Biomedical subjects

Jean-Paul Mornon

Publications and source records attributed to Jean-Paul Mornon.

At least 19 recordsLinked to original sources

PubMed2007

A generalized analysis of hydrophobic and loop clusters within globular protein sequences.

BACKGROUND: Hydrophobic Cluster Analysis (HCA) is an efficient way to compare highly divergent sequences through the implicit secondary structure information directly derived from hydrophobic clusters. However, its efficiency and application are currently limited by the need of user expertise. In order to help the analysis of HCA plots, we report here the structural preferences of hydrophobic cluster species, which are frequently encountered in globular domains of proteins. These species are characterized only by their hydrophobic/non-hydrophobic dichotomy. This analysis has been extended to loop-forming clusters, using an appropriate loop alphabet. RESULTS: The structural behavior of hydrophobic cluster species, which are typical of protein globular domains, was investigated within banks of experimental structures, considered at different levels of sequence redundancy. The 294 more frequent hydrophobic cluster species were analyzed with regard to their association with the different secondary structures (frequencies of association with secondary structures and secondary structure propensities). Hydrophobic cluster species are predominantly associated with regular secondary structures, and a large part (60 %) reveals preferences for alpha-helices or beta-strands. Moreover, the analysis of the hydrophobic cluster amino acid composition generally allows for finer prediction of the regular secondary structure associated with the considered cluster within a cluster species. We also investigated the behavior of loop forming clusters, using a "PGDNS" alphabet. These loop clusters do not overlap with hydrophobic clusters and are highly associated with coils. Finally, the structural information contained in the hydrophobic structural words, as deduced from experimental structures, was compared to the PSI-PRED predictions, revealing that beta-strands and especially alpha-helices are generally over-predicted within the limits of typical beta and alpha hydrophobic clusters. CONCLUSION: The dictionary of hydrophobic clusters described here can help the HCA user to interpret and compare the HCA plots of globular protein sequences, as well as provides an original fundamental insight into the structural bricks of protein folds. Moreover, the novel loop cluster analysis brings additional information for secondary structure prediction on the whole sequence through a generalized cluster analysis (GCA), and not only on regular secondary structures. Such information lays the foundations for developing a new and original tool for secondary structure prediction.

Cluster Analysis↗

PubMed2006

Cernunnos interacts with the XRCC4 x DNA-ligase IV complex and is homologous to the yeast nonhomologous end-joining factor Nej1.

DNA double strand breaks are considered as the most harmful DNA lesions and are repaired by either homologous recombination or nonhomologous end joining (NHEJ). A new NHEJ factor, Cernunnos, has been identified, the defect of which leads to a severe immunodeficiency condition associated with microcephaly and other developmental defects in humans. This presentation is reminiscent to that of DNA-ligase IV deficiency and suggests a possible interplay between Cernunnos and the XRCC4 x DNA-ligase IV complex. We show here that Cernunnos physically interacts with the XRCC4 x DNA-ligase IV complex. Moreover, a combination of sensitive methods of sequence analysis revealed that Cernunnos can be associated with the XRCC4 family of proteins and that it corresponds to the genuine homolog of the yeast Nej1 protein. Altogether these results shed new lights on the last step, the DNA religation, of the NHEJ pathway.

Amino Acid Sequence↗

PubMed2005

Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes.

BACKGROUND: To date, only a few transcription factors have been identified in the genome of the parasite Plasmodium falciparum, the causative agent of malaria. Moreover, no detailed molecular analysis of its basal transcription machinery, which is otherwise well-conserved in the crown group of eukaryotes, has yet been reported. In this study, we have used a combination of sensitive sequence analysis methods to predict the existence of several parasite encoded general transcription factors associated with RNA polymerase II. RESULTS: Several orthologs of general transcription factors associated with RNA polymerase II can be predicted among the hypothetical proteins of the P. falciparum genome using the two-dimensional Hydrophobic Cluster Analysis (HCA) together with profile-based search methods (PSI-BLAST). These predicted orthologous genes encoding putative transcription factors include the large subunit of TFIIA and two candidates for its small subunit, the TFIIE beta-subunit, which would associate with the previously known TFIIE alpha-subunit, the TFIIF beta-subunit, as well as the p62/TFB1 subunit of the TFIIH core. Within TFIID, the putative orthologs of TAF1, TAF2, TAF7 and TAF10 were also predicted. However, no candidates for TAFs with classical histone fold domain (HFD) were found, suggesting an unusual architecture of TFIID complex of RNA polymerase II in the parasite. CONCLUSION: Taken together, these results suggest that more general transcription factors may be present in the P. falciparum proteome than initially thought. The prediction of these orthologous general transcription factors opens the way for further studies dealing with transcriptional regulation in P. falciparum. These alternative and sensitive sequence analysis methods can help to identify candidates for other transcriptional regulatory factors in P. falciparum. They will also facilitate the prediction of biological functions for several orphan proteins from other apicomplexan parasites such as Toxoplasma gondii, Cryptosporidium parvum and Eimeria.

Amino Acid Sequence↗

PubMed2005

The Hedgehog-inducible ubiquitin ligase subunit WSB-1 modulates thyroid hormone activation and PTHrP secretion in the developing growth plate.

WSB-1 is a SOCS-box-containing WD-40 protein of unknown function that is induced by Hedgehog signalling in embryonic structures during chicken development. Here we show that WSB-1 is part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2). The WD-40 propeller of WSB-1 recognizes an 18-amino-acid loop in D2 that confers metabolic instability, whereas the SOCS-box domain mediates its interaction with a ubiquitinating catalytic core complex, modelled as Elongin BC-Cul5-Rbx1 (ECS(WSB-1)). In the developing tibial growth plate, Hedgehog-stimulated D2 ubiquitination via ECS(WSB-1) induces parathyroid hormone-related peptide (PTHrP), thereby regulating chondrocyte differentiation. Thus, ECS(WSB-1) mediates a mechanism by which 'systemic' thyroid hormone can effect local control of the Hedgehog-PTHrP negative feedback loop and thus skeletogenesis.

Amino Acid Sequence↗

PubMed2005

Characterization and study of a kappa-casein-like chymosin-sensitive linkage.

The present report is dealing with the identification, in various unrelated proteins, of protein fragments sharing local sequence and structure similarities with the chymosin-sensitive linkage surrounding the Phe-Met/Ile bond of kappa-caseins. In all these proteins, this linkage is observed within an exposed beta-strand-like structure, as also predicted for kappa-caseins. The structure of one of these fragments, included in glutamine synthetase, particularly superimposes well with the conformation observed for a chymosin inhibitor (CP-113972) within the complex it forms with chymosin and can be similarly accommodated by specificity pockets within the enzyme substrate binding cleft. The effect of the enzyme activity of chymosin was thus tested on glutamine synthetase. Chymosin cut the latter at the Phe-Met linkage, suggesting that this system may locally resemble the kappa-casein/chymosin complex.

Animals↗

PubMed2004

OCRE: a novel domain made of imperfect, aromatic-rich octamer repeats.

SUMMARY: In this study, we describe a novel domain, OCRE, which is shared by the recently identified angiogenic factor VG5Q and a specific family of RNA-binding motif proteins. The OCRE domain is characterized by a 5-fold, imperfectly repeated octameric sequence, which includes a triplet of often-conserved aromatic amino acids predicted to form a beta-strand and in which the slightly modified fifth repeat might act as a repeat terminator. Although the function of this domain remains to be elucidated, the domain architecture of OCRE containing proteins and experimental data suggest a role in RNA metabolism and/or in signalling pathways activated by the tumor necrosis factor superfamily of cytokines.

Angiogenic Proteins↗

PubMed2004

Voro3D: 3D Voronoi tessellations applied to protein structures.

UNLABELLED: Voro3D is an original easy-to-use tool, which provides a brand new point of view on protein structures through the three-dimensional (3D) Voronoi tessellations. To construct the Voronoi cells associated with each amino acid by a number of different tessellation methods, Voro3D uses a protein structure file in the PDB format as an input. After calculation, different structural properties of interest like secondary structures assignment, environment accessibility and exact contact matrices can be derived without any geometrical cut-off. Voro3D provides also a visualization of these tessellations superimposed on the associated protein structure, from which it is possible to model a polygonal protein surface using a model solvent or to quantify, for instance, the contact areas between a protein and a ligand. AVAILABILITY: The software executable file for PC using Windows 98, 2000, NT, XP can be freely downloaded at http://www.lmcp.jussieu.fr/~mornon/voronoi.html CONTACT: franck.dupuis@sanofi-aventis.com; jean-paul-mornon@imcp.jussieu.fr.

Algorithms↗

PubMed2004

Protein secondary structure assignment through Voronoï tessellation.

We present a new automatic algorithm, named VoTAP (Voronoï Tessellation Assignment Procedure), which assigns secondary structures of a polypeptide chain using the list of alpha-carbon coordinates. This program uses three-dimensional Voronoï tessellation. This geometrical tool associates with each amino acid a Voronoï polyhedron, the faces of which unambiguously define contacts between residues. Thanks to the face area, for the contacts close together along the primary structure (low-order contacts) a distinction is made between strong and normal ones. This new definition yields new contact matrices, which are analyzed and used to assign secondary structures. This assignment is performed in two stages. The first one uses contacts between residues close together along the primary structure and is based on data collected on a bank of 282 well-refined nonredundant structures. In this bank, associations were made between the prints defined by these low-order contacts and the assignments performed by different automatic methods. The second step focuses on the strand assignment and uses contacts between distant residues. Comparison with several other automatic assignment methods are presented, and the influence of resolution on the assignment is investigated.

Algorithms↗

PubMed2004

Analysis of fragments induced by simulated lattice protein folding.

The folding process of a set of 42 proteins, representative of the various folds, has been simulated by means of a Monte Carlo method on a discrete lattice, using two different potentials of mean force. Multiple compact fragments of contiguous residues are formed in the simulation, stable in composition, but not in geometry. During time, the number of fragments decreases until one final compact globular state is reached. We focused on the early steps of the folding in order to evidence the maximum number of fragments, provided they are sufficiently stable in sequence. A correlation has been established between these proto fragments and regular secondary-structure elements, whatever their nature, alpha helices or beta strands. Quantitatively, this is revealed by an overall mean one-residue quality factor of nearly 60%, which is better for proteins mainly composed of alpha helices. The correspondence between the number of fragments and the number of secondary-structure elements is of 77% and the regions separating successive fragments are mainly located in loops. Besides, hydrophobic clusters deduced from HCA correspond to fragments with an equivalent accuracy. These results suggest that folding pathways do not contain structurally static intermediate. However, since the beginning of folding, most residues that will later form one given secondary structure are kept close in space by being involved in the same fragment. This aggregation may be a way to accelerate the formation of the native state and enforces the key role played by hydrophobic residues in the formation of the fragments, thus in the folding process itself.

Computer Simulation↗

PubMed2003

Non-intertwined binary patterns of hydrophobic/nonhydrophobic amino acids are considerably better markers of regular secondary structures than nonconstrained patterns.

Patterns of hydrophobic and hydrophilic residues (binary patterns) play an important role in protein architecture and can be roughly categorized into two classes regarding their preferential participation in alpha-helices or beta-strands. However, a single binary pattern can be embedded into different longer patterns carrying opposite structural information and thus cannot be as much informative as expected. Here, we consider conditional binary patterns, or hydrophobic clusters, whose existence is conditioned by the presence of a minimum number of nonhydrophobic residues, called the connectivity distance, that separate two hydrophobic amino acids assumed to belong to two distinct patterns. Conditional binary patterns are distinct from simple ones in that they are not intertwined, i.e., they can not include or be included in other conditional patterns and therefore carry a much more differentiated information, in particular being dramatically better correlated with regular secondary structures (especially beta ones). The distribution of these nonintertwined binary patterns in natural proteins was assessed relative to randomness, evidencing the structural bricks that are favored and disfavored by evolutionary selection. Several connectivity distances as well as several hydrophobic alphabets were tested, evidencing the clear superiority of a connectivity distance of 4, which mimics the minimum current length of loops in globular domains, and of the VILFMYW alphabet, selected from structural data (secondary structure propension and Voronoï tesselation), in highlighting fundamental properties of protein folds.

Amino Acid Sequence↗

PubMed2003

A new protein folding algorithm based on hydrophobic compactness: Rigid Unconnected Secondary Structure Iterative Assembly (RUSSIA). I: Methodology.

We present an algorithm that is able to propose compact models of protein 3D structures, only starting from the prediction of the nature and length of regular secondary structures. Helices are modeled by cylinders and sheets by helicoid surfaces, all strands of a sheet being considered as a single block. It means that relative topology of the strands inside one sheet is a prerequisite. Loops are only considered as constraints, given by the maximal distance between their Calpha extremities according to their sequence length. Unconnected regular secondary structures are reduced to a single point, the center of their hydrophobic faces. These centers are then repeatedly moved in order to obtain a compact hydrophobic core. To prevent secondary structures from interpenetrating, a repulsive term is introduced in the function whose minimization leads to the compact structure. This RUSSIA (Rigid Unconnected Secondary Structure Assembly) algorithm has the advantage of relying on a small number of variables and therefore many initial conformations can be tested. Flexibility is produced in the following way: helices or sheets are allowed to rotate around the direction leading to the center of the model; residues in a sheet can slide along the main direction of the strand where they are embedded. RUSSIA is fast and simple and it produces on a test set several neighbor good models with an r.m.s. to the native structures in the range 1.4-3.7 A. These models can be further treated by statistical potentials used in threading approaches in order to detect the best candidate. The limits of the present method are the following: small proteins with few secondary structures are excluded; multi domain proteins must be split into several compact globular domains from their sequences; sheets of more than five strands and completely buried helices are not treated. In this first paper the algorithm is developed and in Part II, which follows, some applications are presented and the program is evaluated.

Algorithms↗

PubMed2003

A new protein folding algorithm based on hydrophobic compactness: Rigid Unconnected Secondary Structure Iterative Assembly (RUSSIA). II: Applications.

The RUSSIA procedure (Rigid Unconnected Secondary Structure Iterative Assembly) produces structural models of cores of small- and medium-sized proteins. Loops are omitted from this treatment and regular secondary structures are reduced to points, the centers of their hydrophobic faces. This methodology relies on the maximum compactness of the hydrophobic residues, as described in detail in Part I. Starting data are the sequence and the predicted limits and natures of regular secondary structures (alpha or beta). Helices are treated as rigid cylinders, whereas beta-strands are collectively taken into account within beta-sheets modeled by helicoid surfaces. Strands are allowed to shift along their mean axis to allow some flexibility and the alpha-helices can be placed on either side of beta-sheets. Numerous initial conformations are produced by discrete rotations of the helices and sheets around the direction going from the center of their hydrophobic face to the global center of the protein. Selection of proposed models is based upon a criterion lying on the minimization of distances separating hydrophobic residues belonging to different regular secondary structures. The procedure is rapid and appears to be robust relative to the quality of starting data (nature and length of regular secondary structures). This dependence of the quality of the model on secondary structure prediction and in particular the beta-sheet topology, is one of the limits of the present algorithm. We present here some results for a set of 12 proteins (alpha, beta and alpha/beta classes) of lengths 40-166 amino acids. The r.m.s. deviations for core models with respect to the native proteins are in the range 1.4-3.7 A.

Algorithms↗

PubMed2002

Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds.

A three-dimensional Voronoi tessellation of folded proteins is used to analyze geometrical and topological properties of a set of proteins. To each amino acid is associated a central point surrounded by a Voronoi cell. Voronoi cells describe the packing of the amino acids. Special attention is given to reproduction of the protein surface. Once the Voronoi cells are built, a lot of tools from geometrical analysis can be applied to investigate the protein structure; volume of cells, number of faces per cell, and number of sides per face are the usual signatures of the protein structure. A distinct difference between faces related to primary, secondary, and tertiary structures has been observed. Faces threaded by the main-chain have on average more than six edges, whereas those related to helical packing of the amino acid chain have less than five edges. The faces on the protein surface have on average five edges within 1% error. The average number of faces on the protein surface for a given type of amino acid brings a new point of view in the characterization of the exposition to the solvent and the classification of amino acid as hydrophilic or hydrophobic. It may be a convenient tool for model validation.

Algorithms↗

PubMed2002

Towards a new T-fold protein?: the coproporphyrinogen III oxidase sequence matches many structural features from urate oxidase.

Urate oxidase (UOX) and coproporphyrinogen III oxidase (CPO) are two unusual oxidases as they accomplish their catalytic act with no co-factor nor metal ion. They both require molecular oxygen, and lead to hydrogen peroxide in addition to the product. UOX is composed of two contiguous Tunneling-fold domains and CPO appears to be also divided into two structurally equivalent domains. Moreover, each of these putative domains can be coherently aligned on UOX domains. Although their sequences are very distant, we therefore suggest that functional CPO dimer is built around a tunnel, with the substrate sitting above it, on the N- and C-terminal side. This overall model is supported by mutation data and is coherent with the chemical events expected for substrate processing by CPO.

Amino Acid Sequence↗

PubMed2002

Metallo-beta-lactamase fold within nucleic acids processing enzymes: the beta-CASP family.

A separate family of enzymes within the metallo-beta-lactamase fold comprises several important proteins acting on nucleic acid substrates, involved in DNA repair (Artemis, SNM1 and PSO2) and RNA processing [cleavage and polyadenylation specificity factor (CPSF) subunit]. Proteins of this family, named beta-CASP after the names of its representative members, possess specific features relative to those of other metallo-beta-lactamases, that are concentrated in the C-terminal part of the domain. In this study, using sensitive methods of sequence analysis, we identified highly conserved amino acids specific to the beta-CASP family, some of which were unidentified to date, that are predicted to play critical roles in the enzymatic function. The identification and characterisation of all the extant, detectable beta-CASP members within sequence databases and genome data also allowed us to unravel particular sequence features which are likely to be involved in substrate specificity, as well as to describe new but as yet uncharacterised members which may play critical roles in DNA and RNA metabolism.

Amino Acid Motifs↗

PubMed2002

Viral fusion peptides and identification of membrane-interacting segments.

Viral envelope glycoproteins promote infection by mediating fusion between viral and cellular membranes. Fusion occurs after dramatic conformational changes within fusion proteins, leading to the exposure of a short stretch of mostly apolar residues, termed the fusion peptide, which is presumed to insert into the membrane and initiate the fusion process. The typical global composition of fusion peptides, rich in hydrophobic but also in small amino acids such as alanine and glycine, was used here as bait to detect other peptidic segments that can insert into membranes. We so evidenced a similar composition in several cytotoxic peptides, which promote pore formation such as peptides involved in amyloidoses and hydrophobic alpha-hairpins of pore-forming toxins. It is suggested that the structural plasticity observed for several membrane active peptides can be conferred by this particular global amino acid composition, which could be thus used to predict such functional behavior from genome data.

Amino Acid Sequence↗

PubMed2002

The Ig-like structure of the C-terminal domain of lamin A/C, mutated in muscular dystrophies, cardiomyopathy, and partial lipodystrophy.

Lamins are nuclear intermediate filaments that, together with lamin-associated proteins, maintain nuclear shape and provide a structural support for chromosomes and replicating DNA. We have determined the solution structure of the human lamin A/C C-terminal globular domain which contains specific mutations causing four different heritable diseases. This domain encompasses residues 430-545 and adopts an Ig-like fold of type s. We have also characterized by NMR and circular dichroism the structure and thermostability of three mutants, R453W and R482W/Q, corresponding to "hot spots" causing Emery-Dreifuss muscular dystrophy and Dunnigan-type lipodystrophy, respectively. Our structure determination and mutant analyses clearly show that the consequences of the mutations causing muscle-specific diseases or lipodystrophy are different at the molecular level.

Amino Acid Sequence↗

PubMed2002

Modification of a reactive cysteine explains differences between rasburicase and Uricozyme, a natural Aspergillus flavus uricase.

Urate oxidase is used in humans for the control of uric acid in patients receiving chemotherapy. Rasburicase (Fasturtec/Elitek), a recombinant urate oxidase expressed in Saccharomyces cerevisiae, was compared with Uricozyme, the natural enzyme produced by Aspergillus flavus. Rasburicase has a higher purity as demonstrated by SDS/PAGE and chromatographic analysis and a better specific activity. The differences observed for Uricozyme are likely attributable to the previously used purification process, which modifies the enzyme. The production process of rasburicase, on the other hand, preserves the structure of the molecule. MS analysis shows that Uricozyme contains a cysteine adduct on Cys(103). In the crystal structure, the sulphur atom of the cysteine residue in position 103 is orientated to the external surface of the tetramer, whereas the sulphur atom of two other cysteine residues (Cys(35) and Cys(290)) is orientated to the centre of the canal formed by the tetramer. The same adduct is produced by simple incubation of the rasburicase with cysteine.

Aspergillus flavus↗