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Benoit Roux

University of Chicago, Biochemistry, Faculty Member

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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.

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The University of Texas at Austin

Ciria Hernandez

Vanderbilt University

Jared L Ostmeyer

University of Texas Southwestern Medical Center at Dallas

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Papers by Benoit Roux

Mechanism of C-type inactivation in the hERG potassium channel

Science Advances

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...

Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for 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...

Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel

Biochimica et Biophysica Acta (BBA) - Biomembranes, 2016

Potassium (K +) channels are transmembrane proteins that passively and selectively allow K + ions... more Potassium (K +) channels are transmembrane proteins that passively and selectively allow K + ions to flow through them, after opening in response to an external stimulus. One of the most critical functional aspects of their function is their ability to remain very selective for K + over Na + while allowing high-throughput ion conduction at a rate close to the diffusion limit. Classically, it is assumed that the free energy difference between K + and Na + in the pore relative to the bulk solution is the critical quantity at the origin of selectivity. This is the thermodynamic view of ion selectivity. An alternative view assumes that kinetic factor play the dominant role. Recent results from a number of studies have also highlighted the great importance of the multi-ion single file on the selectivity of K + channels. The data indicate that having multiple K + ions bound simultaneously is required for selective K + conduction, and that a reduction in the number of bound K + ions destroys the multi-ion selectivity mechanism utilized by K + channels. In the present study, multi-ion potential of mean force molecular dynamics computations are carried out to clarify the mechanism of ion selectivity in the KcsA channel. The computations show that the multi-ion character of the permeation process is a critical element for establishing the selective ion conductivity through K +-channels.

Energetics of double-ion occupancy in the gramicidin A channel

The journal of physical chemistry. B, Jan 4, 2010

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 ...

Theoretical and computational models of biological ion channels

Quarterly Reviews of Biophysics, 2004

Hydration Number, Topological Control, and Ion Selectivity

The Journal of Physical Chemistry B, 2009

The topological control hypothesis presented by Bostick and Brooks [Proc. Natl. Acad. Sci. USA 10... more The topological control hypothesis presented by Bostick and Brooks [Proc. Natl. Acad. Sci. USA 104:9260, 2007] has sought to explain binding selectivity in potassium channels on the basis of universal environment-independent features related to ion coordination. This leads to the view that ion selectivity is predominantly controlled by the number of ligands coordinating the ion, and that the chemical type of those ligands plays a minor role. The significance of the topological control hypothesis and its ability to predict ion selectivity in protein binding sites are examined. It is shown that the framework encounters increasing difficulties when different protein binding sites with similar coordination numbers are considered.

Computational Studies of Membrane Channels

Structure, 2004

Energetics of ion conduction through the gramicidin channel

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...

Recovery from slow inactivation in K+ channels is controlled by water molecules

Nature, 2013

Perspectives on: Ion selectivity: Ion selectivity in channels and transporters

The Journal of General Physiology, 2011

A multitude of biological processes requires the participation of specific cations, such as H + ,... more A multitude of biological processes requires the participation of specific cations, such as H + , Na + , K + , Ca 2+ , and Mg 2+. Many of these processes can take place only when proteins have the ability to discriminate between different ions with a very high fidelity. How this is possible is a fundamental question that has fascinated scientists for a long time. At the most fundamental level, it is anticipated that ion selectivity must result from a delicate balance of strong interactions. Yet, identifying and quantifying the key microscopic factors is difficult, as many of these cannot be directly measured by experiments. Theory and computations can contribute by providing a virtual route to complement the missing information. Because ion selectivity is often dominated by thermodynamic factors, detailed molecular dynamics (MD) free energy simulations become important tools. This was vividly illustrated early on with studies of ion solvation (Straatsma and Berendsen, 1988; Åqvist, 1990) and ion-selective systems (Lybrand et al., 1986; Grootenhuis and Kollman, 1989; Åqvist, 1992). These pioneering studies inspired our own efforts. In this Perspective, we aim to present our understanding of ion selectivity as it has evolved over approximately 15 years from studies based on various specific structures: gramicidin A channels (e.g.

On the Importance of Atomic Fluctuations, Protein Flexibility, and Solvent in Ion Permeation

The Journal of General Physiology, 2004

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...

Extracellular Blockade of K+ Channels by TEA: Results from Molecular Dynamics Simulations of the KcsA Channel

The Journal of General Physiology, 2001

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 ...

Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels

The Journal of General Physiology, 2011

Fundamental concepts governing ion selectivity in narrow pores are reviewed and the microscopic f... more Fundamental concepts governing ion selectivity in narrow pores are reviewed and the microscopic factors responsible for the lack of selectivity of the NaK channel, which is structurally similar to the K +-selective KcsA channel, are elucidated on the basis of all-atom molecular dynamics free energy simulations. The results on NaK are contrasted and compared with previous studies of the KcsA channel. Analysis indicates that differences in hydration of the cation in the pore of NaK is at the origin of the lack of selectivity of NaK .

Perspectives on: Molecular dynamics and computational methods

The Journal of General Physiology, 2010

Grand canonical Monte Carlo simulations of water in protein environments

The Journal of Chemical Physics, 2004

The grand canonical simulation algorithm is considered as a general methodology to sample the con... more The grand canonical simulation algorithm is considered as a general methodology to sample the configuration of water molecules confined within protein environments. First, the probability distribution of the number of water molecules and their configuration in a region of interest for biochemical simulations, such as the active site of a protein, is derived by considering a finite subvolume in open equilibrium with a large system serving as a bulk reservoir. It is shown that the influence of the bulk reservoir can be represented as a many-body potential of mean force acting on the atoms located inside the subvolume. The grand canonical Monte Carlo ͑GCMC͒ algorithm, augmented by a number of technical advances to increase the acceptance of insertion attempts, is implemented, and tested for simple systems. In particular, the method is illustrated in the case of a pure water box with periodic boundary conditions. In addition, finite spherical systems of pure water and containing a dialanine peptide, are simulated with GCMC while the influence of the surrounding infinite bulk is incorporated using the generalized solvent boundary potential ͓W. Im, S. Bernèche, and B. Roux, J. Chem. Phys. 114, 2924 ͑2001͔͒. As a last illustration of water confined in the interior of a protein, the hydration of the central cavity of the KcsA potassium channel is simulated.

Generalized solvent boundary potential for computer simulations

The Journal of Chemical Physics, 2001

A general approach has been developed to allow accurate simulations of a small region part of a l... more A general approach has been developed to allow accurate simulations of a small region part of a large macromolecular system while incorporating the influence of the remaining distant atoms with an effective boundary potential. The method is called the Generalized Solvent Boundary Potential ͑GSBP͒. By representing the surrounding solvent as a continuum dielectric, both the solvent-shielded static field from the distant atoms of the macromolecule and the reaction field from the dielectric solvent acting on the atoms in the region of interest are included. The static field is calculated once, using the finite-difference Poisson-Boltzmann ͑PB͒ equation, and the result is stored on a discrete grid for efficient simulations. The solvent reaction field is developed using a basis-set expansion whose coefficients correspond to generalized electrostatic multipoles. A matrix representing the reaction field Green's function between those generalized multipoles is calculated only once using the PB equation and stored for efficient simulations. In the present work, the formalism is applied to both spherical and orthorhombic simulation regions for which orthonormal basis-sets exist based on spherical harmonics or cartesian Legendre polynomials. The GSBP method is also tested and illustrated with simple model systems and two detailed atomic systems: the active site region of aspartyl-tRNA synthetase ͑spherical region͒ and the interior of the KcsA potassium channel ͑orthorhombic region͒. Comparison with numerical finite-difference PB calculations shows that GSBP can accurately describe all long-range electrostatic interactions and remain computationally inexpensive.

Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

The Journal of Chemical Physics, 2001

A general method has been developed to include the electrostatic reaction field in Brownian dynam... more A general method has been developed to include the electrostatic reaction field in Brownian dynamics ͑BD͒ simulations of ions diffusing through complex molecular channels of arbitrary geometry. Assuming that the solvent is represented as a featureless continuum dielectric medium, a multipolar basis-set expansion is developed to express the reaction field Green's function. A reaction field matrix, which provides the coupling between generalized multipoles, is calculated only once and stored before the BD simulations. The electrostatic energy and forces are calculated at each time step by updating the generalized multipole moments. The method is closely related to the generalized solvent boundary potential ͓Im et al., J. Chem. Phys. 114, 2924 ͑2001͔͒ which was recently developed to include the influence of distant atoms on a small region part of a large macromolecular system in molecular dynamics simulations. It is shown that the basis-set expansion is accurate and computationally inexpensive for three simple models such as a spherical ionic system, an impermeable membrane system, and a cylindrical pore system as well as a realistic system such as OmpF porin with all atomic details. The influence of the static field and the reaction field on the ion distribution and conductance in the OmpF channel is studied and discussed.

A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N -Methylacetamide

Journal of The American Chemical Society, 2010

Most current biomolecular simulations are based on potential energy functions that treat the elec... more Most current biomolecular simulations are based on potential energy functions that treat the electrostatic energy as a sum of pairwise Coulombic interactions between effective fixed atomic charges. This approximation, in which many-body induced polarization effects are included in an average way, is expected to be satisfactory for a wide range of systems, but less accurate for processes involving the transfer and partition of ions among heterogeneous environments. The limitations of these potential energy functions are perhaps most obvious in studies of ion permeation through membrane channels. In many cases, the pore is so narrow that the permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with protein atoms. Interactions of cations with protein backbone carbonyl oxygens, in particular, play a critical role in several important biological channels. As a first step toward meeting the challenge of developing an accurate explicit accounting for induced polarization effects, the present work combines experiments and computation to characterize the interactions of alkali and halide ions with N-methylacetamide chosen to represent the peptide bond. From solubility measurements, we extract the solvation free energies of KCl and NaCl in liquid N-methylacetamide. Polarizable models based on the Drude oscillator are then developed and compared with available experimental and ab initio data. The good agreement for a range of structural and thermodynamic properties in the gas and condensed phases suggests that the polarizable models provide an accurate representation of ion−amide interactions in biological systems.

Imaging the Electrostatic Potential of Transmembrane Channels: Atomic Probe Microscopy of OmpF Porin

Biophysical Journal, 2002

Free Energy Profiles for H+ Conduction along Hydrogen-Bonded Chains of Water Molecules

Biophysical Journal, 1998

The molecular mechanism for proton conduction along hydrogen-bonded chains, or "proton wires," is... more The molecular mechanism for proton conduction along hydrogen-bonded chains, or "proton wires," is studied with free energy simulations. The complete transport of a charge along a proton wire requires two complementary processes: 1) translocation of an excess proton (propagation of an ionic defect), and 2) reorientation of the hydrogen-bonded chain (propagation of a bonding defect). The potential of mean force profile for these two steps is computed in model systems comprising a single-file chain of nine dissociable and polarizable water molecules represented by the PM6 model of Stillinger and co-workers. Results of molecular dynamics simulations with umbrella sampling indicate that the unprotonated chain is preferably polarized, and that the inversion of its total dipole moment involves an activation free energy of 8 kcal/mol. In contrast, the rapid translocation of an excess H ϩ across a chain extending between two spherical solvent droplets is an activationless process. These results suggest that the propagation of a bonding defect constitutes a limiting step for the passage of several protons along single-file chains of water molecules, whereas the ionic translocation may be fast enough to occur within the lifetime of transient hydrogen-bonded water chains in biological membranes.

Mechanism of C-type inactivation in the hERG potassium channel

Science Advances

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...

Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for 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...

Multi-ion free energy landscapes underscore the microscopic mechanism of ion selectivity in the KcsA channel

Biochimica et Biophysica Acta (BBA) - Biomembranes, 2016

Potassium (K +) channels are transmembrane proteins that passively and selectively allow K + ions... more Potassium (K +) channels are transmembrane proteins that passively and selectively allow K + ions to flow through them, after opening in response to an external stimulus. One of the most critical functional aspects of their function is their ability to remain very selective for K + over Na + while allowing high-throughput ion conduction at a rate close to the diffusion limit. Classically, it is assumed that the free energy difference between K + and Na + in the pore relative to the bulk solution is the critical quantity at the origin of selectivity. This is the thermodynamic view of ion selectivity. An alternative view assumes that kinetic factor play the dominant role. Recent results from a number of studies have also highlighted the great importance of the multi-ion single file on the selectivity of K + channels. The data indicate that having multiple K + ions bound simultaneously is required for selective K + conduction, and that a reduction in the number of bound K + ions destroys the multi-ion selectivity mechanism utilized by K + channels. In the present study, multi-ion potential of mean force molecular dynamics computations are carried out to clarify the mechanism of ion selectivity in the KcsA channel. The computations show that the multi-ion character of the permeation process is a critical element for establishing the selective ion conductivity through K +-channels.

Energetics of double-ion occupancy in the gramicidin A channel

The journal of physical chemistry. B, Jan 4, 2010

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 ...

Theoretical and computational models of biological ion channels

Quarterly Reviews of Biophysics, 2004

Hydration Number, Topological Control, and Ion Selectivity

The Journal of Physical Chemistry B, 2009

The topological control hypothesis presented by Bostick and Brooks [Proc. Natl. Acad. Sci. USA 10... more The topological control hypothesis presented by Bostick and Brooks [Proc. Natl. Acad. Sci. USA 104:9260, 2007] has sought to explain binding selectivity in potassium channels on the basis of universal environment-independent features related to ion coordination. This leads to the view that ion selectivity is predominantly controlled by the number of ligands coordinating the ion, and that the chemical type of those ligands plays a minor role. The significance of the topological control hypothesis and its ability to predict ion selectivity in protein binding sites are examined. It is shown that the framework encounters increasing difficulties when different protein binding sites with similar coordination numbers are considered.

Computational Studies of Membrane Channels

Structure, 2004

Energetics of ion conduction through the gramicidin channel

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...

Recovery from slow inactivation in K+ channels is controlled by water molecules

Nature, 2013

Perspectives on: Ion selectivity: Ion selectivity in channels and transporters

The Journal of General Physiology, 2011

A multitude of biological processes requires the participation of specific cations, such as H + ,... more A multitude of biological processes requires the participation of specific cations, such as H + , Na + , K + , Ca 2+ , and Mg 2+. Many of these processes can take place only when proteins have the ability to discriminate between different ions with a very high fidelity. How this is possible is a fundamental question that has fascinated scientists for a long time. At the most fundamental level, it is anticipated that ion selectivity must result from a delicate balance of strong interactions. Yet, identifying and quantifying the key microscopic factors is difficult, as many of these cannot be directly measured by experiments. Theory and computations can contribute by providing a virtual route to complement the missing information. Because ion selectivity is often dominated by thermodynamic factors, detailed molecular dynamics (MD) free energy simulations become important tools. This was vividly illustrated early on with studies of ion solvation (Straatsma and Berendsen, 1988; Åqvist, 1990) and ion-selective systems (Lybrand et al., 1986; Grootenhuis and Kollman, 1989; Åqvist, 1992). These pioneering studies inspired our own efforts. In this Perspective, we aim to present our understanding of ion selectivity as it has evolved over approximately 15 years from studies based on various specific structures: gramicidin A channels (e.g.

On the Importance of Atomic Fluctuations, Protein Flexibility, and Solvent in Ion Permeation

The Journal of General Physiology, 2004

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...

Extracellular Blockade of K+ Channels by TEA: Results from Molecular Dynamics Simulations of the KcsA Channel

The Journal of General Physiology, 2001

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 ...

Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels

The Journal of General Physiology, 2011

Fundamental concepts governing ion selectivity in narrow pores are reviewed and the microscopic f... more Fundamental concepts governing ion selectivity in narrow pores are reviewed and the microscopic factors responsible for the lack of selectivity of the NaK channel, which is structurally similar to the K +-selective KcsA channel, are elucidated on the basis of all-atom molecular dynamics free energy simulations. The results on NaK are contrasted and compared with previous studies of the KcsA channel. Analysis indicates that differences in hydration of the cation in the pore of NaK is at the origin of the lack of selectivity of NaK .

Perspectives on: Molecular dynamics and computational methods

The Journal of General Physiology, 2010

Grand canonical Monte Carlo simulations of water in protein environments

The Journal of Chemical Physics, 2004

The grand canonical simulation algorithm is considered as a general methodology to sample the con... more The grand canonical simulation algorithm is considered as a general methodology to sample the configuration of water molecules confined within protein environments. First, the probability distribution of the number of water molecules and their configuration in a region of interest for biochemical simulations, such as the active site of a protein, is derived by considering a finite subvolume in open equilibrium with a large system serving as a bulk reservoir. It is shown that the influence of the bulk reservoir can be represented as a many-body potential of mean force acting on the atoms located inside the subvolume. The grand canonical Monte Carlo ͑GCMC͒ algorithm, augmented by a number of technical advances to increase the acceptance of insertion attempts, is implemented, and tested for simple systems. In particular, the method is illustrated in the case of a pure water box with periodic boundary conditions. In addition, finite spherical systems of pure water and containing a dialanine peptide, are simulated with GCMC while the influence of the surrounding infinite bulk is incorporated using the generalized solvent boundary potential ͓W. Im, S. Bernèche, and B. Roux, J. Chem. Phys. 114, 2924 ͑2001͔͒. As a last illustration of water confined in the interior of a protein, the hydration of the central cavity of the KcsA potassium channel is simulated.

Generalized solvent boundary potential for computer simulations

The Journal of Chemical Physics, 2001

A general approach has been developed to allow accurate simulations of a small region part of a l... more A general approach has been developed to allow accurate simulations of a small region part of a large macromolecular system while incorporating the influence of the remaining distant atoms with an effective boundary potential. The method is called the Generalized Solvent Boundary Potential ͑GSBP͒. By representing the surrounding solvent as a continuum dielectric, both the solvent-shielded static field from the distant atoms of the macromolecule and the reaction field from the dielectric solvent acting on the atoms in the region of interest are included. The static field is calculated once, using the finite-difference Poisson-Boltzmann ͑PB͒ equation, and the result is stored on a discrete grid for efficient simulations. The solvent reaction field is developed using a basis-set expansion whose coefficients correspond to generalized electrostatic multipoles. A matrix representing the reaction field Green's function between those generalized multipoles is calculated only once using the PB equation and stored for efficient simulations. In the present work, the formalism is applied to both spherical and orthorhombic simulation regions for which orthonormal basis-sets exist based on spherical harmonics or cartesian Legendre polynomials. The GSBP method is also tested and illustrated with simple model systems and two detailed atomic systems: the active site region of aspartyl-tRNA synthetase ͑spherical region͒ and the interior of the KcsA potassium channel ͑orthorhombic region͒. Comparison with numerical finite-difference PB calculations shows that GSBP can accurately describe all long-range electrostatic interactions and remain computationally inexpensive.

Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

The Journal of Chemical Physics, 2001

A general method has been developed to include the electrostatic reaction field in Brownian dynam... more A general method has been developed to include the electrostatic reaction field in Brownian dynamics ͑BD͒ simulations of ions diffusing through complex molecular channels of arbitrary geometry. Assuming that the solvent is represented as a featureless continuum dielectric medium, a multipolar basis-set expansion is developed to express the reaction field Green's function. A reaction field matrix, which provides the coupling between generalized multipoles, is calculated only once and stored before the BD simulations. The electrostatic energy and forces are calculated at each time step by updating the generalized multipole moments. The method is closely related to the generalized solvent boundary potential ͓Im et al., J. Chem. Phys. 114, 2924 ͑2001͔͒ which was recently developed to include the influence of distant atoms on a small region part of a large macromolecular system in molecular dynamics simulations. It is shown that the basis-set expansion is accurate and computationally inexpensive for three simple models such as a spherical ionic system, an impermeable membrane system, and a cylindrical pore system as well as a realistic system such as OmpF porin with all atomic details. The influence of the static field and the reaction field on the ion distribution and conductance in the OmpF channel is studied and discussed.

A Combined Experimental and Theoretical Study of Ion Solvation in Liquid N -Methylacetamide

Journal of The American Chemical Society, 2010

Most current biomolecular simulations are based on potential energy functions that treat the elec... more Most current biomolecular simulations are based on potential energy functions that treat the electrostatic energy as a sum of pairwise Coulombic interactions between effective fixed atomic charges. This approximation, in which many-body induced polarization effects are included in an average way, is expected to be satisfactory for a wide range of systems, but less accurate for processes involving the transfer and partition of ions among heterogeneous environments. The limitations of these potential energy functions are perhaps most obvious in studies of ion permeation through membrane channels. In many cases, the pore is so narrow that the permeating ion must shed most of its surrounding water molecules and the large energetic loss due to dehydration must be compensated by coordination with protein atoms. Interactions of cations with protein backbone carbonyl oxygens, in particular, play a critical role in several important biological channels. As a first step toward meeting the challenge of developing an accurate explicit accounting for induced polarization effects, the present work combines experiments and computation to characterize the interactions of alkali and halide ions with N-methylacetamide chosen to represent the peptide bond. From solubility measurements, we extract the solvation free energies of KCl and NaCl in liquid N-methylacetamide. Polarizable models based on the Drude oscillator are then developed and compared with available experimental and ab initio data. The good agreement for a range of structural and thermodynamic properties in the gas and condensed phases suggests that the polarizable models provide an accurate representation of ion−amide interactions in biological systems.

Imaging the Electrostatic Potential of Transmembrane Channels: Atomic Probe Microscopy of OmpF Porin

Biophysical Journal, 2002

Free Energy Profiles for H+ Conduction along Hydrogen-Bonded Chains of Water Molecules

Biophysical Journal, 1998

The molecular mechanism for proton conduction along hydrogen-bonded chains, or "proton wires," is... more The molecular mechanism for proton conduction along hydrogen-bonded chains, or "proton wires," is studied with free energy simulations. The complete transport of a charge along a proton wire requires two complementary processes: 1) translocation of an excess proton (propagation of an ionic defect), and 2) reorientation of the hydrogen-bonded chain (propagation of a bonding defect). The potential of mean force profile for these two steps is computed in model systems comprising a single-file chain of nine dissociable and polarizable water molecules represented by the PM6 model of Stillinger and co-workers. Results of molecular dynamics simulations with umbrella sampling indicate that the unprotonated chain is preferably polarized, and that the inversion of its total dipole moment involves an activation free energy of 8 kcal/mol. In contrast, the rapid translocation of an excess H ϩ across a chain extending between two spherical solvent droplets is an activationless process. These results suggest that the propagation of a bonding defect constitutes a limiting step for the passage of several protons along single-file chains of water molecules, whereas the ionic translocation may be fast enough to occur within the lifetime of transient hydrogen-bonded water chains in biological membranes.