François-Yves Dupradeau

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications.

Phenotypic expression of the C282Y/Q283P compound heterozygosity in HFE and molecular modeling of the Q283P mutation effect.

In Caucasians, from 4 to 35% of hereditary hemochromatosis (HH) patients carry a least one chromosome without a common assigned HFE mutation (i.e., C282Y, H63D, and S65C). We have undertaken a D-HPLC scanning of the HFE coding region in such patients in order to identify uncommon mutations liable to explain their high transferrin saturation level. Twenty HH patients from Brittany carrying at least one chromosome without an assigned mutation were selected on the basis of a transferrin saturation level with the following threshold: > or = 60% in men and > or = 50% in women, in the absence of other known causes of iron disorders. This strategy allowed us to detect a heterozygous sequence variant in exon 4 of the HFE gene from one individual who was also heterozygous for C282Y. Subsequent DNA sequencing analysis identified an adenine to cytosine transversion at position 848 which changes amino acid 283 from glutamine to proline (Q283P). Family study revealed a clear association between the C282Y/Q283P compound heterozygote genotype and the development of HH. Molecular modeling studies are in favor of a destabilizing effect of the Q283P mutation on the tertiary structure of the HFE protein. This is the first report of a natural protein variant describing the introduction of a proline in a central beta-strand position. Our approach may have practical implications in screening strategies for hereditary hemochromatosis, molecular diagnosis, and HFE structure-function relationships.

Multimeric Lactoside “Click Clusters” as Tools to Investigate the Effect of Linker Length in Specific Interactions with Peanut Lectin, Galectin-1, and -3

Multimeric lactosides based on carbohydrate scaffolds with valencies ranging from 1 to 4 and different linker lengths were synthesized by a copper‐catalyzed azide–alkyne cycloaddition (CuAAC). The binding affinities and crosslinking abilities of the new “click clusters” toward biologically relevant galectins (gal‐1, gal‐3) and peanut lectin were evaluated by fluorescent polarization assay (FPA) and enzyme‐linked lectin assay (ELLA), respectively. FPA indicated that the binding affinities of the synthetic multilactosides towards the galectins increased proportionally with their lactosyl content, without significant differences due to the spacer length. ELLA evidenced a modest cluster effect for the multivalent conjugates, with a relative potency per lactoside ranging from 2.1 to 3.2. Nearly identical binding affinities were recorded for derivatives differing in the length of the linkers, in agreement with the FPA data. These results demonstrate that this parameter does not significantly influence the recognition process when interactions occur at a single lectin site. Molecular dynamics revealed that glycoconjugates adopt a pseudoglobular structure with a random localization of the lactoside residues. These spatial distributions were observed irrespective of the linker length; this explains the virtually equal affinities recorded by ELLA. In contrast, two‐site “sandwich” ELLA clearly revealed that multivalent derivatives bearing the longest spacers were more efficient for crosslinking lectins. Intrinsic affinities, devoid of aggregation effects, and crosslinking capabilities are, therefore, not directly related phenomena that must be taking into consideration in neoglycoconjugate design for specific applications.

The Q283P amino-acid change in HFE leads to structural and functional consequences similar to those described for the mutated 282Y HFE protein

In Caucasians, 4–35% of hemochromatosis patients carry at least one chromosome without a common HFE mutation (i.e. C282Y, H63D and S65C). Several studies have now shown that iron overload phenotypes in such patients can be associated with uncommon HFE mutations. We previously supported implication of the C282Y/Q283P compound heterozygous genotype in hemochromatosis phenotypes and, based on molecular dynamics simulations, proposed that the Q283P substitution prevents normal folding of the HFE α3-domain. In the current work, we have used HeLa cells carrying wild-type or Q283P-mutant HFE cDNA under the control of a tetracycline-sensitive promoter to functionally characterise the Q283P mutation. Experiments using cells over-expressing wild-type HFE confirm the existence of β2microglobulin(β2m)/HFE and HFE/transferrin receptor 1 (TfR1) interactions, as well as the capacity of HFE to reduce transferrin-mediated iron uptake. In contrast, neither β2m/HFE nor HFE/TfR1 complex formation was detected in cells over-expressing the mutated form of HFE. Moreover, the 283P HFE protein was found to have a very limited effect on the major cellular iron uptake pathway. Combined, our results indicate that the Q283P mutation leads to structural and functional consequences similar to those described for the main hereditary hemochromatosis mutation. As a consequence, our study has implications for the screening of hemochromatosis patients that have one or two copies of HFE which lack the main mutations. It also highlights that protein structure prediction methods could be more generally used to better interpret relationships between rare genotypes and molecular diagnosis of a human inherited disorder.

A 3-dimensional model building by homology of the HFE protein: molecular consequences and application to antibody development.

Genetic hemochromatosis (GH) is a common inherited disease of iron metabolism affecting 2-5 in 1000 individuals of European origin. A candidate gene for GH, namely HFE has been recently characterized. Structural studies of the protein product of the HFE gene are of major interest for a better understanding of the molecular physiopathology in iron overload. We have built a 3-dimensional model of the HFE protein based on congruent with40% homology of sequence identity with HLA-Aw68, another MHC class I molecule. This work presents the first 3-dimensional structure of HFE available in the public domain (http://swift.embl-heidelberg.de/service/francois). The 3-dimensional characteristics of the protein complexed with the beta2-microglobulin are presented. The model has been used to predict immunogenic loops and to develop an antibody able to recognize a protein exhibiting the same molecular weight as HFE. Structural consequences of two common mutations are debated and evolutionary hypotheses are considered in the discussion of the particular biological activity of HFE. This study shows that a strategy based on homology modeling is sufficient to undertake biological investigations.

Bindings of hMRP1 transmembrane peptides with dodecylphosphocholine and dodecyl-β-d-maltoside micelles: a molecular dynamics simulation study.

In this paper, we describe molecular dynamics simulation results of the interactions between four peptides (mTM10, mTM16, TM17 and KTM17) with micelles of dodecylphosphocholine (DPC) and dodecyl-β-d-maltoside (DDM). These peptides represent three transmembrane fragments (TM10, 16 and 17) from the MSD1 and MSD2 membrane-spanning domains of an ABC membrane protein (hMRP1), which play roles in the protein functions. The peptide-micelle complex structures, including the tryptophan accessibility and dynamics were compared to circular dichroism and fluorescence studies obtained in water, trifluoroethanol and with micelles. Our work provides additional results not directly accessible by experiments that give further support to the fact that these peptides adopt an interfacial conformation within the micelles. We also show that the peptides are more buried in DDM than in DPC, and consequently, that they have a larger surface exposure to water in DPC than in DDM. As noted previously by simulations and experiments we have also observed formation of cation-π bonds between the phosphocholine DPC headgroup and Trp peptide residue. Concerning the peptide secondary structures (SS), we find that in TFE their initial helical conformations are maintained during the simulation, whereas in water their initial SS are lost after few nanoseconds of simulation. An intermediate situation is observed with micelles, where the peptides remain partially folded and more structured in DDM than in DPC. Finally, our results show no sign of β-strand structure formation as invoked by far-UV CD experiments even when three identical peptides are simulated either in water or with micelles.