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G Vergoten

Publications and source records attributed to G Vergoten.

At least 19 recordsLinked to original sources
PubMed2006

The SPASIBA force field for chondroitin sulfate: vibrational analysis of D-glucuronic and N-acetyl-D-galactosamine 4-sulfate sodium salts.

Normal-mode analyses were carried out on the two components of the chondroitin 4-sulfate linear glycosaminoglycan, a copolymer implying alternate D-glucuronate beta-(1-->3) and N-acetyl-D-galactosamine 4-sulfate beta-(1-->4) (hereafter named D-galactosamine 4-sulfate) residues. Scaled quantum mechanical calculations (SQM) using the density functional theory approach at different levels of theory (B3LYP/6-31G** and B3LYP/6-31++G**) were performed to obtain correct vibrational assignments. The SPASIBA empirical force field parameters were then obtained from both theoretical predictions and observed IR and Raman data. It is shown that calculations including diffuse functions at the B3LP/6-31++G** level and the introduction of the Na+ counterion are necessary to give correct assignments of the CO2- symmetric (nu(s)) and antisymmetric (nu(a)) stretching modes for the glucuronic carboxylate residue.

Acetylgalactosamine↗
PubMed2005

Theoretical and vibrational spectroscopic analysis of the CO stretching mode of cholesteryl alkanoates: the particular case of the cholesteryl acetate.

Structural and vibrational properties of the CO stretching bond of cholesteryl acetate and related steroids are investigated theoretically and by Micro-Raman spectroscopy. In this work, an analysis of the CO stretching mode for the cholesteryl acetate is presented. Experimental results in crystalline, isotropic liquid and liquid crystal phases are compared with quantum chemical calculations using semi empirical hamiltonians (AM1 and PM3) and the density functional theory. The calculations were performed on isolated molecules with different conformations as found on previous investigations giving strong evidence of their existence. Calculated frequencies are found to be very close to experiments and suggest the possible existence of the predicted conformers.

Alkanes↗
PubMed2005

Density functional theory and empirical derived force fields for the delocalized polaron form of polyaniline. Application to properties determination of an isolated oligomer using molecular dynamics simulations.

Normal mode analyses obtained from quantum chemical calculations at the DFT level of theory have been performed for the repetitive unit of the delocalized bipolaron form of polyaniline (PANI). Empirical molecular mechanics force field parameters were consecutively refined using the SPASIBA software and applied to the molecular dynamics properties of an isolated dodeca oligomer model of the leucoemeraldine form of PANI. It is shown that effects of protonation of the emeraldine base spread over the four rings constituting the repeating unit. Molecular dynamics simulations reveal alternative bendings of the whole chain with a time period of 18-20 ps for the model of PANI under study.

Aniline Compounds↗
PubMed2003

Modified UBFF calculations of the alpha-L-fucopyranose molecule in the crystalline state.

Normal co-ordinate analysis has been realised in the crystalline state using a modified Urey-Bradley-Shimanouchi force field combined with an intermolecular potential energy function that includes van der Waals interactions, some electrostatic terms and an explicit hydrogen bond function. The vibrational spectra of the alpha-L-fucose molecule have been recorded in the crystalline state, in the 4000-500 cm(-1) spectral region for the mid-IR spectra, in the 500-100 cm(-1) spectral region for the far-IR spectra, and in the 4000-20 cm(-1) spectral range for Raman spectra. These spectra constitute the experimental support for the establishment of a force field for the molecule in the crystalline state through a normal co-ordinate analysis.

Crystallization↗
PubMed2003

Harmonic dynamics of alpha- and beta-methyl-D-galactopyranoside in the crystalline state.

The study of the anomeric differences observed on the spectra of methyl-alpha- and methyl-beta-D-galactopyranoside is the essential goal of this investigation. Thus, after a careful examination of the IR and Raman spectra of these two compounds, several differences in the intensities and frequency shifts are observed. This is especially noted in the region 1000-700 cm(-1). In order to make some assignments with more precision, the normal modes analyses of the two compounds are performed in the crystalline state. For this purpose, a modified Urey-Bradley-Shimanouchi force field has been combined with an intermolecular potential energy function. The initial set of force constants comes from those of alpha- and beta-D-galactopyranosyl, then the force constants have been varied, so as to obtain a good agreement between the observed and the calculated vibrational frequencies. The obtained results have finally reproduced the experimental data and have confirmed the previous assignments made for the methyl-alpha- and methyl-beta-D-galactopyranoside. The calculations have demonstrated also the transferability of the set of parameters of the initial force field of D-galactose to methyl-D-galactopyranoside.

Methylgalactosides↗
PubMed2002

Harmonic dynamics of beta-D-fructopyranose.

The vibrational spectra of beta-D-fructopyranose crystals have been recorded in the 4000-400 cm(-1) region using the infrared and in the 4000-20 cm(-1) region using the Raman. These spectra are used as an experimental basis in order to establish a force field for the beta-D-fructopyranose molecule in the crystalline state through a normal co-ordinates analysis. For this purpose, a modified Urey-Bradley-Shimanoushi force field was combined with an intermolecular potential energy function that includes the van-der-Walls interactions, the electrostatic terms, and an explicit hydrogen bond function. The force field parameters are derived from those of beta-D-glucose and are fitted so as to obtain a good agreement between the calculated and the observed frequencies. The results obtained demonstrate the reliability and the transferability of the set of parameters constituting the initial force field. The fitted force field reproduces the experimental spectra to a marked degree of accuracy.

Fructose↗
PubMed2001

Ab initio vibrational calculations on ara-T molecule: application to analysis of IR and Raman spectra.

The FTIR and FT-Raman spectra are reported for the arabinonucleoside ara-T (1-beta-D-arabinofuranosylthymine), which shows antiviral activity. The accurate knowledge of the vibrational modes is a prerequisite for the elucidation of drug-nucleotide and drug-enzyme interactions. The FTIR and FT-Raman spectra of ara-T were recorded from 4000 to 30 cm(-1). A tetradeuterated derivative (deuteration at N3, and hydroxyl groups O'2, O'3, and O'5) was synthesized and the observed isotopic shifts in its spectra were used for the vibrational analysis of ara-T. The theoretical frequencies and the potential energy distribution (PED) of the vibrational modes of ara-T were calculated using the ab initio Hartree-Fock/3-21G method. An assignment of the vibrational spectra of ara-T is proposed considering the scaled PED and the observed band shifts under deuteration. The scaled ab initio frequencies were in reasonable agreement with the experimental data.

Antiviral Agents↗
PubMed2000

New nonbonded interactions calculation strategy for rectangular systems. I. Preliminary molecular dynamics study of solvated Na(+) ion.

A new molecular nonbonded interactions treatment strategy is proposed in the context of rectangular periodic boundary conditions simulations. Several molecular dynamics simulations are performed on a sodium ion in aqueous solution. Box sizes are modified from a cubic to a rectangular shape. The results are compared with those found using a classical spherical cutoff. This new method yields ion-oxygen radial distribution functions in good agreement with experimental results, thus showing its reliability. Severe perturbations in the structural orientation of water molecules in the first shell with the increase of the box length are observed under the classical cutoff method. However, these distorting effects are reduced with the present nonbonded interactions treatment.

Algorithms↗
PubMed2000

Stabilization of proteins by enhancement of inter-residue hydrophobic contacts: lessons of T4 lysozyme and barnase.

Although the hydrophobic interactions are considered as the main contributors to the protein stability, not much examples of protein stabilization by rational increasing of this type of interactions still can be found in literature. This is partly due to the lack of proper theoretical "measure" of hydrophobic interactions and their changes upon mutations. In the present paper the molecular hydrophobicity potential approach is used to assess how the changes in type and the strength of inter-residue contacts upon single amino acid mutations are correlated with the changes in thermodynamic stability of T4 lysozyme and barnase mutants, and which factors affect these correlations. Mutations changing unfavorable hydrophilic-to-hydrophobic contacts into favorable hydrophobic were found to enhance the thermodynamic stability in more than 81 % of cases, if these mutations do not create steric bumps and do not involve proline residues and hydrogen-bonded side-chains. Mutations increasing hydrophobic contributions (according to molecular hydrophobicity potential formalism) lead to increase of thermodynamic stability in more than 94% of cases for certain type of mutations (i.e., mutations not involving charged residues, Pro and residues with side-chain hydrogen bonds, when these mutations do not introduce steric bumps and do not involve strongly exposed residues and residues situated at helix N- and C-cap positions). For this type of mutations the correlation was found between the change in hydrophobic contributions of mutated residues deltaCphob and thermodynamic parameters deltaTm (change in melting temperature) and deltadeltaG (change in free energy of unfolding). Although the correlation coefficients were larger if the experimental structures of mutants were used for the calculations (correlation coefficients r(exp) deltaC,deltaT = .85 and r(exp) deltaC,deltadeltaG = 0.87) than if the modeled structures were used instead (r(mod) deltaC,deltaT = 0.74 and r(mod)deltaC,deltadeltaG = 0.76), the modelled structures of mutants in the vast majority of cases can be used for qualitative predictition of the protein stabilization. Basing on the analysis of mutations increasing hydrophobic contributions in T4 lysozyme the substitution matrix was derived, which can be used to decide which new residue should be put instead the old one to increase the stability of protein. The estimation shows that the number of potential mutation sites for enhancement of hydrophobic interactions in T4 lysozyme is quite large, and only approximately 10 per cent of them were studied thus far. Basing on the current analysis of T4 lysozyme and barnase mutations the algorithm for increasing of protein stability via increasing of hydrophobic interactions for the proteins with known spatial structure is proposed.

Algorithms↗
PubMed2000

4-Mercaptoimidazoles derived from the naturally occurring antioxidant ovothiols 2. Computational and experimental approach of the radical scavenging mechanism.

The radical-scavenging mechanism of fourteen 4-mercaptoimidazoles, derived from the natural family of ovothiols, was studied via a QSAR approach, cyclic voltammetry, ESR and NMR spectroscopy. A significant correlation was found between the DPPH scavenging abilities of test compounds and thermodynamic parameters like overall ease of disulphide formation. The production of a disulphide compound via thiyl radical formation is proposed. Upon DPPH scavenging, hydrogen abstraction from thiols yields transient short-lived thiyl radicals, which were characterised by ESR and rapidly dimerise to form a disulphide compound. Cyclic voltammetry showed that the best DPPH scavengers exhibit low oxidation potentials for their oxidation to disulphides.

Antioxidants↗
PubMed1999

A solvent model for simulations of peptides in bilayers. I. Membrane-promoting alpha-helix formation.

We describe an efficient solvation model for proteins. In this model atomic solvation parameters imitating the hydrocarbon core of a membrane, water, and weak polar solvent (octanol) were developed. An optimal number of solvation parameters was chosen based on analysis of atomic hydrophobicities and fitting experimental free energies of gas-cyclohexane, gas-water, and octanol-water transfer for amino acids. The solvation energy term incorporated into the ECEPP/2 potential energy function was tested in Monte Carlo simulations of a number of small peptides with known energies of bilayer-water and octanol-water transfer. The calculated properties were shown to agree reasonably well with the experimental data. Furthermore, the solvation model was used to assess membrane-promoting alpha-helix formation. To accomplish this, all-atom models of 20-residue homopolypeptides-poly-Leu, poly-Val, poly-Ile, and poly-Gly in initial random coil conformation-were subjected to nonrestrained Monte Carlo conformational search in vacuo and with the solvation terms mimicking the water and hydrophobic parts of the bilayer. All the peptides demonstrated their largest helix-forming tendencies in a nonpolar environment, where the lowest-energy conformers of poly-Leu, Val, Ile revealed 100, 95, and 80% of alpha-helical content, respectively. Energetic and conformational properties of Gly in all environments were shown to be different from those observed for residues with hydrophobic side chains. Applications of the solvation model to simulations of peptides and proteins in the presence of membrane, along with limitations of the approach, are discussed.

1-Octanol↗
PubMed1999

A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices.

We describe application of the implicit solvation model (see the first paper of this series), to Monte Carlo simulations of several peptides in bilayer- and water-mimetic environments, and in vacuum. The membrane-bound peptides chosen were transmembrane segments A and B of bacteriorhodopsin, the hydrophobic segment of surfactant lipoprotein, and magainin2. Their conformations in membrane-like media are known from the experiments. Also, molecular dynamics study of surfactant lipoprotein with different explicit solvents has been reported (Kovacs, H., A. E. Mark, J. Johansson, and W. F. van Gunsteren. 1995. J. Mol. Biol. 247:808-822). The principal goal of this work is to compare the results obtained in the framework of our solvation model with available experimental and computational data. The findings could be summarized as follows: 1) structural and energetic properties of studied molecules strongly depend on the solvent; membrane-mimetic media significantly promote formation of alpha-helices capable of traversing the bilayer, whereas a polar environment destabilizes alpha-helical conformation via reduction of solvent-exposed surface area and packing; 2) the structures calculated in a membrane-like environment agree with the experimental ones; 3) noticeable differences in conformation of surfactant lipoprotein assessed via Monte Carlo simulation with implicit solvent (this work) and molecular dynamics in explicit solvent were observed; 4) in vacuo simulations do not correctly reproduce protein-membrane interactions, and hence should be avoided in modeling membrane proteins.

Amino Acid Sequence↗
PubMed1999

Human chemokine receptors CCR5, CCR3 and CCR2B share common polarity motif in the first extracellular loop with other human G-protein coupled receptors implications for HIV-1 coreceptor function.

Chemokine receptors (CRs) are 7-helix membrane proteins from the family of G-protein coupled receptors (GPCRs). A few human CRs act as cofactors for macrophage-tropic (M-tropic) human immunodeficiency virus type-1 (HIV-1) entry into cells, while others do not. In this study, we describe an application of molecular modeling techniques to delineate common molecular determinants that might be related to coreceptor activity, and the use of the data to identify other GPCRs as putative cofactors for M-tropic HIV-1 entry. Subsequently, the results were confirmed by an experimental approach. The sequences of extracellular domains (ECDs) of CRs were employed in a compatibility search against a database of environmental profiles derived for proteins with known spatial structure. The best-scoring sequence-profile alignments obtained for each ECD were compared in pairs to check for common patterns in residue environments, and consensus sequence-profile fits for ECDs were also derived. Similar hydrophobicity motifs were found in the first extracellular loops of the CRs CCR5, CCR3, and CCR2B, and are all used by M-tropic HIV-1 for cell entry. In contrast, other CRs did not reveal common motifs. However, the same environmental pattern was also delineated in the first extracellular loop of some human GPCRs showing either high (group 1) or low (group 2) degree of similarity of their polarity patterns with those in HIV-1 coreceptors. To address the question of whether the delineated molecular determinant plays a critical role in the receptor-virus binding, three of the identified GPCRs, bradykinin receptor (BRB2) and G-protein receptor (GPR)-CY6 from group 1, and GPR8 from group 2, were cloned and transfected into HeLa-CD4 cells, which are nonpermissive to M-tropic HIV-1 infection. We demonstrate that, similar to CCR5, the two selected GPCRs from group 1 were capable of mediating M-tropic HIV-1 entry, whereas GPR8 from group 2 did not serve as HIV-1 coreceptor. The potential biological significance of the identified structural motif shared by the human CCR5, CCR3, CCR2B and other GPCRs is discussed.

Amino Acid Sequence↗
PubMed1998

Mechanism of inhibition of rat liver bilirubin UDP-glucuronosyltransferase by triphenylalkyl derivatives.

A series of potent and competitive inhibitors of UDP-glucuronosyltransferase derived from 7,7,7-triphenylheptanoic acid has been synthesized in order to probe the active site of the isozyme involved in the glucuronidation of the endogenous toxic compound, bilirubin IX alpha. Like triphenylalkylcarboxylic acids, triphenyl alcohols were found to be very effective competitive inhibitors of the reaction (Ki 12 to 180 microM). Superimposition of the best inhibitors with bilirubin by computer modeling showed a marked spatial similarity, which accounts for the observed competitive-type inhibition. The bulky triphenylmethyl moiety of the inhibitor superimposed well on the part of the bilirubin molecule containing three of the four pyrrole rings. In agreement, substitution of the triphenylmethyl moiety by planar structures such as fluorenyl or indenyl rings completely suppressed the inhibition. In addition, the weak inhibition exerted by the shortest carboxylic acids could be related to the higher acidity of these molecules. The inhibition potency depended on the acidity of the molecules; the more acidic, the less inhibitory, suggesting that the presence of a negative charge on the inhibitor molecule prevents bilirubin glucuronidation. Based on these results, a reaction mechanism for bilirubin glucuronidation is postulated.

Animals↗
PubMed1998

Molecular dynamics simulations of biomembrane models.

A molecular force field dedicated to molecular dynamics simulation of biomembranes was developed. It was parameterized on model compounds related to phospholipids and was able to reproduce at the same time structures, energies, and vibrational spectra. Cross terms in the potential energy function were introduced by solving the redundancy problem among internal coordinates. This force field was used in the 400-ps molecular dynamics simulation of a hydrated bilayer in the gel and liquid crystal phases. The conformational properties of the polar head groups were in particular agreement with the experimental observations using Raman scattering.

Gels↗
PubMed1998

On the use of ultraviolet resonance Raman intensities to elaborate molecular force fields: application to nucleic acid bases and aromatic amino acid residues models.

Normal modes analyses for different molecules with biological interest have been performed and checked via the calculation of resonance Raman intensities. For this purpose, molecular orbital calculations were used to determine bond order changes in the lowest-lying electronic transitions. These bond order changes were used to calculate resonance Raman intensities in order to obtain correct vibrational assignments and reliable force fields.

Amino Acids↗
PubMed1998

Molecular modeling of HIV-1 coreceptor CCR5 and exploring of conformational space of its extracellular domain in molecular dynamics simulation.

The chemokine receptor CCR5 functions as a major fusion coreceptor for macrophage-tropic human immunodeficiency virus entry into cell. Here we report a three-dimensional model of CCR5 built using molecular modeling approach. Because the virus binds to extracellular domain of the receptor, special attention was given to conformational flexibility, hydrogen bonding, and environmental polarity properties of this protein part. Such data were obtained in the result of molecular dynamics study of the extracellular domain. It was shown that during the simulation the extracellular segments form a compact globular domain with numerous long-range hydrogen bonds between them. First loop of the receptor stays quite rigid while N-terminal region and loops 2, 3 are rather flexible. A number of amino acid residues disposed in unfavourable environment and, therefore, potentially involved in binding of CCR5 to viral glycoproteins and chemokines, was delineated. Comparison of the results with available experimental data permits a proposal that such residues in loop-1 and N-terminal part of the receptor are important for HIV-1 entry, while those in loops 2 and 3 participate in ligand binding. Perspectives of rational alteration of virus-binding activity of CCR5 are discussed.

Amino Acid Sequence↗