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J Garnier

Publications and source records attributed to J Garnier.

At least 37 records · Page 2Linked to original sources
PubMed1997

Protein topology recognition from secondary structure sequences: application of the hidden Markov models to the alpha class proteins.

The three-dimensional fold of a protein is described by the organization of its secondary structure elements in 3D space, i.e. its "topology". We find that the protein topology can be recognized from the ID sequence of secondary structure states of the residues alone. Automated recognition is facilitated by use of hidden Markov models (HMMs) to represent topology families of proteins. Such models can be trained on the experimentally observed secondary structure sequences of family members using well established algorithms. Here, we model various topology groups in the alpha class of proteins and identify, from a large database, those proteins having the topology described by each model. The correct topology family for protein secondary structure sequences could be recognized 12 out of 14 times. When the observed secondary structure sequences are replaced with predicted sequences recognition is still achievable 8 out of 14 times. The success rate for observed sequences indicates that our approach will become increasingly useful as the accuracy of secondary prediction algorithms is improved. Our study indicates that the HMMs are useful for protein topology recognition even when no detectable primary amino acid sequence similarity is present. To illustrate the potential utility of our method, protein topology recognition is attempted on leptin, the obese gene product, and the human interleukin-6 sequence, for which fold predictions have been previously published.

Algorithms↗
PubMed1997

Fold recognition using predicted secondary structure sequences and hidden Markov models of protein folds.

We present an analysis of the blind predictions submitted to the fold recognition category for the second meeting on the Critical Assessment of techniques for protein Structure Prediction. Our method achieves fold recognition from predicted secondary structure sequences using hidden Markov models (HMMs) of protein folds. HMMs are trained only with experimentally derived secondary structure sequences of proteins having similar fold, therefore protein structures are described by the models at a remarkably simplified level. We submitted predictions for five target sequences, of which four were later found to be suitable for threading. Our approach correctly predicted the fold for three of them. For a fourth sequence the fold could have been correctly predicted if a better model for its structure was available. We conclude that we have additional evidence that secondary structure information represents an important factor for achieving fold recognition.

Algal Proteins↗
PubMed1997

Incorporating global information into secondary structure prediction with hidden Markov models of protein folds.

Here we propose an approach to include global structural information in the secondary structure prediction procedure based on hidden Markov models (HMMs) of protein folds. We first identify the correct fold or 'topology' of a protein by means of the HMMs of topology families of proteins. Then the most likely structural model for that protein is used to modify the sequence of secondary structure states previously obtained with a prediction algorithm. Our goal is to investigate the effect on the prediction accuracy of including global structural information in the secondary structure prediction scheme, by means of the HMMs. We find that when the HMM of the predicted topology of a protein is used to adjust the secondary structure sequence predicted originally with the Quadratic-Logistic method, the cross-validated prediction accuracy (Q3) improves by 3%. The topology is correctly predicted in 68% of the cases. We conclude that this HMM based approach is a promising tool for effectively incorporating global structural information in the secondary structure prediction scheme.

Algorithms↗
PubMed1996

Improving protein secondary structure prediction with aligned homologous sequences.

Most recent protein secondary structure prediction methods use sequence alignments to improve the prediction quality. We investigate the relationship between the location of secondary structural elements, gaps, and variable residue positions in multiple sequence alignments. We further investigate how these relationships compare with those found in structurally aligned protein families. We show how such associations may be used to improve the quality of prediction of the secondary structure elements, using the Quadratic-Logistic method with profiles. Furthermore, we analyze the extent to which the number of homologous sequences influences the quality of prediction. The analysis of variable residue positions shows that surprisingly, helical regions exhibit greater variability than do coil regions, which are generally thought to be the most common secondary structure elements in loops. However, the correlation between variability and the presence of helices does not significantly improve prediction quality. Gaps are a distinct signal for coil regions. Increasing the coil propensity for those residues occurring in gap regions enhances the overall prediction quality. Prediction accuracy increases initially with the number of homologues, but changes negligibly as the number of homologues exceeds about 14. The alignment quality affects the prediction more than other factors, hence a careful selection and alignment of even a small number of homologues can lead to significant improvements in prediction accuracy.

Amino Acid Sequence↗
PubMed1995

Hyperthermostable mutants of Bacillus licheniformis alpha-amylase: multiple amino acid replacements and molecular modelling.

We have identified previously two critical positions for the thermostability of the highly thermostable alpha-amylase from Bacillus licheniformis. We have now introduced all 19 possible amino acid residues to these two positions, His133 and Ala209. The most favourable substitutions were to Ile and Val, respectively, which both increased the half-life of the enzyme at 80 degrees C by a factor of approximately 3. At both positions a stabilizing effect of hydrophobic residues was observed, although only in the case of position 133 could a clear correlation be drawn between the hydrophobicity of the inserted amino acid and the gain in protein stability. The construction of double mutants showed a cumulative effect of the most favourable and/or deleterious substitutions. Computer modelling was used to generate a 3-D structure of the wild-type protein and to model substitutions at position 209, which lies in the conserved (alpha/beta)8 barrel domain of alpha-amylase; Ala209 would be located at the beginning of the third helix of the barrel, in the bottom of a small cavity facing the fourth helix. The model suggests that replacement by, for example, a valine could fill this cavity and therefore increase intra- and interhelical compactness and hydrophobic interactions.

Amino Acid Sequence↗
PubMed1995

[Iminodimethylation, a method for pharmacomodulation in pyrimido-[3,4-a]-s-triazine series].

Primary amines react with two formaldehydes and compounds presenting two mobile hydrogen atoms, this reaction can be called iminodimethylation. This reaction can be used in order to perform a pharmacomodulation in the pyrimido [3,4-a]-s-triazine series. Against Epidermophyton floccosum, the activity is better when nitrogen 7 is not substituted, when the heroatom in position 2 is 0 instead of S and when an aromatic nucleus is directly linked to the nitrogen atom in position 3.

Antifungal Agents↗
PubMed1994

Monte Carlo study of the effect of beta 2-microglobulin on the binding cleft of the HLA-A2 complex.

Peptide recognition by class I products of the major histocompatibility complex requires association of the class I heavy chain with beta 2-microglobulin. We present results of Monte Carlo simulations of the beta-pleated sheet floor of the human class I MHC molecule, HLA-A2, with and without beta 2-microglobulin. We find a significant effect of beta 2-microglobulin on the side chains of residues near a region that would accommodate the C-terminus of a bound peptide. By modeling simultaneously each loop and its neighboring strand at either end of the class I cleft, we find that beta 2-microglobulin restricts the conformational space of residues that are central to binding peptides. The effect is most pronounced for R97 and H114 and somewhat less important for Y99 and Y116, the latter forming strong hydrogen bonds with neighboring residues in the heavy chain itself.

Amino Acid Sequence↗
PubMed1993

Reconstitution of a high-affinity functional lutropin receptor by coexpression of its extracellular and membrane domains.

The glycoprotein hormone receptors differ from other G protein-coupled receptors by their large extracellular domain which mediates ligand binding. Cooperation between the G-protein coupled membrane domain, the extracellular domain and the hormone in establishing high-affinity binding and efficient transduction is likely to exist. Expression plasmids encoding the full-length porcine LH-hCG receptor (1-696), its extracellular (1-297) and membrane domain (298-696), as well as the alpha and beta subunits of hCG were constructed. We report that coexpression in COS cells of the two LH-hCG receptor domains restores cell surface high-affinity hormone binding and hormone dependent adenylyl cyclase activation, suggesting sufficient interactions between the two receptor domains to reconstitute a complete functional molecule. Moreover, the two hormone subunits and the two receptor domains are able to associate within coexpressing COS cells into an active complex.

Adenylyl Cyclases↗
PubMed1993

Modeling of protein loops by simulated annealing.

A method is presented to model loops of protein to be used in homology modeling of proteins. This method employs the ESAP program of Higo et al. (Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33-43) and is based on a fast Monte Carlo simulation and a simulated annealing algorithm. The method is tested on different loops or peptide segments from immunoglobulin, bovine pancreatic trypsin inhibitor, and bovine trypsin. The predicted structure is obtained from the ensemble average of the coordinates of the Monte Carlo simulation at 300 K, which exhibits the lowest internal energy. The starting conformation of the loop prior to modeling is chosen to be completely extended, and a closing harmonic potential is applied to N, CA, C, and O atoms of the terminal residues. A rigid geometry potential of Robson and Platt (1986, J. Mol. Biol. 188, 259-281) with a united atom representation is used. This we demonstrate to yield a loop structure with good hydrogen bonding and torsion angles in the allowed regions of the Ramachandran map. The average accuracy of the modeling evaluated on the eight modeled loops is 1 A root mean square deviation (rmsd) for the backbone atoms and 2.3 A rmsd for all heavy atoms.

Algorithms↗
PubMed1993

Suppression of fertility in male mice by immunization against LH receptor.

We have investigated the potential contraceptive effects of immunization against the luteinizing hormone (LH) receptor in male mice at the prepubertal stage. Two N-terminal fragments of the porcine LH receptor encoding amino acids 1-297 and 1-370 were produced in large quantities through the Baculovirus insect cell system. We have immunized three-week-old mice from two Balb/c stocks of differing fecundity with Sf9 insect cells producing the short (1-297) or long (1-370) recombinant LH receptor. A booster injection was performed at six weeks using purified antigens. Ten days later, the immunized male mice were mated over a period of two weeks with adult untreated females. After weaning of the first litters, the same partners were mated once again under the same conditions. There was no decrease in the antiserum titers against the antigens over a two-month period. The circulating testosterone decreased as the anti-LH receptor antibodies increased. The fertility of the treated male mice was reduced up to 75%, depending on the mouse stock, the antigen used and the time separating immunization and mating. The impaired fertility was mostly due to male sterilization (up to 60% of sterile mates). The delay between mating and birth was enhanced by the treatment, reflecting delayed fertility and/or delayed male behaviour acquisition.

Animals↗
PubMed1993

Quantification of secondary structure prediction improvement using multiple alignments.

The use of multiple sequence alignments for secondary structure predictions is analysed. Seven different protein families, containing only sequences of known structure, were considered to provide a range of alignment and prediction conditions. Using alignments obtained by spatial superposition of main chain atoms in known tertiary protein structures allowed a mean of 8% in secondary structure prediction accuracy, when compared to those obtained from the individual sequences. Substitution of these alignments by those determined directly from an automated sequence alignment algorithm showed variations in the prediction accuracy which correlated with the quality of the multiple alignments and distance of the primary sequence. Secondary structure predictions can be reliably improved using alignments from an automatic alignment procedure with a mean increase of 6.8%, giving an overall prediction accuracy of 68.5%, if there is a minimum of 25% sequence identity between all sequences in a family.

Amino Acid Sequence↗
PubMed1993

Influence of temperature and substrate concentration on bacterial growth yield in Seine River water batch cultures.

The growth of natural bacterial assemblages was monitored in 3-liter reactors under various temperature and substrate concentration conditions. The oxygen concentration was continuously monitored, and subsamples were taken at short time intervals to determine bacterial number and biomass. The rate of bacterial mortality was also determined. Bacterial growth yield was calculated as the ratio of net production (increase in biomass corrected for mortality) to gross production (net production plus oxygen consumption expressed in carbon units). Averaging 33%, the growth yield did not show any trend with temperatures in the range of 8 to 25 degrees C but increased with the concentration of dissolved organic carbon in the range of 2 to 12 mg of C.liter-1.

Bacteria↗
PubMed1992

Development of an extended simulated annealing method: application to the modeling of complementary determining regions of immunoglobulins.

An extended simulated annealing process (ESAP) has been developed in order to obtain an ensemble of conformations of a peptide segment from a protein fluctuating at a given temperature. The annealing process was performed with a fast Monte Carlo method using the scaled collective variables developed by Noguti and Go. The system was divided into two parts: one consists of one or more peptide segments and is flexible around the main-chain and side-chain torsional angles; the other represents the rest of the molecule and was maintained fixed at the atomic positions determined by x-ray experiments. The target function included the nonbonding atomic interactions and a distance function to anchor the N and C terminal ends of each segment to the fixed part. Three systems of complementary determining regions (CDR) of antibodies were tested and compared to x-ray data: L2 loop (7 residues) of the light chain of lambda-type Bence-Jones protein, H1 and the H2 loops (14 residues) of McPC603, and H1 and H2 loops (12 residues) of HyHEL-5. Each state of CDR conformations was characterized at room temperature by the average of their coordinates (average conformation) and the internal energy. With a limited number of annealing processes (10), starting from the extended conformation, we have obtained states with conformations close to the observed x-ray structures, from 1.1 to 1.7 A root mean square deviation (rmsd) of main-chain atoms depending on the system. These states were identical or within 0.25 A rmsd of those of lowest internal energy. For unknown CDR structures the criteria of lowest internal energies from ESAP can be used to predict hypervariable loop structures in antibodies with an accuracy comparable to other methods.

Amino Acid Sequence↗
PubMed1992

LH receptor RNA and protein levels after hormonal treatment of porcine granulosa cells in primary culture.

Granulosa cells were prepared from small follicles (less than 3 mm) from the ovaries of 5-month-old gilts. They were cultured in plastic dishes coated with a synthetic adhesion peptide in a chemically defined medium supplemented with 2% serum substitute. After 3 days of culture, the cells reached confluence and expression of the LH receptor could be stimulated in a hormonally defined medium. LH receptor RNAs were estimated by autoradiography using Northern blots and dot blots of total cell RNA. LH receptor RNAs were hybridized with a homologous 32P-labelled random-primed DNA probe. The LH receptor was measured using 125I-labelled human chorionic gonadotrophin (hCG) as tracer. Northern blots of LH receptor RNAs revealed a predominant signal of 4.4 kb and two less-intense hybridization bands of 7.5 and 1.9 kb. The 4.4 kb band was used for quantification of LH receptor RNAs because it was the most intense and may be attributed to the full-length messenger RNA. In these conditions, after 72 h stimulation, FSH (0.6 nM), insulin (5 micrograms/ml), oestradiol (30 nM) and deoxycorticosterone (0.3 nM) yielded high LH receptor RNA levels (eight times unstimulated cell level), while dibutyryl cyclic AMP (1 mM), cortisol (5.4 nM), thyroxine (100 nM) and epidermal growth factor (16 pM) gave low LH receptor RNA levels (one to five times). However, the respective amounts of the receptor RNA did not give yield to the same proportion of LH receptor for every factor, indicating some post-transcriptional regulations. The kinetic study of the production of the LH receptor obtained in a defined medium supplemented with FSH, oestradiol and insulin showed that the receptor appeared after 48 h of stimulation and reached a maximum of about 7000 receptors per cell at 72 h. The three hybridization bands on Northern blots evolved in parallel and appeared as early as 24 h. They were at maximal level from 24 to 48 h of stimulation. When the granulosa cells were pulse-treated for 2 h with cycloheximide (10 micrograms/ml), they exhibited a transient rise in LH receptor RNA content which was followed by a delayed receptor increase especially at 72 h of stimulation. Taken together, these results indicate that the LH receptor in primary culture of granulosa cells seems to be regulated by different physiological factors both at the transcriptional and the translational levels.

Amino Acid Sequence↗
PubMed1991

Influence of the local amino acid sequence upon the zones of the torsional angles phi and psi adopted by residues in proteins.

A set of parameters is derived to express the influence of the local amino acid sequence on the torsional angles phi and psi adopted by each residue in a protein. The formalism used, which is based on information theory, evaluates the probability for a given residue to be in a particular zone of the Ramachandran map. Comparisons with crystallographic structures suggest that the method can extract almost all of the available information from the local sequence and show that the local sequence carries only, on average, about 65% of the information necessary for specifying the conformation of a given residue in a protein. The rest is specified by long-range interactions that are specific for each protein fold. The parameters derived here provide a more detailed description of the prediction than other methods in allowing the allocation of the torsional angles for residues having an aperiodic structure and are intended to be used for directing the conformational search in a subsequent simulation of the three-dimensional structure. This method should also predict segments of the polypeptide chain that are the most stable and thus less sensitive to long-range interactions.

Amino Acid Sequence↗