Benoît Roux, Ph.D., is Professor of Biochemistry and Molecular Biophysics at the University of Chicago. He has previously taught at University of Montreal and Weill Medical College of Cornell University.
The fast C-type inactivation displayed by the voltage-activated potassium channel hERG plays a cr... more The fast C-type inactivation displayed by the voltage-activated potassium channel hERG plays a critical role in the repolarization of cardiac cells, and malfunction caused by nonspecific binding of drugs or naturally occurring missense mutations affecting inactivation can lead to pathologies. Because of its impact on human health, understanding the molecular mechanism of C-type inactivation in hERG represents an advance of paramount importance. Here, long–time scale molecular dynamics simulations, free energy landscape calculations, and electrophysiological experiments are combined to address the structural and functional impacts of several disease-associated mutations. Results suggest that C-type inactivation in hERG is associated with an asymmetrical constricted-like conformation of the selectivity filter, identifying F627 side-chain rotation and the hydrogen bond between Y616 and N629 as key determinants. Comparison of hERG with other K+ channels suggests that C-type inactivation...
Proceedings of the National Academy of Sciences of the United States of America, Oct 2, 2017
In many K(+) channels, prolonged activating stimuli lead to a time-dependent reduction in ion con... more In many K(+) channels, prolonged activating stimuli lead to a time-dependent reduction in ion conduction, a phenomenon known as C-type inactivation. X-ray structures of the KcsA channel suggest that this inactivated state corresponds to a "constricted" conformation of the selectivity filter. However, the functional significance of the constricted conformation has become a matter of debate. Functional and structural studies based on chemically modified semisynthetic KcsA channels along the selectivity filter led to the conclusion that the constricted conformation does not correspond to the C-type inactivated state. The main results supporting this view include the observation that C-type inactivation is not suppressed by a substitution of D-alanine at Gly77, even though this modification is believed to lock the selectivity filter into its conductive conformation, whereas it is suppressed following amide-to-ester backbone substitutions at Gly77 and Tyr78, even though these s...
To understand the energetics of double-ion occupancy in gramicidin A (gA) channels, the 2D potent... more To understand the energetics of double-ion occupancy in gramicidin A (gA) channels, the 2D potential of mean force (PMF) is calculated for two ions at different positions along the channel axis. The cross sections of this 2D PMF are compared with available one-ion PMFs to highlight the effect of one ion on the permeation dynamics of the other. It is found that, if the first ion stays on one side in the channel, the second ion has to pass over an additional barrier to move into the outer binding site. At the same time, both outer and inner binding sites for the second ion become shallower than those in the one-ion PMF. The calculated ion-ion repulsion for a doubly occupied channel is about 2 kcal/mol, in good agreement with previous experimental estimates. The number of water molecules inside the channel and their dipole moment are calculated to interpret the energetics of double-ion occupancy. As the first ion moves into the outer binding site and then further into the channel, the ...
Proceedings of the National Academy of Sciences, 2004
The free energy governing K + conduction through gramicidin A channels is characterized by using ... more The free energy governing K + conduction through gramicidin A channels is characterized by using over 0.1 μs of all-atom molecular dynamics simulations with explicit solvent and membrane. The results provide encouraging agreement with experiments and insights into the permeation mechanism. The free energy surface of K + , as a function of both axial and radial coordinates, is calculated. Correcting for simulation artifacts due to periodicity and the lack of hydrocarbon polarizability, the calculated single-channel conductance for K + ions is 0.8 pS, closer to experiment than any previous calculation. In addition, the estimated single ion dissociation constants are within the range of experimental determinations. The relatively small free energy barrier to ion translocation arises from a balance of large opposing contributions from protein, single-file water, bulk electrolyte, and membrane. Mean force decomposition reveals a remarkable ability of the single-file water molecules to st...
Proteins, including ion channels, often are described in terms of some average structure and pict... more Proteins, including ion channels, often are described in terms of some average structure and pictured as rigid entities immersed in a featureless solvent continuum. This simplified view, which provides for a convenient representation of the protein's overall structure, incurs the risk of deemphasizing important features underlying protein function, such as thermal fluctuations in the atom positions and the discreteness of the solvent molecules. These factors become particularly important in the case of ion movement through narrow pores, where the magnitude of the thermal fluctuations may be comparable to the ion pore atom separations, such that the strength of the ion channel interactions may vary dramatically as a function of the instantaneous configuration of the ion and the surrounding protein and pore water. Descriptions of ion permeation through narrow pores, which employ static protein structures and a macroscopic continuum dielectric solvent, thus face fundamental difficu...
TEA is a classical blocker of K+channels. From mutagenesis studies, it has been shown that extern... more TEA is a classical blocker of K+channels. From mutagenesis studies, it has been shown that external blockade by TEA is strongly dependent upon the presence of aromatic residue atShakerposition 449 which is located near the extracellular entrance to the pore (Heginbotham, L., and R. MacKinnon. 1992.Neuron.8:483–491). The data suggest that TEA interacts simultaneously with the aromatic residues of the four monomers. The determination of the 3-D structure of the KcsA channel using X-ray crystallography (Doyle, D.A., J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon. 1998.Science.280:69–77) has raised some issues that remain currently unresolved concerning the interpretation of these observations. In particular, the center of the Tyr82 side chains in KcsA (corresponding to position 449 inShaker) forms a square of 11.8-Å side, a distance which is too large to allow simultaneous interactions of a TEA molecule with the four aromatic side chains. In ...
The fast C-type inactivation displayed by the voltage-activated potassium channel hERG plays a cr... more The fast C-type inactivation displayed by the voltage-activated potassium channel hERG plays a critical role in the repolarization of cardiac cells, and malfunction caused by nonspecific binding of drugs or naturally occurring missense mutations affecting inactivation can lead to pathologies. Because of its impact on human health, understanding the molecular mechanism of C-type inactivation in hERG represents an advance of paramount importance. Here, long–time scale molecular dynamics simulations, free energy landscape calculations, and electrophysiological experiments are combined to address the structural and functional impacts of several disease-associated mutations. Results suggest that C-type inactivation in hERG is associated with an asymmetrical constricted-like conformation of the selectivity filter, identifying F627 side-chain rotation and the hydrogen bond between Y616 and N629 as key determinants. Comparison of hERG with other K+ channels suggests that C-type inactivation...
Proceedings of the National Academy of Sciences of the United States of America, Oct 2, 2017
In many K(+) channels, prolonged activating stimuli lead to a time-dependent reduction in ion con... more In many K(+) channels, prolonged activating stimuli lead to a time-dependent reduction in ion conduction, a phenomenon known as C-type inactivation. X-ray structures of the KcsA channel suggest that this inactivated state corresponds to a "constricted" conformation of the selectivity filter. However, the functional significance of the constricted conformation has become a matter of debate. Functional and structural studies based on chemically modified semisynthetic KcsA channels along the selectivity filter led to the conclusion that the constricted conformation does not correspond to the C-type inactivated state. The main results supporting this view include the observation that C-type inactivation is not suppressed by a substitution of D-alanine at Gly77, even though this modification is believed to lock the selectivity filter into its conductive conformation, whereas it is suppressed following amide-to-ester backbone substitutions at Gly77 and Tyr78, even though these s...
To understand the energetics of double-ion occupancy in gramicidin A (gA) channels, the 2D potent... more To understand the energetics of double-ion occupancy in gramicidin A (gA) channels, the 2D potential of mean force (PMF) is calculated for two ions at different positions along the channel axis. The cross sections of this 2D PMF are compared with available one-ion PMFs to highlight the effect of one ion on the permeation dynamics of the other. It is found that, if the first ion stays on one side in the channel, the second ion has to pass over an additional barrier to move into the outer binding site. At the same time, both outer and inner binding sites for the second ion become shallower than those in the one-ion PMF. The calculated ion-ion repulsion for a doubly occupied channel is about 2 kcal/mol, in good agreement with previous experimental estimates. The number of water molecules inside the channel and their dipole moment are calculated to interpret the energetics of double-ion occupancy. As the first ion moves into the outer binding site and then further into the channel, the ...
Proceedings of the National Academy of Sciences, 2004
The free energy governing K + conduction through gramicidin A channels is characterized by using ... more The free energy governing K + conduction through gramicidin A channels is characterized by using over 0.1 μs of all-atom molecular dynamics simulations with explicit solvent and membrane. The results provide encouraging agreement with experiments and insights into the permeation mechanism. The free energy surface of K + , as a function of both axial and radial coordinates, is calculated. Correcting for simulation artifacts due to periodicity and the lack of hydrocarbon polarizability, the calculated single-channel conductance for K + ions is 0.8 pS, closer to experiment than any previous calculation. In addition, the estimated single ion dissociation constants are within the range of experimental determinations. The relatively small free energy barrier to ion translocation arises from a balance of large opposing contributions from protein, single-file water, bulk electrolyte, and membrane. Mean force decomposition reveals a remarkable ability of the single-file water molecules to st...
Proteins, including ion channels, often are described in terms of some average structure and pict... more Proteins, including ion channels, often are described in terms of some average structure and pictured as rigid entities immersed in a featureless solvent continuum. This simplified view, which provides for a convenient representation of the protein's overall structure, incurs the risk of deemphasizing important features underlying protein function, such as thermal fluctuations in the atom positions and the discreteness of the solvent molecules. These factors become particularly important in the case of ion movement through narrow pores, where the magnitude of the thermal fluctuations may be comparable to the ion pore atom separations, such that the strength of the ion channel interactions may vary dramatically as a function of the instantaneous configuration of the ion and the surrounding protein and pore water. Descriptions of ion permeation through narrow pores, which employ static protein structures and a macroscopic continuum dielectric solvent, thus face fundamental difficu...
TEA is a classical blocker of K+channels. From mutagenesis studies, it has been shown that extern... more TEA is a classical blocker of K+channels. From mutagenesis studies, it has been shown that external blockade by TEA is strongly dependent upon the presence of aromatic residue atShakerposition 449 which is located near the extracellular entrance to the pore (Heginbotham, L., and R. MacKinnon. 1992.Neuron.8:483–491). The data suggest that TEA interacts simultaneously with the aromatic residues of the four monomers. The determination of the 3-D structure of the KcsA channel using X-ray crystallography (Doyle, D.A., J.M. Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon. 1998.Science.280:69–77) has raised some issues that remain currently unresolved concerning the interpretation of these observations. In particular, the center of the Tyr82 side chains in KcsA (corresponding to position 449 inShaker) forms a square of 11.8-Å side, a distance which is too large to allow simultaneous interactions of a TEA molecule with the four aromatic side chains. In ...
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