Catherine Etchebest - Academia.edu (original) (raw)
Papers by Catherine Etchebest
Cet article est dedie a la presentation de differentes methodes bioinformatiques visant a analyse... more Cet article est dedie a la presentation de differentes methodes bioinformatiques visant a analyser et a predire la structure des macromolecules biologiques, proteines et acides nucleiques. Il souligne l’importance de la structure 3D pour comprendre la fonction de ces macromolecules et l’apport des methodes de prediction de la structure a partir de la sequence. Il fournit des informations pour comprendre les principes des methodes de bioinformatique structurale et des recommandations pour la mise en œuvre d’une demarche de prediction. Une liste non exhaustive d’outils et de bases de donnees utiles est proposee, associee a une bibliographie recente.
Virus Research, Sep 1, 2022
Blood Cells, Molecules, and Diseases
Frontiers in Physiology
The K+ channel activated by the Ca2+, KCNN4, has been shown to contribute to red blood cell dehyd... more The K+ channel activated by the Ca2+, KCNN4, has been shown to contribute to red blood cell dehydration in the rare hereditary hemolytic anemia, the dehydrated hereditary stomatocytosis. We report two de novo mutations on KCNN4, We reported two de novo mutations on KCNN4, V222L and H340N, characterized at the molecular, cellular and clinical levels. Whereas both mutations were shown to increase the calcium sensitivity of the K+ channel, leading to channel opening for lower calcium concentrations compared to WT KCNN4 channel, there was no obvious red blood cell dehydration in patients carrying one or the other mutation. The clinical phenotype was greatly different between carriers of the mutated gene ranging from severe anemia for one patient to a single episode of anemia for the other patient or no documented sign of anemia for the parents who also carried the mutation. These data compared to already published KCNN4 mutations question the role of KCNN4 gain-of-function mutations in ...
Journal of Biomolecular Structure & Dynamics, Feb 1, 1985
Computations on the energy profiles for Na+ in the gramicidin A (GA) channel have been extended b... more Computations on the energy profiles for Na+ in the gramicidin A (GA) channel have been extended by introducing the effect, previously neglected, of the amino acid side chains of GA, fixed in their most stable conformations. The calculations have been performed in two approximations: 1) with the ethanolamine tail fixed in its most stable conformation, 2) with the tail allowed to optimize its conformation upon the progression of the ion. In both approximations the overall shape of the energy profile is very similar to that obtained in the absence of the side chains. One observes, however, a general lowering of the profile upon the adjunction of the side chains. The analysis of the factors responsible for this energy lowering indicates that it is due essentially to the electrostatic and polarisation components of the interaction which interplay differently, however, in the different parts of the channel. A particular role is attributed in this respect to the tryptophan residues of GA. The role of the 4 tryptophans present, Trp 15, 13, 11 and 9, is individualized by stripping of one of them at a time. The strongest effect on the energy deepening is due to Trp 13 and is particularly prominent in the entrance zone at 14.5A from the center of the channel. The result indicates the possibility of investigating theoretically the effect on the energy profiles of the substitution of the "natural" side chain by others.
Journal of Molecular Graphics, Mar 1, 1992
Two efficient algorithms have been developed which allow amino acid side chain conformations to b... more Two efficient algorithms have been developed which allow amino acid side chain conformations to be optimized rapidly for a given peptide backbone conformation. Both these approaches are based on the assumption that each side chain can be represented by a small number of rotameric states. These states have been obtained by a dynamic cluster analysis of a large data base of known crystallographic structures. Successful applications of these algorithms to the prediction of known protein conformations are presented.
Chemical Physics Letters, 1982
ABSTRACT
Theoretica chimica acta, 1982
ABSTRACT
International Journal of Molecular Sciences, Feb 24, 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Protein Engineering Design & Selection, Apr 1, 1997
which gathered representations of side-chain conformations by Minato-ku, Tokyo 108, Japan analyzi... more which gathered representations of side-chain conformations by Minato-ku, Tokyo 108, Japan analyzing the side-chain torsion angles of various proteins in A method of side-chain prediction without calculating the Brookhaven Protein Data Bank (Bernstein et al., 1977). the potential function is introduced. It is based on the However, even if this library was used, the number of combinaassumption that similar side-chain conformations have a tions of side-chain conformations is still huge. similar structural environment around the side chains. The Recently, the Dead-End-Elimination Theorem (Desmet et al., environment information is represented by vectors that 1992; Lasters and Desmet, 1993; Leach, 1994; Tanimura were obtained from principle component analysis and et al., 1994), which detects side-chain conformations absolutely represented by the variance of positions of main-chain incompatible with those at the global minimum, was reported atoms around side chains. This information was added to to obtain the global minimum energy conformation. This the side-chain library (rotamer library) made from Xmethod can predict side-chain conformations relatively rapidly, ray structures. Side-chain conformations were constructed because the number of combinations searched is smaller than using this side-chain library without using potential functhat of all combinations. tions. An optimal solution was determined by comparing The potential function, especially the van der Waals potential, environmental information with the backbone conformais strongly influenced by small changes in side-chain conformation around the side chain to be predicted and native ones tions. Side-chain conformations in the protein interior are in the library. The method was performed for 15 proteins determined by the tight packing of atoms and even a small whose structures were known. The result for the rootoverlap of atoms makes the potential value very large. This mean-square deviation between the predicted and X-ray means that Ponder and Richard's rotamer library may not have side-chain conformations was~1.5 Å (the value for core enough side-chain conformations to obtain the best solution residues was~1.1 Å) and the percentage of predicted χ 1 for various proteins. angles correct within 40°was~65% (75% for the core). To avoid this difficulty, the prediction must be performed The computational time was short (~60 s for the prediction by using a large rotamer library which includes a large number of proteins with 200 amino acid residues). About 70% of of side-chain conformations, which should make the evaluation of conformations faster than that in the currently used methods. the side-chain conformations were constructed by location As one approach, Laughton (1994) performed the prediction of the main-chain atoms around the central C β atom and using a large library including environmental information taken the average of r.m.s.d. was~1.4 Å (for core residues the from the X-ray structure. This method limited the generation average was~1.0 Å). of side-chain conformations by a local three-dimensional Keywords: database searching/homology modeling/prediction homology defined for each side-chain conformation. After of side-chain conformations/principal component analysis/siderestricting side-chain conformations, an optimal solution was chain library evaluated with a Monte Carlo procedure. However, this method calculated the potential function for a large number of conformations and then the running time was long.
Methods in molecular biology, 2017
This chapter describes a protocol to establish a three-dimensional (3D) model of a protein and to... more This chapter describes a protocol to establish a three-dimensional (3D) model of a protein and to explore its conformational landscape. It combines predictions from up-to-date bioinformatics methods with low-resolution experimental data. It also proposes to examine rapidly the dynamics of the protein using molecular dynamics simulations with a coarse-grained force field. Tools for analyzing these trajectories are suggested as well as those for constructing all-atoms models. Thus, starting from a protein sequence and using free software, the user can get important conformational information, which might improve the knowledge about the protein function.
NATO advanced study institutes series, 1994
Predicting protein structure using computer simulation is still very much in its infancy. Protein... more Predicting protein structure using computer simulation is still very much in its infancy. Proteins are far from being easy systems to treat, firstly, because of their size, typically involving many thousands of atoms and, secondly, because of their complex structures which are stabilised by many weak interactions between sites often distant from one another in terms of the primary amino acid sequence. As a result of these features, current simulation techniques, even with the help of the fastest computers presently available, are far from being able to explain the folding pathways which lead from the denatured to the native state of typical globular proteins.
Jerusalem Symposia on Quantum Chemistry and Biochemistry, 1995
A strategy for modelling transmembrane c~-helix bundles has been investigated. Results concerning... more A strategy for modelling transmembrane c~-helix bundles has been investigated. Results concerning the rotational orientations of the helices are described and perspectives for extensions of the method are discussed.
BioMedInformatics, Apr 6, 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Journal of Chemical Information and Modeling, Feb 13, 2023
Journal of Biomolecular Structure & Dynamics, Feb 8, 2023
Transfusion, Feb 6, 2023
Octafunctionalized spherosilsesquioxanes (Q 8 M 8 H), decorated with Si−H functions, could be use... more Octafunctionalized spherosilsesquioxanes (Q 8 M 8 H), decorated with Si−H functions, could be used to design, by coupling via hydrosilylation with α-methoxy-ω-undecenyl poly(ethylene oxide)s (PEOs), organic− inorganic nanocomposite structures. 1 H, 13 C, and 29 Si NMR; size exclusion chromatography; and Fourier transfrom infrared spectroscopy were used to follow the grafting reaction and determine the molar mass and the functionality of the different species. Hybrid star-shaped poly(ethylene oxide)s of precise molar mass and functionality could be isolated by fractional precipitation of the raw reaction product. Absolute molar masses of the purified star-shaped PEOs, calculated with the assumption of a functionality of 8, were comparable when measured by light scattering in methanol and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Small-angle X-ray scattering was employed to determine their molecular and structural characteristics, representing the versatility and innovative aspect to this study. Both differential scanning calorimetry and optical microscopy were utilized to elaborate and analyze the thermal properties and crystallization, respectively, of the hybrid stars. Further ongoing work is being carried out currently to investigate and foresee the use of longer PEO branches onto the core.
bioRxiv (Cold Spring Harbor Laboratory), Mar 15, 2022
Flaviviruses comprise a large group of arboviral species that are distributed in several countrie... more Flaviviruses comprise a large group of arboviral species that are distributed in several countries of the tropics, neotropics, and some temperate zones. Since they can produce neurological pathologies or vascular damage, there has been intense research seeking better diagnosis and treatments for their infections in the last decades. The flavivirus NS1 protein is a relevant clinical target because it is involved in viral replication, immune evasion, and virulence. Being a key factor in endothelial and tissue-specific modulation, NS1 has been largely studied to understand the molecular mechanisms exploited by the virus to reprogram host cells. A central part of the viral maturation processes is the NS1 oligomerization because many stages rely on these protein-protein assemblies. In the present study, the self-associations of NS1 proteins from Zika, Dengue, and West Nile viruses are examined through constant-pH coarse-grained biophysical simulations. Free energies of interactions were estimated for different oligomeric states and pH conditions. Our results show that these proteins can form both dimers and tetramers under conditions near physiological pH even without the presence of lipids. Moreover, pH plays an important role mainly controlling the regimes where van der Waals interactions govern their association. Finally, despite the similarity at the sequence level, we found that each flavivirus has a well-characteristic protein-protein interaction profile. These specific features can provide new hints for the development of binders both for better diagnostic tools and the formulation of new therapeutic drugs.
Biophysical Journal, Feb 1, 2018
BMC Biochemistry, Oct 31, 2007
Background: Aminopeptidase B (Ap-B; EC 3.4.11.6) catalyzes the cleavage of basic residues at the ... more Background: Aminopeptidase B (Ap-B; EC 3.4.11.6) catalyzes the cleavage of basic residues at the N-terminus of peptides and processes glucagon into miniglucagon. The enzyme exhibits, in vitro, a residual ability to hydrolyze leukotriene A 4 into the pro-inflammatory lipid mediator leukotriene B 4. The potential bi-functional nature of Ap-B is supported by close structural relationships with LTA 4 hydrolase (LTA 4 H ; EC 3.3.2.6). A structure-function analysis is necessary for the detailed understanding of the enzymatic mechanisms of Ap-B and to design inhibitors, which could be used to determine the complete in vivo functions of the enzyme. Results: The rat Ap-B cDNA was expressed in E. coli and the purified recombinant enzyme was characterized. 18 mutants of the H 325 EXXHX 18 E 348 Zn 2+-binding motif were constructed and expressed. All mutations were found to abolish the aminopeptidase activity. A multiple alignment of 500 sequences of the M1 family of aminopeptidases was performed to identify 3 sub-families of exopeptidases and to build a structural model of Ap-B using the x-ray structure of LTA 4 H as a template. Although the 3D structures of the two enzymes resemble each other, they differ in certain details. The role that a loop, delimiting the active center of Ap-B, plays in discriminating basic substrates, as well as the function of consensus motifs, such as RNP1 and Armadillo domain are discussed. Examination of electrostatic potentials and hydrophobic patches revealed important differences between Ap-B and LTA 4 H and suggests that Ap-B is involved in protein-protein interactions. Conclusion: Alignment of the primary structures of the M1 family members clearly demonstrates the existence of different sub-families and highlights crucial residues in the enzymatic activity of the whole family. E. coli recombinant enzyme and Ap-B structural model constitute powerful tools for investigating the importance and possible roles of these conserved residues in Ap-B, LTA 4 H and M1 aminopeptidase catalytic sites and to gain new insight into their physiological functions. Analysis of Ap-B structural model indicates that several interactions between Ap-B and proteins can occur and suggests that endopeptidases might form a complex with Ap-B during hormone processing.
Cet article est dedie a la presentation de differentes methodes bioinformatiques visant a analyse... more Cet article est dedie a la presentation de differentes methodes bioinformatiques visant a analyser et a predire la structure des macromolecules biologiques, proteines et acides nucleiques. Il souligne l’importance de la structure 3D pour comprendre la fonction de ces macromolecules et l’apport des methodes de prediction de la structure a partir de la sequence. Il fournit des informations pour comprendre les principes des methodes de bioinformatique structurale et des recommandations pour la mise en œuvre d’une demarche de prediction. Une liste non exhaustive d’outils et de bases de donnees utiles est proposee, associee a une bibliographie recente.
Virus Research, Sep 1, 2022
Blood Cells, Molecules, and Diseases
Frontiers in Physiology
The K+ channel activated by the Ca2+, KCNN4, has been shown to contribute to red blood cell dehyd... more The K+ channel activated by the Ca2+, KCNN4, has been shown to contribute to red blood cell dehydration in the rare hereditary hemolytic anemia, the dehydrated hereditary stomatocytosis. We report two de novo mutations on KCNN4, We reported two de novo mutations on KCNN4, V222L and H340N, characterized at the molecular, cellular and clinical levels. Whereas both mutations were shown to increase the calcium sensitivity of the K+ channel, leading to channel opening for lower calcium concentrations compared to WT KCNN4 channel, there was no obvious red blood cell dehydration in patients carrying one or the other mutation. The clinical phenotype was greatly different between carriers of the mutated gene ranging from severe anemia for one patient to a single episode of anemia for the other patient or no documented sign of anemia for the parents who also carried the mutation. These data compared to already published KCNN4 mutations question the role of KCNN4 gain-of-function mutations in ...
Journal of Biomolecular Structure & Dynamics, Feb 1, 1985
Computations on the energy profiles for Na+ in the gramicidin A (GA) channel have been extended b... more Computations on the energy profiles for Na+ in the gramicidin A (GA) channel have been extended by introducing the effect, previously neglected, of the amino acid side chains of GA, fixed in their most stable conformations. The calculations have been performed in two approximations: 1) with the ethanolamine tail fixed in its most stable conformation, 2) with the tail allowed to optimize its conformation upon the progression of the ion. In both approximations the overall shape of the energy profile is very similar to that obtained in the absence of the side chains. One observes, however, a general lowering of the profile upon the adjunction of the side chains. The analysis of the factors responsible for this energy lowering indicates that it is due essentially to the electrostatic and polarisation components of the interaction which interplay differently, however, in the different parts of the channel. A particular role is attributed in this respect to the tryptophan residues of GA. The role of the 4 tryptophans present, Trp 15, 13, 11 and 9, is individualized by stripping of one of them at a time. The strongest effect on the energy deepening is due to Trp 13 and is particularly prominent in the entrance zone at 14.5A from the center of the channel. The result indicates the possibility of investigating theoretically the effect on the energy profiles of the substitution of the "natural" side chain by others.
Journal of Molecular Graphics, Mar 1, 1992
Two efficient algorithms have been developed which allow amino acid side chain conformations to b... more Two efficient algorithms have been developed which allow amino acid side chain conformations to be optimized rapidly for a given peptide backbone conformation. Both these approaches are based on the assumption that each side chain can be represented by a small number of rotameric states. These states have been obtained by a dynamic cluster analysis of a large data base of known crystallographic structures. Successful applications of these algorithms to the prediction of known protein conformations are presented.
Chemical Physics Letters, 1982
ABSTRACT
Theoretica chimica acta, 1982
ABSTRACT
International Journal of Molecular Sciences, Feb 24, 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Protein Engineering Design & Selection, Apr 1, 1997
which gathered representations of side-chain conformations by Minato-ku, Tokyo 108, Japan analyzi... more which gathered representations of side-chain conformations by Minato-ku, Tokyo 108, Japan analyzing the side-chain torsion angles of various proteins in A method of side-chain prediction without calculating the Brookhaven Protein Data Bank (Bernstein et al., 1977). the potential function is introduced. It is based on the However, even if this library was used, the number of combinaassumption that similar side-chain conformations have a tions of side-chain conformations is still huge. similar structural environment around the side chains. The Recently, the Dead-End-Elimination Theorem (Desmet et al., environment information is represented by vectors that 1992; Lasters and Desmet, 1993; Leach, 1994; Tanimura were obtained from principle component analysis and et al., 1994), which detects side-chain conformations absolutely represented by the variance of positions of main-chain incompatible with those at the global minimum, was reported atoms around side chains. This information was added to to obtain the global minimum energy conformation. This the side-chain library (rotamer library) made from Xmethod can predict side-chain conformations relatively rapidly, ray structures. Side-chain conformations were constructed because the number of combinations searched is smaller than using this side-chain library without using potential functhat of all combinations. tions. An optimal solution was determined by comparing The potential function, especially the van der Waals potential, environmental information with the backbone conformais strongly influenced by small changes in side-chain conformation around the side chain to be predicted and native ones tions. Side-chain conformations in the protein interior are in the library. The method was performed for 15 proteins determined by the tight packing of atoms and even a small whose structures were known. The result for the rootoverlap of atoms makes the potential value very large. This mean-square deviation between the predicted and X-ray means that Ponder and Richard's rotamer library may not have side-chain conformations was~1.5 Å (the value for core enough side-chain conformations to obtain the best solution residues was~1.1 Å) and the percentage of predicted χ 1 for various proteins. angles correct within 40°was~65% (75% for the core). To avoid this difficulty, the prediction must be performed The computational time was short (~60 s for the prediction by using a large rotamer library which includes a large number of proteins with 200 amino acid residues). About 70% of of side-chain conformations, which should make the evaluation of conformations faster than that in the currently used methods. the side-chain conformations were constructed by location As one approach, Laughton (1994) performed the prediction of the main-chain atoms around the central C β atom and using a large library including environmental information taken the average of r.m.s.d. was~1.4 Å (for core residues the from the X-ray structure. This method limited the generation average was~1.0 Å). of side-chain conformations by a local three-dimensional Keywords: database searching/homology modeling/prediction homology defined for each side-chain conformation. After of side-chain conformations/principal component analysis/siderestricting side-chain conformations, an optimal solution was chain library evaluated with a Monte Carlo procedure. However, this method calculated the potential function for a large number of conformations and then the running time was long.
Methods in molecular biology, 2017
This chapter describes a protocol to establish a three-dimensional (3D) model of a protein and to... more This chapter describes a protocol to establish a three-dimensional (3D) model of a protein and to explore its conformational landscape. It combines predictions from up-to-date bioinformatics methods with low-resolution experimental data. It also proposes to examine rapidly the dynamics of the protein using molecular dynamics simulations with a coarse-grained force field. Tools for analyzing these trajectories are suggested as well as those for constructing all-atoms models. Thus, starting from a protein sequence and using free software, the user can get important conformational information, which might improve the knowledge about the protein function.
NATO advanced study institutes series, 1994
Predicting protein structure using computer simulation is still very much in its infancy. Protein... more Predicting protein structure using computer simulation is still very much in its infancy. Proteins are far from being easy systems to treat, firstly, because of their size, typically involving many thousands of atoms and, secondly, because of their complex structures which are stabilised by many weak interactions between sites often distant from one another in terms of the primary amino acid sequence. As a result of these features, current simulation techniques, even with the help of the fastest computers presently available, are far from being able to explain the folding pathways which lead from the denatured to the native state of typical globular proteins.
Jerusalem Symposia on Quantum Chemistry and Biochemistry, 1995
A strategy for modelling transmembrane c~-helix bundles has been investigated. Results concerning... more A strategy for modelling transmembrane c~-helix bundles has been investigated. Results concerning the rotational orientations of the helices are described and perspectives for extensions of the method are discussed.
BioMedInformatics, Apr 6, 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Journal of Chemical Information and Modeling, Feb 13, 2023
Journal of Biomolecular Structure & Dynamics, Feb 8, 2023
Transfusion, Feb 6, 2023
Octafunctionalized spherosilsesquioxanes (Q 8 M 8 H), decorated with Si−H functions, could be use... more Octafunctionalized spherosilsesquioxanes (Q 8 M 8 H), decorated with Si−H functions, could be used to design, by coupling via hydrosilylation with α-methoxy-ω-undecenyl poly(ethylene oxide)s (PEOs), organic− inorganic nanocomposite structures. 1 H, 13 C, and 29 Si NMR; size exclusion chromatography; and Fourier transfrom infrared spectroscopy were used to follow the grafting reaction and determine the molar mass and the functionality of the different species. Hybrid star-shaped poly(ethylene oxide)s of precise molar mass and functionality could be isolated by fractional precipitation of the raw reaction product. Absolute molar masses of the purified star-shaped PEOs, calculated with the assumption of a functionality of 8, were comparable when measured by light scattering in methanol and by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Small-angle X-ray scattering was employed to determine their molecular and structural characteristics, representing the versatility and innovative aspect to this study. Both differential scanning calorimetry and optical microscopy were utilized to elaborate and analyze the thermal properties and crystallization, respectively, of the hybrid stars. Further ongoing work is being carried out currently to investigate and foresee the use of longer PEO branches onto the core.
bioRxiv (Cold Spring Harbor Laboratory), Mar 15, 2022
Flaviviruses comprise a large group of arboviral species that are distributed in several countrie... more Flaviviruses comprise a large group of arboviral species that are distributed in several countries of the tropics, neotropics, and some temperate zones. Since they can produce neurological pathologies or vascular damage, there has been intense research seeking better diagnosis and treatments for their infections in the last decades. The flavivirus NS1 protein is a relevant clinical target because it is involved in viral replication, immune evasion, and virulence. Being a key factor in endothelial and tissue-specific modulation, NS1 has been largely studied to understand the molecular mechanisms exploited by the virus to reprogram host cells. A central part of the viral maturation processes is the NS1 oligomerization because many stages rely on these protein-protein assemblies. In the present study, the self-associations of NS1 proteins from Zika, Dengue, and West Nile viruses are examined through constant-pH coarse-grained biophysical simulations. Free energies of interactions were estimated for different oligomeric states and pH conditions. Our results show that these proteins can form both dimers and tetramers under conditions near physiological pH even without the presence of lipids. Moreover, pH plays an important role mainly controlling the regimes where van der Waals interactions govern their association. Finally, despite the similarity at the sequence level, we found that each flavivirus has a well-characteristic protein-protein interaction profile. These specific features can provide new hints for the development of binders both for better diagnostic tools and the formulation of new therapeutic drugs.
Biophysical Journal, Feb 1, 2018
BMC Biochemistry, Oct 31, 2007
Background: Aminopeptidase B (Ap-B; EC 3.4.11.6) catalyzes the cleavage of basic residues at the ... more Background: Aminopeptidase B (Ap-B; EC 3.4.11.6) catalyzes the cleavage of basic residues at the N-terminus of peptides and processes glucagon into miniglucagon. The enzyme exhibits, in vitro, a residual ability to hydrolyze leukotriene A 4 into the pro-inflammatory lipid mediator leukotriene B 4. The potential bi-functional nature of Ap-B is supported by close structural relationships with LTA 4 hydrolase (LTA 4 H ; EC 3.3.2.6). A structure-function analysis is necessary for the detailed understanding of the enzymatic mechanisms of Ap-B and to design inhibitors, which could be used to determine the complete in vivo functions of the enzyme. Results: The rat Ap-B cDNA was expressed in E. coli and the purified recombinant enzyme was characterized. 18 mutants of the H 325 EXXHX 18 E 348 Zn 2+-binding motif were constructed and expressed. All mutations were found to abolish the aminopeptidase activity. A multiple alignment of 500 sequences of the M1 family of aminopeptidases was performed to identify 3 sub-families of exopeptidases and to build a structural model of Ap-B using the x-ray structure of LTA 4 H as a template. Although the 3D structures of the two enzymes resemble each other, they differ in certain details. The role that a loop, delimiting the active center of Ap-B, plays in discriminating basic substrates, as well as the function of consensus motifs, such as RNP1 and Armadillo domain are discussed. Examination of electrostatic potentials and hydrophobic patches revealed important differences between Ap-B and LTA 4 H and suggests that Ap-B is involved in protein-protein interactions. Conclusion: Alignment of the primary structures of the M1 family members clearly demonstrates the existence of different sub-families and highlights crucial residues in the enzymatic activity of the whole family. E. coli recombinant enzyme and Ap-B structural model constitute powerful tools for investigating the importance and possible roles of these conserved residues in Ap-B, LTA 4 H and M1 aminopeptidase catalytic sites and to gain new insight into their physiological functions. Analysis of Ap-B structural model indicates that several interactions between Ap-B and proteins can occur and suggests that endopeptidases might form a complex with Ap-B during hormone processing.