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See detailReplacing explicit water and lipids by implicit representation in molecular dynamics simulations
Steinhauer, Sven ULg; Crowet, Jean-Marc ULg; Lins, Laurence ULg et al

Poster (2012, September 11)

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are ... [more ▼]

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are not accessible by experimental methods(Lindahl, 2008). By now, many biologically relevant processes for drug design, toxicological studies and other fields of application, can not be performed by atomistic MD simulations (Lindahl, 2008). <br />In MD, the necessary time effort for carrying out a simulation is considerable and depends mainly on (1) the complexity of the simulated system (2) the simulated time scale (3) the simulation method (4) the efficiency of used hardware and software algorithms. Carried out MD simulations nowadays may still take weeks of calculation on high end computers. <br /> <br />In practice, biologically relevant processes, as e.g. protein folding, take usually place above the time scale of milli seconds. They can take up to the order of some thousands of seconds (in case of the folding of membrane proteins). Molecular dynamics computer simulations have reached the scale of micro seconds for simulations of systems where each atom was described and simulated over time.(Lindahl, 2008) <br /> <br />Nevertheless, MD has risen to an important promoter methodology for many different fields of application. By replacing bunches of atoms by artificial particles, complexity of the systems can be reduced. This method is called the coarse grain method (CG). Biggin and Bond (2008) found an acceleration of their simulation processes for self assembling membrane / protein systems in water by factor 100. They estimated one to two days of calculation for a simulated time scale of 0.1 to 0.2 micro seconds for their systems. <br /> <br />Implicit force fields like "IMPALA", aim to describe water and/or membrane molecules in simulations by a couple of simple and partially precalculable equations. “IMPALA” is a force field initially developed by our laboratory. Using this method, thousands of water and lipid molecules can be replaced, leading to a reduced complexity of the system to be simulated. <br />"IMPALA"(Ducarme et al., 1998) based on the assumption of rigid peptides and aimed to find the insertion characteristics of such in membranes. Elimination of the necessity for simulating the aqueous and lipid phase atom by atom in the software package "Gromacs"(Berendsen et al., 1995) will permit both: a gain of speed, as it was already the case for the introduction of the coarse grain method, and a gain of precision by turning rigid molecules flexible through "Gromacs". Our current work is the integration of the "IMPALA" implicit force field into "Gromacs". <br /> <br />Biggin, P.C. & Bond, P.J. Molecular dynamics simulations of membrane proteins. Methods Mol. Biol. 443, 147-60(2008). <br />Berendsen, et al. (1995) Comp. Phys. Comm. 91: 43-56. <br />Ducarme, P., Rahman, M. & Brasseur, R. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins 30, 357-71(1998). <br />Lindahl, E.R. (2008). Molecular dynamics simulations. Methods Mol. Biol. 443, 3-23. [less ▲]

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See detailCharacterizing of protein dataset with GO ontology
Dmitrieva, Joelia Borisnova; Florea, B; Li, N et al

Poster (2012, September 09)

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See detailPlasma membrane localization of StREM1.3 Remorin is mediated by conformational changes in a novel C-terminal anchor and required for the restriction of PVX movement.
Perraki, Artemis; Cacas, Jean-Luc; Crowet, Jean-Marc ULg et al

in Plant Physiology (2012), 160(1),

The formation of plasma membrane (PM) micro-domains plays a crucial role in the regulation of membrane signalling and trafficking. Remorins are a plant-specific family of proteins organized in six ... [more ▼]

The formation of plasma membrane (PM) micro-domains plays a crucial role in the regulation of membrane signalling and trafficking. Remorins are a plant-specific family of proteins organized in six phylogenetic groups, and Remorins of the group 1 are among the few plant proteins known to specifically associate with membrane rafts. As such, they are valuable to understand the molecular bases for PM lateral organization in plants. However, little is known about the structural determinants underlying group 1 Remorins specific association with membrane rafts. We used a structure-function approach to identify a short C-terminal anchor (RemCA) indispensable and sufficient for tight direct binding of Solanum tuberosum REMORIN 1.3 (StREM1.3) to the PM. RemCA switches from unordered to an alpha-helical structure in a non-polar environment. Protein structure modelling indicates that RemCA folds into a tight hairpin of amphipathic helices. Consistently, mutations reducing RemCA amphipathy abolished StREM1.3 PM localization. Furthermore, RemCA directly binds to biological membranes in vitro, shows higher affinity for Detergent-Insoluble Membranes (DIM) lipids, and targets YFP to DIMs in vivo. Mutations in RemCA resulting in cytoplasmic StREM1.3 localization abolish StREM1.3 function in restricting potato virus X movement. The mechanisms described here provide new insights on the control and function of lateral segregation of plant PM. [less ▲]

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See detailCharacterization of the interaction of xylose-based bolaamphiphiles with biomimetic membrane systems
Nasir, Mehmet Nail ULg; Legrand, Vincent; Gatard, Sylvain et al

Conference (2012, July)

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See detailCalcium-induced conformational changes of the elicitor and membrane-active fengycin
Nasir, Mehmet Nail ULg; Lins, Laurence ULg; Ongena, Marc ULg et al

Poster (2012, April)

Fengycin is a natural lipopeptide synthetized by Bacillus subtilis strains. It is characterized by strong antifungal and low hemolytic activities. It seems also play a role in the promoting of elicitor ... [more ▼]

Fengycin is a natural lipopeptide synthetized by Bacillus subtilis strains. It is characterized by strong antifungal and low hemolytic activities. It seems also play a role in the promoting of elicitor activities of other compounds. The target of the biological activities of fengycin is supposed to be plasma membrane of sensitive cells. Even though the natural fengycin from has been discovered 25 years ago, nowadays, there is an increase of interest for this compound because of its potent applications. Until 15 years ago, the primary structure of fengycin was a matter of open debate before the publication of the corrected structure obtained by nuclear magnetic resonance and mass spectroscopy techniques. Although the infrared and ultraviolet absorption spectra of the lipopeptide were measured, no detailed analysis of these data was performed probably because of the unconventional sequence of the lipopeptide making these kinds of analyses complicated. In this work, our attempt was to analyze the conformational properties of fengycin as well as the calcium-induced changes using two complementary spectroscopic methods, Fourrier transformed infrared spectroscopy (FTIR) and circular dichroism (CD). In a first step, we have characterized the conformational properties of pure fengycin. The lipopeptide adopts turn conformation in trifluoroethanol, a membrane-mimicking solvent. D-aminoacids seem to be involved in intra molecular hydrogen bonds. In a second step, we have investigated the role played by Ca2+ ions on the possible conformational changes of fengycin. The addition of calcium gives rise to important modifications of the conformation. As fengycin has two glutamate residues, calcium is supposed to bind to their side chains. In conclusion, we have demonstrated that the conformation of fengycin is closely depending of the environment and the presence of calcium ions play an important role on the conformational changes of the lipopeptide. Moreover, spectra obtained both FTIR and CD methods ascertain the presence of turn conformation. [less ▲]

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See detailHow does elicitor and antimicrobial fengycin interact with plasma membranes of sensitive cells ?
Nasir, Mehmet Nail ULg; Eeman, Marc; Lins, Laurence ULg et al

Conference (2012, April)

Fengycin is characterized by its strong antifungal and low hemolytic activities. It has also been recently demonstrated that it has plant elicitor properties and is also able to enhance the elicitors’ ... [more ▼]

Fengycin is characterized by its strong antifungal and low hemolytic activities. It has also been recently demonstrated that it has plant elicitor properties and is also able to enhance the elicitors’ activity of surfactin. The cell target of its biological activities is supposed to be plasma membrane. In spite of these interesting biological activities, fengycin has not been extensively investigated probably because of the difficulties related to its production. In a first time; we have characterized the interfacial properties of fengycin by tensiometry measurements and demonstrated that this surface activity was pH-dependent. In a second time; we have investigated the interactions of the lipopeptide with membrane lipids using model membranes such as Langmuir monolayers and multilammelar vesicles (MLVs). Our results indicate that the lipopeptide was able to penetrate into different lipid monolayers showing a preference for sterol-containing monolayers. In order to better understand the mechanism of the interactions of fengycin with membranes at the molecular level, MLVs with or without fengycin have been analyzed by spectroscopic techniques. We have shown that conformational changes of the lipopeptide occurred in the presence of lipids and they were more significant in the presence of sterol. Moreover, tyrosine residues of the lipopeptide seem to play an important role in these interactions. In conclusion, we have determined that the surface-active behavior as well as the conformation of fengycin depends on its environment. We have also showed that the lipopeptide does not interact with all class of lipids in the same way and presents a preference for sterols. The presence of key groups within peptide cycle has also been supposed for the biological activities of the lipopeptide. [less ▲]

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See detailReplacing explicit water and membrane molecules in molecular dynamics simulation to boost simulation speed
Steinhauer, Sven ULg; Crowet, Jean-Marc ULg; Lins, Laurence ULg et al

Poster (2012, February 10)

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are ... [more ▼]

Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are not accessible by experimental methods(Lindahl, 2008). By now, many biologically relevant processes for drug design, toxicological studies and other fields of application, can not be performed by atomistic MD simulations (Lindahl, 2008). In MD, the necessary time effort for carrying out a simulation is considerable and depends mainly on (1) the complexity of the simulated system (2) the simulated time scale (3) the simulation method (4) the efficiency of used hardware and software algorithms. Carried out MD simulations nowadays may still take weeks of calculation on high end computers. In practice, biologically relevant processes, as e.g. protein folding, take usually place above the time scale of milli seconds. They can take up to the order of some thousands of seconds (in case of the folding of membrane proteins). Molecular dynamics computer simulations have reached the scale of micro seconds for simulations of systems where each atom was described and simulated over time.(Lindahl, 2008) Nevertheless, MD has risen to an important promoter methodology for many different fields of application. By replacing bunches of atoms by artificial particles, complexity of the systems can be reduced. This method is called the coarse grain method (CG). Biggin and Bond (2008) found an acceleration of their simulation processes for self assembling membrane / protein systems in water by factor 100. They estimated one to two days of calculation for a simulated time scale of 0.1 to 0.2 micro seconds for their systems. Implicit force fields like "IMPALA", aim to describe water and/or membrane molecules in simulations by a couple of simple and partially precalculable equations. “IMPALA” is a force field initially developed by our laboratory. Using this method, thousands of water and lipid molecules can be replaced, leading to a reduced complexity of the system to be simulated. "IMPALA"(Ducarme et al., 1998) based on the assumption of rigid peptides and aimed to find the insertion characteristics of such in membranes. Elimination of the necessity for simulating the aqueous and lipid phase atom by atom in the software package "Gromacs"(Berendsen et al., 1995) will permit both: a gain of speed, as it was already the case for the introduction of the coarse grain method, and a gain of precision by turning rigid molecules flexible through "Gromacs". Our current work is the integration of the "IMPALA" implicit force field into "Gromacs". Biggin, P.C. & Bond, P.J. Molecular dynamics simulations of membrane proteins. Methods Mol. Biol. 443, 147-60(2008). Berendsen, et al. (1995) Comp. Phys. Comm. 91: 43-56. Ducarme, P., Rahman, M. & Brasseur, R. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins 30, 357-71(1998). Lindahl, E.R. (2008). Molecular dynamics simulations. Methods Mol. Biol. 443, 3-23. [less ▲]

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See detailMulti-Scale Simulation of the Simian Immunodeficiency Virus Fusion Peptide.
Crowet, Jean-Marc ULg; Parton, Daniel L.; Hall, Benjamin A. et al

in Journal of Physical Chemistry B (2012)

Fusion peptides of type I fusion glycoproteins are structural elements of several enveloped viruses which enable the fusion between host and virus membranes. It is generally suggested that these peptides ... [more ▼]

Fusion peptides of type I fusion glycoproteins are structural elements of several enveloped viruses which enable the fusion between host and virus membranes. It is generally suggested that these peptides can promote the early fusion steps by inducing membrane curvature and that they adopt a tilted helical conformation in membranes. Although this property has been the subject of several experimental and in silico studies, an extensive sampling of the membrane peptide interaction has not yet been done. In this study, we performed coarse-grained molecular dynamic simulations in which the lipid bilayer self-assembles around the peptide. The simulations indicate that the SIV fusion peptide can adopt two different orientations in a DPPC bilayer, a major population which adopts a tilted interfacial orientation and a minor population which is perpendicular to the bilayer. The simulations also indicate that for the SIV mutant that does not induce fusion in vitro the tilt is abolished. [less ▲]

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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 detailInteraction network of antimicrobial peptides of Arabidopsis thaliana, based on hith-throughput yeast two-hybrid screening
Damon, Coralie ULg; Dmitrieva, Joelia Borisnova; Muhovski, Yordan et al

in Plant Physiology & Biochemistry (2012)

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See detailLiquid Crystalline Phases Induced by the Hydroxyl Group Stereochemistry of Amphiphilic Carbohydrate Bicatenary Derivatives
Razafindralambo, Hary ULg; Richel, Aurore ULg; Paquot, Michel ULg et al

in Journal of Physical Chemistry B (2012), 116(13), 3998-4005

Liquid-crystals (LC) may exist in different phases depending upon the orientational and positional orders of molecules in the material. Here, we demonstrate that the class of LC state induced by ... [more ▼]

Liquid-crystals (LC) may exist in different phases depending upon the orientational and positional orders of molecules in the material. Here, we demonstrate that the class of LC state induced by amphiphilic carbohydrate bicatenary derivatives is strictly a hydroxyl group stereochemistry-dependent. This statement results from the experimental and theoretical investigations of surface film (2D) and bulk solid (3D) thermal behavior of synthetic stereoisomers n-tetradecyl (-D-n-tetradecyl) galacto- and gluco-pyranosiduronate, with an axial (GalA-C14/14) or equatorial (GlcA-C14/14) hydroxyl group at the fourth carbon, respectively. Surface pressure-area isotherms (283 K to 310 K), differential scanning calorimetry thermograms (223 K to 573 K), and polarized optical textures (298-363 K) reveal that GlcA-C14/14 organizes as a smectic LC-like phase (positional or lateral order) whereas the analogous stereoisomeric GalA-C14/14 behaves as a nematic LC-like phase (orientational order). Thermodynamic investigations and molecular dynamics models computed under similar temperature conditions provide consistent data with physical properties resulting from experimental approaches. [less ▲]

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See detailInteraction of Hexadecylbetainate Chloride with Biological Relevant Lipids
Nsimba Zakanda, Francis; Lins, Laurence ULg; Nott, Katherine ULg et al

in Langmuir (2012), 28(7), 3524-3533

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See detaild-Xylose-based bolaamphiphiles: Synthesis and influence of the spacer nature on their interfacial and membrane properties
Deleu, Magali ULg; Gatard, Sylvain; Payen, Emeline et al

in Comptes Rendus Chimie (2012), 15

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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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