Yves Chapron - Academia.edu (original) (raw)
Papers by Yves Chapron
European Biophysics Journal, 1996
Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules ... more Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules in their hydrophobic cavity. Moreover, cyclodextrins show a hemolytic activity when mM concentrations are added to blood. This hemolysis is commonly interpreted as a massive dissociation of phospholipids from the cell membrane due to the formation of complexes with the cyclodextrins. In the literature, a complexation between c~-cyclodextrin (~ CD) and phosphatidylinositol (PI) specific to the inositol headgroup has been proposed. But the need for the detailed interaction mechanism between the two molecules motivated the present work based on molecular dynamics simulations. Investigation of long range electrostatic interactions shows that a mutual approach of the molecules is only possible when the primary hydroxyl side of ~ CD faces the inositol headgroup of PI. This orientation is also the most favourable from adiabatic-and free-energy profiles calculated along a reaction coordinate that leads to an inclusion of PI into c~CD. For free energy simulations, partial hydration of the model has been used. A study of glycosidic bond dihedral angles in ~ CD shows an increase in dihedral fluctuations before complexation and a dihedral "freezing" once the complex is formed.
Carbohydrate Research, Jun 1, 1996
1H-31P NMR spectroscopy and molecular dynamics (MD) have been used to investigate the myo-inosito... more 1H-31P NMR spectroscopy and molecular dynamics (MD) have been used to investigate the myo-inositol 2-phosphate (MY2P) inclusion complex in α-cyclodextrin (α-CD). From spectral analyses, it has not been possible to estimate the stoichiometric ratio of MY2P to α-CD, however several geometrical constraints between the two molecules have been deduced from nuclear Overhauser effects and chemical shift measurements. Based on a MD study, a model for the α-CD-MY2P interaction is proposed showing the possible coexistence of loose and tight inclusion of MY2P into α-CD.
European Biophysics Journal, 1996
Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules ... more Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules in their hydrophobic cavity. Moreover, cyclodextrins show a hemolytic activity when mM concentrations are added to blood. This hemolysis is commonly interpreted as a massive dissociation of phospholipids from the cell membrane due to the formation of complexes with the cyclodextrins. In the literature, a complexation between c~-cyclodextrin (~ CD) and phosphatidylinositol (PI) specific to the inositol headgroup has been proposed. But the need for the detailed interaction mechanism between the two molecules motivated the present work based on molecular dynamics simulations. Investigation of long range electrostatic interactions shows that a mutual approach of the molecules is only possible when the primary hydroxyl side of ~ CD faces the inositol headgroup of PI. This orientation is also the most favourable from adiabatic-and free-energy profiles calculated along a reaction coordinate that leads to an inclusion of PI into c~CD. For free energy simulations, partial hydration of the model has been used. A study of glycosidic bond dihedral angles in ~ CD shows an increase in dihedral fluctuations before complexation and a dihedral "freezing" once the complex is formed.
European Biophysics Journal, 1996
Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules ... more Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules in their hydrophobic cavity. Moreover, cyclodextrins show a hemolytic activity when mM concentrations are added to blood. This hemolysis is commonly interpreted as a massive dissociation of phospholipids from the cell membrane due to the formation of complexes with the cyclodextrins. In the literature, a complexation between c~-cyclodextrin (~ CD) and phosphatidylinositol (PI) specific to the inositol headgroup has been proposed. But the need for the detailed interaction mechanism between the two molecules motivated the present work based on molecular dynamics simulations. Investigation of long range electrostatic interactions shows that a mutual approach of the molecules is only possible when the primary hydroxyl side of ~ CD faces the inositol headgroup of PI. This orientation is also the most favourable from adiabatic-and free-energy profiles calculated along a reaction coordinate that leads to an inclusion of PI into c~CD. For free energy simulations, partial hydration of the model has been used. A study of glycosidic bond dihedral angles in ~ CD shows an increase in dihedral fluctuations before complexation and a dihedral "freezing" once the complex is formed.
Biochemical and Biophysical Research Communications, 1989
Carbohydrate Research, Jun 1, 1996
1H-31P NMR spectroscopy and molecular dynamics (MD) have been used to investigate the myo-inosito... more 1H-31P NMR spectroscopy and molecular dynamics (MD) have been used to investigate the myo-inositol 2-phosphate (MY2P) inclusion complex in α-cyclodextrin (α-CD). From spectral analyses, it has not been possible to estimate the stoichiometric ratio of MY2P to α-CD, however several geometrical constraints between the two molecules have been deduced from nuclear Overhauser effects and chemical shift measurements. Based on a MD study, a model for the α-CD-MY2P interaction is proposed showing the possible coexistence of loose and tight inclusion of MY2P into α-CD.
Journal of Pharmaceutical Sciences, Aug 1, 1997
Abstract It has been suggested that the interaction of cyclodextrins with the lipid components of... more Abstract It has been suggested that the interaction of cyclodextrins with the lipid components of the erythrocyte membranes is the determining factor in the hemolysis induced by these cyclic oligosaccharides. In the case of α-cyclodextrin (cyclomaltohexose), phospholipids ...
Biochemical and Biophysical Research Communications, 1989
Journal of Colloid and Interface Science, Nov 1, 2009
Molecular dynamics (MD) simulations of a montmorillonite / water interface at the pore scale were... more Molecular dynamics (MD) simulations of a montmorillonite / water interface at the pore scale were carried out at 0.1 mol L-1 NaCl concentration in order to constrain cation, anion and water distribution and mobility influenced by the mineral surface. MD results enabled anion exclusion and cation condensation at the surface to be quantified. MD derived values could then be compared with macroscopic model results obtained from the modified Gouy-Chapman (MGC) theory. While the Na concentration profile is well reproduced in the diffuse layer, anion exclusion is overestimated by the MGC theory in our experimental conditions. We also showed that MD simulations can be used to constrain Basic Stern model parameters or, in combination with zeta potential measurements, can be used to constrain triple layer model (TLM) parameters by providing suitable values for the capacitance values. Na sorption intrinsic equilibrium constant values for clay basal surfaces are given accordingly.
Journal of Pharmaceutical Sciences, Aug 1, 1997
Abstract It has been suggested that the interaction of cyclodextrins with the lipid components of... more Abstract It has been suggested that the interaction of cyclodextrins with the lipid components of the erythrocyte membranes is the determining factor in the hemolysis induced by these cyclic oligosaccharides. In the case of α-cyclodextrin (cyclomaltohexose), phospholipids ...
Journal of Colloid and Interface Science, Nov 1, 2009
Molecular dynamics (MD) simulations of a montmorillonite / water interface at the pore scale were... more Molecular dynamics (MD) simulations of a montmorillonite / water interface at the pore scale were carried out at 0.1 mol L-1 NaCl concentration in order to constrain cation, anion and water distribution and mobility influenced by the mineral surface. MD results enabled anion exclusion and cation condensation at the surface to be quantified. MD derived values could then be compared with macroscopic model results obtained from the modified Gouy-Chapman (MGC) theory. While the Na concentration profile is well reproduced in the diffuse layer, anion exclusion is overestimated by the MGC theory in our experimental conditions. We also showed that MD simulations can be used to constrain Basic Stern model parameters or, in combination with zeta potential measurements, can be used to constrain triple layer model (TLM) parameters by providing suitable values for the capacitance values. Na sorption intrinsic equilibrium constant values for clay basal surfaces are given accordingly.
Springer eBooks, 1990
Photoexcitation induces a hyperpolarization of the plasma membrane of the rod outer segment, and ... more Photoexcitation induces a hyperpolarization of the plasma membrane of the rod outer segment, and it is now clearly established that this hyperpolarization results from a decrease of cGMP* concentration which directly regulates the opening of sodium channels of this membrane (see Haynes and Yau, Chapter 3 in this volume, and Hanke and Simmoteit, Chapter 4 in this volume; for a review, see Pugh and Cobbs(1)). cGMP-dependent sodium channels are also present in the membranes of the disks.(2–7)
Springer eBooks, 1990
Photoexcitation induces a hyperpolarization of the plasma membrane of the rod outer segment, and ... more Photoexcitation induces a hyperpolarization of the plasma membrane of the rod outer segment, and it is now clearly established that this hyperpolarization results from a decrease of cGMP* concentration which directly regulates the opening of sodium channels of this membrane (see Haynes and Yau, Chapter 3 in this volume, and Hanke and Simmoteit, Chapter 4 in this volume; for a review, see Pugh and Cobbs(1)). cGMP-dependent sodium channels are also present in the membranes of the disks.(2–7)
Építőanyag, 2010
Better understanding of the forces between modified or unmodified nanoparticles would be benefici... more Better understanding of the forces between modified or unmodified nanoparticles would be beneficial for developing new strategies for the production of engineered nanoparticle suspensions, as well as for predicting their fate and transport in the environment. Molecularlevel simulations, such as Molecular Dynamics can be useful for understanding the interactions between colloidal nanoparticles, but simulations of very large systems are constrained by the long calculation times and require enormous computer resources. A new computation approach that combines series of cycles of Rigid Body Dynamics and Molecular Dynamics has been applied to the study of the interaction of a lysophospholipidic micelle with polyacrylic acid. The results obtained show that the method makes it possible to reach a stationary interaction structure quite rapidly. The method is ready to be applied to the study of the interaction of a wide range of nanoparticles of industrial, environmental or biological interest via a widely-used and freelyaccessible computer code.
Építőanyag, 2010
Better understanding of the forces between modified or unmodified nanoparticles would be benefici... more Better understanding of the forces between modified or unmodified nanoparticles would be beneficial for developing new strategies for the production of engineered nanoparticle suspensions, as well as for predicting their fate and transport in the environment. Molecularlevel simulations, such as Molecular Dynamics can be useful for understanding the interactions between colloidal nanoparticles, but simulations of very large systems are constrained by the long calculation times and require enormous computer resources. A new computation approach that combines series of cycles of Rigid Body Dynamics and Molecular Dynamics has been applied to the study of the interaction of a lysophospholipidic micelle with polyacrylic acid. The results obtained show that the method makes it possible to reach a stationary interaction structure quite rapidly. The method is ready to be applied to the study of the interaction of a wide range of nanoparticles of industrial, environmental or biological interest via a widely-used and freelyaccessible computer code.
Theoretical Chemistry Accounts, Feb 15, 1999
The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular ... more The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular dynamics techniques both in vacuum and within an explicit hydrated L-a-dilauroyl-phosphatidylethanolamine environment. In-vacuum simulations show that a highly cooperative structural transition occurs frequently within the a-helical transmembrane domain which converts to local p-helices. We show that the a-helix alteration does not depend upon the force ®eld or initial side-chain conformations but is intimately related to the sequence. The membrane-like environment does not prevent the structural transition in the helix but slows down the peptide dynamics indicating that the appearance of a p-bulge is not an artifact of the vacuum approximation. The consequences of p-helix formation could be very huge for the ErbB-2 receptor which is involved in numerous human cancers and also for other membrane proteins wherein similar local structures are also observed experimentally.
Theoretical Chemistry Accounts, Feb 15, 1999
The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular ... more The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular dynamics techniques both in vacuum and within an explicit hydrated L-a-dilauroyl-phosphatidylethanolamine environment. In-vacuum simulations show that a highly cooperative structural transition occurs frequently within the a-helical transmembrane domain which converts to local p-helices. We show that the a-helix alteration does not depend upon the force ®eld or initial side-chain conformations but is intimately related to the sequence. The membrane-like environment does not prevent the structural transition in the helix but slows down the peptide dynamics indicating that the appearance of a p-bulge is not an artifact of the vacuum approximation. The consequences of p-helix formation could be very huge for the ErbB-2 receptor which is involved in numerous human cancers and also for other membrane proteins wherein similar local structures are also observed experimentally.
Journal of Theoretical Biology, May 1, 2000
Transmissible subacute spongiform encephalopathies (TSE) are animal and human neurodegenerative d... more Transmissible subacute spongiform encephalopathies (TSE) are animal and human neurodegenerative diseases. The nature of the transmissible agent remains unknown. The speci"c molecular marker of these diseases is the abnormal isoform of the prion protein (PrP). This protein is encoded by a cellular gene and accumulates in a pathological isoform (PrPres) which is partially resistant to proteolysis. The tridimensional structure of this protein remains theoretical. F. Cohen proposed one of the most realistic models. According to this model and from molecular mechanics calculation, we suggest a PrP oligomeric ionic channel model that may be involved in TSE-induced neuronal apoptosis.
Journal of Theoretical Biology, May 1, 2000
Transmissible subacute spongiform encephalopathies (TSE) are animal and human neurodegenerative d... more Transmissible subacute spongiform encephalopathies (TSE) are animal and human neurodegenerative diseases. The nature of the transmissible agent remains unknown. The speci"c molecular marker of these diseases is the abnormal isoform of the prion protein (PrP). This protein is encoded by a cellular gene and accumulates in a pathological isoform (PrPres) which is partially resistant to proteolysis. The tridimensional structure of this protein remains theoretical. F. Cohen proposed one of the most realistic models. According to this model and from molecular mechanics calculation, we suggest a PrP oligomeric ionic channel model that may be involved in TSE-induced neuronal apoptosis.
Journal of Pharmaceutical Sciences, 1998
A nuclear magnetic resonance (NMR) spectroscopy and molecular modeling study of the interaction b... more A nuclear magnetic resonance (NMR) spectroscopy and molecular modeling study of the interaction between R-cyclodextrin (R-CD) and phospholipids with serine, ethanolamine, or choline headgroups is presented. The experimental approach is based on 31 P and 1 H NMR measurements on small unilamellar vesicles (SUV), multilamellar systems (MLV), and aqueous suspensions of lipids using a direct complex preparation with R-CD. Molecular dynamics computer simulations are used to investigate the trajectory of R-CD in the vicinity of a membrane surface and the influence of the charge and dipole moment of the phospholipid headgroups. These factors of charge and orientation of dipole moment seem to play a key role in the interaction of phospholipids with R-CD and reflect very well the experimentally observed selectivity of the phospholipid −R-CD approach. However, with this approach, there is no evidence for the formation of a complex with the phospholipid headgroup (except for phosphatidylinositol) that results from electrostatic forces. Rather, after a possible extraction of the lipid from the membrane, a classical inclusion of the sn-2 chain in the cavity of R-CD occurs. This step depends on the alkyl chain length and saturation state of the lipids as well as on their organization (i.e., as vesicles or dispersions). Based on our results, chemical modifications of the R-CD molecule to control the hemolytic properties of R-CD are discussed.
European Biophysics Journal, 1996
Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules ... more Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules in their hydrophobic cavity. Moreover, cyclodextrins show a hemolytic activity when mM concentrations are added to blood. This hemolysis is commonly interpreted as a massive dissociation of phospholipids from the cell membrane due to the formation of complexes with the cyclodextrins. In the literature, a complexation between c~-cyclodextrin (~ CD) and phosphatidylinositol (PI) specific to the inositol headgroup has been proposed. But the need for the detailed interaction mechanism between the two molecules motivated the present work based on molecular dynamics simulations. Investigation of long range electrostatic interactions shows that a mutual approach of the molecules is only possible when the primary hydroxyl side of ~ CD faces the inositol headgroup of PI. This orientation is also the most favourable from adiabatic-and free-energy profiles calculated along a reaction coordinate that leads to an inclusion of PI into c~CD. For free energy simulations, partial hydration of the model has been used. A study of glycosidic bond dihedral angles in ~ CD shows an increase in dihedral fluctuations before complexation and a dihedral "freezing" once the complex is formed.
Carbohydrate Research, Jun 1, 1996
1H-31P NMR spectroscopy and molecular dynamics (MD) have been used to investigate the myo-inosito... more 1H-31P NMR spectroscopy and molecular dynamics (MD) have been used to investigate the myo-inositol 2-phosphate (MY2P) inclusion complex in α-cyclodextrin (α-CD). From spectral analyses, it has not been possible to estimate the stoichiometric ratio of MY2P to α-CD, however several geometrical constraints between the two molecules have been deduced from nuclear Overhauser effects and chemical shift measurements. Based on a MD study, a model for the α-CD-MY2P interaction is proposed showing the possible coexistence of loose and tight inclusion of MY2P into α-CD.
European Biophysics Journal, 1996
Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules ... more Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules in their hydrophobic cavity. Moreover, cyclodextrins show a hemolytic activity when mM concentrations are added to blood. This hemolysis is commonly interpreted as a massive dissociation of phospholipids from the cell membrane due to the formation of complexes with the cyclodextrins. In the literature, a complexation between c~-cyclodextrin (~ CD) and phosphatidylinositol (PI) specific to the inositol headgroup has been proposed. But the need for the detailed interaction mechanism between the two molecules motivated the present work based on molecular dynamics simulations. Investigation of long range electrostatic interactions shows that a mutual approach of the molecules is only possible when the primary hydroxyl side of ~ CD faces the inositol headgroup of PI. This orientation is also the most favourable from adiabatic-and free-energy profiles calculated along a reaction coordinate that leads to an inclusion of PI into c~CD. For free energy simulations, partial hydration of the model has been used. A study of glycosidic bond dihedral angles in ~ CD shows an increase in dihedral fluctuations before complexation and a dihedral "freezing" once the complex is formed.
European Biophysics Journal, 1996
Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules ... more Cyclodextrins are cyclic oligosaccharides known for their ability to include substrate molecules in their hydrophobic cavity. Moreover, cyclodextrins show a hemolytic activity when mM concentrations are added to blood. This hemolysis is commonly interpreted as a massive dissociation of phospholipids from the cell membrane due to the formation of complexes with the cyclodextrins. In the literature, a complexation between c~-cyclodextrin (~ CD) and phosphatidylinositol (PI) specific to the inositol headgroup has been proposed. But the need for the detailed interaction mechanism between the two molecules motivated the present work based on molecular dynamics simulations. Investigation of long range electrostatic interactions shows that a mutual approach of the molecules is only possible when the primary hydroxyl side of ~ CD faces the inositol headgroup of PI. This orientation is also the most favourable from adiabatic-and free-energy profiles calculated along a reaction coordinate that leads to an inclusion of PI into c~CD. For free energy simulations, partial hydration of the model has been used. A study of glycosidic bond dihedral angles in ~ CD shows an increase in dihedral fluctuations before complexation and a dihedral "freezing" once the complex is formed.
Biochemical and Biophysical Research Communications, 1989
Carbohydrate Research, Jun 1, 1996
1H-31P NMR spectroscopy and molecular dynamics (MD) have been used to investigate the myo-inosito... more 1H-31P NMR spectroscopy and molecular dynamics (MD) have been used to investigate the myo-inositol 2-phosphate (MY2P) inclusion complex in α-cyclodextrin (α-CD). From spectral analyses, it has not been possible to estimate the stoichiometric ratio of MY2P to α-CD, however several geometrical constraints between the two molecules have been deduced from nuclear Overhauser effects and chemical shift measurements. Based on a MD study, a model for the α-CD-MY2P interaction is proposed showing the possible coexistence of loose and tight inclusion of MY2P into α-CD.
Journal of Pharmaceutical Sciences, Aug 1, 1997
Abstract It has been suggested that the interaction of cyclodextrins with the lipid components of... more Abstract It has been suggested that the interaction of cyclodextrins with the lipid components of the erythrocyte membranes is the determining factor in the hemolysis induced by these cyclic oligosaccharides. In the case of α-cyclodextrin (cyclomaltohexose), phospholipids ...
Biochemical and Biophysical Research Communications, 1989
Journal of Colloid and Interface Science, Nov 1, 2009
Molecular dynamics (MD) simulations of a montmorillonite / water interface at the pore scale were... more Molecular dynamics (MD) simulations of a montmorillonite / water interface at the pore scale were carried out at 0.1 mol L-1 NaCl concentration in order to constrain cation, anion and water distribution and mobility influenced by the mineral surface. MD results enabled anion exclusion and cation condensation at the surface to be quantified. MD derived values could then be compared with macroscopic model results obtained from the modified Gouy-Chapman (MGC) theory. While the Na concentration profile is well reproduced in the diffuse layer, anion exclusion is overestimated by the MGC theory in our experimental conditions. We also showed that MD simulations can be used to constrain Basic Stern model parameters or, in combination with zeta potential measurements, can be used to constrain triple layer model (TLM) parameters by providing suitable values for the capacitance values. Na sorption intrinsic equilibrium constant values for clay basal surfaces are given accordingly.
Journal of Pharmaceutical Sciences, Aug 1, 1997
Abstract It has been suggested that the interaction of cyclodextrins with the lipid components of... more Abstract It has been suggested that the interaction of cyclodextrins with the lipid components of the erythrocyte membranes is the determining factor in the hemolysis induced by these cyclic oligosaccharides. In the case of α-cyclodextrin (cyclomaltohexose), phospholipids ...
Journal of Colloid and Interface Science, Nov 1, 2009
Molecular dynamics (MD) simulations of a montmorillonite / water interface at the pore scale were... more Molecular dynamics (MD) simulations of a montmorillonite / water interface at the pore scale were carried out at 0.1 mol L-1 NaCl concentration in order to constrain cation, anion and water distribution and mobility influenced by the mineral surface. MD results enabled anion exclusion and cation condensation at the surface to be quantified. MD derived values could then be compared with macroscopic model results obtained from the modified Gouy-Chapman (MGC) theory. While the Na concentration profile is well reproduced in the diffuse layer, anion exclusion is overestimated by the MGC theory in our experimental conditions. We also showed that MD simulations can be used to constrain Basic Stern model parameters or, in combination with zeta potential measurements, can be used to constrain triple layer model (TLM) parameters by providing suitable values for the capacitance values. Na sorption intrinsic equilibrium constant values for clay basal surfaces are given accordingly.
Springer eBooks, 1990
Photoexcitation induces a hyperpolarization of the plasma membrane of the rod outer segment, and ... more Photoexcitation induces a hyperpolarization of the plasma membrane of the rod outer segment, and it is now clearly established that this hyperpolarization results from a decrease of cGMP* concentration which directly regulates the opening of sodium channels of this membrane (see Haynes and Yau, Chapter 3 in this volume, and Hanke and Simmoteit, Chapter 4 in this volume; for a review, see Pugh and Cobbs(1)). cGMP-dependent sodium channels are also present in the membranes of the disks.(2–7)
Springer eBooks, 1990
Photoexcitation induces a hyperpolarization of the plasma membrane of the rod outer segment, and ... more Photoexcitation induces a hyperpolarization of the plasma membrane of the rod outer segment, and it is now clearly established that this hyperpolarization results from a decrease of cGMP* concentration which directly regulates the opening of sodium channels of this membrane (see Haynes and Yau, Chapter 3 in this volume, and Hanke and Simmoteit, Chapter 4 in this volume; for a review, see Pugh and Cobbs(1)). cGMP-dependent sodium channels are also present in the membranes of the disks.(2–7)
Építőanyag, 2010
Better understanding of the forces between modified or unmodified nanoparticles would be benefici... more Better understanding of the forces between modified or unmodified nanoparticles would be beneficial for developing new strategies for the production of engineered nanoparticle suspensions, as well as for predicting their fate and transport in the environment. Molecularlevel simulations, such as Molecular Dynamics can be useful for understanding the interactions between colloidal nanoparticles, but simulations of very large systems are constrained by the long calculation times and require enormous computer resources. A new computation approach that combines series of cycles of Rigid Body Dynamics and Molecular Dynamics has been applied to the study of the interaction of a lysophospholipidic micelle with polyacrylic acid. The results obtained show that the method makes it possible to reach a stationary interaction structure quite rapidly. The method is ready to be applied to the study of the interaction of a wide range of nanoparticles of industrial, environmental or biological interest via a widely-used and freelyaccessible computer code.
Építőanyag, 2010
Better understanding of the forces between modified or unmodified nanoparticles would be benefici... more Better understanding of the forces between modified or unmodified nanoparticles would be beneficial for developing new strategies for the production of engineered nanoparticle suspensions, as well as for predicting their fate and transport in the environment. Molecularlevel simulations, such as Molecular Dynamics can be useful for understanding the interactions between colloidal nanoparticles, but simulations of very large systems are constrained by the long calculation times and require enormous computer resources. A new computation approach that combines series of cycles of Rigid Body Dynamics and Molecular Dynamics has been applied to the study of the interaction of a lysophospholipidic micelle with polyacrylic acid. The results obtained show that the method makes it possible to reach a stationary interaction structure quite rapidly. The method is ready to be applied to the study of the interaction of a wide range of nanoparticles of industrial, environmental or biological interest via a widely-used and freelyaccessible computer code.
Theoretical Chemistry Accounts, Feb 15, 1999
The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular ... more The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular dynamics techniques both in vacuum and within an explicit hydrated L-a-dilauroyl-phosphatidylethanolamine environment. In-vacuum simulations show that a highly cooperative structural transition occurs frequently within the a-helical transmembrane domain which converts to local p-helices. We show that the a-helix alteration does not depend upon the force ®eld or initial side-chain conformations but is intimately related to the sequence. The membrane-like environment does not prevent the structural transition in the helix but slows down the peptide dynamics indicating that the appearance of a p-bulge is not an artifact of the vacuum approximation. The consequences of p-helix formation could be very huge for the ErbB-2 receptor which is involved in numerous human cancers and also for other membrane proteins wherein similar local structures are also observed experimentally.
Theoretical Chemistry Accounts, Feb 15, 1999
The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular ... more The structure and dynamics of the ErbB-2 transmembrane domain have been examined using molecular dynamics techniques both in vacuum and within an explicit hydrated L-a-dilauroyl-phosphatidylethanolamine environment. In-vacuum simulations show that a highly cooperative structural transition occurs frequently within the a-helical transmembrane domain which converts to local p-helices. We show that the a-helix alteration does not depend upon the force ®eld or initial side-chain conformations but is intimately related to the sequence. The membrane-like environment does not prevent the structural transition in the helix but slows down the peptide dynamics indicating that the appearance of a p-bulge is not an artifact of the vacuum approximation. The consequences of p-helix formation could be very huge for the ErbB-2 receptor which is involved in numerous human cancers and also for other membrane proteins wherein similar local structures are also observed experimentally.
Journal of Theoretical Biology, May 1, 2000
Transmissible subacute spongiform encephalopathies (TSE) are animal and human neurodegenerative d... more Transmissible subacute spongiform encephalopathies (TSE) are animal and human neurodegenerative diseases. The nature of the transmissible agent remains unknown. The speci"c molecular marker of these diseases is the abnormal isoform of the prion protein (PrP). This protein is encoded by a cellular gene and accumulates in a pathological isoform (PrPres) which is partially resistant to proteolysis. The tridimensional structure of this protein remains theoretical. F. Cohen proposed one of the most realistic models. According to this model and from molecular mechanics calculation, we suggest a PrP oligomeric ionic channel model that may be involved in TSE-induced neuronal apoptosis.
Journal of Theoretical Biology, May 1, 2000
Transmissible subacute spongiform encephalopathies (TSE) are animal and human neurodegenerative d... more Transmissible subacute spongiform encephalopathies (TSE) are animal and human neurodegenerative diseases. The nature of the transmissible agent remains unknown. The speci"c molecular marker of these diseases is the abnormal isoform of the prion protein (PrP). This protein is encoded by a cellular gene and accumulates in a pathological isoform (PrPres) which is partially resistant to proteolysis. The tridimensional structure of this protein remains theoretical. F. Cohen proposed one of the most realistic models. According to this model and from molecular mechanics calculation, we suggest a PrP oligomeric ionic channel model that may be involved in TSE-induced neuronal apoptosis.
Journal of Pharmaceutical Sciences, 1998
A nuclear magnetic resonance (NMR) spectroscopy and molecular modeling study of the interaction b... more A nuclear magnetic resonance (NMR) spectroscopy and molecular modeling study of the interaction between R-cyclodextrin (R-CD) and phospholipids with serine, ethanolamine, or choline headgroups is presented. The experimental approach is based on 31 P and 1 H NMR measurements on small unilamellar vesicles (SUV), multilamellar systems (MLV), and aqueous suspensions of lipids using a direct complex preparation with R-CD. Molecular dynamics computer simulations are used to investigate the trajectory of R-CD in the vicinity of a membrane surface and the influence of the charge and dipole moment of the phospholipid headgroups. These factors of charge and orientation of dipole moment seem to play a key role in the interaction of phospholipids with R-CD and reflect very well the experimentally observed selectivity of the phospholipid −R-CD approach. However, with this approach, there is no evidence for the formation of a complex with the phospholipid headgroup (except for phosphatidylinositol) that results from electrostatic forces. Rather, after a possible extraction of the lipid from the membrane, a classical inclusion of the sn-2 chain in the cavity of R-CD occurs. This step depends on the alkyl chain length and saturation state of the lipids as well as on their organization (i.e., as vesicles or dispersions). Based on our results, chemical modifications of the R-CD molecule to control the hemolytic properties of R-CD are discussed.