Biomedical subjects

E Feytmans

Publications and source records attributed to E Feytmans.

At least 19 recordsLinked to original sources

PubMed1998

Assessing protein structures with a non-local atomic interaction energy.

We describe a new approach, based on the energy of non-local interactions, to assess protein structures. The method uses a very sensitive and accurate atomic mean force potential (AMFP) to calculate the non-local energy profile (NL-profile) of a proteins structure. Several protein models, built using the comparative modeling technique and containing several errors, were evaluated. These models exhibit a good stereochemistry and have been previously checked with different, widely used, methods that failed to detect the errors. The AMFP-derived energy profiles are able to correlate high scores with point errors and misalignments in the models. The point errors are frequently found in loops or regions of structural differences between the template and the target protein. The misalignments are clearly detected with very high scores. The performance of the method was also tested for the assessment of X-ray solved protein structures. In a data set of 143 well solved and non-redundant protein structures, we find that the average energy Z-scores, obtained from AMFP, increase as the resolution decreases. In the case of structures that have already been described as having an unusual stereochemistry, very high Z-scores are obtained. Moreover, energy calculations for some pairs of obsolete and replacement proteins always show higher Z-scores for the obsolete proteins. Finally, two particular cases show the usefulness of the profiles in the assessment of X-ray solved protein structures. First, the NL-profile of a protein structure refined in the incorrect space group has very high scores in several regions. One region has already been described to be out-of-register with the density map of the structure. The NL-profile of the re-refined structure with the correct space group is vastly improved. In the second case, the method is able to accurately point out disordered residues, even if the atoms of these residues do not violate the sum of the van der Waals radii. ANOLEA, the program used to calculate the NL-profile of a protein structure containing one or more chains is accessible through the World Wide Web at: http://www.fundp.ac.be/pub/ANOLEA.html.

Crystallography, X-Ray↗

PubMed1998

Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions.

MOTIVATION: The prediction reliability of seven multiple alignment servers currently available on the Internet (ClustalW, MAP, PIMA, Block Maker, MSA, MEME and Match-Box) has been evaluated in terms of power (sensitivity) and confidence (selectivity). Therefore, the alignments obtained have been respectively compared to refined structural alignments for 20 families of related proteins with low levels of identity. RESULTS: Results clearly show that any powerful method remains reliable when the rate of identity falls. For some methods, power and confidence decrease linearly with the rate of identity, while other methods emphasize reliability at the cost of a lower power. Increasing the number of related sequences included in the alignment may either improve or decrease the quality of the predictions substantially. For some methods, the gain in power or in confidence is quite systematic; for others, the effect of the addition of homologous sequences is highly unpredictable. Extracting the consensus between two different methods may increase the overall confidence of the predictions tremendously. Our conclusions induce users of sequence alignment methods on the Internet to select the most suitable technique according to their requirements in terms of selectivity and sensitivity. AVAILABILITY: The aligned sequences of the 20 alignments of structure can be obtained automatically by sending the message 'send: cabios_tests.txt' by e-mail to 'matchbox@biq.fundp.ac.be'. CONTACT: eric.depiereux@fundp.ac.be

Computer Communication Networks↗

PubMed1997

Bivalent cations stabilize yeast alcohol dehydrogenase I.

The thermostability of yeast alcohol dehydrogenase (ADH) I is strongly dependent on the presence of NaCl, a salt that is almost neutral on the Hofmeister scale, which suggests that solvent-accessible electrostatic repulsion might play a role in the inactivation of the enzyme. Moreover, CaCl2 and MgCl2 are able to stabilize the enzyme at millimolar concentrations. Ca2+ stabilizes yeast ADH I by preventing the dissociation of the reduced form of the enzyme and by preventing the unfolding of the oxidized form of the enzyme. An analysis of several chimaeric ADHs suggests that Ca2+ is fixed by the Asp-236 and Glu-101 side chains in yeast ADH I, but that Ca2+ can be displaced by replacing Met-168 by an Arg residue, as suggested by a three-dimensional model of the enzyme structure. These results indicate that electrostatic repulsion can cause protein unfolding and/or dissociation. It is proposed that yeast ADH I binds Mg2+ in vivo.

Alcohol Dehydrogenase↗

PubMed1997

Novel knowledge-based mean force potential at atomic level.

We present a new approach at the atomic level for the development of knowledge-based mean force potentials (MFPs) that can be used in fold recognition, ab initio structure prediction, comparative modelling and molecular recognition. Our method is based on atom-type definitions, raising the total frequency of the pairwise distributions and leading to very accurate and specific distance-dependent energy functions. Forty different heavy atom types were defined depending on their bond connectivity, chemical nature and location level (side-chain or backbone). Using this approach it has been possible to obtain average frequencies of pairwise contacts about 15 times higher than the ones obtained using the classic way of one heavy atom definition for each amino acid (i.e. alpha-carbon, beta-carbon, virtual centroid or virtual beta-carbon co-ordinates). In this paper we use this approach to develop a MFP that can be used in fold recognition and we compare it with a classic MFP at the amino acid level compiled from the alpha-carbon distances between the different amino acid pairs. Both potentials involve all the pairwise contacts extracted from a non-redundant folds database of 180 protein chains with a sequence identity threshold of 25%. The pairwise energy functions of the MFP at the atomic level have a deep and very well defined minimum for each pairwise interaction, in contrast to the same curves obtained from the MFP developed at the amino acid level, which generally have multiple minima with similar depth. Our results also show that this MFP is able to produce very similar energy profiles for couples of proteins that share a very low sequence identity but are closely related at the structural level. When these profiles are plotted considering the structure-structure alignment, they are mostly superimposed, showing a correlation with the structure-structure similarity. In the same test, the MFP at the amino acid level fails to produce similar profiles. We suggest that using this MFP at the atomic level in the last stages of fold recognition or threading, when some candidates are available, can improve the sequence-structure alignments and, therefore, the final models. We also discuss the possibility of using this approach in the development of new MFPs to be used in ab initio structure prediction, comparative modelling and molecular recognition procedures.

Amino Acids↗

PubMed1997

Mutagenesis of charged residues in a conserved sequence in the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase.

Arg-136, Glu-137, Arg-138 and Arg-139 are conserved in all sequences of the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase. Their role was studied by site-directed mutagenesis. All the mutations had little, if any, effect on fructose-2,6-bisphosphatase activity. Mutations of Arg-136 and Glu-137 into Ala caused only minor modifications of phosphofructo-2-kinase activity. In contrast, mutation of Arg138 into Ala increased 280-fold the Km for fructose 6-phosphate of phosphofructo-2-kinase. Mutation of Arg-139 into Ala resulted in decreases in phosphofructo-2-kinase Vmax/Km for MgATP and fructose 6-phosphate 600-fold and 5000-fold respectively. Mutation of Arg-139 into Lys and Gln increased the Km of phosphofructo-2-kinase for MgATP (20-fold and 25-fold respectively) and for fructose 6-phosphate (8-fold and 13-fold), and the IC50 for MgADP (30-fold and 50-fold) and for magnesium citrate (7-fold and 25-fold). However, these two mutations did not affect nucleotide binding, as measured by quenching of intrinsic fluorescence. The changes in kinetic properties induced by mutations could not be attributed to structural changes. It is proposed that Arg-138 is involved in fructose 6-phosphate binding and that Arg-139 is probably involved in the stabilization of the transition state and so participates in catalysis.

Adenosine Triphosphate↗

PubMed1997

Modelling the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase on adenylate kinase.

Simultaneous multiple alignment of available sequences of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase revealed several segments of conserved residues in the 2-kinase domain. The sequence of the kinase domain was also compared with proteins of known three-dimensional structure. No similarity was found between the kinase domain of 6-phosphofructo-2-kinase and 6-phosphofructo-1-kinase. This questions the modelling of the 2-kinase domain on bacterial 6-phosphofructo-1-kinase that has previously been proposed [Bazan, Fletterick and Pilkis (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 9642-9646]. However, sequence similarities were found between the 2-kinase domain and several nucleotide-binding proteins, the most similar being adenylate kinase. A structural model of the 2-kinase domain based on adenylate kinase is proposed. It accommodates all the results of site-directed mutagenesis studies carried out to date on residues in the 2-kinase domain. It also allows residues potentially involved in catalysis and/or substrate binding to be predicted.

Adenylate Kinase↗

PubMed1997

Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability.

MOTIVATION: The Match-Box software comprises protein sequence alignment tools based on strict statistical thresholds of similarity between protein segments. The method circumvents the gap penalty requirement: gaps being the result of the alignment and not a governing parameter of the procedure. The reliable conserved regions outlined by Match-Box are particularly relevant for homology modelling of protein structures, prediction of essential residues for site-directed mutagenesis and oligonucleotide design for cloning homologous genes by polymerase chain reaction (PCR). RESULTS: The method produces reliable results, as assessed by tests performed on protein families of known structures and of low sequence similarity. A reliability score is computed in relation to a threshold of similarity progressively raised to extend the aligned regions to their maximal length, up to the significance limit of matching segments. The score obtained at each position is printed below the sequences and allows a discriminant reading of each aligned region. AVAILABILITY: Sequences may be submitted to a Web server at http://www.fundp.ac.be/sciences/biologie/bms/+ ++matchbox_submit.html or sent by e-mail to matchbox/biq.fundp.ac.be (help available by just mailing help).

Algorithms↗

PubMed1997

ANOLEA: a www server to assess protein structures.

ANOLEA (Atomic Non-Local Environment Assessment) is a www server that performs energy calculations at the atomic level in protein structures. The calculations involve the non-local interactions between all the heavy atoms of the twenty standard amino acids in the molecule. The input of the server is a PDB file containing one or more protein chains. The output is an energy profile, which gives an energy value for each amino acid of the protein. High energy zones (HEZs) in the profile correlate with errors or with potential interacting zones of proteins. The output of the server also displays the structure in three dimensions, pointing out the high energy amino acids in the protein. This option requires the CHIME plug-in, which is freely available on Internet and makes possible, in real time, to rotate, translate and change the point of view and presentation of the molecule in three dimensions. Thus, a fast analysis of a protein structure can be done using a personal computer connected to Internet. The server is available at: http:@www.fundp.ac.be/pub/ANOLEA.html.

Amino Acids↗

PubMed1995

Identification of residues potentially involved in the interactions between subunits in yeast alcohol dehydrogenases.

The lack of crystal structure for tetrameric yeast alcohol dehydrogenases (ADHs) has precluded, until now, the identification of the residues involved in subunit contacts. In order to address this question, we have characterized the thermal stability and dissociation propensity of native ADH I and ADH II isozymes as well as of several chimeric (ADH I-ADH II) enzymes. Three groups of substitutions affecting the thermostability have been identified among the 24 substitutions observed between isozymes I and II. The first group contains a Cys277-->Ser substitution, located at the interface between subunits in a three-dimensional model of ADH I, based on the crystallographic structure of the dimeric horse liver ADH. In the second group, the Asp236-->Asn substitution is located in the same interaction zone on the model. The stabilizing effect of this substitution can result from the removal of a charge repulsion between subunits. It is shown that the effect of these two groups of substitutions correlates with changes in dissociation propensities. The third group contains the Met168-->Arg substitution that increases the thermal stability, probably by the formation of an additional salt bridge between subunits through the putative interface. These data suggest that at least part of the subunit contacts observed in horse liver ADH are located at homologous positions in yeast ADHs.

Alcohol Dehydrogenase↗

PubMed1995

Knowledge-based modeling of the D-lactate dehydrogenase three-dimensional structure.

A three-dimensional structure of the NAD-dependent D-lactate dehydrogenase of Lactobacillus bulgaricus is modeled using the structure of the formate dehydrogenase of Pseudomonas sp. as template. Both sequences share only 22% of identical residues. Regions for knowledge-based modeling are defined from the structurally conserved regions predicted by multiple alignment of a set of related protein sequences with low homology. The model of the D-LDH subunit shows, as for the formate dehydrogenase, an alpha/beta structure, with a catalytic domain and a coenzyme binding domain. It points out the catalytic histidine (His-296) and supports the hypothetical catalytic mechanism. It also suggests that the other residues involved in the active site are Arg-235, possibly involved in the binding of the carboxyl group of the pyruvate, and Phe-299, a candidate for stabilizing the methyl group of the substrate.

Amino Acid Sequence↗

PubMed1993

Prediction of structurally conserved regions of D-specific hydroxy acid dehydrogenases by multiple alignment with formate dehydrogenase.

We propose a multiple alignment of the sequence of formate dehydrogenase with the D-specific 2-hydroxy acid dehydrogenases family. Structurally conserved regions are predicted for those sequences corresponding to important regions of the catalytic and the coenzyme binding domains defined from the known three-dimensional structure of the formate dehydrogenase, namely the nicotinamide binding site (beta D to beta F) and the beta A-loop-alpha B region containing the typical glycine pattern of the adenosine binding site, the catalytic histidine/aspartic acid pair and an arginine probably involved in the interaction with the carboxyl group of the substrate.

Alcohol Oxidoreductases↗

PubMed1993

Similarities between alanine dehydrogenase and the N-terminal part of pyridine nucleotide transhydrogenase and their possible implication in the virulence mechanism of Mycobacterium tuberculosis.

Recent developments in simultaneous multiple alignment methods of protein sequences allow prediction of structural similarity in related proteins. Alanine dehydrogenase and the N-terminal sequence of pyridine nucleotide transhydrogenase were compared for their sequences. High similarities of sequences were observed especially in their NAD(H)-binding sites. These similarities suggest that antibodies which recognized the alanine dehydrogenase of Mycobacterium tuberculosis can also be directed against the membrane bound pyridine nucleotide transhydrogenase. If this is the case, the virulent property of this pathogen could be linked to its higher synthesis of NADPH necessary for its anabolism.

Alanine Dehydrogenase↗

PubMed1992

MATCH-BOX: a fundamentally new algorithm for the simultaneous alignment of several protein sequences.

Original algorithms for simultaneous alignment of protein sequences are presented, including sequence clustering and within- or between-groups multiple alignment. The way of matching similar regions is fundamentally new. Complete matches are formed by segments more similar than expected by random, according to a given probability limit. Any classic or user-defined score matrix can be used to express the similarity between the residues. The algorithm seeks for complete matches common to all the sequences without performing pairwise alignment and regardless of gap weighting. An automatic screening delineates all the similar regions (boxes) that may be defined for a given maximal shift between the sequences. The shift can be large enough to allow the matching of any region of a sequence with any region of another one. It can also be short and used to refine the alignment around anchor points. The algorithm provides the most likely optimal alignment and a comprehensive list of the alignment dilemma. Duality between automatism and interactivity is provided. Depending on the problem complexity, a final alignment is obtained fully automatically or requires some interactive handling to discriminate alternative pathways.

Algorithms↗

PubMed1991

Simultaneous and multivariate alignment of protein sequences: correspondence between physicochemical profiles and structurally conserved regions (SCR).

A general protein sequence alignment methodology for detecting a priori unknown common structural and functional regions is described. The method proposed in this paper is based on two basic requirements for a meaningful alignment. First, each sequence or segment of a sequence is characterized by a multivariate physicochemical profile. Second, the alignment is performed by considering all the sequences simultaneously, and the algorithm detects those regions that form a set of similar profiles. In order to test the structural meaning of the alignment obtained from the sequences, quantitative comparisons are performed with structurally conserved regions (SCR) determined from the X-ray structures of three serine proteases. Results suggest that the limits of the SCR may be predicted from the similarities between the physicochemical profiles of the sequences. The procedures are not completely automated. The final step requires a visual screening of alternative pathways in order to determine an optimal alignment.

Algorithms↗

PubMed1991

Saturation of hepatic transport of taurocholate in rats in vivo.

A single intravenous injection of [14C]taurocholate was followed up in blood and bile of rats submitted to steady intravenous infusions of taurocholate (TC) at rates of 0.0, 0.5, 1.0, and 1.5 mumol.min-1.100 g body wt-1 for at least 30 min. The transport rate constants and the amounts of TC in different compartments were estimated by weighted least-squares adjustment of a six-compartment model to the experimental data (3 compartments for TC distribution in blood, 2 compartments for liver, and 1 compartment for sinusoidal blood space). The saturation of the TC excretion rate was reached at 0.8 mumol.min-1.100 g body wt-1. It was characterized by a decrease of both the uptake and excretion rate constants, by an increase of the ratio of the amounts of TC in the two intrahepatic compartments (H'/H), and by an intrahepatic TC concentration of approximately 2 mM. When tauroursodeoxycholate (TUDC) was infused at a rate of 0.5 mumol.min-1.100 g body wt-1 together with TC at a rate of 1.5 mumol.min-1.100 g body wt-1, the TC excretion rate increased to 1.2 mumol.min-1.100 g body wt-1, and the excretion rate constant and H'/H decreased toward control values. These results support the hypothesis that the saturation of the transport of TC is due to TC hepatotoxicity and can be reduced by TUDC. Michaelis-Menten parameters, derived from saturation curves for both uptake and excretion steps, closely matched earlier results, thus confirming the good descriptive capacity of the model.

Animals↗

PubMed1991

Compartmental analysis of steady-state taurocholate transport kinetics by isolated rat hepatocytes.

We used compartmental modeling to describe taurocholate transport by isolated rat liver cells in suspension. Cells are preincubated in the presence of unlabeled taurocholate. When a steady-state for taurocholate is reached, radiolabeled taurocholate is added to the medium and its exchange kinetics between the medium and the cells are followed over time. Because the studies are performed under steady-state conditions, the kinetics can be described by linear compartmental models. We found a closed two-compartment model sufficient to describe the steady-state transport data. Simulations reveal that if the pools of free and bound intracellular taurocholate exchange rapidly, the cells will behave as a single, kinetically homogeneous compartment and intracellular events will not influence the exchange kinetics of taurocholate between the medium and the cells. The two-compartment model was used to study the concentration dependence of taurocholate transport by isolated cells. Steady-state transport rates and taurocholate concentrations in the medium and the cells were calculated using the model equations. Taurocholate influx, accumulation and efflux processes were studied simultaneously by examining the relationship between appropriate combinations of these variables. Application of this approach to study the inhibition of taurocholate transport by taurochenodeoxycholate is illustrated. In conclusion, this method provides a complementary approach to initial rate studies, which are generally used to investigate bile acid transport by isolated cells.

Animals↗

PubMed1990

Direct observation of sexual competition in Drosophila melanogaster: the mutant white in competition with other genotypes.

When two types of Drosophila are in competition, the frequency dependence of mating success routinely is measured in our laboratory by direct observation of mating pairs in "Elens-Wattiaux" observation chambers. The present experiments concern white mutants (used here as a reference standard) in competition with three other genotypes: wild-type Canton S, "giant" gt wa, and "giant" gt13z/w+ Y/C(1)Dx, y f. From the present observations, the frequency dependence of mating success seems a very common phenomenon: a rare-type sexual advantage exists for females and for males. Sexual activity of male and female white mutants is significantly higher when food is present in the mating chamber. Males of the other strains also are more active in the presence of food. Homogamic matings are more frequent among gt13z/w+ Y/C(1)Dx, y f flies.

Animals↗

PubMed1989

Compartmental modeling of the hepatic transport of taurocholate in the rat in vivo.

Compartmental analysis was used to study the hepatobiliary transport of taurocholate (TC) in the rat in vivo. The available data are the following: [14C]TC kinetics in blood and bile, weighting factors associated with these data and computed from a theoretical variability model, and TC excretion rate in bile. The lumped model that best fits the data contains five compartments: three compartments for TC distribution in blood and two compartments for the liver. It includes a compartmental representation of the laminar flow of bile in the collecting catheter. This model overestimates TC concentration in blood. A perfusion model that includes a compartment representing explicitly the sinusoidal TC concentration gradient was developed. TC concentration in blood estimated by this model is in good agreement with direct measurements, showing that the perfused model has a better descriptive capacity than the lumped model. The amounts of TC estimated in the two hepatic compartments are similar to values previously published.

Animals↗