Four-alpha-helix bundle with designed anesthetic binding pockets. Part I: structural and dynamical analyses

Influence of Krypton Gas Nanobubbles on the Activity of Pepsin

The fact that biologically inert gases can significantly affect the biological function of proteins still lacks a full understanding because they are usually chemically stable and weakly absorbed by biological molecules. Recently, nanobubbles were proposed to play an important role in the activity of a protein (Scientific reports 2013, 3; Scientific reports 2017, 7, 10176). In this study, we developed a controllable method to produce high-concentration krypton (Kr) gas nanobubbles in pure water and measured the concentration influence of those Kr nanobubbles on pepsin protein activity. By combining high-sensitivity synchrotron radiation X-ray fluorescence techniques with a nanoparticle tracking analysis technology, we provided strong evidence that the observed "nanoparticles" were indeed Kr nanobubbles. Activity measurements showed that the activity would be inhibited by the existence of Kr nanobubbles and could be recovered by degassing. More importantly, the inhibition extent of pepsin activity was dominated by the number of nanobubbles in solution. More nanobubbles would cause more inhibition of pepsin activity. Furthermore, the structures of pepsin could be changed by nanobubbles, which might be the reason for inhabitation of activity. Our results would provide a further understanding of the mechanisms of the biological effects of inert gases.

Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC

Experimental chemical shifts (CS) from solution and solid state magic-angle-spinning nuclear magnetic resonance (NMR) spectra provide atomic level information for each amino acid within a protein or protein complex. However, structure determination of large complexes and assemblies based on NMR data alone remains challenging due to the complexity of the calculations. Here, we present a hardware accelerated strategy for the estimation of NMR chemical-shifts of large macromolecular complexes based on the previously published PPM_One software. The original code was not viable for computing large complexes, with our largest dataset taking approximately 14 hours to complete. Our results show that serial code refactoring and parallel acceleration brought down the time taken of the software running on an NVIDIA Volta 100 (V100) Graphic Processing Unit (GPU) to 46.71 seconds for our largest dataset of 11.3 million atoms. We use OpenACC, a directive-based programming model for porting the application to a heterogeneous system consisting of x86 processors and NVIDIA GPUs. Finally, we demonstrate the feasibility of our approach in systems of increasing complexity ranging from 100K to 11.3M atoms.

Nuclear magnetic resonance (NMR) spectroscopy yields chemical shifts (CSs) which reveal chemical details of the environment of an atom in a protein. Computer estimation of CSs require the calculation of several contributing terms including interatomic distances, ring current effects and the formation of hydrogen bonds. Here, taking advantage of graphic processing units (GPUs), the estimation of chemical shifts are accelerated thus enabling the determination of the CSs for large systems, encompassing millions of atoms. The rapid determination of CSs enables the use of CS-based validation for other molecular dynamics computations.

Solution NMR Studies of Anesthetic Interactions with Ion Channels

NMR spectroscopy is one of the major tools to provide atomic resolution protein structural information. It has been used to elucidate the molecular details of interactions between anesthetics and ion channels, to identify anesthetic binding sites, and to characterize channel dynamics and changes introduced by anesthetics. In this chapter, we present solution NMR methods essential for investigating interactions between ion channels and general anesthetics, including both volatile and intravenous anesthetics. Case studies are provided with a focus on pentameric ligand-gated ion channels and the voltage-gated sodium channel NaChBac.

Exploring the Effects on Lipid Bilayer Induced by Noble Gases via Molecular Dynamics Simulations

Noble gases seem to have no significant effect on the anesthetic targets due to their simple, spherical shape. However, xenon has strong narcotic efficacy and can be used clinically, while other noble gases cannot. The mechanism remains unclear. Here, we performed molecular dynamics simulations on phospholipid bilayers with four kinds of noble gases to elucidate the difference of their effects on the membrane. Our results showed that the sequence of effects on membrane exerted by noble gases from weak to strong was Ne, Ar, Kr and Xe, the same order as their relative narcotic potencies as well as their lipid/water partition percentages. Compared with the other three kinds of noble gases, more xenon molecules were distributed between the lipid tails and headgroups, resulting in membrane’s lateral expansion and lipid tail disorder. It may contribute to xenon’s strong anesthetic potency. The results are well consistent with the membrane mediated mechanism of general anesthesia.

Strong hyperconjugative interactions in isolated and water complexes of desflurane: a theoretical investigation

Ab initio MP2/aug-cc-pvDZ and density functional B3LYP calculations with the 6-311++G(d,p) basis set are performed to investigate the conformation of desflurane (CHF2OCHFCF3), its acidity/basicity and its interaction with one water molecule. The calculations include the optimized geometries, the harmonic frequencies of relevant vibrational modes, the binding energies with water, and a detailed natural bond orbital (NBO) analysis Iincluding the NBO charges, the hybridization of the C atoms and the intra- and intermolecular hyperconjugations. The relative energies of the two most stable conformers are discussed as a function of the total hyperconjugative energies resulting from the interaction of lone pairs of the O and F atoms to the different antibonding orbitals of desflurane. The proton affinity is the same for both conformers but the acidity of the CH bond is larger for the less stable conformer. The binding energies of the complexes of two desflurane conformers with one water molecule range from -2.75 to -3.23 kcal mol(-1). Depending on the structure of the complexes, the CH bonds involved in the interaction are contracted or elongated. The σ*(CH) occupation predominates over the hybridization effect in determining the CH bond length. There is an unexpected charge transfer to the external OH bond of the water molecule. This effect is in good agreement with theoretical data on the complexes between fluorinated dimethyl ethers and water and seems to depend on the number of F atoms implanted on the ether molecule.

Design and biophysical characterization of a monomeric four-alpha-helix bundle protein Aα₄ with affinity for the volatile anesthetic halothane

A monomeric four-α-helix bundle protein Aα₄ was designed as a step towards investigating the interaction of volatile general anesthetics with their putative membrane protein targets. The alpha helices, connected by glycine loops, have the sequence A, B, B', A'. The DNA sequence was designed to make the helices with the same amino acid sequences (helix A and A', B and B', respectively) as different as possible, while using codons which are favorable for expression in E. coli. The protein was bacterially expressed and purified to homogeneity using reversed-phase HPLC. Protein identity was verified using MALDI-TOF mass spectrometry. Far-UV circular dichroism spectroscopy confirmed the predominantly alpha-helical nature of the protein Aα₄. Guanidinium chloride induced denaturation showed that the monomeric four-α-helix bundle protein Aα₄ is considerably more stable compared to the dimeric di-α-helical protein (Aα₂-L38M)₂. The sigmoidal character of the unfolding reaction is conserved while the sharpness of the transition is increased 1.8-fold. The monomeric four-α-helix bundle protein Aα₄ bound halothane with a dissociation constant (K(d)) of 0.93 ± 0.02mM, as shown by both tryptophan fluorescence quenching and isothermal titration calorimetry. This monomeric four-α-helix bundle protein can now be used as a scaffold to incorporate natural central nervous system membrane protein sequences in order to examine general anesthetic interactions with putative targets in detail.

General anesthetics predicted to block the GLIC pore with micromolar affinity

Although general anesthetics are known to modulate the activity of ligand-gated ion channels in the Cys-loop superfamily, there is at present neither consensus on the underlying mechanisms, nor predictive models of this modulation. Viable models need to offer quantitative assessment of the relative importance of several identified anesthetic binding sites. However, to date, precise affinity data for individual sites has been challenging to obtain by biophysical means. Here, the likely role of pore block inhibition by the general anesthetics isoflurane and propofol of the prokaryotic pentameric channel GLIC is investigated by molecular simulations. Microscopic affinities are calculated for both single and double occupancy binding of isoflurane and propofol to the GLIC pore. Computations are carried out for an open-pore conformation in which the pore is restrained to crystallographic radius, and a closed-pore conformation that results from unrestrained molecular dynamics equilibration of the structure. The GLIC pore is predicted to be blocked at the micromolar concentrations for which inhibition by isofluorane and propofol is observed experimentally. Calculated affinities suggest that pore block by propofol occurs at signifcantly lower concentrations than those for which inhibition is observed: we argue that this discrepancy may result from binding of propofol to an allosteric site recently identified by X-ray crystallography, which may cause a competing gain-of-function effect. Affinities of isoflurane and propofol to the allosteric site are also calculated, and shown to be 3 mM for isoflurane and for propofol; both anesthetics have a lower affinity for the allosteric site than for the unoccupied pore.

Although general anesthesia is performed every day on thousands of people, its detailed microscopic mechanisms are not known. What is known is that general anesthetic drugs modulate the activity of ion channels in the central nervous system. These channels are proteins that open in response to binding of neurotransmitter molecules, creating an electric current through the cell membrane and thus propagating nerve impulses between cells. One possible mechanism for ion channel inhibition by anesthetics is that the drugs bind inside the pore of the channels, blocking ion current. Here we investigate such a pore block mechanism by computing the strength of the drugs' interaction with the pore – and hence the likelihood of binding, in the case of GLIC, a bacterial channel protein. The results, obtained from numerical simulations of atomic models of GLIC, indicate that the anesthetics isoflurane and propofol have a tendency to bind in the pore that is strong enough to explain blocking of the channel, even at low concentration of the drugs.

Recognition of anesthetic barbiturates by a protein binding site: a high resolution structural analysis

Barbiturates potentiate GABA actions at the GABA_A receptor and act as central nervous system depressants that can induce effects ranging from sedation to general anesthesia. No structural information has been available about how barbiturates are recognized by their protein targets. For this reason, we tested whether these drugs were able to bind specifically to horse spleen apoferritin, a model protein that has previously been shown to bind many anesthetic agents with affinities that are closely correlated with anesthetic potency. Thiopental, pentobarbital, and phenobarbital were all found to bind to apoferritin with affinities ranging from 10–500 µM, approximately matching the concentrations required to produce anesthetic and GABAergic responses. X-ray crystal structures were determined for the complexes of apoferritin with thiopental and pentobarbital at resolutions of 1.9 and 2.0 Å, respectively. These structures reveal that the barbiturates bind to a cavity in the apoferritin shell that also binds haloalkanes, halogenated ethers, and propofol. Unlike these other general anesthetics, however, which rely entirely upon van der Waals interactions and the hydrophobic effect for recognition, the barbiturates are recognized in the apoferritin site using a mixture of both polar and nonpolar interactions. These results suggest that any protein binding site that is able to recognize and respond to the chemically and structurally diverse set of compounds used as general anesthetics is likely to include a versatile mixture of both polar and hydrophobic elements.

Binding of small molecules to cavity forming mutants of a de novo designed protein

A central goal of protein design is to devise novel proteins for applications in biotechnology and medicine. Many applications, including those focused on sensing and catalysis will require proteins that recognize and bind to small molecules. Here, we show that stably folded α-helical proteins isolated from a binary patterned library of designed sequences can be mutated to produce binding sites capable of binding a range of small aromatic compounds. Specifically, we mutated two phenylalanine side chains to alanine in the known structure of de novo protein S-824 to create buried cavities in the core of this four-helix bundle. The parental protein and the Phe→Ala variants were exposed to mixtures of compounds, and selective binding was assessed by saturation transfer difference NMR. The affinities of benzene and a number of its derivatives were determined by pulse field gradient spin echo NMR, and several of the compounds were shown to bind the mutated protein with micromolar dissociation constants. These studies suggest that stably folded de novo proteins from binary patterned libraries are well-suited as scaffolds for the design of binding sites.

New insights into the molecular mechanisms of general anaesthetics

This paper provides new insights of how general anaesthetic research should be carried out in the future by an analysis of what we know, what we do not know and what we would like to know. I describe previous hypotheses on the mechanism of action of general anaesthetics (GAs) involving membranes and protein receptors. I provide the reasons why the GABA type A receptor, the NMDA receptor and the glycine receptor are strong candidates for the sites of action of GAs. I follow with a review on attempts to provide a mechanism of action, and how future research should be conducted with the help of physical and chemical methods.

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 interaction between the general anesthetic halothane and a model ion channel protein, III: Molecular dynamics simulation incorporating a cyanophenylalanine spectroscopic probe

A nitrile-derived amino acid, Phe(CN), has been used as an internal spectroscopic probe to study the binding of an inhalational anesthetic to a model membrane protein. The infrared spectra from experiment showed a blue-shift of the nitrile vibrational frequency in the presence of the anesthetic halothane. To interpret the infrared results and explore the nature of the interaction between halothane and the model protein, all-atom molecular dynamics (MD) simulations have been used to probe the structural and dynamic properties of the protein in the presence and absence of one halothane molecule. The frequency shift analyzed from MD simulations agrees well with the experimental infrared results. Decomposition of the forces acting on the nitrile probes demonstrates an indirect impact on the probes from halothane, namely a change of the protein's electrostatic local environment around the probes induced by halothane. Although the halothane remains localized within the designed hydrophobic binding cavity, it undergoes a significant amount of translational and rotational motion, modulated by the interaction of the trifluorine end of halothane with backbone hydrogens of the residues forming the cavity. This dominant interaction between halothane and backbone hydrogens outweighs the direct interaction between halothane and the nitrile groups, making it a good "spectator" probe of the halothane-protein interaction. These MD simulations provide insight into action of anesthetic molecules on the model membrane protein, and also support the further development of nitrile-labeled amino acids as spectroscopic probes within the designed binding cavity.

Mechanism of interaction between the general anesthetic halothane and a model ion channel protein, I: Structural investigations via X-ray reflectivity from Langmuir monolayers

We previously reported the synthesis and structural characterization of a model membrane protein comprised of an amphiphilic 4-helix bundle peptide with a hydrophobic domain based on a synthetic ion channel and a hydrophilic domain with designed cavities for binding the general anesthetic halothane. In this work, we synthesized an improved version of this halothane-binding amphiphilic peptide with only a single cavity and an otherwise identical control peptide with no such cavity, and applied x-ray reflectivity to monolayers of these peptides to probe the distribution of halothane along the length of the core of the 4-helix bundle as a function of the concentration of halothane. At the moderate concentrations achieved in this study, approximately three molecules of halothane were found to be localized within a broad symmetric unimodal distribution centered about the designed cavity. At the lowest concentration achieved, of approximately one molecule per bundle, the halothane distribution became narrower and more peaked due to a component of approximately 19A width centered about the designed cavity. At higher concentrations, approximately six to seven molecules were found to be uniformly distributed along the length of the bundle, corresponding to approximately one molecule per heptad. Monolayers of the control peptide showed only the latter behavior, namely a uniform distribution along the length of the bundle irrespective of the halothane concentration over this range. The results provide insight into the nature of such weak binding when the dissociation constant is in the mM regime, relevant for clinical applications of anesthesia. They also demonstrate the suitability of both the model system and the experimental technique for additional work on the mechanism of general anesthesia, some of it presented in the companion parts II and III under this title.

Anesthetic modulation of protein dynamics: insight from an NMR study

Mistic (membrane integrating sequence for translation of integral membrane protein constructs) comprises the four-alpha-helix bundle scaffold found in the transmembrane domains of the Cys-loop receptors that are plausible targets for general anesthetics. Nuclear magnetic resonance (NMR) studies of anesthetic halothane interaction with Mistic in dodecyl phosphocholine (DPC) micelles provide an experimental basis for understanding molecular mechanisms of general anesthesia. Halothane was found to interact directly with Mistic, mostly in the interfacial loop regions. Although the presence of halothane had little effect on Mistic structure, (15)N NMR relaxation dispersion measurements revealed that halothane affected Mistic's motion on the microsecond-millisecond time scale. Halothane shifted the equilibrium of chemical exchange in some residues and made the exchange faster or slower in comparison to the original state in the absence of halothane. The motion on the microsecond-millisecond time scale in several residues disappeared in response to the addition of halothane. Most of the residues experiencing halothane-induced dynamics changes also exhibited profound halothane-induced changes in chemical shift, suggesting that dynamics modification of these residues might result from their direct interaction with halothane molecules. Allosteric modulation by halothane also contributed to dynamics changes, as reflected in residues I52 and Y82 where halothane introduction brought about dynamics changes but not chemical shift changes. The study suggests that inhaled general anesthetics could act on proteins via altering protein motion on the microsecond-millisecond time scale, especially motion in the flexible loops that link different alpha helices. The validation of anesthetic effect on protein dynamics that are potentially correlated with protein functions is a critical step in unraveling the mechanisms of anesthetic action on proteins.

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.