> <i></i> 45: 19 6105-6114<br/>

http://publicationslist.org/a.thomas/refid19 2009-05-11T11:18:14Z

Rational design of peptides is a challenge, which would benefit from a better knowledge of the rules of sequence-structure-function relationships. Peptide structures can be approached by spectroscopy and NMR techniques but data from these approaches too frequently diverge. Structures can also be calculated in silico from primary sequence information using three algorithms: Pepstr, Robetta, and Pep...<br/><br/>Annick Thomas, Sébastien Deshayes, Marc Decaffmeyer, Marie Hélène Van Eyck, Benoit Charloteaux, Robert Brasseur (2006) <i>Proteins</i> <i></i> <i></i> 65: 4 889-897<br/>

http://publicationslist.org/a.thomas/refid17 2009-05-11T11:18:14Z

Nature has selected peptide motifs for protein functions. It is clear that specific sequence motifs can identify families of enzymes. These sequence motifs are one dimensional signatures and nature has also developed two dimension motifs which cannot be read in the one dimension of sequence language but can be detected in the three dimensional properties of a secondary structure. One of such motif...<br/><br/>Annick Thomas, Robert Brasseur (2006) <i>Curr Protein Pept Sci</i> <i></i> <i></i> 7: 6 523-527<br/>

http://publicationslist.org/a.thomas/refid28 2009-05-11T11:18:55Z

The interaction of the native Alzheimer's peptide C-terminal fragment Abeta (29-42), and two mutants (G33A and G37A) with neutral lipid bilayers made of POPC and POPE in a 9:1 molar ratio was investigated by solid-state NMR. This fragment and the lipid composition were selected because they represent the minimum requirement for the fusogenic activity of the Alzheimer's peptide. The chemical shifts...<br/><br/>Stéphanie Ravault, Olivier Soubias, Olivier Saurel, Annick Thomas, Robert Brasseur, Alain Milon (2005) <i>Protein Sci</i> <i></i> <i></i> 14: 5 1181-1189<br/>

http://publicationslist.org/a.thomas/refid27 2009-05-11T11:18:55Z

We analyzed structural features of 11,038 direct atomic contacts (either electrostatic, H-bonds, hydrophobic, or other van der Waals interactions) extracted from 139 protein-DNA and 49 protein-RNA nonhomologous complexes from the Protein Data Bank (PDB). Globally, H-bonds are the most frequent interactions (approximately 50%), followed by van der Waals, hydrophobic, and electrostatic interactions....<br/><br/>Diane Lejeune, Nicolas Delsaux, Benoît Charloteaux, Annick Thomas, Robert Brasseur (2005) <i>Proteins</i> <i></i> <i></i> 61: 2 258-271<br/>

http://publicationslist.org/a.thomas/refid26 2009-05-11T11:18:14Z

Pancreatic lipase is a soluble globular protein that must undergo structural modifications before it can hydrolyze oil droplets coated with bile salts. The binding of colipase and movement of the lipase lid open access to the active site. Mechanisms triggering lid mobility are unclear. The *KNILSQIVDIDGI* fragment of the lid of the human pancreatic lipase is predicted by molecular modeling to be a...<br/><br/>Annick Thomas, Maya Allouche, Frédéric Basyn, Robert Brasseur, Brigitte Kerfelec (2005) <i>J Biol Chem</i> <i></i> <i></i> 280: 48 40074-40083<br/>

http://publicationslist.org/a.thomas/refid30 2009-05-11T11:18:55Z

Using a semiempirical quantum mechanical procedure (FCPAC) we have calculated the partial atomic charges of amino acids from 494 high-resolution protein structures. To analyze the influence of the protein's environment, we considered each residue under two conditions: either as the center of a tripeptide with PDB structure geometry (free) or as the center of 13-16 amino acid clusters extracted fro...<br/><br/>Annick Thomas, Alain Milon, Robert Brasseur (2004) <i>Proteins</i> <i></i> <i></i> 56: 1 102-109<br/>

http://publicationslist.org/a.thomas/refid29 2009-05-11T11:18:55Z

Site-directed mutagenesis experiments combined with fluorescence microscopy shed light on the role of Escherichia coli FtsW, a membrane protein belonging to the SEDS family that is involved in peptidoglycan assembly during cell elongation, division, and sporulation. This essential cell division protein has 10 transmembrane segments (TMSs). It is a late recruit to the division site and is required ...<br/><br/>Soumya Pastoret, Claudine Fraipont, Tanneke den Blaauwen, Benoît Wolf, Mirjam E G Aarsman, André Piette, Annick Thomas, Robert Brasseur, Martine Nguyen-Distèche (2004) <i>J Bacteriol</i> <i></i> <i></i> 186: 24 8370-8379<br/>

http://publicationslist.org/a.thomas/refid32 2009-05-11T11:18:55Z

The lipid-destabilizing properties of the N-terminal domain of the GP2 of Ebola virus were investigated. Our results suggest that the domain of Ebola virus needed for fusion is shorter than that previously reported. The fusogenic properties of this domain are related to its oblique orientation at the lipid/water interface owing to an asymmetric distribution of the hydrophobic residues when helical...<br/><br/>B Adam, L Lins, V Stroobant, A Thomas, R Brasseur (2004) <i>J Virol</i> <i></i> <i></i> 78: 4 2131-2136<br/>

http://publicationslist.org/a.thomas/refid31 2009-05-11T11:18:55Z

In the present study, an extensive analysis of the aromatic Tyr-X interactions is performed on a data set of 593 PDB structures, X being Phe, His, Tyr, and Trp. The nonredundant Tyr-X pairs (2645) were retained and separated by both the residue distance in the sequence and the secondary structures they bridge. Similar to the Phe-X and His-X pairs, the far-sequence Tyr-X pairs (X partner > five apa...<br/><br/>Rita Meurisse, Robert Brasseur, Annick Thomas (2004) <i>Proteins</i> <i></i> <i></i> 54: 3 478-490<br/>

http://publicationslist.org/a.thomas/refid34 2009-05-11T11:18:55Z

We analyzed the total, hydrophobic, and hydrophilic accessible surfaces (ASAs) of residues from a nonredundant bank of 587 3D structure proteins. In an extended fold, residues are classified into three families with respect to their hydrophobicity balance. As expected, residues lose part of their solvent-accessible surface with folding but the three groups remain. The decrease of accessibility is ...<br/><br/>Laurence Lins, Annick Thomas, Robert Brasseur (2003) <i>Protein Sci</i> <i></i> <i></i> 12: 7 1406-1417<br/>

http://publicationslist.org/a.thomas/refid36 2009-05-11T11:18:55Z

Few structures of membrane proteins are known and their relationships with the membrane are unclear. In a previous report, 20 X-ray structures of transmembrane proteins were analyzed in silico for their orientation in a 36A-thick membrane [J. Mol. Graph. Model. 20 (2001) 235]. In this paper, we use the same approach to analyze how the insertion of the X-ray structures varies with the bilayer thick...<br/><br/>Frederic Basyn, Benoit Spies, Olivier Bouffioux, Annick Thomas, Robert Brasseur (2003) <i>J Mol Graph Model</i> <i></i> <i></i> 22: 1 11-21<br/>

http://publicationslist.org/a.thomas/refid37 2009-05-11T11:19:18Z

Amyloid peptide (Abeta) is a 40/42-residue proteolytic fragment of a precursor protein (APP), implicated in the pathogenesis of Alzheimer's disease. The hypothesis that interactions between Abeta aggregates and neuronal membranes play an important role in toxicity has gained some acceptance. Previously, we showed that the C-terminal domain (e.g. amino acids 29-42) of Abeta induces membrane permeab...<br/><br/>Marie-Paule Mingeot-Leclercq, Laurence Lins, Mariam Bensliman, Annick Thomas, Françoise Van Bambeke, Jacques Peuvot, André Schanck, Robert Brasseur (2003) <i>Biochim Biophys Acta</i> <i></i> <i></i> 1609: 1 28-38<br/>

http://publicationslist.org/a.thomas/refid33 2009-05-11T11:18:55Z

What determines the shape of the allowed regions in the Ramachandran plot? Although Ramachandran explained these regions in terms of 1-4 hard-sphere repulsions, there are discrepancies with the data where, in particular, the alphaR, alphaL, and beta-strand regions are diagonal. The alphaR-region also varies along the alpha-helix where it is constrained at the center and the amino terminus but diff...<br/><br/>Bosco K Ho, Annick Thomas, Robert Brasseur (2003) <i>Protein Sci</i> <i></i> <i></i> 12: 11 2508-2522<br/>

http://publicationslist.org/a.thomas/refid35 2009-05-11T11:18:55Z

Several studies have analysed aromatic interactions, involving mostly phenylalanine, tyrosine and tryptophan. Only a few studies have considered histidine as an interacting aromatic residue. An extensive analysis of aromatic His-X interactions is performed here on a data set of 593 PDB structures: 68% of the histidine are involved in aromatic pairs and 1271 non-redundant His-X pairs were analysed....<br/><br/>Rita Meurisse, Robert Brasseur, Annick Thomas (2003) <i>Biochim Biophys Acta</i> <i></i> <i></i> 1649: 1 85-96<br/>

http://publicationslist.org/a.thomas/refid40 2009-05-11T11:19:18Z

The lipid-interacting properties of the N-terminal domain of human apolipoprotein C-III (apo C-III) were investigated. By molecular modeling, we predicted that the 6-20 fragment of apo C-III is obliquely orientated at the lipid/water interface owing to an asymmetric distribution of the hydrophobic residues when helical. This is characteristic of 'tilted peptides' originally discovered in viral fus...<br/><br/>L Lins, C Flore, L Chapelle, P J Talmud, A Thomas, R Brasseur (2002) <i>Protein Eng</i> <i></i> <i></i> 15: 6 513-520<br/>

http://publicationslist.org/a.thomas/refid39 2009-05-11T11:19:18Z

In a data set of 593 nonhomologous proteins from the PDB, we have analyzed the pairing of phenylalanine, tyrosine, tryptophan, and histidine residues with their closest aromatic partner. The frequency distribution of the shortest interatomic distance of partners is bimodal with a sharp peak at approximately 3.8 A and a wider one at a longer distance. Only the 3.8 A peak corresponds to direct ring-...<br/><br/>Annick Thomas, Rita Meurisse, Benoit Charloteaux, Robert Brasseur (2002) <i>Proteins</i> <i></i> <i></i> 48: 4 628-634<br/>

http://publicationslist.org/a.thomas/refid38 2009-05-11T11:19:18Z

We have collected all aromatic pairs (3152) involving an N-phenyl partner in a dataset of 593 proteins of the PDB: 728 of these pairs involve a partner residue less than 6 apart in the sequence. These near-sequence Phe-X pairs correspond to specific conformations that stabilize secondary structures, mainly alpha-helices when the residues are 1, 3, and 4 apart, and beta-strands when they are 2 apar...<br/><br/>Annick Thomas, Rita Meurisse, Robert Brasseur (2002) <i>Proteins</i> <i></i> <i></i> 48: 4 635-644<br/>

http://publicationslist.org/a.thomas/refid45 2009-05-11T11:19:18Z

Pex are created to extract numeric and string descriptions of protein structures from PDB files. This concerns covalent bond lengths and angles, secondary structures, residues in interaction, H-bond lengths and geometry, etc. Several kinds of Pex are generated: (1) general feature (GF-Pex); (2) H-bond (H-Pex); and (3) accessible surface (AS-Pex) and force potential (FP-Pex). We describe the genera...<br/><br/>A Thomas, O Bouffioux, D Geeurickx, R Brasseur (2001) <i>Proteins</i> <i></i> <i></i> 43: 1 28-36<br/>

http://publicationslist.org/a.thomas/refid46 2009-05-11T11:19:18Z

The human VPAC(1) receptor for vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase activating peptide belongs to the class II family of G-protein-coupled receptors with seven transmembrane segments. Like for all class II receptors, the extracellular N-terminal domain of the human VPAC(1) receptor plays a predominant role in peptide ligand recognition. To determine the three-dimensi...<br/><br/>L Lins, A Couvineau, C Rouyer-Fessard, P Nicole, J J Maoret, M Benhamed, R Brasseur, A Thomas, M Laburthe (2001) <i>J Biol Chem</i> <i></i> <i></i> 276: 13 10153-10160<br/>

http://publicationslist.org/a.thomas/refid44 2009-05-11T11:19:18Z

We use the H-Pex (Thomas et al., this issue) to analyze the main chain interactions in 131 proteins. In antiparallel beta-sheets, the geometry of the N...O bond is: median N...O distances, 2.9 SA, C==O...N angles at 154 degrees and the C alpha--C==O...H angles are dispersed around 3 degrees. In some instances, the other side of the C==O axis is occupied by a HC alpha. As recently supported by Varg...<br/><br/>A Thomas, N Benhabiles, R Meurisse, R Ngwabije, R Brasseur (2001) <i>Proteins</i> <i></i> <i></i> 43: 1 37-44<br/>

http://publicationslist.org/a.thomas/refid2 2009-05-11T11:19:50Z

We screened a cDNA bank of rabbit gastric fundic mucosa by two-hybrid assays looking for binding partners of the N-terminal domain of the rabbit gastric H,K-ATPase. We extracted five clones sharing more than 90% sequence identity. The longest clone codes for a protein sharing a high identity (96 and 96.8%, respectively) with a fragment of the membrane domain, from Arg-835 to Ser-873, plus the majo...<br/><br/>F Festy, J C Robert, R Brasseur, A Thomas (2001) <i>J Biol Chem</i> <i></i> <i></i> 276: 11 7721-7726<br/>

http://publicationslist.org/a.thomas/refid43 2009-05-11T11:19:18Z

In a previous study, Hughes et al. [Proc. Natl. Acad. Sci. USA 93 (1996) 2065-2070] demonstrated that the amyloid peptide is able to interact with itself in a two-hybrid system and that interaction is specific. They further supported that the method could be used to define the sequences that might be important in nucleation-dependent aggregation. The sequence of the amyloid peptide can be split in...<br/><br/>F Festy, L Lins, G Péranzi, J N Octave, R Brasseur, A Thomas (2001) <i>Biochim Biophys Acta</i> <i></i> <i></i> 1546: 2 356-364<br/>

http://publicationslist.org/a.thomas/refid41 2009-05-11T11:19:18Z

Over the past few years, several three-dimensional (3-D) structures of membrane proteins have been described with increasing accuracy, but their relationship with membranes are still not well understood. Recently, we have developed an empirical method, Integral Membrane Protein and Lipid Association (IMPALA), to predict the insertion of molecules (lipids, drugs) into lipid bilayers (Proteins 30 (1...<br/><br/>F Basyn, B Charloteaux, A Thomas, R Brasseur (2001) <i>J Mol Graph Model</i> <i></i> <i></i> 20: 3 235-244<br/>

http://publicationslist.org/a.thomas/refid42 2009-05-11T11:19:18Z

Tilted peptides are short sequence fragments (10-20 residues long) that possess an asymmetric hydrophobicity gradient along their sequence when they are helical. Due to this gradient, they adopt a tilted orientation towards a single lipid/water interface and destabilize the lipids. We have detected those peptides in many different proteins with various functions. While being all tilted-oriented at...<br/><br/>L Lins, B Charloteaux, A Thomas, R Brasseur (2001) <i>Proteins</i> <i></i> <i></i> 44: 4 435-447<br/>

http://publicationslist.org/a.thomas/refid4 2009-05-11T11:19:50Z

The widespread neuropeptide vasoactive intestinal peptide (VIP) has two receptors VPAC(1) and VPAC(2). Solid-phase syntheses of VIP analogs in which each amino acid has been changed to alanine (Ala scan) or glycine was achieved and each analog was tested for: (i) three-dimensional structure by ab initio molecular modeling; (ii) ability to inhibit (125)I-VIP binding (K(i)) and to stimulate adenylyl...<br/><br/>P Nicole, L Lins, C Rouyer-Fessard, C Drouot, P Fulcrand, A Thomas, A Couvineau, J Martinez, R Brasseur, M Laburthe (2000) <i>J Biol Chem</i> <i></i> <i></i> 275: 31 24003-24012<br/>

http://publicationslist.org/a.thomas/refid6 2009-05-11T11:15:46Z

Inner ear fluids and cerebrospinal fluid show remarkably stable ionic concentrations, particularly that of K(+) and H(+), but the mechanisms which control the homeostasis of these media are not well understood. We investigated a possible role of the gastric H, K-ATPase (gH,K-ATPase) pump in this control since this pump is known to be expressed in other tissues than gastric parietal cells. Here, we...<br/><br/>E Lecain, J C Robert, A Thomas, P Tran Ba Huy (2000) <i>Hear Res</i> 149: 1-2 147-154<br/>

http://publicationslist.org/a.thomas/refid3 2009-05-11T11:19:50Z

A simple method for predicting residues involved in protein interaction sites is proposed. In the absence of any structural report, the procedure identifies linear stretches of sequences as "receptor-binding domains" (RBDs) by analysing hydrophobicity distribution. The sequences of two databases of non-homologous interaction sites eliciting various biological activities were tested; 59-80 % were d...<br/><br/>X Gallet, B Charloteaux, A Thomas, R Brasseur (2000) <i>J Mol Biol</i> <i></i> <i></i> 302: 4 917-926<br/>

http://publicationslist.org/a.thomas/refid1 2009-05-11T11:19:50Z

A continuous membrane model (IMPALA) was previously developed to predict how hydrophobic spans of proteins insert in membranes (Mol. Mod. 2 (1996) 27). Using that membrane model, we looked for the interactions between several hydrophobic spans. We used the glycophorin A dimer as an archetype of polytopic protein to validate the approach. We find that the native complex do not dislocate when it is ...<br/><br/>P Ducarme, A Thomas, R Brasseur (2000) <i>Biochim Biophys Acta</i> <i></i> <i></i> 1509: 1-2 148-154<br/>

http://publicationslist.org/a.thomas/refid5 2009-05-11T11:19:50Z

The structural gene of the H-NS protein, a global regulator of bacterial metabolism, has been identified in the group of enterobacteria as well as in closely related bacteria, such as Erwinia chrysanthemi and Haemophilus influenzae. Isolated outside these groups, the BpH3 protein of Bordetella pertussis exhibits a low amino acid conservation with H-NS, particularly in the N-terminal domain. To obt...<br/><br/>P Bertin, N Benhabiles, E Krin, C Laurent-Winter, C Tendeng, E Turlin, A Thomas, A Danchin, R Brasseur (1999) <i>Mol Microbiol</i> <i></i> <i></i> 31: 1 319-329<br/>

http://publicationslist.org/a.thomas/refid57 2009-05-11T11:23:29Z

1. Cimetidine was more potent 4 hr after a single injection of 25 or 100 mg/kg body wt in increasing gastric pH than other H2 receptor antagonists, ranitidine and famotidine but was less efficient than H+/K(+)-ATPase inhibitors. Omeprazole rose proventricular and gizzard pH at a lower dose than SCH 28080 and Ro 18-5364 (30, 50 and 200 mg/kg body wt, respectively). 2. Proventricular and gizzard pH ...<br/><br/>F Guinotte, J Gautron, A Soumarmon, J C Robert, G Peranzi, Y Nys (1993) <i>Comp Biochem Physiol Comp Physiol</i> <i></i> <i></i> 106: 2 319-327<br/>

http://publicationslist.org/a.thomas/refid47 2009-05-11T11:22:10Z

Several antibodies against the gastric H+/K(+)-ATPase were analysed for the topological and sequence location of their epitopes. Topological mapping was done by comparing indirect immunofluorescent staining in intact and permeabilised rat parietal cells. Epitope definition was by Western analysis of intact and of trypsin or V8-proteinase-fragmented hog gastric ATPase combined with N-terminal seque...<br/><br/>F Mercier, D Bayle, M Besancon, T Joys, J M Shin, M J Lewin, C Prinz, M A Reuben, A Soumarmon, H Wong (1993) <i>Biochim Biophys Acta</i> <i></i> <i></i> 1149: 1 151-165<br/>

http://publicationslist.org/a.thomas/refid58 2009-05-11T11:23:29Z

1. The tubulovesicles of hog and rabbit gastric parietal cells were immunopurified from microsomes using monoclonal antibodies against the (H+, K+)-ATPase. 2. The best yields of immunoprecipitation were obtained with an ATPase/mAb molar ratio of 0.3: the immunoprecipitate contained 79 and 90% of the hog and rabbit microsomal PNPPase activity respectively and K(+)-stimulated ATPase specific activit...<br/><br/>D Bayle, F Benkouka, J C Robert, G Peranzi, A Soumarmon (1992) <i>Comp Biochem Physiol B</i> <i></i> <i></i> 101: 4 519-525<br/>

http://publicationslist.org/a.thomas/refid48 2009-05-11T11:22:10Z

The monoclonal antibody (mAb) 95-111 binds the alpha subunit of (H+,K+)-ATPase and inhibits the K(+)-ATPase activity. To map the epitope, all of the partial sequences of the alpha subunit were expressed in Escherichia coli HB101 using rabbit alpha subunit cDNA restriction fragments ligated into PuEx vector. Bacterial recombinant lysates were separated by sodium dodecyl sulfate-gel electrophoresis,...<br/><br/>D Bayle, J C Robert, K Bamberg, F Benkouka, A M Cheret, M J Lewin, G Sachs, A Soumarmon (1992) <i>J Biol Chem</i> <i></i> <i></i> 267: 27 19060-19065<br/>

http://publicationslist.org/a.thomas/refid49 2009-05-11T11:22:10Z

The fundic mucosa of resting and acid-secreting rabbit stomachs were freeze-fractured and replicated to compare the intramembranous particles on the parietal cell tubulovesicles (rest) and canaliculus (secretion). The particles were counted and their shadow diameters were measured using an image analysis program. The tubulovesicles bore 9,726 +/- 400 particles per microns2 (mean +/- SD), having a ...<br/><br/>G Péranzi, D Bayle, M J Lewin, A Soumarmon (1991) <i>Biol Cell</i> <i></i> <i></i> 73: 2-3 163-171<br/>

http://publicationslist.org/a.thomas/refid59 2009-05-11T11:23:29Z

A monoclonal antibody (mAb 95-111) was used to titrate the amounts of H+/K(+)-ATPase in subcellular fractions of the fundus of rats, pigs, rabbits and humans. All four had similar amounts of H+/K(+)-ATPase: 2.1 +/- 0.5 (human), 1.9 +/- 0.4 (rabbit), 4.4 +/- 0.5 (rat) and 4.2 +/- 0.8 (hog) mg ATPase/g wet tissue. The antigen concentrations and H+/K(+)-ATPase enzymatic activities of subcellular frac...<br/><br/>J C Robert, F Benkouka, D Bayle, F Hervatin, A Soumarmon (1990) <i>Biochim Biophys Acta</i> <i></i> <i></i> 1024: 1 167-172<br/>

http://publicationslist.org/a.thomas/refid60 2009-05-11T11:23:29Z

The ontogeny of rat H+/K+-ATPase was studied between foetal day 18 and neonatal day 18, using a specific monoclonal antibody (95-111 mAb). The H+/K+-ATPase content of gastric subcellular membranes was assayed and the ATPase subunits were characterized by Western blot. The epithelium density in parietal cells was measured by immunohistochemistry. H+/K+-ATPase was present in the 18-day-old foetuses ...<br/><br/>F Hervatin, F Benkouka, J C Robert, G Péranzi, A Soumarmon (1989) <i>Biochim Biophys Acta</i> <i></i> <i></i> 985: 3 320-324<br/>

http://publicationslist.org/a.thomas/refid50 2009-05-11T11:22:10Z

A mouse monoclonal antibody was raised against hog gastric membranes. This antibody (95-111 mAb) has a very high affinity for the 95 kDalton band of H+/K(+)-ATPase-enriched membranes, and does not react with Na+/K(+)-ATPase. The epitope is located on the tubulovesicles and canaliculi of the parietal cells. The 95-111 mAb also inhibits the ATP hydrolytic activity, decreases the steady-state phospho...<br/><br/>F Benkouka, G Péranzi, J C Robert, M J Lewin, A Soumarmon (1989) <i>Biochim Biophys Acta</i> <i></i> <i></i> 987: 2 205-211<br/>

http://publicationslist.org/a.thomas/refid51 2009-05-11T11:22:10Z

Gastric acid secretion results from the activity of a specific ATPase, the (H+,K+)-ATPase. This enzyme, discovered in 1973, exchanges H+ for K+. It has two ATP binding sites, both involved in enzyme activity, whose affinities vary as a function of the H+ and K+ concentrations. Hydrolysis of ATP at the highest affinity site leads to the synthesis of a covalent aspartyl phosphate which accumulates i...<br/><br/>A Soumarmon, M J Lewin (1986) <i>Biochimie</i> <i></i> <i></i> 68: 12 1287-1291<br/>

http://publicationslist.org/a.thomas/refid53 2009-05-11T11:22:10Z

Gastric (H+ + K+)-ATPase was reconstituted into artificial phosphatidylcholine/cholesterol liposomes by means of a freeze-thaw-sonication technique. Upon addition of MgATP, active H+ transport was observed, with a maximal rate of 2.1 mumol X mg-1 X min-1, requiring the presence of 100 mM K+ at the intravesicular site. However, in the absence of ATP an H+-K+ exchange with a maximal rate of 0.12 mum...<br/><br/>A T Skrabanja, P Asty, A Soumarmon, J Joep, H H de Pont, M J Lewin (1986) <i>Biochim Biophys Acta</i> <i></i> <i></i> 860: 1 131-136<br/>

http://publicationslist.org/a.thomas/refid54 2009-05-11T11:22:10Z

We have previously shown that an active (H+ + K+)-ATPase can be extracted from gastric apical membranes using n-octylglucoside (Soumarmon, A., Grelac, F. and Lewin, M.J.M. (1983) Biochim. Biophys. Acta 732, 579-585). This extract contained an holomeric enzyme of 390-420 kDa and contained 68% of the K+-stimulated ATPase specific activity originally present. We demonstrate here that inactivation, in...<br/><br/>A Soumarmon, J C Robert, M J Lewin (1986) <i>Biochim Biophys Acta</i> <i></i> <i></i> 860: 1 109-117<br/>

http://publicationslist.org/a.thomas/refid52 2009-05-11T11:22:10Z

(H+ + K+)-ATPase-enriched membranes from hog stomachs were tested for their capacity to autophosphorylate using [gamma-32P]ATP or [gamma-35S]ATP[S] as phosphate donors. The radioactive polypeptides were characterized by SDS-PAGE. In the presence of Mg2+ and 5 microM [gamma-32P]ATP, rapid and transient incorporation of 32P occurred at 0 degrees C. Radioactivity was essentially found in the major po...<br/><br/>A Soumarmon, F Pierrang, J C Robert, F Benkouka, M J Lewin (1986) <i>Biochim Biophys Acta</i> <i></i> <i></i> 863: 1 82-90<br/>

http://publicationslist.org/a.thomas/refid55 2009-05-11T11:22:10Z

Proteoliposomes containing the hog gastric H+,K+-ATPase were prepared from cholate and n-octyl glucoside extracts of native microsomes. Experiments were presented which show reconstitution-dependent selective purification of a 94-kDa peptide capable of Rb+/Rb+ exchange and active H+ transport. The absence of selective enrichment of residual protein contamination in this material suggests but does ...<br/><br/>E Rabon, R D Gunther, A Soumarmon, S Bassilian, M Lewin, G Sachs (1985) <i>J Biol Chem</i> <i></i> <i></i> 260: 18 10200-10207<br/>

http://publicationslist.org/a.thomas/refid56 2009-05-11T11:22:10Z

NADH-cytochrome b5 reductase from hog gastric microsomes was studied with respect to substrate dependence, optimum pH, thermal denaturation as well as anti-cytochrome b5 antibodies and different ions. The reduction of potassium ferricyanide by the enzyme was specific for NADH. Using potassium ferricyanide or trypsin-solubilized liver cytochrome b5 (Tb5) as substrates, enzyme activity was inhibited...<br/><br/>D Ghesquier, J C Robert, A Soumarmon, M Abastado, F Grelac, M J Lewin (1985) <i>Comp Biochem Physiol B</i> <i></i> <i></i> 80: 1 165-169<br/>