Molecular dynamics simulations of C2F6 effects on gramicidin A: implications of the mechanisms of general anesthesia

VIBRATIONAL INFRARED LIFETIME OF THE ANESTHETIC NITROUS OXIDE GAS IN SOLUTION

The lifetime of the asymmetric fundamental stretching 2218 cm-1 vibration of the anesthetic gas nitrous oxide ( N 2 O ) dissolved in octanol and olive oil is reported. These solvents are model systems commonly used to assess anesthetic potency. Picosecond time-scale molecular dynamics simulations have suggested that protein dynamics or membrane dynamics play a role in the molecular mechanism of anesthetic action. Ultrafast infrared spectroscopy with 100 fs time resolution is an ideal tool to probe dynamics of anesthetic molecules on such timescales. Pump-probe studies centered at the peak of the vibrational band yield a lifetime of 55 ± 1 ps in olive oil and 52 ± 1 ps in octanol. The similarity of lifetimes suggests that energy relaxation of the anesthetic is determined primarily by the hydrophobic nature of the environment, consistent with models of anesthetic action. The results show that nitrous oxide is a good model system for probing anesthetic-solvent interactions using nonlinear infrared spectroscopy.

Modulation of KvAP unitary conductance and gating by 1-alkanols and other surface active agents

The actions of alcohols and anesthetics on ion channels are poorly understood. Controversy continues about whether bilayer restructuring is relevant to the modulatory effects of these surface active agents (SAAs). Some voltage-gated K channels (Kv), but not KvAP, have putative low affinity alcohol-binding sites, and because KvAP structures have been determined in bilayers, KvAP could offer insights into the contribution of bilayer mechanics to SAA actions. We monitored KvAP unitary conductance and macroscopic activation and inactivation kinetics in PE:PG/decane bilayers with and without exposure to classic SAAs (short-chain 1-alkanols, cholesterol, and selected anesthetics: halothane, isoflurane, chloroform). At levels that did not measurably alter membrane specific capacitance, alkanols caused functional changes in KvAP behavior including lowered unitary conductance, modified kinetics, and shifted voltage dependence for activation. A simple explanation is that the site of SAA action on KvAP is its entire lateral interface with the PE:PG/decane bilayer, with SAA-induced changes in surface tension and bilayer packing order combining to modulate the shape and stability of various conformations. The KvAP structural adjustment to diverse bilayer pressure profiles has implications for understanding desirable and undesirable actions of SAA-like drugs and, broadly, predicts that channel gating, conductance and pharmacology may differ when membrane packing order differs, as in raft versus nonraft domains.

Computational studies on the interactions of inhalational anesthetics with proteins

Despite the widespread clinical use of anesthetics since the 19th century, a clear understanding of the mechanism of anesthetic action has yet to emerge. On the basis of early experiments by Meyer, Overton, and subsequent researchers, the cell's lipid membrane was generally concluded to be the primary site of action of anesthetics. However, later experiments with lipid-free globular proteins, such as luciferase and apoferritin, shifted the focus of anesthetic action to proteins. Recent experimental studies, such as photoaffinity labeling and mutagenesis on membrane proteins, have suggested specific binding sites for anesthetic molecules, further strengthening the proteocentric view of anesthetic mechanism. With the increased availability of high-resolution crystal structures of ion channels and other integral membrane proteins, as well as the availability of powerful computers, the structure-function relationship of anesthetic-protein interactions can now be investigated in atomic detail. In this Account, we review recent experiments and related computer simulation studies involving interactions of inhalational anesthetics and proteins, with a particular focus on membrane proteins. Globular proteins have long been used as models for understanding the role of protein-anesthetic interactions and are accordingly examined in this Account. Using selected examples of membrane proteins, such as nicotinic acetyl choline receptor (nAChR) and potassium channels, we address the issues of anesthetic binding pockets in proteins, the role of conformation in anesthetic effects, and the modulation of local as well as global dynamics of proteins by inhaled anesthetics. In the case of nicotinic receptors, inhalational anesthetic halothane binds to the hydrophobic cavity close to the M2-M3 loop. This binding modulates the dynamics of the M2-M3 loop, which is implicated in allosterically transmitting the effects to the channel gate, thus altering the function of the protein. In potassium channels, anesthetic molecules preferentially potentiate the open conformation by quenching the motion of the aromatic residues implicated in the gating of the channel. These simulations suggest that low-affinity drugs (such as inhalational anesthetics) modulate the protein function by influencing local as well as global dynamics of proteins. Because of intrinsic experimental limitations, computational approaches represent an important avenue for exploring the mode of action of anesthetics. Molecular dynamics simulations-a computational technique frequently used in the general study of proteins-offer particular insight in the study of the interaction of inhalational anesthetics with membrane proteins.

Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective

Hemagglutinins (HA's) from duck, swine, and human influenza viruses have previously been shown to prefer avian and human glycan receptor analogues with distinct topological profiles, pentasaccharides LSTa (alpha-2,3 linkage) and LSTc (alpha-2,6 linkage), in comparative molecular dynamics studies. On the basis of detailed analyses of the dynamic motions of the receptor binding domains (RBDs) and interaction energy profiles with individual glycan residues, we have identified approximately 30 residue positions in the RBD that present distinct profiles with the receptor analogues. Glycan binding constrained the conformational space sampling by the HA. Electrostatic steering appeared to play a key role in glycan binding specificity. The complex dynamic behaviors of the major SSE and trimeric interfaces with or without bound glycans suggested that networks of interactions might account for species specificity in these low affinity and high avidity (multivalent) interactions between different HA and glycans. Contact frequency, energetic decomposition, and H-bond analyses revealed species-specific differences in HA-glycan interaction profiles, not readily discernible from crystal structures alone. Interaction energy profiles indicated that mutation events at the set of residues such as 145, 156, 158, and 222 would favor human or avian receptor analogues, often through interactions with distal asialo-residues. These results correlate well with existing experimental evidence, and suggest new opportunities for simulation-based vaccine and drug development.

Four-alpha-helix bundle with designed anesthetic binding pockets. Part II: halothane effects on structure and dynamics

As a model of the protein targets for volatile anesthetics, the dimeric four-alpha-helix bundle, (Aalpha(2)-L1M/L38M)(2), was designed to contain a long hydrophobic core, enclosed by four amphipathic alpha-helices, for specific anesthetic binding. The structural and dynamical analyses of (Aalpha(2)-L1M/L38M)(2) in the absence of anesthetics (another study) showed a highly dynamic antiparallel dimer with an asymmetric arrangement of the four helices and a lateral accessing pathway from the aqueous phase to the hydrophobic core. In this study, we determined the high-resolution NMR structure of (Aalpha(2)-L1M/L38M)(2) in the presence of halothane, a clinically used volatile anesthetic. The high-solution NMR structure, with a backbone root mean-square deviation of 1.72 A (2JST), and the NMR binding measurements revealed that the primary halothane binding site is located between two side-chains of W15 from each monomer, different from the initially designed anesthetic binding sites. Hydrophobic interactions with residues A44 and L18 also contribute to stabilizing the bound halothane. Whereas halothane produces minor changes in the monomer structure, the quaternary arrangement of the dimer is shifted by about half a helical turn and twists relative to each other, which leads to the closure of the lateral access pathway to the hydrophobic core. Quantitative dynamics analyses, including Modelfree analysis of the relaxation data and the Carr-Purcell-Meiboom-Gill transverse relaxation dispersion measurements, suggest that the most profound anesthetic effect is the suppression of the conformational exchange both near and remote from the binding site. Our results revealed a novel mechanism of an induced fit between anesthetic molecule and its protein target, with the direct consequence of protein dynamics changing on a global rather than a local scale. This mechanism may be universal to anesthetic action on neuronal proteins.

Molecular dynamics simulations of ternary membrane mixture: phosphatidylcholine, phosphatidic acid, and cholesterol

A ternary mixture of 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl phosphatidic acid (POPA), and cholesterol (CHOL) works effectively for a functional conformation of nicotinic acetylcholine receptor (nAChR) that can undergo agonist-induced conformation changes, but POPC alone can stabilize only a desensitized state of nAChR. To gain insights into the lipid mixture that has strong impact to nAChR functions, we performed more than 50 ns all atom molecular dynamic (MD) simulations at 303 K on a fully hydrated bilayer consisting of 240 POPC, 80 POPA, and 80 CHOL (3:1:1). The MD simulation revealed various interactions between different types of molecular pairs that ultimately regulated lipid organization. The heterogeneous interactions among three different constituents resulted in a broad spectrum of lipid properties, including extensive distributions of average area per lipid and varied lipid ordering as a function of lipid closeness to CHOL. Higher percentage of POPA than POPC had close association with CHOL, which coincided with relatively higher ordering of POPA molecules in their acyl chains near lipid head groups. Lower fraction of gauche dihedrals was also found in the same region of POPA. Although the CHOL molecules had the effects on the enhancement of surrounding lipid order, relatively low lipid order parameters and high fraction of gauche bonds were observed in the ternary mixture. Collectively, these results suggest that the dynamical structure of the ternary system could be determinant for a functional nAChR.

Fluorescence quenching of gramicidin D in model membranes by halothane

Inhaled anesthetics were introduced in surgery over a century ago. To this day, the molecular mechanism of anesthetic action remains largely unknown. However, ion-channels of neuronal membranes are believed to be the most- likely molecular targets of inhaled anesthetics. In the study presented here, we investigated the interaction of a simplified ion-channel system, gramicidin, with halothane, a small haloalkane inhaled anesthetic in various environments. Fluorescence-quenching experiments of gramicidin D in dioleoylphosphatidylcholine (DOPC) large unilamellar vesicles (LUVS) have shown that halothane can directly interact with the ion channel (KSV = 66 M–1). Halothane quenched the fluorescence from tryptophan residues located at the lipid bilayer – aqueous interfaces as well as those tryptophans located deeper in the bilayer. Quenching data from gramicidin D in sodium dodecyl sulfide (SDS) micelles revealed that the tryptophan residues located at the micelle–solvent interface were preferentially quenched by halothane (KSV = 22 M–1). In 1-octanol, fluorescence quenching was observed, but with a lower KSV value (KSV = 6 M–1) than in DOPC LUVS and SDS micelles. Taken together, these results indicate that halothane interactions with gramicidin, mediated by a lipid bilayer, are the strongest, and that the mechanism of anesthetic action may also be lipid-mediated.

Steered Molecular Dynamics Simulations of Na+ Permeation across the Gramicidin A Channel

The potential of mean forces (PMF) governing Na+ permeation through gramicidin A (gA) channels with explicit water and membrane was characterized using steered molecular dynamics (SMD) simulations. Constant-force SMD with a steering force parallel to the channel axis revealed at least seven energy wells in each monomer of the channel dimer. Except at the channel dimer interface, each energy well is associated with at least three and at most four backbone carbonyl oxygens and two water oxygens in a pseudo-hexahedral or pseudo-octahedral coordination with the Na+ ion. Repeated constant-velocity SMD by dragging a Na+ ion from each energy well in opposite directions parallel to the channel axis allowed the computation of the PMF across the gA channel, revealing a global minimum corresponding to Na+ binding sites near the entrance of gA at +/-9.3 A from the geometric center of the channel. The effect of volatile anesthetics on the PMF was also analyzed in the presence of halothane molecules. Although the accuracy of the current PMF calculation from SMD simulations is not yet sufficient to quantify the PMF difference with and without anesthetics, the comparison of the overall PMF profiles nevertheless confirms that the anesthetics cause insignificant changes to the structural makeup of the free energy wells along the channel and the overall permeation barrier. On average, the PMF appears less rugged in the outer part of the channel in the presence of anesthetics, consistent with our earlier finding that halothane interaction with anchoring residues makes the gA channel more dynamic. A causal relationship was observed between the reorientation of the coordinating backbone carbonyl oxygen and Na+ transit from one energy well to another, suggesting the possibility that even minute changes in the conformation of pore-lining residues due to dynamic motion could be sufficient to trigger the ion permeation. Because some of the carbonyl oxygens contribute to Na+ coordination in two adjacent energy wells, our SMD results reveal that the atomic picture of ion "hopping" through a gA channel actually involves a Na+ ion being carried in a relay by the coordinating oxygens from one energy well to the next. Steered molecular dynamics complements other computational approaches as an attractive means for the atomistic interpretation of experimental permeation studies.

ROLES OF BILAYER MATERIAL PROPERTIES IN FUNCTION AND DISTRIBUTION OF MEMBRANE PROTEINS

Structural, compositional, and material (elastic) properties of lipid bilayers exert strong influences on the interactions of water-soluble proteins and peptides with membranes, the distribution of transmembrane proteins in the plane of the membrane, and the function of specific membrane channels. Theoretical and experimental studies show that the binding of either cytoplasmic proteins or extracellular peptides to membranes is regulated by the presence of charged lipids and that the sorting of transmembrane proteins into or out of membrane microdomains (rafts) depends on several factors, including bilayer material properties governed by the presence of cholesterol. Recent studies have also shown that bilayer material properties modify the permeability of membrane pores, formed either by protein channels or by cell-lytic peptides.