Gérard Vergoten

PhytAMP: a database dedicated to antimicrobial plant peptides

Plants produce small cysteine-rich antimicrobial peptides as an innate defense against pathogens. Based on amino acid sequence homology, these peptides were classified mostly as α-defensins, thionins, lipid transfer proteins, cyclotides, snakins and hevein-like. Although many antimicrobial plant peptides are now well characterized, much information is still missing or is unavailable to potential users. The compilation of such information in one centralized resource, such as a database would therefore facilitate the study of the potential these peptide structures represent, for example, as alternatives in response to increasing antibiotic resistance or for increasing plant resistance to pathogens by genetic engineering. To achieve this goal, we developed a new database, PhytAMP, which contains valuable information on antimicrobial plant peptides, including taxonomic, microbiological and physicochemical data. Information is very easy to extract from this database and allows rapid prediction of structure/function relationships and target organisms and hence better exploitation of plant peptide biological activities in both the pharmaceutical and agricultural sectors. PhytAMP may be accessed free of charge at http://phytamp.pfba-lab.org.

An Acetylation/Deacetylation-SUMOylation switch through a phylogenetically conserved ΨKxEP motif in the tumor suppressor HIC1 (Hypermethylated in Cancer 1) regulates transcriptional repression activity

ABSTRACT Tumor suppressor HIC1 (hypermethylated in cancer 1) is a gene that is essential for mammalian development, epigenetically silenced in many human tumors, and involved in a complex pathway regulating P53 tumor suppression activity. HIC1 encodes a sequence-specific transcriptional repressor containing five Krüppel-like C2H2 zinc fingers and an N-terminal BTB/POZ repression domain. Here, we show that endogenous HIC1 is SUMOylated in vivo on a phylogenetically conserved lysine, K314, located in the central region which is a second repression domain. K314R mutation does not influence HIC1 subnuclear localization but significantly reduces its transcriptional repression potential, as does the mutation of the other conserved residue in the ψKXE consensus, E316A, or the overexpression of the deSUMOylase SSP3/SENP2. Furthermore, HIC1 is acetylated in vitro by P300/CBP. Strikingly, the K314R mutant is less acetylated than wild-type HIC1, suggesting that this lysine is a target for both SUMOylation and acetylation. We further show that HIC1 transcriptional repression activity is positively controlled by two types of deacetylases, SIRT1 and HDAC4, which increase the deacetylation and SUMOylation, respectively, of K314. Knockdown of endogenous SIRT1 by the transfection of short interfering RNA causes a significant loss of HIC1 SUMOylation. Thus, this dual-deacetylase complex induces either a phosphorylation-dependent acetylation-SUMOylation switch through a ψKXEXXSP motif, as previously shown for MEF2, or a phosphorylation-independent switch through a ψKXEP motif, as shown here for HIC1, since P317A mutation severely impairs HIC1 acetylation. Finally, our results demonstrate that HIC1 is a target of the class III deacetylase SIRT1 and identify a new posttranslational modification step in the P53-HIC1-SIRT1 regulatory loop.

A Solvent Model for Simulations of Peptides in Bilayers. I. Membrane-Promoting α-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.

Lectin activities of cytokines: functions and putative carbohydrate-recognition domains.

The discovery that some cytokines have carbohydrate-binding (lectin) properties opens new concepts in the understanding of their mechanism of action. The carbohydrate-recognition domain (CRD), which is localized at the opposite of the receptor-binding domain, makes these molecules bi-functional. The expression of the biological activity of the cytokine relies on its carbohydrate-binding activity, which allows the association of the cytokine receptor with molecular complexes comprising the specific kinase/phosphatase involved in receptor phosphorylation/dephosphorylation and in specific signal transduction. As a correlate, a cytokine can act only on cells possessing both the receptor and the ligand. Two cytokines using the same receptor can have different target cells and functions because of their different lectin activities. Based on a few examples, the CRD can be predicted based on the 3-D structures of the molecules.

Vibrational molecular force field of model compounds with biologic interest II: harmonic dynamics of both anomers of glucose in the crystalline state

Combining the modified Urey–Bradley–Shimanouchi intramolecular potential energy function with an appropriate intermolecular energy function, normal coordinate calculations have been performed for both α and β anomers of glucose and for some deuterated analogs in the crystalline state. The overall agreement between the observed and calculated frequencies leads to an average error on the order of 3 and 5 cm−1 for α and β glucose, respectively. In both cases, it is shown that the intermolecular potential energy terms are essential to reproduce perfectly the whole spectra, in particular for the hydroxyl stretching region, the anomeric and crystalline spectral regions, and the low‐frequency range. Moreover, the intermolecular interactions have a nonnegligible influence on the value of the intramolecular force constants. But, the potential energy distribution of vibrational modes are in accord with previous works performed for an isolated molecule. It is also important to point out that approximately the same set of force constants has been used for both molecules, differences existing only for the atoms involved in the anomeric configuration. Likewise, different charge distributions have been calculated and tested with different value of the dielectric constant. Charges determined by the AM1 quantum mechanical procedure with a value of 3 for the dielectric constant have the merit to reproduce quite well the whole spectra and in particular the frequency range below 200 cm−1.

The structures and vibrational frequencies of a series of alkanes using the SPASIBA force field

Abstract The spectroscopic potential energy function SPASIBA is applied to a series of alkanes. SPASIBA is actually a hybrid of the AMBER force field and the Urey-Bradley-Shimanouchi force field. The parameters of the energy function are optimized to give best fit to the observed vibrational spectra and structures of the series of alkanes, including a few deuterated analogs. The test molecules are methane, ethane and ethane- d 6 , propane, trans - and gauche-n -butane, cyclohexane and its fully deuterated analog, isobutane, 2-methylbutane, neopentane, 2,2,3,3-tetramethylpentane, n -octane and n -decane. A set of 18 independent force constants is found to be sufficient to represent the vibrational frequencies accurately, and the standard deviation between the observed and calculated frequencies is 13 cm −1 . Although such an accuracy was obtained using a consistent valence force field with a comparable number of adjustable parameters, 21, this potential has the merit to be expressed in a more physical way and, consequently, can be applied very easily and successfully to all the molecules without delocalized electrons and highly strained energies.

Force-field and vibrational spectra of oligosaccharides with different glycosidic linkages—Part I. Trehalose dihydrate, sophorose monohydrate and laminaribiose

Abstract The vibrational spectra of the disaccharides, trehalose dihydrate, sophorose monohydrate and laminaribiose, have been recorded in the crystalline state in the 4000-100 cm−1 spectral region for the IR spectra and in the 4000-20 cm−1 spectral range for the Raman spectra. These three disaccharides exhibit the same monosaccharide composition (i.e. glucose residue), but differ in the position and configuration of the glycosidic linkage (α, 1-1; β, 1-2 and β, 1-3 for trehalose, sophorose and laminaribiose, respectively). Most of these spectra have not yet been reported, particularly in the low frequency range. They constitute the basis of theoretical calculations of normal modes of vibration. Normal coordinate analysis has been made in the crystalline state using a modified Urey-Bradley-Shimanouchi intramolecular potential energy combined with a specific intermolecular potential energy function. The force field parameters are transformed from initial works on both anomers of glucose. The vibrational assignments of the observed bands are made on the basis of the potential energy distributions. It appears that the greatest part of the vibrational modes is very highly coupled vibrations. The calculated vibrational frequencies agree very well with the observed frequencies in the whole spectra, particularly in the “fingerprint” regions and in the low frequency range. The bands observed at 733, 773 and 755 cm−1 for trehalose dihydrate, sophorose monohydrate and laminaribiose, respectively, are calculated at 728, 772 and 755 cm−1 and are due to bending modes of heavy atoms involved in the corresponding glycosidic linkage C1O1C′x. Moreover, some known characteristic structural regions may be divided into different parts that have a specific significance. Ale standard deviation between calculated and observed frequencies below 1500 cm−1 leads to values of 3.0, 3.7 and 4.2 cm−1 for the three disaccharides, respectively.

Force field and vibrational spectra of oligosaccharides with different glycosidic linkages—Part II. Maltose monohydrate, cellobiose and gentiobiose

Abstract Complete Raman and IR spectra of maltose monohydrate, cellobiose and gentiobiose have been recorded in the crystalline state. These three disaccharides present the same monosaccharide composition of the glucose molecule and the remaining studied position (1–4 and 1–6) of the glycosidic linkage. Moreover, maltose and cellobiose present the different configurations of the glycosidic linkage α, 1–4 and β, 1–4, respectively. These data will constitute the support for theoretical calculations of normal modes of vibration. The assignments of the calculated bands of vibration will be made on the basis of the potential energy distributions using a modified Urey—Bradley—Shimanouchi intramolecular potential energy combined with a specific intermolecular potential energy function. The calculations show that using a correct initial force field, it is possible to reproduce correctly the density of observed vibrational states for large molecules such as disaccharides. The standard deviation between calculated and observed frequencies, below 1500 cm −1 , leads to values of 4.7, 4.2 and 4.6 cm − for maltose monohydrate, cellobiose and gentiobiose, respectively. Our previous investigations on trehalose dihydrate, sophorose monohydrate and laminaribiose are confirmed in this study and complete the previous assignments for the whole set of disaccharides.

Vibrational spectra of 4-methylimidazole: assignment of modes and calculation of Raman and resonance Raman intensities at the ab initio 6-31G level

Abstract Fourier transform infrared (FT-IR) and Raman (FT-R) spectra of 4-methylimidazole and its N-deuterated analogue were obtained for the solid and the aqueous solution. Assignments of the observed band wavenumbers are discussed by comparison with normal mode wavenumbers and IR and Raman intensities calculated from ab initio 6-31G force fields and optimized geometries for both 4- and 5-methylimidazole. The latter molecules are considered to be similar to two tautomers which are assumed to be present in aqueous solution in particular. These assignments were applied to the calculation of the resonance Raman relative intensities for the excited states corresponding to the lowest lying π → π∗ orbital excitations, obtained from the change in bond order and the L−1 matrix. Compared with the observed band intensities at resonance in Raman spectra recorded with excitation at 218 nm, the agreement appears to be excellent for several modes.

Antimicrobial properties of aqueous extracts from three medicinal plants growing wild in arid regions of Tunisia

Seed extracts of three plant species that grow wild in the arid regions of Tunisia, Juniperus phoenicea L. (Cupressaceae), Pistacia atlantica Desf. (Anacardiaceae), and Oudneya africana R. Br. (Brassicaceae), were examined for antimicrobial activity against bacterial food pathogens. Aqueous extracts were prepared and then precipitated with methanol or acetone. Extracted acetone fractions (pH 7.2) showed powerful antimicrobial activity, especially against Listeria monocytogenes, Listeria innocua, and Listeria ivanovii (Gram-positive) and were also active against Gram-negative strains Escherichia coli and Pseudomonas aeruginosa. Extracts selected for high antimicrobial activity were stable in the presence of organic solvents (chloroform, hexane, acetonitrile, methanol, and acetone), and withstand thermal treatments up to 100°C for 30 min. L. monocytogenes LSD530 and E. coli ATCC 25922 appeared to be inhibited by Juniperus and Pistacia extracts with a minimum concentration of 1.56 and 3. 12 mg/mL, respectively. This study established the potential of medicinal plants growing wild in arid regions of Tunisia as a source of antimicrobial agents.