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Xavier Daura

Publications and source records attributed to Xavier Daura.

16 recordsLinked to original sources
PubMed2006

Biomolecular modeling: Goals, problems, perspectives.

Computation based on molecular models is playing an increasingly important role in biology, biological chemistry, and biophysics. Since only a very limited number of properties of biomolecular systems is actually accessible to measurement by experimental means, computer simulation can complement experiment by providing not only averages, but also distributions and time series of any definable quantity, for example, conformational distributions or interactions between parts of systems. Present day biomolecular modeling is limited in its application by four main problems: 1) the force-field problem, 2) the search (sampling) problem, 3) the ensemble (sampling) problem, and 4) the experimental problem. These four problems are discussed and illustrated by practical examples. Perspectives are also outlined for pushing forward the limitations of biomolecular modeling.

Computer Simulation↗
PubMed2005

On the influence of charged side chains on the folding-unfolding equilibrium of beta-peptides: a molecular dynamics simulation study.

The influence of charged side chains on the folding-unfolding equilibrium of beta-peptides was investigated by means of molecular dynamics simulations. Four different peptides containing only negatively charged side chains, positively charged side chains, both types of charged side chains (with the ability to form stabilizing salt bridges) or no charged side chains were studied under various conditions (different simulation temperatures, starting structures and solvent environment). The NMR solution structure in methanol of one of the peptides (A) has already been published; the synthesis and NMR analysis of another peptide (B) is described here. The other peptides (C and D) studied herein have hitherto not been synthesized. All four peptides A-D are expected to adopt a left-handed 3(14)-helix in solution as well as in the simulations. The resulting ensembles of structures were analyzed in terms of conformational space sampled by the peptides, folding behavior, structural properties such as hydrogen bonding, side chain-side chain and side chain-backbone interactions and in terms of the level of agreement with the NMR data available for two of the peptides. It was found that the presence of charged side chains significantly slows down the folding process in methanol solution due to the stabilization of intermediate conformers with side chain-backbone interactions. In water, where the solvent competes with the solute-solute polar interactions, the folding process to the 3(14)-helix is faster in the simulations.

Hydrogen Bonding↗
PubMed2005

Engineering the E. coli beta-galactosidase for the screening of antiviral protease inhibitors.

Site-specific proteolysis is essential in many fundamental cellular and viral processes. It has been previously shown that the Escherichia coli beta-galactosidase can be useful for the high-throughput screening of human immunodeficiency virus type 1 protease inhibitors. Here, by using crystallographic and functional data of the bacterial enzyme, we have identified a new accommodation site between amino acids 581 and 582, in a solvent-exposed and flexible beta-turn of domain III. The placement of the model peptide reproducing the matrix-capsid (p17/p24) gag cleavage sequence renders a highly active and efficiently digested chimeric construct. The use of this insertion site, that increases the cleavage potential of this reporter enzyme, can improve the sensitivity and dynamic range of the antiviral drug assay. This simple and highly specific analytical test may also be extended to the screening of other specific protease inhibitors by a convenient colorimetric assay.

Amino Acid Substitution↗
PubMed2005

Molecular-dynamics simulations of C- and N-terminal peptide derivatives of GCN4-p1 in aqueous solution.

We report the investigation of two 16-residue peptides in aqueous solution by means of molecular-dynamics simulations. The peptides constitute the C- and N-terminal halves of the 33-residue monomer whose dimer constitutes the leucine zipper of the yeast transcriptional activator, denoted GCN4-p1. To examine a hypothesis about coiled-coil formation, in which the C-terminal half contains a helix-formation trigger site absent in the N-terminal half, experimental studies of the two peptides have determined their helix propensities under several conditions of temperature, pH, and salt concentration with circular dichroism. An NMR experiment provides additional evidence. At temperatures of 278 and 325 K and pH 7.5, mixtures of alpha- and pi-helical secondary structure constitute the most probable conformations in both C- and N-terminal halves. A bifurcated salt bridge between Arg25 and Glu22/20 correlates with the structural fluctuations of the C-terminal half. It also exhibits a persistent loop at the N-terminal end involving the side chains of His18 and Glu22, which is reminiscent of helix-capping boxes. Nonreversible unfolding appears to occur abruptly in the Arg25 mutant, suggesting a cooperative event. Analysis does not indicate that the N-terminal half is less stable than the C-terminal half, indicating that 100 ns is too short a period to observe complete unfolding.

Amino Acid Sequence↗
PubMed2004

Molecular dynamics simulations of peptides containing an unnatural amino acid: dimerization, folding, and protein binding.

We have performed molecular dynamics (MD) simulations to study the dimerization, folding, and binding to a protein of peptides containing an unnatural amino acid. NMR studies have shown that the substitution of one residue in a tripeptide beta-strand by the unnatural amino acid Hao (5-HO2CCONH-2-MeO-C6H3-CO-NHNH2) modifies the conformational flexibility of the beta-strand and the hydrogen-bonding properties of its two edges: The number of hydrogen-bond donors and acceptors increases at one edge, whereas at the other, they are sterically hindered. In simulations in chloroform, the Hao-containing peptide 9 (i-PrCO-Phe-Hao-Val-NHBu) forms a beta-sheet-like hydrogen-bonded dimer, in good agreement with the available experimental data. Addition of methanol to the solution induces instability of this beta-sheet, as confirmed by the experiments. MD simulations also reproduce the folding of the synthetic peptide 1a (i-PrCO-Hao-Ut-Phe-Ile-Leu-NHMe) into a beta-hairpin-like structure in chloroform. Finally, the Hao-containing peptide, Ac-Ala-Hao-Ala-NHMe, is shown to form a stable complex with the Ras analogue, Rap1 A, in water at room temperature. Together with the available experimental data, these simulation studies indicate that Hao-containing peptides may serve as inhibitors of beta-sheet interactions between proteins.

Amino Acids, Aromatic↗
PubMed2004

Modelling of the complex between a 15-residue peptide from mSos2 and the N-terminal SH3 domain of Grb2 by molecular-dynamics simulation.

Under specific conditions, the complex formed by the adaptor protein Grb2 and the guanine-nucleotide exchange factor Sos2 is responsible for the activation of Ras, a low-molecular-weight GTPase involved in the control of cell proliferation and differentiation. The interaction between the N-terminal SH3 domain of the mouse Grb2 and one of its potential target sequences in the mouse, Sos2, a 15-residue peptide corresponding to residues 1264-1278, had been studied by NMR. However, the resulting data provided very limited information on the structure of the peptide and its interaction with the protein. Here, we present results from a molecular-dynamics simulation aimed at producing a realistic, atomic model for the interaction between the N-terminal SH3 domain of Grb2 and the SPLLPKLPPKTYKRE peptide from Sos2. In the simulation, the peptide adopts an extended conformation over the protein's binding surface. The proposed polyproline-type-II helicity appears only locally, and the peptide displays substantial flexibility. It is found that the peptide residues Lys10 to Tyr12 could be responsible for most of the specificity of the interaction.

Amino Acid Sequence↗
PubMed2004

beta-hairpin folding and stability: molecular dynamics simulations of designed peptides in aqueous solution.

The structural properties of a 10-residue and a 15-residue peptide in aqueous solution were investigated by molecular dynamics simulation. The two designed peptides, SYINSDGTWT and SESYINSDGTWTVTE, had been studied previously by NMR at 278 K and the resulting model structures were classified as 3:5 beta-hairpins with a type I + G1 beta-bulge turn. In simulations at 278 K, starting from the NMR model structure, the 3:5 beta-hairpin conformers proved to be stable over the time period evaluated (30 ns). Starting from an extended conformation, simulations of the decapeptide at 278 K, 323 K and 353 K were also performed to study folding. Over the relatively short time scales explored (30 ns at 278 K and 323 K, 56 ns at 353 K), folding to the 3:5 beta-hairpin could only be observed at 353 K. At this temperature, the collapse to beta-hairpin-like conformations is very fast. The conformational space accessible to the peptide is entirely dominated by loop structures with different degrees of beta-hairpin character. The transitions between different types of ordered loops and beta-hairpins occur through two unstructured loop conformations stabilized by a single side-chain interaction between Tyr2 and Trp9, which facilitates the changes of the hydrogen-bond register. In agreement with previous experimental results, beta-hairpin formation is initially driven by the bending propensity of the turn segment. Nevertheless, the fine organization of the turn region appears to be a late event in the folding process.

Amino Acid Sequence↗
PubMed2003

Circular dichroism spectra of beta-peptides: sensitivity to molecular structure and effects of motional averaging.

Circular dichroism spectra of two beta-peptides, i.e. peptides composed of beta-amino acids, calculated using ensembles of configurations obtained by molecular dynamics simulation are presented. The calculations were based on 200 ns simulations of a beta-heptapeptide in methanol at 298 K and 340 K and a 50 ns simulation of a beta-hexapeptide in methanol at 340 K. In the simulations the peptides sampled both folded (helical) and unfolded structures. Trajectory structures with common backbone conformations were identified and grouped into clusters. The CD spectra were calculated for individual structures, based on peptide-group dipole transition moments obtained from semi-empirical molecular orbital theory and using the so-called matrix method. The single-structure spectra were then averaged over entire trajectories and over clusters of structures. Although certain features of the experimental CD spectra of the beta-peptides are reproduced by the trajectory-average spectra, there exist clear differences between the two sets of spectra in both wavelength and peak intensities. The analysis of individual contributions to the average spectra shows that, in general, the interpretation of a CD signal in terms of a single structure is not possible. Moreover, there is a large variation in the CD spectra calculated for a set of individual structures that belong to the same cluster, even when a structurally tight clustering criterion is used. This indicates that the CD spectra of these peptides are very sensitive to small local structural differences.

Circular Dichroism↗
PubMed2003

A novel approach for designing simple point charge models for liquid water with three interaction sites.

A simultaneous improvement of the diffusion and dielectric properties of the simple point charge (SPC) model for liquid water appears to be very difficult with conventional reparametrization of the commonly used Lennard-Jones and Coulomb interaction functions and without including a self-energy correction in the effective pair-potential as is done in the SPC/E model. Here, a different approach to circumvent this problem is presented. A short-range interaction term, which corrects the oxygen-oxygen energy at small distances by small amounts of energy, was introduced in the nonbonded interaction function. This additional force-field term allows to derive new parameter sets for SPC-like water models that yield better agreement with experimental data on liquid water. Based on previous investigations of the force-field parameter dependence of the water properties of SPC-like models, the necessary parameter changes to obtain a lower diffusion coefficient and a larger dielectric permittivity were specified and accordingly six new models were developed. They all represent an improvement over SPC in terms of structural and diffusional properties, four of them show better dielectric properties also. One model, SPC/S, has been characterized in more detail, and represents most properties of liquid water better than SPC while avoiding the larger discrepancies with experimental values regarding density, thermal compressibility, energy, and free energy of the SPC/E model. We conclude that the use of a simple, short-ranged additional oxygen-oxygen interaction term makes a simultaneous improvement of the diffusion coefficient and the dielectric properties of water feasible.

Journal Article↗
PubMed2003

Procarboxypeptidase A from the insect pest Helicoverpa armigera and its derived enzyme. Two forms with new functional properties.

Although there is a significant knowledge about mammalian metallocarboxypeptidases, the data available on this family of enzymes is very poor for invertebrate forms. Here we present the biochemical characterization of a metallocarboxypeptidase from the insect Helicoverpa armigera (Lepidoptera: Noctuidae), a devastating pest spread in subtropical regions of Europe, Asia, Africa and Oceania. The zymogen of this carboxypeptidase (PCPAHa) has been expressed at high levels in a Pichia pastoris system and shown to display the characteristics of the enzyme purified from the insect midgut. The in vitro activation process of the proenzyme differs significantly from the mammalian ones. The lysine-specific endoprotease LysC activates PCPAHa four times more efficiently than trypsin, the general activating enzyme for all previously studied metalloprocarboxypeptidases. LysC and trypsin independently use two different activation targets and the presence of sugars in the vicinity of the LysC activation point affects the activation process, indicating a possible modulation of the activation mechanism. During the activation with LysC the prodomain is degraded, while the carboxypeptidase moiety remains intact except for a C-terminal octapeptide that is rapidly released. Interestingly, the sequence at the cleavage point for the release of the octapeptide is also found at the boundary between the activation peptide and the enzyme moieties. The active enzyme (CPAHa) is shown to have a very broad substrate specificity, as it appears to be the only known metallocarboxypeptidase capable of efficiently hydrolysing basic and aliphatic residues and, to a much lower extent, acidic residues. Two carboxypeptidase inhibitors, from potato and leech, were tested against CPAHa. The former, of vegetal origin, is the most efficient metallocarboxypeptidase inhibitor described so far, with a Ki in the pm range.

Amino Acid Sequence↗
PubMed2002

Can one derive the conformational preference of a beta-peptide from its CD spectrum?

CD spectroscopy is often used to elucidate the secondary structure of peptides built from non-natural amino acids such as beta-amino acids. The interpretation of such CD spectra is not always unambiguous. Here, we present a case where two beta-hexapeptides, a dimethyl-beta-hexapeptide indicated as DM-BHP (A) and its nonmethylated analogue indicated as BHP (B), exhibit similar CD spectra, whereas they are expected to differ in secondary structure. The structural properties of both peptides were studied by molecular dynamics simulation, and from the resulting trajectories, the corresponding CD spectra were calculated. Starting from a fully extended conformation, BHP is observed to form a 3(14)-helix, while DM-BHP remains unfolded. However, even though these two peptides hardly share any conformations, their calculated CD spectra are alike and show the same features as the experimentally measured ones. Our results imply that a particular CD pattern can be induced by spatially different structures, which makes it difficult to derive the conformational preference of a peptide from its CD spectrum alone. To gain more insight into the relationship between the preferred conformation of a peptide and its CD spectrum, more accurate methods to calculate the CD spectrum for a given conformation are required.

Circular Dichroism↗
PubMed2002

Assessing equilibration and convergence in biomolecular simulations.

If molecular dynamics simulations are used to characterize the folding of peptides or proteins, a wide range of conformational states needs to be sampled. This study reports an analysis of peptide simulations to identify the best methods for assessing equilibration and sampling in these systems where there is significant conformational disorder. Four trajectories of a beta peptide in methanol and four trajectories of an alpha peptide in water, each of 5 ns in length, have been studied. Comparisons have also been made with two 50-ns trajectories of the beta peptide in methanol. The convergence rates of quantities that probe both the extent of conformational sampling and the local dynamical properties have been characterized. These include the numbers of hydrogen bonds populated, clusters identified, and main chain torsion angle transitions in the trajectories. The relative equilibrium rates of different quantities are found to vary significantly between the two systems studied reflecting both the differences in peptide primary structure and the different solvents used. A cluster analysis of the simulation trajectories is identified as a very effective method for judging the convergence of the simulations. This is particularly the case if the analysis includes a comparison of multiple trajectories calculated for the same system from different starting structures.

Amino Acid Sequence↗
PubMed2001

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Journal Article↗