References of "Brasseur, Robert"
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See detailIn silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues.
Beaufays, Jérôme ULg; Lins, Laurence ULg; Thomas, Annick ULg et al

in Journal of Peptide Science : An Official Publication of the European Peptide Society (2012), 18(1), 17-24

We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio ... [more ▼]

We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio calculation procedure, to the calculation of peptides with non-proteinogenic amino acids. Indeed, such peptides cannot be predicted by homology or threading. We compare the calculated models with NMR and X-ray models and for the cyclic peptides, with models predicted by other in silico procedures (Pep-Fold and I-Tasser). For cyclic peptides, on a set of 38 peptides, average root mean square deviation of backbone atoms (BB-RMSD) was 3.8 and 4.1 A for Peplook and Pep-Fold, respectively. The best results are obtained with I-Tasser (2.5 A) although evaluations were biased by the fact that the resolved Protein Data Bank models could be used as template by the server. Peplook and Pep-Fold give similar results, better for short (up to 20 residues) than for longer peptides. For peptides with non-proteinogenic residues, performances of Peplook are sound with an average BB-RMSD of 3.6 A for 'non-natural peptides' and 3.4 A for peptides combining non-proteinogenic residues and cyclic structure. These results open interesting possibilities for the design of peptidic drugs. Copyright (c) 2011 European Peptide Society and John Wiley & Sons, Ltd. [less ▲]

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See detailModeling of non-covalent complexes of the cell-penetrating peptide CADY and its siRNA cargo.
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Deshayes, Sebastien et al

in Biochimica et Biophysica Acta (2012)

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with siRNAs in water. Neither the structure of CADY nor that of the complexes is resolved. We have calculated and analyzed 3D ... [more ▼]

CADY is a cell-penetrating peptide spontaneously making non-covalent complexes with siRNAs in water. Neither the structure of CADY nor that of the complexes is resolved. We have calculated and analyzed 3D models of CADY and of the non-covalent CADY-siRNA complexes in order to understand their formation and stabilization. Data from the ab initio calculations and molecular dynamics support that, in agreement with the experimental data, CADY is a polymorphic peptide partly helical. Taking into consideration the polymorphism of CADY, we calculated and compared several complexes with peptide/siRNA ratios of up to 40. Four complexes were run by using molecular dynamics. The initial binding of CADYs is essentially due to the electrostatic interactions of the arginines with siRNA phosphates. Due to a repetitive arginine motif (XLWR(K)) in CADY and to the numerous phosphate moieties in the siRNA, CADYs can adopt multiple positions at the siRNA surface leading to numerous possibilities of complexes. Nevertheless, several complex properties are common: an average of 14+/-1 CADYs is required to saturate a siRNA as compared to the 12+/-2 CADYs experimentally described. The 40 CADYs/siRNA that is the optimal ratio for vector stability always corresponds to two layers of CADYs per siRNA. When siRNA is covered by the first layer of CADYs, the peptides still bind despite the electrostatic repulsion. The peptide cage is stabilized by hydrophobic CADY-CADY contacts thanks to CADY polymorphism. The analysis demonstrates that the hydrophobicity, the presence of several positive charges and the disorder of CADY are mandatory to make stable the CADY-siRNA complexes. [less ▲]

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See detailMonolayer Properties of Uronic Acid Bicatenary Derivatives at the Air-Water Interface: Effect of Hydroxyl Group Stereochemistry Evidenced by Experimental and Computational Approaches
Razafindralambo, Hary ULg; Richel, Aurore ULg; Wathelet, Bernard ULg et al

in Physical Chemistry Chemical Physics [=PCCP] (2011), 13(33), 1529115298

By screening uronic acid-based surfactant interfacial properties, the effect of the hydroxyl group stereochemistry (OH-4) on the conformation of bicatenary (disubstituted) derivatives at the air–water ... [more ▼]

By screening uronic acid-based surfactant interfacial properties, the effect of the hydroxyl group stereochemistry (OH-4) on the conformation of bicatenary (disubstituted) derivatives at the air–water interface has been evidenced by experimental and computational approaches. Physical and optical properties of a monolayer characterized by Langmuirfilmbalance, Brewster angle microscopy, and ellipsometry at 20°C reveal that the derivative of glucuronate (C14/14–GlcA) forms a more expanded monolayer, and shows a transition state under compression, in the opposite to that of galacturonate (C14/14–GalA). Both films are very mechanically resistant (compression modulus > 300m Nm-1) and stable (collapse pressure exceeding 60mNm-1), while that of C14/14–GalA exhibits a very high compression modulus up to 600mNm-1 like films in the solid state. Computational approaches provide single and assembly molecular models that corroborate the molecule expansion degree and interactions data from experimental results. Differences in the molecular conformation and film behaviours of uronic acid bicatenary derivatives at the air–water interface are attributed to the intra-H-bonding formation, which is more favourable with an OH-4 in the axial (C14/14–GalA) than in the equatorial position (C14/14–GlcA). [less ▲]

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See detailA new in-silico method for determination of helical transmembrane domains based on the PepLook scan: application to IL-2Rbeta and IL-2Rgammac receptor chains.
Charlois, Yan; Lins, Laurence ULg; Brasseur, Robert ULg

in BMC Structural Biology (2011), 11

BACKGROUND: Modeling of transmembrane domains (TMDs) requires correct prediction of interfacial residues for in-silico modeling and membrane insertion studies. This implies the defining of a target ... [more ▼]

BACKGROUND: Modeling of transmembrane domains (TMDs) requires correct prediction of interfacial residues for in-silico modeling and membrane insertion studies. This implies the defining of a target sequence long enough to contain interfacial residues. However, too long sequences induce artifactual polymorphism: within tested modeling methods, the longer the target sequence, the more variable the secondary structure, as though the procedure were stopped before the end of the calculation (which may in fact be unreachable). Moreover, delimitation of these TMDs can produce variable results with sequence based two-dimensional prediction methods, especially for sequences showing polymorphism. To solve this problem, we developed a new modeling procedure using the PepLook method. We scanned the sequences by modeling peptides from the target sequence with a window of 19 residues. RESULTS: Using sequences whose NMR-structures are already known (GpA, EphA1 and Erb2-HER2), we first determined that the hydrophobic to hydrophilic accessible surface area ratio (ASAr) was the best criterion for delimiting the TMD sequence. The length of the helical structure and the Impala method further supported the determination of the TMD limits. This method was applied to the IL-2Rbeta and IL-2Rgamma TMD sequences of Homo sapiens, Rattus norvegicus, Mus musculus and Bos taurus. CONCLUSIONS: We succeeded in reducing the variation in the TMD limits to only 2 residues and in gaining structural information. [less ▲]

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See detailThe Pseudomonas aeruginosa membranes: A target for a new amphiphilic aminoglycoside derivative?
Ouberai, M.; El Garch, F.; Bussiere, A. et al

in Biochimica et biophysica acta (2011)

Aminoglycosides are among the most potent antimicrobials to eradicate Pseudomonas aeruginosa. However, the emergence of resistance has clearly led to a shortage of treatment options, especially for ... [more ▼]

Aminoglycosides are among the most potent antimicrobials to eradicate Pseudomonas aeruginosa. However, the emergence of resistance has clearly led to a shortage of treatment options, especially for critically ill patients. In the search for new antibiotics, we have synthesized derivatives of the small aminoglycoside, neamine. The amphiphilic aminoglycoside 3',4',6-tri-2-naphtylmethylene neamine (3',4',6-tri-2NM neamine) has appeared to be active against sensitive and resistant P. aeruginosa strains as well as Staphylococcus aureus strains (Baussanne et al., 2010). To understand the molecular mechanism involved, we determined the ability of 3',4',6-tri-2NM neamine to alter the protein synthesis and to interact with the bacterial membranes of P. aeruginosa or models mimicking these membranes. Using atomic force microscopy, we observed a decrease of P. aeruginosa cell thickness. In models of bacterial lipid membranes, we showed a lipid membrane permeabilization in agreement with the deep insertion of 3',4',6-tri-2NM neamine within lipid bilayer as predicted by modeling. This new amphiphilic aminoglycoside bound to lipopolysaccharides and induced P. aeruginosa membrane depolarization. All these effects were compared to those obtained with neamine, the disubstituted neamine derivative (3',6-di-2NM neamine), conventional aminoglycosides (neomycin B and gentamicin) as well as to compounds acting on lipid bilayers like colistin and chlorhexidine. All together, the data showed that naphthylmethyl neamine derivatives target the membrane of P. aeruginosa. This should offer promising prospects in the search for new antibacterials against drug- or biocide-resistant strains. [less ▲]

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See detailStudy of the specific lipid binding properties of Abêta 11-22 fragment at endosomal pH
Ravault, Stéphanie; Milon, Alain; Brasseur, Robert ULg et al

Conference (2010, February)

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See detailStandardized evaluation of protein stability.
Thomas, Annick ULg; Joris, Bernard ULg; Brasseur, Robert ULg

in Biochimica et Biophysica Acta (2010)

We compare Mean Force Potential values of a large series of PDB models of proteins and peptides and find that either as monomers or polymers, proteins longer than 200-250 residues have equivalent MFP ... [more ▼]

We compare Mean Force Potential values of a large series of PDB models of proteins and peptides and find that either as monomers or polymers, proteins longer than 200-250 residues have equivalent MFP values that are averaged to -65+/-3kcal/aa. This value is named the standard or stability value. The standard value is reached irrespective of sequences and 3D folds. Peptides are too short to follow the rule and frequently exist as populations of conformers; one exception are peptides in amyloid fibrils. Fibrils surpass the standard value in accordance with their uppermost stability. In parallel, we calculate median MFP values of amino acids in stably folded PDB models of proteins: median values vary from -25 for Gly to -115kcal/aa for Trp. These median values are used to score primary sequences of proteins: all sequences converge to a mean value of -63.5+/-2.5kcal/aa i.e. only 1.5kcal less than the folded model standard. Sequences from unfolded proteins have lower values. This supports the conclusion that sequences carry in an important message and more specifically that diversity of amino acids in sequences is mandatory for stability. We also use the median amino acid MFP to score residue stability in 3D folds. This demonstrates that 3D folds are compromises between fragments of high and fragments of low scores and that functional residues are often, but not always in the extreme score values. The approach opens to possibilities of evaluating any 3D model, of detecting functional residues and should help in conducting mutation assays. [less ▲]

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See detailRealistic modeling approaches of structure-function properties of CPPs in non-covalent complexes.
Thomas, Annick ULg; Lins, Laurence ULg; Divita, G. et al

in Biochimica et Biophysica Acta (2010)

Transfers of cargoes into cells by means of carrier peptides are multi-steps biological phenomenon the mechanisms of which are unclear. We here discuss bases of realistic in silico molecular modeling ... [more ▼]

Transfers of cargoes into cells by means of carrier peptides are multi-steps biological phenomenon the mechanisms of which are unclear. We here discuss bases of realistic in silico molecular modeling approaches of the formation of non-covalent complexes considering CPPs and cargo diversities. [less ▲]

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See detailAcylated and unacylatedghrelin binding to membranes and to ghrelin receptor: Towards a better understanding of the underlying mechanisms
Staes, Edith; Absil, Pierre-Antoine; Lins, Laurence ULg et al

in Biochimica et Biophysica Acta - Biomembranes (2010), 1798

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See detailCholesterol interaction with proteins that partition into membrane domains: an overview.
Epand, Richard M; Thomas, Annick ULg; Brasseur, Robert ULg et al

in Sub Cellular Biochemistry (2010), 51

Biological membranes are complex structures composed largely of proteins and lipids. These components have very different structural and physical properties and consequently they do not form a single ... [more ▼]

Biological membranes are complex structures composed largely of proteins and lipids. These components have very different structural and physical properties and consequently they do not form a single homogeneous mixture. Rather components of the mixture are more enriched in some regions than in others. This can be demonstrated with simple lipid mixtures that spontaneously segregate components so as to form different lipid phases that are immiscible with one another. The segregation of molecular components of biological membranes also involves proteins. One driving force that would promote the segregation of membrane components is the preferential interaction between a protein and certain lipid components. Among the varied lipid components of mammalian membranes, the structure and physical properties of cholesterol is quite different from that of other major membrane lipids. It would therefore be expected that in many cases proteins would have very different energies of interaction with cholesterol vs. those of other membrane lipids. This would be sufficient to cause segregation of components in membranes. The factors that facilitate the interaction of proteins with cholesterol are varied and are not yet completely understood. However, there are certain groups that are present in some proteins that facilitate interaction of the protein with cholesterol. These groups include saturated acyl chains of lipidated proteins, as well as certain amino acid sequences. Although there is some understanding as to why these particular groups favour interaction with cholesterol, our knowledge of these molecular features is not sufficiently developed to allow for the design of agents that will modify such binding. [less ▲]

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See detailInsight into the cellular uptake mechanism of a secondary amphipathic cell penetrating peptide for siRNA delivery.
Konate, K.; Crombez, L.; Deshayes, S. et al

in Biochemistry (2010)

Delivery of siRNA remains a major limitation to their clinical application and several technologies have been proposed to improve their cellular uptake. We recently described a peptide-based nanoparticle ... [more ▼]

Delivery of siRNA remains a major limitation to their clinical application and several technologies have been proposed to improve their cellular uptake. We recently described a peptide-based nanoparticle system for efficient delivery of siRNA into primary cell lines: CADY. CADY is a secondary amphipathic peptide that forms stable complexes with siRNA and improves their cellular uptake independently of the endosomal pathway. In the present work, we have combined molecular modelling, spectroscopy and membrane interaction approaches, in order to gain further insight into CADY/siRNA particle mechanism of interaction with biological membrane. We demonstrate that CADY forms stable complexes with siRNA and binds phospholipids tightly, mainly through electrostatic interactions. Binding to siRNA or phospholipids triggers a conformational transition of CADY from an unfolded state to an -helical structure, thereby stabilizing CADY/siRNA complexes and improving their interactions with cell membranes. Therefore, we propose that CADY cellular membrane interaction is driven by its structural polymorphism which enables stabilization of both electrostatic and hydrophobic contacts with surface membrane proteoglycan and phospholipids. [less ▲]

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See detailStructural features conferring dual Geranyl/Farnesyl diphosphate synthase activity to an aphid prenyltransferase
Vandermoten, Sophie ULg; Santini, Sébastien; Haubruge, Eric ULg et al

in Insect Biochemistry and Molecular Biology (2009), 39(10), 707-716

In addition to providing lipid chains for protein prenylation, short-chain isoprenyl diphosphate synthases (scIPPSs) play a pivotal role in the biosynthesis of numerous mevalonate pathway end-products ... [more ▼]

In addition to providing lipid chains for protein prenylation, short-chain isoprenyl diphosphate synthases (scIPPSs) play a pivotal role in the biosynthesis of numerous mevalonate pathway end-products, including insect juvenile hormone and terpenoid pheromones. For this reason, they are being considered as targets for pesticide development. Recently, we characterized an aphid scIPPS displaying dual geranyl diphosphate (GPP; C10)/farnesyl diphosphate (FPP; C15) synthase activity in vitro. To identify the mechanism(s) responsible for this dual activity, we assessed the product selectivity of aphid scIPPSs bearing mutations at Gln107 and/or Leu110, the fourth and first residue upstream from the “first aspartate-rich motif” (FARM), respectively. All but one resulted in significant changes in product chain-length selectivity, effectively increasing the production of either GPP (Q107E, L110W) or FPP (Q107F, Q107F–L110A); the other mutation (L110A) abolished activity. Although some of these effects could be attributed to changes in steric hindrance within the catalytic cavity, molecular dynamics simulations identified other contributing factors, including residue-ligand Van der Waals interactions and the formation of hydrogen bonds or salt bridges between Gln107 and other residues across the catalytic cavity, which constitutes a novel product chain-length determination mechanism for scIPPSs. Thus the aphid enzyme apparently evolved to maintain the capacity to produce both GPP and FPP through a balance between these mechanisms. [less ▲]

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See detailPepLook Scale-Up Prediction of protein structures
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Brasseur, Robert ULg

Poster (2009, August 27)

Besides experimental approaches for peptide structures determination which results often differ with assay conditions, there is, to our knowledge, only three in silico methods available for the prediction ... [more ▼]

Besides experimental approaches for peptide structures determination which results often differ with assay conditions, there is, to our knowledge, only three in silico methods available for the prediction of peptide structures: Pepstruct, Rosetta and PepLook. The latter was developed by the CBMN (1, 2) based on the fact that any protein PDB model can be re-constructed in silico using a restricted subset of φψ couples of angles (3). As PepLook was able to predict conformation of peptides and protein fragments, like cell penetrating peptides (CPPs) (1) and the hydrophobic segment of DGKє (4) with good accuracy, we are testing whether PepLook could be used for the prediction of complete protein structures. To reach this goal, PepLook is used to predict the conformation of peptidic fragments along the protein sequences. The sequence is scanned with different sizes of windows shifted along the sequence from the first to the last residue. For each sequence window, the 99 PepLook models of structure are analysed and compared to the PDB model. PepLook scans are running for five proteins, α-synuclein (1XQ8), a Zinc endoprotease (1C7K), Ubiquitin (1UBQ), Cytochrome b562 (256B) and Lysozyme (3LZT, 1AM7), using different window lengths (7, 9, 11, 15, 17, 21, 23 and 27 residues) by sliding steps of 1 residue. Since this approach requires huge calculation time, we present here the preliminary results. [less ▲]

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See detailStudy of thermomyces ianuginosa lipase in the presence of tributyrylglycerol and water
Santini, Sébastien; Crowet, Jean-Marc ULg; Thomas, Annick ULg et al

in Biophysical Journal (2009), 96(12), 4814-4825

The Thermomyces lanuginosa lipase has been extensively studied in industrial and biotechnological research because of its potential for triacylglycerol transformation. This protein is known to catalyze ... [more ▼]

The Thermomyces lanuginosa lipase has been extensively studied in industrial and biotechnological research because of its potential for triacylglycerol transformation. This protein is known to catalyze both hydrolysis at high water contents and transesterification in quasi-anhydrous conditions. Here, we investigated the Thermomyces lanuginosa lipase structure in solution in the presence of a tributyrin aggregate using 30 ns molecular-dynamics simulations. The water content of the active-site groove was modified between the runs to focus on the protein-water molecule interactions and their implications for protein structure and protein-lipid interactions. The simulations confirmed the high plasticity of the lid fragment and showed that lipid molecules also bind to a secondary pocket beside the lid. Together, these results strongly suggest that the lid plays a role in the anchoring of the protein to the aggregate. The simulations also revealed the existence of a polar channel that connects the active-site groove to the outside solvent. At the inner extremity of this channel, a tyrosine makes hydrogen bonds with residues interacting with the catalytic triad. This system could function as a pipe (polar channel) controlled by a valve (the tyrosine) that could regulate the water content of the active site. [less ▲]

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See detailDetection and characterization of tilted peptides in amyloid proteins
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Brasseur, Robert ULg

Poster (2009, April 25)

The study of amyloidogenic proteins is of interest in biochemistry because these proteins undergo conformational changes and aggregation. Both processes are largely implicated in several diseases ... [more ▼]

The study of amyloidogenic proteins is of interest in biochemistry because these proteins undergo conformational changes and aggregation. Both processes are largely implicated in several diseases including Alzheimer’s, Parkinson’s or Creutzfeldt-Jakob’s disease. These phenomena are not completely understood, either at a structural or energetical point of view. Tilted peptides are short protein fragment (11 to 19 residues) that adopt a tilted orientation when inserted into biological membranes and destabilise them. Recently, tilted peptides have been detected in two amyloidogenic proteins involved in neurodegenerative diseases; the amyloid  peptide responsible for Alzheimer’s disease, and the PrP protein that causes Creutzfeldt-Jakob’s disease. Tilted peptides could be responsible for the neurotoxic effects of these proteins. Due to their destabilising properties, they could interact directly with the membrane leading to cell death. Tilted peptides could also be involved in the transconformational process of the proteins. The aim of this work is to detect tilted fragments in other amyloidogenic proteins by molecular modelling and to study some of these peptides experimentally to evidence their lipid destabilizing properties, their structure and their toxicity. Twenty-four tilted peptides from 18 different proteins have been detected among 53 amyloidogenic proteins and 7 peptides were tested experimentally. The results support the hypothesis that some tilted peptides could be involved in transconformational processes and/or cytotoxicity related to amyloidogenic proteins. [less ▲]

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See detailPepLook Scale-Up: Prediction of protein structures
Crowet, Jean-Marc ULg; Brasseur, Robert ULg; Lins, Laurence ULg

Conference (2009, January 27)

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