Carmen Domene - Academia.edu (original) (raw)
Papers by Carmen Domene
Tetrahedron Letters, 2005
Direct computation of the π-current density, that is, the ‘ring current’, of anthranil (1) and it... more Direct computation of the π-current density, that is, the ‘ring current’, of anthranil (1) and its isomers 1,2-benzisoxazole (2) and benzoxazole (3) reveals different patterns of current flow: isomers 2 and 3 sustain strong benzene-like currents in the six-membered and bifurcated flow in the five-membered ring, whereas, in keeping with its lower thermodynamic stability, 1 has only a perimeter circulation
Proceedings of The National Academy of Sciences, 2010
Journal of Molecular Biology, 2009
Potassium channels are a diverse family of integral membrane proteins through which K+ can pass s... more Potassium channels are a diverse family of integral membrane proteins through which K+ can pass selectively. There is ongoing debate about the nature of conformational changes associated with the opening/closing and conductive/nonconductive states of potassium channels. The channels partly exert their function by varying their conductance through a mechanism known as C-type inactivation. Shortly after the activation of K+ channels,
Proteins-structure Function and Bioinformatics, 2009
Previous studies have reported that the KcsA potassium channel has an osmotic permeability coeffi... more Previous studies have reported that the KcsA potassium channel has an osmotic permeability coefficient of 4.8 x 10(-12) cm3/s, giving it a significantly higher osmotic permeability coefficient than that of some membrane channels specialized in water transport. This high osmotic permeability is proposed to occur when the channel is depleted of potassium ions, the presence of which slow down the water permeation process. The atomic structure of the potassium-depleted KcsA channel and the mechanisms of water permeation have not been well characterized so far. Here, all-atom molecular dynamics simulations, in conjunction with an umbrella sampling strategy and a nonequilibrium approach to simulate pressure gradients are employed to illustrate the permeation of water in the absence of ions through the KcsA K+ channel. Equilibrium molecular dynamics simulations (95 ns combined total length) identified a possible structure of the potassium-depleted KcsA channel, and umbrella sampling calculations (160 ns combined total length) revealed that this structure is not permeable by water molecules moving along the channel axis. The simulation of a pressure gradient across the channel (30 ns combined total length) identified an alternative permeation pathway with a computed osmotic permeability of approximately (2.7 +/- 0.9) x 10(-13) cm3/s. Water fluxes along this pathway did not proceed through collective water motions or transitions to vapor state. All of the major results of this study were robust against variations in a wide set of simulation parameters (force field, water model, membrane model, and channel conformation).
Journal of The American Chemical Society, 2008
The chemical-physical basis for K + permeation and selectivity in K + channels has been the focus... more The chemical-physical basis for K + permeation and selectivity in K + channels has been the focus of attention of many theoretical and computational studies since the first crystal structure was obtained by the Mackinnon lab in 1998. Most of the previous studies reported focused on atomic descriptions of permeation events in the selectivity filter of K + channels in their closed conformation. In this Article, a comparative analysis of permeation events in the KirBac1.1 K + channel in a closed-and an open-state model is presented. The availability of models of the same channel in two different conformations has made this comparative analysis possible. All-atom molecular dynamics simulations of both models in a membrane environment have been carried out. As previously suggested by many studies of this and other K + channels, when the channel is closed the ion conduction involves transitions between two main sites of the selectivity filter, with two K + ions each coordinated by eight carbonyl oxygens of the protein and separated by a water molecule. In contrast, in our open-state model, three to four K + ions move in a concerted motion during the permeation process. The selectivity filter, though maintaining a certain degree of flexibility to cope with these cooperative events, appears to be more "symmetrical" and robust in the simulations of the open-state channel when it is occupied by an average of three ions. Therefore, it appears as if the occupation of the pore depends upon the global conformation of the channel. Due to the complexity of these systems, only single conduction events have been described by means of molecular dynamics trajectories. To complement these results and describe the energetics of ion permeation and ionic fluxes, continuum approaches (Poisson-Boltzmann and Poisson-Nernst-Planck theory) have been also employed. Gulbis, J. M.; Antcliff, J. F.; Rahman, T.; Lowe, E. D.; Jochen, Z.; Cuthbertson, J.; Ashcroft, F. M.; Ezaki, T.; Doyle,
![Research paper thumbnail of On the lack of ring-current aromaticity of (heteroatom) [N]radialenes and their dianions](https://attachments.academia-assets.com/44845568/thumbnails/1.jpg)
](Chemistry-a European Journal, 2007
Current-density maps, calculated at the ab initio RHF//6-31G**/ CTOCD-DZ level, show no significa... more Current-density maps, calculated at the ab initio RHF//6-31G**/ CTOCD-DZ level, show no significant π ring current in planar equilateral geometries ofneutral and dianionic [N]radialenes, oxocarbons and thiocarbons CNYNq- (Y=CH2, O, S; N=4, 5, 6; q=0 (1a-12 a), 2 (1b-12b)). Only the N=3 deltate dianions C3Y3 2- (Y=CH2, O, S (1b, 5b and 9b)) have discernible π ring current, and then
Journal of The American Chemical Society, 2008
The translocation of ions and water across cell membranes is a prerequisite for many of life's pr... more The translocation of ions and water across cell membranes is a prerequisite for many of life's processes. K + channels are a diverse family of integral membrane proteins through which K + can pass selectively. There is an ongoing debate about the nature of conformational changes associated with the opening and closing and conductive and nonconductive states of potassium (K + ) channels. These changes depend on the membrane potential, the K + concentration gradient, and large scale motions of transmembrane helices and associated residues. Experiments also suggest that local structural changes in the selectivity filter may act as the dominant gate referred to as C-type inactivation. Herein we present an extensive computational study on KirBac, which supports the existence of a physical gate or constriction in the selectivity filter (SF) of K + channels. Our computations identify a new selectivity filter structure, which is likely associated with C-type inactivation. Specifically, the four peptide chains that comprise the filter adopt an unusual structure in which their dihedrals alternate between left-and right-handed Ramachandran angles, which also justifies the need for conservation of glycine in the K + selectivity filter, since it is the only residue able to play this bifunctional role.
Proceedings of The National Academy of Sciences, 2009
Potassium channels can conduct passively K ؉ ions with rates of up to Ϸ10 8 ions per second at ph... more Potassium channels can conduct passively K ؉ ions with rates of up to Ϸ10 8 ions per second at physiological conditions, and they are selective to these species by a factor of 10 4 over Na ؉ ions. Ion conduction has been proposed to involve transitions between 2 main states, with 2 or 3 K ؉ ions occupying the selectivity filter separated by an intervening water molecule. The largest free energy barrier of such a process was reported to be of the order of 2-3 kcal mol ؊1 . Here, we present an alternative mechanism for conduction of K ؉ in potassium channels where site vacancies are involved, and we propose that coexistence of several ion permeation mechanisms is energetically possible. Conduction can be described as a more anarchic phenomenon than previously characterized by the concerted translocations of K ؉ -water-K ؉ .
IEEE Transactions on Nanobioscience, 2005
Molecular modeling and simulations enable extrapolation for the structure of bacterial potassium ... more Molecular modeling and simulations enable extrapolation for the structure of bacterial potassium channels to the function of their mammalian homologues. Molecular dynamics simulations have revealed the concerted single-file motion of potassium ions and water molecules through the selectivity filter of K channels and the role of filter flexibility in ion permeation and in "fast gating." Principal components analysis of extended
Biophysical Journal, 2004
The bacterial channel KirBac1.1 provides a structural homolog of mammalian inward rectifier potas... more The bacterial channel KirBac1.1 provides a structural homolog of mammalian inward rectifier potassium (Kir) channels. The conformational dynamics of the selectivity filter of Kir channels are of some interest in the context of possible permeation and gating mechanisms for this channel. Molecular dynamics simulations of KirBac have been performed on a 10-ns timescale, i.e., comparable to that of ion permeation.
ACS nano, Jan 14, 2015
Classical MD simulations combined with docking calculations, potential of mean force estimates wi... more Classical MD simulations combined with docking calculations, potential of mean force estimates with the umbrella sampling method, and MM-PBSA energy calculations reveal that C60 may block K+ channels with two mechanisms: a low affinity blockage from the extracellular side, and an open-channel block from the intracellular side. The presence of a low affinity binding-site at the extracellular entrance of the channel is in agreement with the experimental results showing a fast and reversible block without use-dependence, from the extracellular compartment. Our simulation protocol suggests the existence of another binding site for C60 located in the channel cavity at the intracellular entrance of the selectivity filter. The escape barrier from this binding site is ~21 kcal/mol making the corresponding kinetic rate of the order of minutes. The analysis of the change in Solvent Accessible Surface Area upon C60 binding shows that binding at this site is governed purely by shape complementa...
The journal of physical chemistry. B, Jan 20, 2014
The lactose repressor, LacI, finds its DNA target sites via a process that is faster than what it... more The lactose repressor, LacI, finds its DNA target sites via a process that is faster than what it is expected from a diffusion-driven mechanism. This is possible thanks to nonspecific binding of LacI to DNA, followed by diffusion along the DNA molecule. The diffusion of the protein along DNA might lead to a fast-searching mechanism only if LacI binds with comparable strength to different nonspecific sequences and if, in addition, the value of the binding energy remarkably decreases in the presence of a binding site. The first condition would be favored by loose interactions with the base edges, while the second would take advantage from the opposite situation. In order to understand how the protein satisfies these two opposing requirements, the DNA recognition process was studied by a combination of umbrella sampling and metadynamics simulations. The simulations revealed that when aligned with a specific sequence, LacI establishes polar interactions with the base edges that require ...
Biophysical journal, 2003
Interactions of Na(+), K(+), Rb(+), and Cs(+) ions within the selectivity filter of a potassium c... more Interactions of Na(+), K(+), Rb(+), and Cs(+) ions within the selectivity filter of a potassium channel have been investigated via multiple molecular dynamics simulations (total simulation time, 48 ns) based on the high resolution structure of KcsA, embedded in a phospholipid bilayer. As in simulations based on a lower resolution structure of KcsA, concerted motions of ions and water within the filter are seen. Despite the use of a higher resolution structure and the inclusion of four buried water molecules thought to stabilize the filter, this region exhibits a significant degree of flexibility. In particular, pronounced distortion of filter occurs if no ions are present within it. The two most readily permeant ions, K(+) and Rb(+), are similar in their interactions with the selectivity filter. In contrast, Na(+) ions tend to distort the filter by binding to a ring of four carbonyl oxygens. The larger Cs(+) ions result in a small degree of expansion of the filter relative to the x-...
Current opinion in drug discovery & development, 2003
Several ion channel structures have recently been determined, including MthK (a bacterial K+ chan... more Several ion channel structures have recently been determined, including MthK (a bacterial K+ channel in an open state), KirBac (a bacterial homolog of mammalian inward rectifier K+ channels), KvAP (a bacterial voltage-activated K+ channel) and the pore domain of the nicotinic acetylcholine receptor. Analysis of these structures has increased our understanding of the molecular mechanisms underlying channel gating. A hydrophobic gate appears to operate in a number of channels. Structures of ligand binding domains provide some clues as to how ligand-induced conformational changes control channel gating, but further experimental and computational studies are required before a full picture emerges.
is currently unknown. In this work, we use density gradient centrifugation and liposome coflotati... more is currently unknown. In this work, we use density gradient centrifugation and liposome coflotation analysis to demonstrate that the anchoring energy of the Dengue E protein in anionic membranes composed of POPCþPOPG is much greater than in membranes composed of POPCþPOPE.
The interactions between membrane proteins and their lipid bilayer environment play important rol... more The interactions between membrane proteins and their lipid bilayer environment play important roles in the stability and function of such proteins. Extended (15-20 ns) molecular dynamics simulations have been used to explore the interactions of two membrane proteins with phosphatidylcholine bilayers. One protein (KcsA) is an a-helix bundle and embedded in a palmitoyl oleoyl phosphatidylcholine bilayer; the other (OmpA) is a b-barrel outer-membrane protein and is in a dimyristoyl phosphatidylcholine bilayer. The simulations enable analysis in detail of a number of aspects of lipid-protein interactions. In particular, the interactions of aromatic amphipathic side chains (i.e., Trp, Tyr) with lipid headgroups, and ''snorkeling'' interactions of basic side chains (i.e., Lys, Arg) with phosphate groups are explored. Analysis of the number of contacts and of H-bonds reveal fluctuations on an ;1-to 5-ns timescale. There are two clear bands of interacting residues on the surface of KcsA, whereas there are three such bands on OmpA. A large number of Arg-phosphate interactions are seen for KcsA; for OmpA, the number of basic-phosphate interactions is smaller and shows more marked fluctuations with respect to time. Both classes of interaction occur in clearly defined interfacial regions of width ;1 nm. Analysis of lateral diffusion of lipid molecules reveals that ''boundary'' lipid molecules diffuse at about half the rate of bulk lipid. Overall, these simulations present a dynamic picture of lipid-protein interactions: there are a number of more specific interactions but even these fluctuate on an ;1-to 5-ns timescale.
Molecular pharmaceutics, Jan 3, 2015
Voltage-gated potassium channels of the Kv1 family play a crucial role in the generation and tran... more Voltage-gated potassium channels of the Kv1 family play a crucial role in the generation and transmission of electrical signals in excitable cells affecting neuronal and cardiac activities. Small-molecule blockage of these channels has been proposed to occur via a cooperative mechanism involving two main blocking sites: the inner-pore site located below the selectivity filter, and a side-pocket cavity located between the pore and the voltage-sensor. Using 0.5-s molecular dynamics simulation trajectories complemented by docking calculations, the potential binding sites of the PAP-1 (5-(4-phenoxybutoxy) psoralen) blocker to the crystal structure of Kv1.2 channel have been studied. The presence of both mentioned blocking sites at Kv1.2 is confirmed, adding evidence in favor of a cooperative channel blockage mechanism. These observations provide insight into drug modulation that will guide further developments of Kv inhibitors.
Zinc-α2-glycoprotein (ZAG) is an adipokine with an MHC class I-like protein fold. Even though zin... more Zinc-α2-glycoprotein (ZAG) is an adipokine with an MHC class I-like protein fold. Even though zinc causes ZAG to precipitate from plasma during protein purification, no zinc binding has been identified to date. Using mass spectrometry, we demonstrated that ZAG contains one strongly bound zinc ion, predicted to lie close to the α1 and α2 helical groove. UV, CD and fluorescence spectroscopies detected weak zinc binding to holo-ZAG, which can bind up to 15 zinc ions. Zinc binding to 11-(dansylamino) undecanoic acid was enhanced by holo-ZAG. Zinc binding may be important for ZAG binding to fatty acids and the β-adrenergic receptor.
In the cell, signals are conveyed by interacting protein molecules. Electron microscopy can provi... more In the cell, signals are conveyed by interacting protein molecules. Electron microscopy can provide information on the nature of these interactions, especially for large protein complexes. Our projects address the role of protein/protein interactions in the control of signalling processing through the study of four important systems by using electron microscopy and combining the results with information from X-ray diffraction
Tetrahedron Letters, 2005
Direct computation of the π-current density, that is, the ‘ring current’, of anthranil (1) and it... more Direct computation of the π-current density, that is, the ‘ring current’, of anthranil (1) and its isomers 1,2-benzisoxazole (2) and benzoxazole (3) reveals different patterns of current flow: isomers 2 and 3 sustain strong benzene-like currents in the six-membered and bifurcated flow in the five-membered ring, whereas, in keeping with its lower thermodynamic stability, 1 has only a perimeter circulation
Proceedings of The National Academy of Sciences, 2010
Journal of Molecular Biology, 2009
Potassium channels are a diverse family of integral membrane proteins through which K+ can pass s... more Potassium channels are a diverse family of integral membrane proteins through which K+ can pass selectively. There is ongoing debate about the nature of conformational changes associated with the opening/closing and conductive/nonconductive states of potassium channels. The channels partly exert their function by varying their conductance through a mechanism known as C-type inactivation. Shortly after the activation of K+ channels,
Proteins-structure Function and Bioinformatics, 2009
Previous studies have reported that the KcsA potassium channel has an osmotic permeability coeffi... more Previous studies have reported that the KcsA potassium channel has an osmotic permeability coefficient of 4.8 x 10(-12) cm3/s, giving it a significantly higher osmotic permeability coefficient than that of some membrane channels specialized in water transport. This high osmotic permeability is proposed to occur when the channel is depleted of potassium ions, the presence of which slow down the water permeation process. The atomic structure of the potassium-depleted KcsA channel and the mechanisms of water permeation have not been well characterized so far. Here, all-atom molecular dynamics simulations, in conjunction with an umbrella sampling strategy and a nonequilibrium approach to simulate pressure gradients are employed to illustrate the permeation of water in the absence of ions through the KcsA K+ channel. Equilibrium molecular dynamics simulations (95 ns combined total length) identified a possible structure of the potassium-depleted KcsA channel, and umbrella sampling calculations (160 ns combined total length) revealed that this structure is not permeable by water molecules moving along the channel axis. The simulation of a pressure gradient across the channel (30 ns combined total length) identified an alternative permeation pathway with a computed osmotic permeability of approximately (2.7 +/- 0.9) x 10(-13) cm3/s. Water fluxes along this pathway did not proceed through collective water motions or transitions to vapor state. All of the major results of this study were robust against variations in a wide set of simulation parameters (force field, water model, membrane model, and channel conformation).
Journal of The American Chemical Society, 2008
The chemical-physical basis for K + permeation and selectivity in K + channels has been the focus... more The chemical-physical basis for K + permeation and selectivity in K + channels has been the focus of attention of many theoretical and computational studies since the first crystal structure was obtained by the Mackinnon lab in 1998. Most of the previous studies reported focused on atomic descriptions of permeation events in the selectivity filter of K + channels in their closed conformation. In this Article, a comparative analysis of permeation events in the KirBac1.1 K + channel in a closed-and an open-state model is presented. The availability of models of the same channel in two different conformations has made this comparative analysis possible. All-atom molecular dynamics simulations of both models in a membrane environment have been carried out. As previously suggested by many studies of this and other K + channels, when the channel is closed the ion conduction involves transitions between two main sites of the selectivity filter, with two K + ions each coordinated by eight carbonyl oxygens of the protein and separated by a water molecule. In contrast, in our open-state model, three to four K + ions move in a concerted motion during the permeation process. The selectivity filter, though maintaining a certain degree of flexibility to cope with these cooperative events, appears to be more "symmetrical" and robust in the simulations of the open-state channel when it is occupied by an average of three ions. Therefore, it appears as if the occupation of the pore depends upon the global conformation of the channel. Due to the complexity of these systems, only single conduction events have been described by means of molecular dynamics trajectories. To complement these results and describe the energetics of ion permeation and ionic fluxes, continuum approaches (Poisson-Boltzmann and Poisson-Nernst-Planck theory) have been also employed. Gulbis, J. M.; Antcliff, J. F.; Rahman, T.; Lowe, E. D.; Jochen, Z.; Cuthbertson, J.; Ashcroft, F. M.; Ezaki, T.; Doyle,
Chemistry-a European Journal, 2007
Current-density maps, calculated at the ab initio RHF//6-31G**/ CTOCD-DZ level, show no significa... more Current-density maps, calculated at the ab initio RHF//6-31G**/ CTOCD-DZ level, show no significant π ring current in planar equilateral geometries ofneutral and dianionic [N]radialenes, oxocarbons and thiocarbons CNYNq- (Y=CH2, O, S; N=4, 5, 6; q=0 (1a-12 a), 2 (1b-12b)). Only the N=3 deltate dianions C3Y3 2- (Y=CH2, O, S (1b, 5b and 9b)) have discernible π ring current, and then
Journal of The American Chemical Society, 2008
The translocation of ions and water across cell membranes is a prerequisite for many of life's pr... more The translocation of ions and water across cell membranes is a prerequisite for many of life's processes. K + channels are a diverse family of integral membrane proteins through which K + can pass selectively. There is an ongoing debate about the nature of conformational changes associated with the opening and closing and conductive and nonconductive states of potassium (K + ) channels. These changes depend on the membrane potential, the K + concentration gradient, and large scale motions of transmembrane helices and associated residues. Experiments also suggest that local structural changes in the selectivity filter may act as the dominant gate referred to as C-type inactivation. Herein we present an extensive computational study on KirBac, which supports the existence of a physical gate or constriction in the selectivity filter (SF) of K + channels. Our computations identify a new selectivity filter structure, which is likely associated with C-type inactivation. Specifically, the four peptide chains that comprise the filter adopt an unusual structure in which their dihedrals alternate between left-and right-handed Ramachandran angles, which also justifies the need for conservation of glycine in the K + selectivity filter, since it is the only residue able to play this bifunctional role.
Proceedings of The National Academy of Sciences, 2009
Potassium channels can conduct passively K ؉ ions with rates of up to Ϸ10 8 ions per second at ph... more Potassium channels can conduct passively K ؉ ions with rates of up to Ϸ10 8 ions per second at physiological conditions, and they are selective to these species by a factor of 10 4 over Na ؉ ions. Ion conduction has been proposed to involve transitions between 2 main states, with 2 or 3 K ؉ ions occupying the selectivity filter separated by an intervening water molecule. The largest free energy barrier of such a process was reported to be of the order of 2-3 kcal mol ؊1 . Here, we present an alternative mechanism for conduction of K ؉ in potassium channels where site vacancies are involved, and we propose that coexistence of several ion permeation mechanisms is energetically possible. Conduction can be described as a more anarchic phenomenon than previously characterized by the concerted translocations of K ؉ -water-K ؉ .
IEEE Transactions on Nanobioscience, 2005
Molecular modeling and simulations enable extrapolation for the structure of bacterial potassium ... more Molecular modeling and simulations enable extrapolation for the structure of bacterial potassium channels to the function of their mammalian homologues. Molecular dynamics simulations have revealed the concerted single-file motion of potassium ions and water molecules through the selectivity filter of K channels and the role of filter flexibility in ion permeation and in "fast gating." Principal components analysis of extended
Biophysical Journal, 2004
The bacterial channel KirBac1.1 provides a structural homolog of mammalian inward rectifier potas... more The bacterial channel KirBac1.1 provides a structural homolog of mammalian inward rectifier potassium (Kir) channels. The conformational dynamics of the selectivity filter of Kir channels are of some interest in the context of possible permeation and gating mechanisms for this channel. Molecular dynamics simulations of KirBac have been performed on a 10-ns timescale, i.e., comparable to that of ion permeation.
ACS nano, Jan 14, 2015
Classical MD simulations combined with docking calculations, potential of mean force estimates wi... more Classical MD simulations combined with docking calculations, potential of mean force estimates with the umbrella sampling method, and MM-PBSA energy calculations reveal that C60 may block K+ channels with two mechanisms: a low affinity blockage from the extracellular side, and an open-channel block from the intracellular side. The presence of a low affinity binding-site at the extracellular entrance of the channel is in agreement with the experimental results showing a fast and reversible block without use-dependence, from the extracellular compartment. Our simulation protocol suggests the existence of another binding site for C60 located in the channel cavity at the intracellular entrance of the selectivity filter. The escape barrier from this binding site is ~21 kcal/mol making the corresponding kinetic rate of the order of minutes. The analysis of the change in Solvent Accessible Surface Area upon C60 binding shows that binding at this site is governed purely by shape complementa...
The journal of physical chemistry. B, Jan 20, 2014
The lactose repressor, LacI, finds its DNA target sites via a process that is faster than what it... more The lactose repressor, LacI, finds its DNA target sites via a process that is faster than what it is expected from a diffusion-driven mechanism. This is possible thanks to nonspecific binding of LacI to DNA, followed by diffusion along the DNA molecule. The diffusion of the protein along DNA might lead to a fast-searching mechanism only if LacI binds with comparable strength to different nonspecific sequences and if, in addition, the value of the binding energy remarkably decreases in the presence of a binding site. The first condition would be favored by loose interactions with the base edges, while the second would take advantage from the opposite situation. In order to understand how the protein satisfies these two opposing requirements, the DNA recognition process was studied by a combination of umbrella sampling and metadynamics simulations. The simulations revealed that when aligned with a specific sequence, LacI establishes polar interactions with the base edges that require ...
Biophysical journal, 2003
Interactions of Na(+), K(+), Rb(+), and Cs(+) ions within the selectivity filter of a potassium c... more Interactions of Na(+), K(+), Rb(+), and Cs(+) ions within the selectivity filter of a potassium channel have been investigated via multiple molecular dynamics simulations (total simulation time, 48 ns) based on the high resolution structure of KcsA, embedded in a phospholipid bilayer. As in simulations based on a lower resolution structure of KcsA, concerted motions of ions and water within the filter are seen. Despite the use of a higher resolution structure and the inclusion of four buried water molecules thought to stabilize the filter, this region exhibits a significant degree of flexibility. In particular, pronounced distortion of filter occurs if no ions are present within it. The two most readily permeant ions, K(+) and Rb(+), are similar in their interactions with the selectivity filter. In contrast, Na(+) ions tend to distort the filter by binding to a ring of four carbonyl oxygens. The larger Cs(+) ions result in a small degree of expansion of the filter relative to the x-...
Current opinion in drug discovery & development, 2003
Several ion channel structures have recently been determined, including MthK (a bacterial K+ chan... more Several ion channel structures have recently been determined, including MthK (a bacterial K+ channel in an open state), KirBac (a bacterial homolog of mammalian inward rectifier K+ channels), KvAP (a bacterial voltage-activated K+ channel) and the pore domain of the nicotinic acetylcholine receptor. Analysis of these structures has increased our understanding of the molecular mechanisms underlying channel gating. A hydrophobic gate appears to operate in a number of channels. Structures of ligand binding domains provide some clues as to how ligand-induced conformational changes control channel gating, but further experimental and computational studies are required before a full picture emerges.
is currently unknown. In this work, we use density gradient centrifugation and liposome coflotati... more is currently unknown. In this work, we use density gradient centrifugation and liposome coflotation analysis to demonstrate that the anchoring energy of the Dengue E protein in anionic membranes composed of POPCþPOPG is much greater than in membranes composed of POPCþPOPE.
The interactions between membrane proteins and their lipid bilayer environment play important rol... more The interactions between membrane proteins and their lipid bilayer environment play important roles in the stability and function of such proteins. Extended (15-20 ns) molecular dynamics simulations have been used to explore the interactions of two membrane proteins with phosphatidylcholine bilayers. One protein (KcsA) is an a-helix bundle and embedded in a palmitoyl oleoyl phosphatidylcholine bilayer; the other (OmpA) is a b-barrel outer-membrane protein and is in a dimyristoyl phosphatidylcholine bilayer. The simulations enable analysis in detail of a number of aspects of lipid-protein interactions. In particular, the interactions of aromatic amphipathic side chains (i.e., Trp, Tyr) with lipid headgroups, and ''snorkeling'' interactions of basic side chains (i.e., Lys, Arg) with phosphate groups are explored. Analysis of the number of contacts and of H-bonds reveal fluctuations on an ;1-to 5-ns timescale. There are two clear bands of interacting residues on the surface of KcsA, whereas there are three such bands on OmpA. A large number of Arg-phosphate interactions are seen for KcsA; for OmpA, the number of basic-phosphate interactions is smaller and shows more marked fluctuations with respect to time. Both classes of interaction occur in clearly defined interfacial regions of width ;1 nm. Analysis of lateral diffusion of lipid molecules reveals that ''boundary'' lipid molecules diffuse at about half the rate of bulk lipid. Overall, these simulations present a dynamic picture of lipid-protein interactions: there are a number of more specific interactions but even these fluctuate on an ;1-to 5-ns timescale.
Molecular pharmaceutics, Jan 3, 2015
Voltage-gated potassium channels of the Kv1 family play a crucial role in the generation and tran... more Voltage-gated potassium channels of the Kv1 family play a crucial role in the generation and transmission of electrical signals in excitable cells affecting neuronal and cardiac activities. Small-molecule blockage of these channels has been proposed to occur via a cooperative mechanism involving two main blocking sites: the inner-pore site located below the selectivity filter, and a side-pocket cavity located between the pore and the voltage-sensor. Using 0.5-s molecular dynamics simulation trajectories complemented by docking calculations, the potential binding sites of the PAP-1 (5-(4-phenoxybutoxy) psoralen) blocker to the crystal structure of Kv1.2 channel have been studied. The presence of both mentioned blocking sites at Kv1.2 is confirmed, adding evidence in favor of a cooperative channel blockage mechanism. These observations provide insight into drug modulation that will guide further developments of Kv inhibitors.
Zinc-α2-glycoprotein (ZAG) is an adipokine with an MHC class I-like protein fold. Even though zin... more Zinc-α2-glycoprotein (ZAG) is an adipokine with an MHC class I-like protein fold. Even though zinc causes ZAG to precipitate from plasma during protein purification, no zinc binding has been identified to date. Using mass spectrometry, we demonstrated that ZAG contains one strongly bound zinc ion, predicted to lie close to the α1 and α2 helical groove. UV, CD and fluorescence spectroscopies detected weak zinc binding to holo-ZAG, which can bind up to 15 zinc ions. Zinc binding to 11-(dansylamino) undecanoic acid was enhanced by holo-ZAG. Zinc binding may be important for ZAG binding to fatty acids and the β-adrenergic receptor.
In the cell, signals are conveyed by interacting protein molecules. Electron microscopy can provi... more In the cell, signals are conveyed by interacting protein molecules. Electron microscopy can provide information on the nature of these interactions, especially for large protein complexes. Our projects address the role of protein/protein interactions in the control of signalling processing through the study of four important systems by using electron microscopy and combining the results with information from X-ray diffraction