Ion channel gating and proton transport

A model of ion channel gating has been proposed (J. Biomol. Struct. Dyn. 19 (2002) 725). It includes the following. (1) There is a bacterial channel for which an X-ray structure is known (KcsA) that opens (‘gates’) with a drop in pH. In the proposal, a proton gates this channel by adding a charge to the glutamate residues that form the center of the gating region. It is postulated that two water molecules form a strong short hydrogen bond when the glutamates plus the water have a −2 charge. Adding a proton leads to a normal, weak, hydrogen bond, and the groups can separate, opening the channel. 98 calculations support this part of the proposal (J. Phys. Chem. B 105 (2001) 5298). (2) Voltage gated channels contain six transmembrane (TM) segments in each of four domains. We suggest that the additional four TM segments (KcsA has two) act as a voltage-to-proton current transducer. In the model, the first step in gating is proton tunneling (J. Phys. Chem. A 102 (1998) 7181), followed by a proton cascade. Calculations supporting the latter step are presented here. One of the eukaryotic TM segments, S4, is known to be involved in gating. This segment has arginines (occasionally lysine) at every third amino acid. The arginines appear capable of transmitting a proton, or possibly a proton cascade (three per S4 would produce the observed charge movement (‘gating current’) that precedes gating). We have carried out density functional calculations, using 98, on a system that includes: one pair of guanidinium groups, the side chains of arginines responsible for carrying the proton current; a mobile proton; one, two or three water molecules. Several guanidinium spacings have been tried, all in the range of carbon–carbon distances 4–6 Å. The potential energy surface was computed for each, and a minimum path found for the proton, at B3LYP/6-311G** level. It was found that the proton, under some conditions, could follow a path between guanidiniums that had no barriers greater than a few kT (thermal energy), thereby supporting the proposal that protons could move along the chain of guanidiniums.     

Molecular dynamics and brownian dynamics investigation of ion permeation and anesthetic halothane effects on a proton-gated ion channel

Bacterial Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) is activated to cation permeation upon lowering the solution pH. Its function can be modulated by anesthetic halothane. In the present work, we integrate molecular dynamics (MD) and Brownian dynamics (BD) simulations to elucidate the ion conduction, charge selectivity, and halothane modulation mechanisms in GLIC, based on recently resolved X-ray crystal structures of the open-channel GLIC. MD calculations of the potential of mean force (PMF) for a Na(+) revealed two energy barriers in the extracellular domain (R109 and K38) and at the hydrophobic gate of transmembrane domain (I233), respectively. An energy well for Na(+) was near the intracellular entrance: the depth of this energy well was modulated strongly by the protonation state of E222. The energy barrier for Cl(-) was found to be 3-4 times higher than that for Na(+). Ion permeation characteristics were determined through BD simulations using a hybrid MD/continuum electrostatics approach to evaluate the energy profiles governing the ion movement. The resultant channel conductance and a near-zero permeability ratio (P(Cl)/P(Na)) were comparable to experimental data. On the basis of these calculations, we suggest that a ring of five E222 residues may act as an electrostatic gate. In addition, the hydrophobic gate region may play a role in charge selectivity due to a higher dehydration energy barrier for Cl(-) ions. The effect of halothane on the Na(+) PMF was also evaluated. Halothane was found to perturb salt bridges in GLIC that may be crucial for channel gating and open-channel stability, but had no significant impact on the single ion PMF profiles.     

Solid-state 35/37Cl NMR spectroscopy of hydrochloride salts of amino acids implicated in chloride ion transport channel selectivity: opportunities at 900 MHz

The results of a detailed systematic chlorine solid-state NMR study of several hydrochloride salts of amino acids implicated in chloride ion transport channel selectivity are reported. (35)Cl and (37)Cl NMR spectra have been obtained for stationary and/or magic-angle spinning powdered samples of the following compounds on 500 and/or 900 MHz spectrometers: DL-arginine HCl monohydrate, L-lysine HCl, L-serine HCl, L-glutamic acid HCl, L-proline HCl, L-isoleucine HCl, L-valine HCl, L-phenylalanine HCl, and glycine HCl. Spectral analyses provide information on the anisotropic properties and relative orientations of the chlorine electric field gradient and chemical shift (CS) tensors, which are intimately related to the local molecular and electronic structure. Data obtained at 900 MHz provide unique examples of the effects of CS anisotropy on the NMR spectrum of a quadrupolar nucleus. The range of chlorine quadrupolar coupling constants (C(Q)) measured, -6.42 to 2.03 MHz, demonstrates the sensitivity of this parameter to the chloride ion environment and suggests the applicability of chlorine solid-state NMR as a novel experimental tool for defining chloride binding environments in larger ion channel systems. Salts of hydrophobic amino acids are observed to tend to exhibit larger values of C(Q) than salts of hydrophilic amino acids. A simple model for rationalizing the observed trend in C(Q) is proposed. For salts for which neutron diffraction structures are available, we identify a quantum chemical method which reproduces experimental values of C(Q) with a root-mean-square deviation of 0.1 MHz and a correlation coefficient of 0.9998. On the basis of this, chlorine NMR tensors are predicted for the Cl(-) binding site in ClC channels.     

Carboxylate anion diminishes chloride transport through a synthetic, self-assembled transmembrane pore

Six amphiphilic heptapeptides with the structure (C18H37)2NCOCH2OCH2CO-(Gly)3-Pro-(Gly)n-(Glx)-(Gly)m-O(CH2)6CH3, in which Glx represents glutamic acid or its benzyl ester and n+m=2, have been studied. In addition, the glutamate residue in the GGGPGGE sequence was esterified by fluorescent 1-pyrenemethanol. These compounds insert into phospholipid bilayers and form anion-conducting pores. Hill plots based on carboxyfluorescein release indicate that the pores are at least dimeric. Studies that involved ion-selective electrode techniques showed that transport of chloride varied with the position of glutamate within the peptide chain and whether glutamic acid was present as the free acid or its benzyl ester. Chloride transport activity was significantly higher for the glutamate esters than for free carboxylates irrespective of the glutamate position. Activity was highest when the glutamate residue in approximately (Gly)3-Pro-(Xxx)3 approximately was closest to the C terminus of the peptide. A fluorescent pyrene residue was introduced to probe the aggregation state of the amphiphile. The selectivity of the pore for Cl(-) over K+ was maintained even when the carboxylate anion was present within it. Complexation of Cl(-) by the ionophoric peptides was confirmed by negative ion mass spectrometry. Planar bilayer voltage clamp experiments confirmed that pores with more than one conductance state may form in these dynamic, self-assembled pores.     

Hierarchical multiscale simulation of electrokinetic transport in silica nanochannels at the point of zero charge

Effects of nanoscale confinement and partial charges that stem from quantum calculations are investigated in silica slit channels filled with 1 M KCl at the point of zero charge by using a hierarchical multiscale simulation methodology. Partial charges of both bulk and surface atoms from ab initio quantum calculations that take into account bond polarization and electronegativity are used in molecular dynamics (MD) simulations to obtain ion and water concentration profiles for channel widths of 1.1, 2.1, 2.75, and 4.1 nm. The interfacial electron density profiles of simulations matched well with that of recent X-ray reflectivity experiments. By simulating corresponding channels with no partial charges, it was observed that the partial charges affect the concentration profiles and transport properties such as diffusion coefficients and mobilities up to a distance of about 3 sigma(O)(-)(O) from the surface. Both in uncharged and partially charged cases, oscillations in concentration profiles of K(+) and Cl(-) ions give rise to an electro-osmotic flow in the presence of an external electric field, indicating the presence of an electric double layer at net zero surface charge, contrary to the expectations from classical continuum theory. I-V curves in a channel-bath system using ionic mobilities from MD simulations were significantly different for channels with and without partial charges for channel widths less than 4.1 nm.     

Voltage-Mediated Water Dynamics Enables On-Demand Transport of Sugar Molecules in Two-Dimensional Channels

The constructing of artificial channels with gating functions is an important undertaking for gaining insight into biological process and achieving efficient bionic functions. Typically, controllable transport within such channels relies on either electrostatic or specific interactions between the transporting species and the channel. However, for molecules with weak interactions with the channel, achieving precise gating of the transport remains a significant challenge. In this regard, this study proposes a voltage gating membrane of two-dimensional channels that selectively transport of neutral molecules glucose with a dimension of 0.60 nm. The permeation of glucose is switched on/off by electrochemically manipulating the water dynamics in the nanochannel. Voltage driven-intercalation of ion into the two-dimensional channel causes water to stratify and move closer to the channel walls, thereby resulting in the channel center being emptier for glucose diffusion. Due to the sub-nanometer size dimension of the channel, selective permeation of glucose over sucrose is also achieved in this approach.     

Role of Arg123 in Light‐driven Anion Pump Mechanisms of pharaonis Halorhodopsin†

Halorhodopsin (HR) acts as a light‐driven chloride pump which transports a chloride ion from the extracellular (EC) to the cytoplasmic space during a photocycle reaction that includes some photointermediates initiated by illumination. To understand the chloride uptake mechanisms, we focused on a basic residue Arg123 of HR from Natronomonas pharaonis (NpHR), which is the only basic residue located in the EC half ion channel. By the measurements of the visible absorption spectra in the dark and the light‐induced inward current through the membrane, it was shown that the chloride binding and transport ability of NpHR completely disappeared by the change of arginine to glutamine. From flashphotolysis analysis, the photocycle of R123Q differed from that of wildtype NpHR completely. The response of the R123H mutant depended on pH. These facts imply that the positive charge at position 123 is essential for chloride binding in the ground state and for the chloride uptake under illumination. On the basis of the molecular structures of HR and the anion‐transportable mutants of bacteriorhodopsin, the effects of the positive charge and the conformational change of the Arg123 side chain as well as the chloride‐pumping mechanism are discussed.     

DFT study on the interaction between monomeric aluminium and chloride ion in aqueous solution

The interaction of monomeric aluminium and chloride ion in aqueous solution is investigated by density functional theory (DFT) calculations. The computational results show that it is difficult for Cl(-) to enter the inner-coordination shell of aluminium complexes by replacing the bound water molecules, independent of pH and the concentration of Cl(-). However, pH and the concentration of Cl(-) might influence the conformations, bond lengths and natural charge populations of monomeric aluminium complexes to a given extent. Based on the computed Gibbs energies, pK(a) values of various hydrolysis species in the presence and absence of Cl(-) are evaluated, respectively. It is concluded that pK(a) increases with the introduction of Cl(-).     

Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family

Understanding the mechanisms of gating and ion permeation in biological channels and receptors has been a long-standing challenge in biophysics. Recent advances in structural biology have revealed the architecture of a number of transmembrane channels and allowed detailed, molecular-level insight into these systems. Herein, we have examined the barriers to ion conductance and origins of ion selectivity in models of the cationic human alpha7 nicotinic acetylcholine receptor (nAChR) and the anionic alpha1 glycine receptor (GlyR), based on the structure of Torpedo nAChR. Molecular dynamics simulations were used to determine water density profiles along the channel length, and they established that both receptor pores were fully hydrated. The very low water density in the middle of the nAChR pore indicated the existence of a hydrophobic constriction. By contrast, the pore of GlyR was lined with hydrophilic residues and remained well-hydrated throughout. Adaptive biasing force simulations allowed us to reconstruct potentials of mean force (PMFs) for chloride and sodium ions in the two receptors. For the nicotinic receptor we observed barriers to ion translocation associated with rings of hydrophobic residues-Val13' and Leu9'-in the middle of the transmembrane domain. This finding further substantiates the hydrophobic gating hypothesis for nAChR. The PMF revealed no significant hydrophobic barrier for chloride translocation in GlyR. For both receptors nonpermeant ions displayed considerable barriers. Thus, the overall electrostatics and the presence of rings of charged residues at the entrance and exit of the channels were sufficient to explain the experimentally observed anion and cation selectivity.     

Photodissociation of propargyl chloride at 193 nm

The photodissociation of propargyl chloride (C3H3Cl) has been studied at 193 nm. Ion imaging experiments with state-selective detection of the Cl atoms and single-photon ionization of the C3H3 radicals were performed, along with measurements of the Cl + C3H3 and HCl + C3H2 recoil kinetic energy distributions, using a scattering apparatus with electron bombardment ionization detection to resolve the competing Cl and HCl elimination channels. The experiments allow the determination of the Cl (2P3/2) and Cl (2P1/2) (hereafter Cl) branching fractions associated with the C-Cl bond fission, which are determined to be 0.5 +/- 0.1 for both channels. Although prior translational spectroscopy studies by others had concluded that the low velocity signal at the Cl+ mass was due to daughter fragments of the HCl elimination products, the present work shows that Cl atoms are produced with a bimodal recoil kinetic energy distribution. The major C-Cl bond fission channel, with a narrow recoil kinetic energy distribution peaking near 40 kcal/mol, produces both Cl and Cl, whereas the minor (5%) channel, partitioning much less energy to relative kinetic energy, produces only ground spin-orbit state Cl atoms. The maximum internal energy of the radicals produced in the low-recoil-kinetic-energy channel is consistent with this channel producing electronically excited propargyl radicals. Finally, in contrast to previous studies, the present work determines the HCl recoil kinetic energy distribution and identifies the possible contribution to this spectrum from propargyl radicals cracking to C3+ ions in the mass spectrometer.     

A photodissociation study of CH2BrCl in the A-band using the time-sliced ion velocity imaging method

Employing a high-resolution (velocity resolution deltanu/nu<1.5%) time-sliced ion velocity imaging apparatus, we have examined the photodissociation of CH2BrCl in the photon energy range of 448.6-618.5 kJ/mol (193.3-266.6 nm). Precise translational and angular distributions for the dominant Br(2P32) and Br(2P12) channels have been determined from the ion images observed for Br(2P32) and Br(2P12). In confirmation with the previous studies, the kinetic-energy distributions for the Br(2P12) channel are found to fit well with one Gaussian function, whereas the kinetic- energy distributions for the Br(2P32) channel exhibit bimodal structures and can be decomposed into a slow and a fast Gaussian component. The observed kinetic-energy distributions are consistent with the conclusion that the formation of the Br(2P32) and Br(2P12) channels takes place on a repulsive potential-energy surface, resulting in a significant fraction (0.40-0.47) of available energy to appear as translational energy for the photo fragments. On the basis of the detailed kinetic-energy distributions and anisotropy parameters obtained in the present study, together with the specific features and relative absorption cross sections of the excited 2A', 1A", 3A', 4A', and 2A" states estimated in previous studies, we have rationalized the dissociation pathways of CH2BrCl in the A-band, leading to the formation of the Br(2P32) and Br(2P12) channels. The analysis of the ion images observed at 235 nm for Cl(2P(32,12)) provides strong evidence that the formation of Cl mainly arises from the secondary photodissociation process CH2Cl + hnu --> CH2 + Cl.     

Products, rate constants and mechanisms of gas-phase reactions of CX(3)(+), CX(2)(+), CX(+) (X = F and/or Cl) and Cl(+) with 1,1,1- and 1,1,2-trichlorotrifluoroethane.

The gas-phase ion chemistry of 1,1,1- and 1,1,2-trichlorotrifluoroethane was investigated with an ion trap mass spectrometer. Following electron ionization both compounds (M) fragment to [M - Cl](+), CX(3)(+), CX(2)(+), CX(+) (X = F and/or Cl) and Cl(+). The reactivity of each of these fragments towards their neutral precursors was studied to obtain product and kinetic data. Whereas [M - Cl](+), CCl(3)(+) and CCl(2)F(+) cations are unreactive under the experimental conditions used, all other species react via halide abstraction to give [M - Cl](+) and, to a far lesser extent, [M - F](+). In addition, CX(2)(+) ions form CClX(2)(+) in a process which formally amounts to chlorine atom abstraction, but more likely involves chloride ion abstraction followed by charge transfer. CX(+) ions also form minor amounts of CX(3)(+) product ions, possibly via chloride abstraction followed by or concerted with dihalocarbene elimination from the (incipient) [M - Cl](+) ion. Trivalent carbenium ions are less reactive than divalent species, which in turn are less reactive than the monovalent ions (reaction efficiencies are given in parentheses): CF(3)(+)(0.70) < CF(2)(+)(0.78) < CF(+)(0.96). More interestingly, within each family of ions reactivity increases with the number of fluorine substituents (e.g. CF(2)(+) > CFCl(+) > CCl(2)(+) and CF(+) > CCl(+)), i.e. reactivity increases with the ion thermochemical stability, as measured by available standard free enthalpies of formation. Evaluation of the energetics involved shows that reactions are largely driven by the stability of the neutrals more than of the ions. Finally, the products observed in the reaction of Cl(+) are attributed to ionization of the neutral via charge transfer and fragmentation.     

氯代甲苯双电荷离子的单分子解离反应研究

研究了在70 eV电子轰击电离条件下，氯代甲苯及氯化苄产生的双电荷离子[C_7H_7Cl]~(2＋)、[C_7H_6Cl]~(2＋·)和[C_7H_5Cl]~(2＋)为母体的两种类型单分子解离反应．主要讨论了亚稳双电荷离子的异构化反应、失H解高的“偶电子规则”以及单分子电荷分离过渡态的结构．     

Ion channel formation from a calix[4]arene amide that binds HCl

The ion transport activity of calix[4]arene tetrabutylamide 1,3-alt 2 was studied in liposomes, planar lipid bilayers, and HEK-293 cells. These experiments, when considered together with (1)H NMR and X-ray crystallography data, indicate that calix[4]arene tetrabutylamide 2 (1) forms ion channels in bilayer membranes, (2) mediates ion transport across cell membranes at positive holding potential, (3) alters the pH inside liposomes experiencing a Cl(-) gradient, and (4) shows a significant Cl(-)/SO(4)(2)(-) transport selectivity. An analogue, calix[4]arene tetramethylamide 1, self-assembles in the presence of HCl to generate solid-state structures with chloride-filled and water-filled channels. Structureminus signactivity studies indicate that the hydrophobicity, amide substitution, and macrocyclic framework of the calixarene are essential for HCl binding and transport. Calix[4]arene tetrabutylamide 2 is a rare example of an anion-dependent, synthetic ion channel.     

Altering the activity of syringomycin E via the membrane dipole potential

The membrane dipole potential is responsible for the modulation of numerous biological processes. It was previously shown (Ostroumova, O. S.; Kaulin, Y. A.; Gurnev, P. A.; Schagina, L. V. Langmuir 2007, 23, 6889-6892) that variations in the dipole potential lead to changes in the channel properties of the antifungal lipodepsipeptide syringomycin E (SRE). Here, data are presented demonstrating the effect of the membrane dipole potential on the channel-forming activity of SRE. A rise in the dipole potential is accompanied by both an increase in the minimum SRE concentration required for the detection of single channels at fixed voltage and a decrease in the steady-state number of open SRE channels at a given SRE concentration and voltage. These alterations are determined by several factors: gating charge, connected with translocations of lipid and SRE dipoles during channel formation, the bilayer-water solution partitioning of SRE, and the chemical work related to conformational changes during channel formation.     

Dynamics of Cl (2Pj) atom formation in the photodissociation of fumaryl chloride (ClCO - CH = CH - COCl) at 235 nm: a resonance enhanced multiphoton ionization (REMPI) time-of-flight (TOF) study

The photodissociation dynamics of fumaryl chloride (ClCO-CH═CH-COCl) has been studied in a supersonic molecular beam around 235 nm using resonance enhanced multiphoton ionization (REMPI) time-of-flight (TOF) technique by detecting the nascent state of the primary chlorine atom. A single laser has been used for excitation of fumaryl chloride and the REMPI detection of chlorine atoms in their spin-orbit states, Cl ((2)P(3/2)) and Cl* ((2)P(1/2)). We have determined the translational energy distribution, the recoil anisotropy parameter, β, and the spin-orbit branching ratio for chlorine atom elimination channels. To obtain these, measured polarization-dependent and state-specific TOF profiles are converted into kinetic energy distributions, using a least-squares fitting method, taking into account the fragment recoil anisotropies, β(i). The TOF profiles for both Cl and Cl* are found to be independent of laser polarization; i.e., β is well characterized by a value of 0.0, within the experimental uncertainties. Two components, namely, the fast and the slow, are observed in the translational energy distribution, P(E(T)), of Cl and Cl* atoms, and assigned to be formed from different potential energy surfaces. The average translational energies for the fast components of the Cl and Cl* channels are 14.9 ± 1.6 and 16.8 ± 1.6 kcal/mol, respectively. Similarly, for the slow components, the average translational energies of the Cl and Cl* channels are 3.4 ± 0.8 and 3.1 ± 0.8 kcal/mol, respectively. The energy partitioning into the translational modes is interpreted with the help of various models, such as impulsive and statistical models. Apart from the chlorine atom elimination channel, molecular hydrogen chloride (HCl) elimination is also observed in the photodissociation process. The HCl product has been detected, using a REMPI scheme in the region of 236-237 nm. The observation of the molecular HCl in the dissociation process highlights the importance of the relaxation process, in which the initially excited parent molecule relaxes to the ground state from where the molecular (HCl) elimination takes place.     

Molecular design and synthesis of artificial ion channels based on cyclic peptides containing unnatural amino acids

A series of novel cyclic peptides composed of 3 to 5 dipeptide units with alternating natural-unnatural amino acid units, have been designed and synthesized, employing 5-(N-alkanoylamino)-3-aminobenzoic acid with a long alkanoyl chain as the unnatural amino acid. All cyclic peptides with systematically varying pore size, shape, and lipophilicity are found to form ion channels with a conductance of ca. 9 pS in aqueous KCl (500 mM) upon examination by the voltage clamp method. These peptide channels are cation selective with the permeability ratio P(Cl(-))/P(K(+)) of around 0.17. The ion channels formed by the neutral, cationic, and anionic cyclic peptides containing L-alanine, L-lysine, and L-aspartate, respectively, show the monovalent cation selectivity with the permeability ratio P(Na(+))/P(K(+)) of ca. 0.39. On the basis of structural information provided by voltage-dependent blockade of the single channel current of all the tested peptides by Ca(2+), we inferred that each channel is formed from a dimer of the peptide with its peptide ring constructing the channel entrance and its alkanoyl chains lining across the membrane to build up the channel pore. The experimental results are consistent with an idea that the rate of ion conduction is determined by the nature of the hydrophobic alkanoyl chain region, which is common to all the channels.     

Charge effects for differentiation of oligodeoxynucleotide isomers containing 8-oxo-dG residues

Dissociation reactions of a series of multiply charged oligodeoxynucleotide (ODN) 12-mer anions were studied using an ion trap mass spectrometer. These mixed nucleobase 12-mers fragment first by loss of a neutral nucleobase (A, G, C, and/or 5-methyl-cytosine) followed by cleavage at 3' C-O bond of the sugar from which the base is lost to produce the complementary sequence ions, i.e., [a - B] and w type of ions. No detectable loss of 8-oxo-guanine and/or thymine from these 12-mers is observed under gentle collision conditions in the ion trap. The primary loss of a nucleobase and the subsequent backbone cleavage to generate sequence ions strongly depend on the charge state of the parent molecular ion. For low charge states (2- and 3-), product ions due to the loss of a neutral guanine base and related sequence ions are dominant in the tandem mass spectra. However, preferential loss of a neutral adenine becomes the primary reaction channel from the 5- charge state of the molecular ion. Such charge state dependent fragmentation behavior was utilized to determine the site of 8-oxo-dG residue in a series of structural isomers. The position of 8-oxo-dG residue can be simply determined from the fragmentation pattern of 3- charge state, but not of 5- charge state. It is suggested that in addition to specific modification that affects the N-glycosidic bond strength, total charge content of an ODN is an important factor for determining the differential fragmentation behavior.     

Ion channels from linear and branched bola-amphiphiles

The synthesis and characterization of the ion channel activity of three new bola-amphiphiles is described. These compounds are conceptually derived from a previously reported bis-cyclophane bola-amphiphile through opening of the cyclophanes to acyclic structures and were found to readily form ion channels in planar bilayer membranes as assessed by bilayer clamp single-channel analysis. All three compounds behaved very similarly: the dominant channels formed by all three are Ohmic with specific conductance of 10 +/- 1 pS (NaCl electrolyte) and 39 +/- 1 pS (CsCl electrolyte). Single-ion permeability ratios, determined from dissymmetric electrolyte experiments, showed the selectivity P(Cs(+)) > P(Na(+)) > P(Cl(-)). Less frequently, lower conductance channels were also observed to act independently of the dominant channels. The lifetimes of the dominant channels range from 70 to 280 ms for the three compounds with some very long-lived openings (20-40 s) observed for two of the three. The lower conductance states have shorter lifetimes. This study demonstrates that bis-macrocyclic compounds are not essential for channel formation by bola-amphiphiles, and opens a new class of channel-forming compounds for structure-activity optimization.     

Permeation and gating in proteins: kinetic Monte Carlo reaction path following

We present a new Monte Carlo technique, kinetic Monte Carlo reaction path following (kMCRPF), for the computer simulation of permeation and large-scale gating transitions in protein channels. It combines ideas from Metropolis Monte Carlo (MMC) and kinetic Monte Carlo (kMC) algorithms, and is particularly suitable when a reaction coordinate is well defined. Evolution of transition proceeds on the reaction coordinate by small jumps (kMC technique) toward the nearest lowest-energy uphill or downhill states, with the jumps thermally activated (constrained MMC). This approach permits navigation among potential minima on an energy surface, finding the minimum-energy paths and determining their associated free-energy profiles. The methodological and algorithmic strategies underlying the kMCRPF method are described. We have tested it using an analytical model and applied it to study permeation through the curvilinear ClC chloride and aquaporin pores and to gating in the gramicidin A channel. These studies of permeation and gating in real proteins provide extensive procedural tests of the method.