N. Boutonnet - Academia.edu (original) (raw)
Papers by N. Boutonnet
It has been shown that the insertion of antigenic peptides of the foot-and-mouse disease virus (F... more It has been shown that the insertion of antigenic peptides of the foot-and-mouse disease virus (FMDV) into specific sites of the bacterial enzyme β-galactosidase causes a severe reduction of the activity of this enzyme which can be recovered upon antibody binding to the inserted antigenic peptide [1]. In principle, the recovery of β-galactosidase activity upon antigen-antibody binding allows the detection of antibodies by simple colorimetric quantification of β-galactosidase activity in a homogeneous test system, involving only the antigenic fusion protein, a chromogenic substrate and a serum sample for testing. The lack of three-dimensional (3D) structural information on the chimeric proteins renders their modeling requisite to understand at the molecular level the chimeric enzyme inactivation and reactivation upon antibody binding. For this purpose, we have determined 3D models of chimeric β-galactosidase by comparative modeling and structure prediction techniques.
Proteins, 1998
We present a fully automatic structural classification of supersecondary structure units, consist... more We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded beta strands, preceded or followed by an alpha helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the alpha helix and beta hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the o...
Proteins Structure Function and Bioinformatics
We present a fully automatic structural classification of supersecondary structure units, consist... more We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded beta strands, preceded or followed by an alpha helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the alpha helix and beta hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the orientation, preferences in the left/right handedness of the alpha-beta connection are observed. These preferences can be explained by favorable side by side packing of the alpha helix and the beta hairpin, local interactions in the region of the alpha-beta connection or stabilizing environments in the parent protein. Furthermore, fold recognition procedures and structure prediction algorithms coupled to database-derived potentials suggest that the preferable nature of these arrangements does not imply their intrinsic stability. They usually accommodate a large number of sequences, of which only a subset is predicted to stabilize the motif. The motifs predicted as stable could correspond to nuclei formed at the very beginning of the folding process.
Nucleosides and Nucleotides, 1999
In this work we examined different aspects of the photo-reaction of Ru(TAP)2 (DIP) (TAP = 1,4,5,8... more In this work we examined different aspects of the photo-reaction of Ru(TAP)2 (DIP) (TAP = 1,4,5,8-tetraazaphenanthrene; DIP = 4,7 diphenylphenanthroline) with guanine by studying synthetic oligonucleotide conjugates in which the metal complex is tethered to the oligonucleotide.
Proteins, 1998
We present a fully automatic structural classification of supersecondary structure units, consist... more We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded beta strands, preceded or followed by an alpha helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the alpha helix and beta hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the o...
Protein Engineering Design and Selection, 1995
A fully automatic procedure for aligning two protein structures is presented. It uses as sole str... more A fully automatic procedure for aligning two protein structures is presented. It uses as sole structural similarity measure the root mean square (r.m.s.) deviation of superimposed backbone atoms (N, C alpha, C and O) and is designed to yield optimal solutions with respect to this measure. In a first step, the procedure identifies protein segments with similar conformations in both proteins. In a second step, a novel multiple linkage clustering algorithm is used to identify segment combinations which yield optimal global structure alignments. Several structure alignments can usually be obtained for a given pair of proteins, which are exploited here to define automatically the common structural core of a protein family. Furthermore, an automatic analysis of the clustering trees is described which enables detection of rigid-body movements between structure elements. To illustrate the performance of our procedure, we apply it to families of distantly related proteins. One groups the three alpha + beta proteins ubiquitin, ferredoxin and the B1-domain of protein G. Their common structure motif consists of four beta-strands and the only alpha-helix, with one strand and the helix being displaced as a rigid body relative to the remaining three beta-strands. The other family consists of beta-proteins from the Greek key group, in particular actinoxanthin, the immunoglobulin variable domain and plastocyanin. Their consensus motif, composed of five beta-strands and a turn, is identified, mostly intact, in all Greek key proteins except the trypsins, and interestingly also in three other beta-protein families, the lipocalins, the neuraminidases and the lectins. This result provides new insights into the evolutionary relationships in the very diverse group of all beta-proteins.
Journal of Virology, 2002
It has been proposed that the ectodomain of human immunodeficiency virus type 1 (HIV-1) gp41 (e-g... more It has been proposed that the ectodomain of human immunodeficiency virus type 1 (HIV-1) gp41 (e-gp41), involved in HIV entry into the target cell, exists in at least two conformations, a pre-hairpin intermediate and a fusion-active hairpin structure. To obtain more information on the structure-sequence relationship in e-gp41, we performed in silico a full single-amino-acid substitution analysis, resulting in a Fold Compatible Database (FCD) for each conformation. The FCD contains for each residue position in a given protein a list of values assessing the energetic compatibility (ECO) of each of the 20 natural amino acids at that position. Our results suggest that FCD predictions are in good agreement with the sequence variation observed for well-validated e-gp41 sequences. The data show that at a minECO threshold value of 5 kcal/mol, about 90% of the observed patient sequence variation is encompassed by the FCD predictions. Some inconsistent FCD predictions at N-helix positions packing against residues of the C helix suggest that packing of both peptides may involve some flexibility and may be attributed to an altered orientation of the C-helical domain versus the N-helical region. The permissiveness of sequence variation in the C helices is in agreement with FCD predictions. Comparison of N-core and triple-hairpin FCDs suggests that the N helices may impose more constraints on sequence variation than the C helices. Although the observed sequences of e-gp41 contain many multiple mutations, our method, which is based on single-point mutations, can predict the natural sequence variability of e-gp41 very well.
Journal of Molecular Biology, 1995
changes such as those occurring upon substrate binding or in different Biologie 13 crystal forms ... more changes such as those occurring upon substrate binding or in different Biologie 13 crystal forms of the same protein. Using, as sole information, the atomic coordinates of a pair of protein structures, the procedure first generates rue Pierre et Marie Curie Paris, 75005, France structure alignments, which optimize the root-mean-square deviation of the backbone atoms. To this end, equivalent secondary structures and/or 2 Unité de Conformation des loops from both proteins are combined by a multiple linkage hierarchic Macromolécules Biologiques clustering algorithm, which generates several intertwined clustering trees.
Chemistry - A European Journal, 1999
ABSTRACT A series of 17-mer oligonucleotides labeled with [Ru(tap)2(dip)]2+ (tap = 1,4,5,8-tetraa... more ABSTRACT A series of 17-mer oligonucleotides labeled with [Ru(tap)2(dip)]2+ (tap = 1,4,5,8-tetraazaphenanthrene; dip = 4,7-diphenylphenanthroline) at position 5 of an uracil residue in the middle of the sequence (e.g. see scheme) have been prepared and characterized. The luminescence of the chemically attached complex is quenched by hybridization with the complementary sequence, when it contains guanines in the vicinity of the Ru site. This electron-transfer quenching process generates a photoproduct on the illuminated duplex, that is responsible for an irreversible photocrosslinking of the two strands.
Biopolymers, 1993
The present study is aimed at understanding the effects of DNA sequence, local conformation, and ... more The present study is aimed at understanding the effects of DNA sequence, local conformation, and curvature on groove geometry. Energy-optimized structures are obtained by Jumna methodology; groove geometry is analyzed by a recently developed technique that allows an accurate and continuous measurement of width and depth. The mechanics of groove deformations is also studied and analyzed in terms of helicoidal parameters.
Biophysical Journal, 2002
The yield of hole injection into guanines of different oligonucleotide duplexes by a photooxidizi... more The yield of hole injection into guanines of different oligonucleotide duplexes by a photooxidizing tethered Ru(II) complex is examined by measuring the luminescence quenching of the excited complex. This yield is investigated as a function of the anchoring site of the complex (on a thymine nucleobase in the middle of the sequence or on the 5Ј terminal phosphate) and the number and position of the guanine bases as compared with the site of attachment of the Ru(II) compound. In contrast to other studies, the tethered complex, [Ru(tap) 2 (dip)] 2ϩ , is a non-intercalating compound and has been shown previously to produce an irreversible photocrosslinking between the two strands as the ultimate step of hole injection. The study of luminescence quenching of the anchored complex by emission intensity and lifetime measurements for the different duplexes indicates that a direct contact between the complex and the guanine nucleobase is needed for the electron transfer to take place. Moreover, for none of the sequences a clear contribution of a static quenching is evidenced independently of the two types of attachment of the [Ru(tap) 2 (dip)] 2ϩ complex to the oligonucleotide. A comparison of the fastest hole-injection process by electron transfer to the excited anchored [Ru(tap) 2 (dip)] 2ϩ , with the rate of the photo-electron transfer between the same complex free in solution and guanosine-5Ј-monophosphate, indicates that the hole injection by the anchored complex is slower by a factor of 10 at least. A bad overlap between donor and acceptor orbitals is probably the cause of this slow rate, which could be attributed to some steric hindrance induced by the complex linker.
It has been shown that the insertion of antigenic peptides of the foot-and-mouse disease virus (F... more It has been shown that the insertion of antigenic peptides of the foot-and-mouse disease virus (FMDV) into specific sites of the bacterial enzyme β-galactosidase causes a severe reduction of the activity of this enzyme which can be recovered upon antibody binding to the inserted antigenic peptide [1]. In principle, the recovery of β-galactosidase activity upon antigen-antibody binding allows the detection of antibodies by simple colorimetric quantification of β-galactosidase activity in a homogeneous test system, involving only the antigenic fusion protein, a chromogenic substrate and a serum sample for testing. The lack of three-dimensional (3D) structural information on the chimeric proteins renders their modeling requisite to understand at the molecular level the chimeric enzyme inactivation and reactivation upon antibody binding. For this purpose, we have determined 3D models of chimeric β-galactosidase by comparative modeling and structure prediction techniques.
Proteins, 1998
We present a fully automatic structural classification of supersecondary structure units, consist... more We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded beta strands, preceded or followed by an alpha helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the alpha helix and beta hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the o...
Proteins Structure Function and Bioinformatics
We present a fully automatic structural classification of supersecondary structure units, consist... more We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded beta strands, preceded or followed by an alpha helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the alpha helix and beta hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the orientation, preferences in the left/right handedness of the alpha-beta connection are observed. These preferences can be explained by favorable side by side packing of the alpha helix and the beta hairpin, local interactions in the region of the alpha-beta connection or stabilizing environments in the parent protein. Furthermore, fold recognition procedures and structure prediction algorithms coupled to database-derived potentials suggest that the preferable nature of these arrangements does not imply their intrinsic stability. They usually accommodate a large number of sequences, of which only a subset is predicted to stabilize the motif. The motifs predicted as stable could correspond to nuclei formed at the very beginning of the folding process.
Nucleosides and Nucleotides, 1999
In this work we examined different aspects of the photo-reaction of Ru(TAP)2 (DIP) (TAP = 1,4,5,8... more In this work we examined different aspects of the photo-reaction of Ru(TAP)2 (DIP) (TAP = 1,4,5,8-tetraazaphenanthrene; DIP = 4,7 diphenylphenanthroline) with guanine by studying synthetic oligonucleotide conjugates in which the metal complex is tethered to the oligonucleotide.
Proteins, 1998
We present a fully automatic structural classification of supersecondary structure units, consist... more We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded beta strands, preceded or followed by an alpha helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the alpha helix and beta hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the o...
Protein Engineering Design and Selection, 1995
A fully automatic procedure for aligning two protein structures is presented. It uses as sole str... more A fully automatic procedure for aligning two protein structures is presented. It uses as sole structural similarity measure the root mean square (r.m.s.) deviation of superimposed backbone atoms (N, C alpha, C and O) and is designed to yield optimal solutions with respect to this measure. In a first step, the procedure identifies protein segments with similar conformations in both proteins. In a second step, a novel multiple linkage clustering algorithm is used to identify segment combinations which yield optimal global structure alignments. Several structure alignments can usually be obtained for a given pair of proteins, which are exploited here to define automatically the common structural core of a protein family. Furthermore, an automatic analysis of the clustering trees is described which enables detection of rigid-body movements between structure elements. To illustrate the performance of our procedure, we apply it to families of distantly related proteins. One groups the three alpha + beta proteins ubiquitin, ferredoxin and the B1-domain of protein G. Their common structure motif consists of four beta-strands and the only alpha-helix, with one strand and the helix being displaced as a rigid body relative to the remaining three beta-strands. The other family consists of beta-proteins from the Greek key group, in particular actinoxanthin, the immunoglobulin variable domain and plastocyanin. Their consensus motif, composed of five beta-strands and a turn, is identified, mostly intact, in all Greek key proteins except the trypsins, and interestingly also in three other beta-protein families, the lipocalins, the neuraminidases and the lectins. This result provides new insights into the evolutionary relationships in the very diverse group of all beta-proteins.
Journal of Virology, 2002
It has been proposed that the ectodomain of human immunodeficiency virus type 1 (HIV-1) gp41 (e-g... more It has been proposed that the ectodomain of human immunodeficiency virus type 1 (HIV-1) gp41 (e-gp41), involved in HIV entry into the target cell, exists in at least two conformations, a pre-hairpin intermediate and a fusion-active hairpin structure. To obtain more information on the structure-sequence relationship in e-gp41, we performed in silico a full single-amino-acid substitution analysis, resulting in a Fold Compatible Database (FCD) for each conformation. The FCD contains for each residue position in a given protein a list of values assessing the energetic compatibility (ECO) of each of the 20 natural amino acids at that position. Our results suggest that FCD predictions are in good agreement with the sequence variation observed for well-validated e-gp41 sequences. The data show that at a minECO threshold value of 5 kcal/mol, about 90% of the observed patient sequence variation is encompassed by the FCD predictions. Some inconsistent FCD predictions at N-helix positions packing against residues of the C helix suggest that packing of both peptides may involve some flexibility and may be attributed to an altered orientation of the C-helical domain versus the N-helical region. The permissiveness of sequence variation in the C helices is in agreement with FCD predictions. Comparison of N-core and triple-hairpin FCDs suggests that the N helices may impose more constraints on sequence variation than the C helices. Although the observed sequences of e-gp41 contain many multiple mutations, our method, which is based on single-point mutations, can predict the natural sequence variability of e-gp41 very well.
Journal of Molecular Biology, 1995
changes such as those occurring upon substrate binding or in different Biologie 13 crystal forms ... more changes such as those occurring upon substrate binding or in different Biologie 13 crystal forms of the same protein. Using, as sole information, the atomic coordinates of a pair of protein structures, the procedure first generates rue Pierre et Marie Curie Paris, 75005, France structure alignments, which optimize the root-mean-square deviation of the backbone atoms. To this end, equivalent secondary structures and/or 2 Unité de Conformation des loops from both proteins are combined by a multiple linkage hierarchic Macromolécules Biologiques clustering algorithm, which generates several intertwined clustering trees.
Chemistry - A European Journal, 1999
ABSTRACT A series of 17-mer oligonucleotides labeled with [Ru(tap)2(dip)]2+ (tap = 1,4,5,8-tetraa... more ABSTRACT A series of 17-mer oligonucleotides labeled with [Ru(tap)2(dip)]2+ (tap = 1,4,5,8-tetraazaphenanthrene; dip = 4,7-diphenylphenanthroline) at position 5 of an uracil residue in the middle of the sequence (e.g. see scheme) have been prepared and characterized. The luminescence of the chemically attached complex is quenched by hybridization with the complementary sequence, when it contains guanines in the vicinity of the Ru site. This electron-transfer quenching process generates a photoproduct on the illuminated duplex, that is responsible for an irreversible photocrosslinking of the two strands.
Biopolymers, 1993
The present study is aimed at understanding the effects of DNA sequence, local conformation, and ... more The present study is aimed at understanding the effects of DNA sequence, local conformation, and curvature on groove geometry. Energy-optimized structures are obtained by Jumna methodology; groove geometry is analyzed by a recently developed technique that allows an accurate and continuous measurement of width and depth. The mechanics of groove deformations is also studied and analyzed in terms of helicoidal parameters.
Biophysical Journal, 2002
The yield of hole injection into guanines of different oligonucleotide duplexes by a photooxidizi... more The yield of hole injection into guanines of different oligonucleotide duplexes by a photooxidizing tethered Ru(II) complex is examined by measuring the luminescence quenching of the excited complex. This yield is investigated as a function of the anchoring site of the complex (on a thymine nucleobase in the middle of the sequence or on the 5Ј terminal phosphate) and the number and position of the guanine bases as compared with the site of attachment of the Ru(II) compound. In contrast to other studies, the tethered complex, [Ru(tap) 2 (dip)] 2ϩ , is a non-intercalating compound and has been shown previously to produce an irreversible photocrosslinking between the two strands as the ultimate step of hole injection. The study of luminescence quenching of the anchored complex by emission intensity and lifetime measurements for the different duplexes indicates that a direct contact between the complex and the guanine nucleobase is needed for the electron transfer to take place. Moreover, for none of the sequences a clear contribution of a static quenching is evidenced independently of the two types of attachment of the [Ru(tap) 2 (dip)] 2ϩ complex to the oligonucleotide. A comparison of the fastest hole-injection process by electron transfer to the excited anchored [Ru(tap) 2 (dip)] 2ϩ , with the rate of the photo-electron transfer between the same complex free in solution and guanosine-5Ј-monophosphate, indicates that the hole injection by the anchored complex is slower by a factor of 10 at least. A bad overlap between donor and acceptor orbitals is probably the cause of this slow rate, which could be attributed to some steric hindrance induced by the complex linker.