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R Bonneau

Publications and source records attributed to R Bonneau.

17 recordsLinked to original sources
PubMed2001

Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.

This study explores the use of multiple sequence alignment (MSA) information and global measures of hydrophobic core formation for improving the Rosetta ab initio protein structure prediction method. The most effective use of the MSA information is achieved by carrying out independent folding simulations for a subset of the homologous sequences in the MSA and then identifying the free energy minima common to all folded sequences via simultaneous clustering of the independent folding runs. Global measures of hydrophobic core formation, using ellipsoidal rather than spherical representations of the hydrophobic core, are found to be useful in removing non-native conformations before cluster analysis. Through this combination of MSA information and global measures of protein core formation, we significantly increase the performance of Rosetta on a challenging test set. Proteins 2001;43:1-11.

Algorithms↗
PubMed2001

Rosetta in CASP4: progress in ab initio protein structure prediction.

Rosetta ab initio protein structure predictions in CASP4 were considerably more consistent and more accurate than previous ab initio structure predictions. Large segments were correctly predicted (>50 residues superimposed within an RMSD of 6.5 A) for 16 of the 21 domains under 300 residues for which models were submitted. Models with the global fold largely correct were produced for several targets with new folds, and for several difficult fold recognition targets, the Rosetta models were more accurate than those produced with traditional fold recognition models. These promising results suggest that Rosetta may soon be able to contribute to the interpretation of genome sequence information.

Protein Conformation↗
PubMed2001

Ab initio protein structure prediction: progress and prospects.

Considerable recent progress has been made in the field of ab initio protein structure prediction, as witnessed by the third Critical Assessment of Structure Prediction (CASP3). In spite of this progress, much work remains, for the field has yet to produce consistently reliable ab initio structure prediction protocols. In this work, we review the features of current ab initio protocols in an attempt to highlight the foundations of recent progress in the field and suggest promising directions for future work.

Algorithms↗
PubMed2001

Photochemistry of methoxyhydroquinone and methoxy-p-benzoquinone in solution related to the photoyellowing of the lignocellulosics.

The photoreactivity of methoxy-p-benzoquinone (MQ) and methoxyhydroquinone (MHQ) in dilute solution (10(-4)-10(-3) M) was studied using continuous irradiation and laser flash photolysis (LFP). The quinone irradiated in degassed tetrahydrofuran (THF) gives MHQ and an adduct with the solvent. Only the formation of hydroquinone is observed in ethanol, and hydroxylation is evidenced in water, whereas the compound is stable in CCl4. The bis-quinone, 4,4'-dimethoxybiphenyl-2,5,2',5'-bisquinone, and the dibenzofurane-quinone, 8-hydroxy-3,7-dimethoxydibenzofuran-1,4-quinone, are formed in the presence of MHQ, whereas the reactivity is low with ethylconiferyl alcohol. When MHQ is irradiated selectively in degassed THF, the formation of MQ and of the bis-hydroquinone, 4,4'-dimethoxy-2,5,2',5'-tetrahydroxy-biphenyl, are observed. The dimer is oxidized photochemically or thermally into the mono- or bis-quinones, the process being accelerated in alkaline medium. The formation of the dimers is strongly favored by the contiguous presence of quinone and hydroquinone. When MHQ is selectively irradiated in the presence of transethylconiferaldehyde (EtC), quinone formation and isomerization of EtC are observed. LFP experiments, performed with a selective excitation of MQ, indicate that the triplet state of the quinone is strongly quenched by MHQ to conduce to a semiquinone radical. The interaction between 3MQ* and MQ is mainly driven by an electron transfer process according to the similar value of the quenching rate constant found with another electron donor compound such as 1,4-dimethoxybenzene. By contrast, no strong quenching of 3EtC* by MHQ was observed. It is proposed that the photochemistry of the couple MQ/MHQ is governed by the formation of encounter complex between either 3MQ* and MHQ or 3MHQ* and MQ. Consequently, the fast part of the photoyellowing of lignocellulosics does not appear to involve the couple MHQ/MQ or MHQ/etherified coniferaldehyde, but more likely a combination of oxidation of the hydroquinone by ground-state oxygen and photohydration of the formed quinone from its triplet state, giving inter-alia more colored o-quinonoid type molecules.

Benzoquinones↗
PubMed1999

Ab initio protein structure prediction of CASP III targets using ROSETTA.

To generate structures consistent with both the local and nonlocal interactions responsible for protein stability, 3 and 9 residue fragments of known structures with local sequences similar to the target sequence were assembled into complete tertiary structures using a Monte Carlo simulated annealing procedure (Simons et al., J Mol Biol 1997; 268:209-225). The scoring function used in the simulated annealing procedure consists of sequence-dependent terms representing hydrophobic burial and specific pair interactions such as electrostatics and disulfide bonding and sequence-independent terms representing hard sphere packing, alpha-helix and beta-strand packing, and the collection of beta-strands in beta-sheets (Simons et al., Proteins 1999;34:82-95). For each of 21 small, ab initio targets, 1,200 final structures were constructed, each the result of 100,000 attempted fragment substitutions. The five structures submitted for the CASP III experiment were chosen from the approximately 25 structures with the lowest scores in the broadest minima (assessed through the number of structural neighbors; Shortle et al., Proc Natl Acad Sci USA 1998;95:1158-1162). The results were encouraging: highlights of the predictions include a 99-residue segment for MarA with an rmsd of 6.4 A to the native structure, a 95-residue (full length) prediction for the EH2 domain of EPS15 with an rmsd of 6.0 A, a 75-residue segment of DNAB helicase with an rmsd of 4.7 A, and a 67-residue segment of ribosomal protein L30 with an rmsd of 3.8 A. These results suggest that ab initio methods may soon become useful for low-resolution structure prediction for proteins that lack a close homologue of known structure.

Algorithms↗
PubMed1994

Spatial distribution of DNA ploidy in colorectal carcinoma.

This paper reports on the phenomenon of heterogeneity of DNA distribution in colorectal carcinoma. The aim of this study was to find a new strategy in sampling methodology as a solution to the heterogeneity problem by studying ploidy topography. The study was carried out by using image analysis for densitometric measurements of tissue imprints of 19 colorectal specimens after Feulgen staining. Heterogeneity of ploidy in colorectal carcinoma is well known; therefore, we wished to determine whether this heterogeneity is random within different parts of a colorectal tumour. For each tumour, five systematic and reproducible samples were taken from the peripheral, intermediate and central tumoural areas. In addition two samples were taken from adjacent non-tumoural areas: one from the proximal and the other from the distal site with respect to the neoplastic lesion. By using image analysis three parameters were obtained. Mean DNA content was computed for each sample and expressed in arbitrary units (DNA-a.u.) from the measurement of integrated optical density according to the Beer Lambert law. Secondly mean DNA content expressed in relative units (DNA-r.u.) was computed according to an internal euploid control. Finally entropy was computed from each histogram of DNA content. Experimental design was based on a repeated measures analysis of variance with a priori orthogonal comparisons. We found that DNA content and particularly entropy are not randomly distributed. Furthermore, there was a significant difference between the two non-tumoural epithelia.

Colorectal Neoplasms↗
PubMed1991

Plexiform fibrohistiocytic tumor.

Two groups of cells, one rounded or oval and the other spindle-shaped, were found in a case of plexiform fibrohistiocytic tumor. Immunohistochemistry was strongly positive for alpha smooth muscle actin in most cells of both types but stronger in the spindle-shaped cells, suggesting a myofibroblastic origin. This was in correlation with electron microscopic findings which revealed fibroblasts, myofibroblasts and some undifferentiated mesenchymal cells. However, factor XIIIa was negative suggesting that this tumor does not originate from dermal dendrocytes.

Adolescent↗
PubMed1984

[Merkel's tumor].

Explore the source record for details and available documents.

Adolescent↗
PubMed1983

Neuromuscular choristoma. A clinicopathologic study of two cases.

Neuromuscular choristoma, also known as benign "triton" tumor, is an uncommon peripheral nerve tumor usually occurring in early childhood. We report two cases, a 6-year-old girl with a solitary tumor of the supraclavicular fossa, and a 14-year-old girl with multiple small neuromuscular choristomas surrounding a recurrent massive musculoaponeurotic fibromatosis of the right axilla. These choristomas were bound firmly to the involved nerves, and consisted histologically of bundles of mature striated muscle fibers intermingled with myelinated nerve fibers. Our review of the literature indicates that these tumors are benign, regress with time, do not recur, and are usually not accompanied by functional impairment of the affected nerves before biopsy, so that wide or complete excision should not be attempted. Histogenetically, the striated muscle fibers in the nerves probably derive from nondifferentiated ectomesenchymal cells.

Adolescent↗
PubMed1978

Complications of water-soluble contrast lumbar myelography. Review of the literature and case report.

A historic review of the development of water-soluble contrast materials for lumbar myelography is presented. This is followed by a discussion of their advantages and complications, as well as a case report of convulsive segmental myoclonus, hypotension, and death after myelography associated with the use of dimeglumine locarmate (Dimer-X). A new nonionic material, metrizamide (Amipaque), is discussed, and its current clinical status is summarized.

Aged↗
PubMedDate not supplied

Functional inferences from blind ab initio protein structure predictions.

Ab initio protein structure prediction methods have improved dramatically in the past several years. Because these methods require only the sequence of the protein of interest, they are potentially applicable to the open reading frames in the many organisms whose sequences have been and will be determined. Ab initio methods cannot currently produce models of high enough resolution for use in rational drug design, but there is an exciting potential for using the methods for functional annotation of protein sequences on a genomic scale. Here we illustrate how functional insights can be obtained from low-resolution predicted structures using examples from blind ab initio structure predictions from the third and fourth critical assessment of structure prediction (CASP3, CASP4) experiments.

Computational Biology↗