Effect of increased chain packing on gramicidin-lipid interactions

Synthesis and characterization of glucose-bis(pyrazole)-Cu(II)/Ni(II) complexes and their in vitro DNA binding studies

The D-glucose-bis pyrazolyl complexes of Cu(II) 1 and Ni(II) 2 were synthesized and characterized by elemental analysis, molar conductance measurements and spectroscopic methods. The solution structures of the complex have been assessed to square pyramidal using electronic absorption and electronic paramagnetic resonance (EPR) spectroscopy. The interaction of 1 and 2 with calf thymus DNA (CT DNA) has been carried out by absorption, emission, viscometric and electrochemical methods. The intrinsic binding constant K(b) was determined as 13.4x10(5) M(-1), 4.5x10(5) M(-1) for 1 and 2, respectively suggestive of strong binding of complexes with DNA. Furthermore, higher value of K(b) for 1 implies that this complex interacts more strongly with CT DNA in comparison to 2. The quenching constant "K" of 1 and 2 obtained from emission spectral methods was 1.33, 0.55, respectively. Complex 1 hydrolytically cleaved pBR322 supercoiled DNA in absence of an activating agent. The enhanced cleavage of pBR322 DNA was observed in presence of ascorbic acid as a reducing agent, 1 also displays efficient photonuclease activity through double strand DNA breaks when irradiated at 365 nm through mechanistic pathway involving hydroxyl radicals. In addition to the above binding studies, an in vitro binding study of complex 1 with protein human serum albumin (HSA), tyrptophan and mixtures of HSA, L-tryptophan with CT DNA was carried out. The in vitro "binding study" also supports that 1 shows higher binding affinity towards CT DNA.

The gramicidin ion channel: A model membrane protein

The linear peptide gramicidin forms prototypical ion channels specific for monovalent cations and has been extensively used to study the organization, dynamics and function of membrane-spanning channels. In recent times, the availability of crystal structures of complex ion channels has challenged the role of gramicidin as a model membrane protein and ion channel. This review focuses on the suitability of gramicidin as a model membrane protein in general, and the information gained from gramicidin to understand lipid-protein interactions in particular. Special emphasis is given to the role and orientation of tryptophan residues in channel structure and function and recent spectroscopic approaches that have highlighted the organization and dynamics of the channel in membrane and membrane-mimetic media.

Determination of the 19F NMR chemical shielding tensor and crystal structure of 5-fluoro-dl-tryptophan

5-Fluoro-dl-tryptophan (5F-Trp) is a very sensitive probe used to investigate orientation and dynamics of biomacromolecules at the in situ level. In order to establish a (19)F NMR strategy, the crystal structure and (19)F chemical shielding tensor of 5F-Trp are reported. A novel approach was developed to use F-F homonuclear dipole-dipole coupling information to analyze single-crystal NMR data without determining crystal orientations. The measured values for the principal components of the shielding tensor are sigma(11)=0.9, sigma(22)=-63.3, and sigma(33)=-82.9 ppm relative to TFA in D(2)O. The principal axes of the shielding tensors coincide with the indole ring symmetry, which makes it a straightforward and powerful tool to monitor protein alignment in oriented environments. Hartree-Fock (HF) and density functional theory (DFT) calculations of the chemical shielding tensors are also reported.

Mixed Langmuir monolayers of gramicidin A and fluorinated alcohols

Mixed monolayers of gramicidin A (GA) and three alcohols, differing in the degree of fluorination, namely C18OH, F18OH, and F8H10OH have been investigated by means of: surface manometry (pi-A isotherms) and Brewster angle microscopy (BAM) aiming at finding appropriate molecules for incorporating gramicidin A for a biosensor design. Our results proved that only the semifluorinated alcohol is appropriate material for this purpose since it forms miscible and homogeneous monolayers with GA within the whole concentration range. The experimental results have been supported by the calculations of van der Waals energy profiles using the Insight II program. Both the hydrogenated and perfluorinated alcohols were found to aggregate at higher surface pressures, which exclude their application for gramicidin-based biosensor construction.

Gramicidin A Channel in a Matrix from a Semifluorinated Surfactant Monolayer

Gramicidin A, a polypeptide antibiotic forming transmembrane ion channels, has been incorporated into a Langmuir monolayer formed by a semifluorinated alkane (SFA). In this work, partially fluorinated tetracosane, perfluorohexyloctadecane (F6H18), has been applied, aiming at finding a suitable matrix for gramicidin A to be transferred onto solid support for a biosensor design. For this purpose, the physiological conditions were of special interest (mixed monolayers containing low gramicidin proportion and the surface pressure of 30 mN/m). Mixed monolayers of gramicidin and SFA were found to be miscible within the whole range of mole fractions. A very significant increase of the stability of SFA monolayer has been found in the presence of gramicidin, even at such a low proportion as X(gramicidin) = 0.1, which is reflected in a 3.5-fold increase of the collapse pressure value of mixed monolayer as compared to the film from pure SFA. This interesting phenomenon has been interpreted as being due to the existence of a strong dipole-dipole interaction between both film-forming molecules. Opposite sign of the measured electric surface potential for gramicidin and SFA, resulting from different directions of the dipole moment vectors in both film molecules, implies that the ordered, antiparallel orientation of the dipole moments in the mixed gramicidin/SFA system can be responsible for its extremely high stability.

Miscibility of Gramicidin A−Ethyl Nonadecanoate in Langmuir Monolayers in the Presence of Salts Dissolved in the Subphase

The behavior of binary mixed Langmuir monolayers from gramicidin A (GA) and ethyl nonadecanoate (EN), spread on aqueous subphases containing NaCl and CaCl2, was investigated on the basis of the analysis of surface pressure-average area per molecule (pi-A) isotherms complemented with Brewster angle microscopy (BAM) images. Compression modulus versus surface pressure (C(S-1)-pi) curves indicate the existence of interactions in the GA-EN mixed monolayers at low surface pressures (below 5 mN m(-1)). However, for mixtures in which the ester is the predominant component, both GA and EN are miscible within regions from fully expanded to collapse. To examine the interactions between both components in the studied system, values of the mean molecular area per molecule (A12) were plotted as a function of molar fraction of gramicidin A (X(GA)). A12-X(GA) plots exhibit negative deviations from ideality at high surface pressures, wherein beta-helices of GA are vertically oriented in respect to the interface. However, at surface pressures below the plateau transition, which is due to reorientation of GA, the binary system obeys the additive rule. Brewster angle microscopy (BAM) was applied for a direct visualization of the monolayers morphologies. The obtained images prove that for molar ratios of GA > or = 0.3 and at surface pressures above 5 mN m(-1), both components are immiscible at the interface. The observed negative deviations from the additively rule were attributed to the formation of a three-dimensional phase in the mixed film, which provokes its contraction at the interface.

Structural restraints and heterogeneous orientation of the gramicidin A channel closed state in lipid bilayers

Although there have been several decades of literature illustrating the opening and closing of the monovalent cation selective gramicidin A channel through single channel conductance, the closed conformation has remained poorly characterized. In sharp contrast, the open-state dimer is one of the highest resolution structures yet characterized in a lipid environment. To shift the open/closed equilibrium dramatically toward the closed state, a lower peptide/lipid molar ratio and, most importantly, long-chain lipids have been used. For the first time, structural evidence for a monomeric state has been observed for the native gramicidin A peptide. Solid-state NMR spectroscopy of single-site (15)N-labeled gramicidin in uniformly aligned bilayers in the L(alpha) phase have been observed. The results suggest a kinked structure with considerable orientational heterogeneity. The C-terminal domain is well structured, has a well-defined orientation in the bilayer, and appears to be in the bilayer interfacial region. On the other hand, the N-terminal domain, although appearing to be well structured and in the hydrophobic core of the bilayer, has a broad range of orientations relative to the bilayer normal. The structure is not just half of the open-state dimer, and neither is the structure restricted to the surface of the bilayer. Consequently, the monomeric or closed state appears to be a hybrid of these two models from the literature.

Membrane tension accelerates rate-limiting voltage-dependent activation and slow inactivation steps in a Shaker channel

A classical voltage-sensitive channel is tension sensitive—the kinetics of Shaker and S3–S4 linker deletion mutants change with membrane stretch (Tabarean, I.V., and C.E. Morris. 2002. Biophys. J. 82:2982–2994.). Does stretch distort the channel protein, producing novel channel states, or, more interestingly, are existing transitions inherently tension sensitive? We examined stretch and voltage dependence of mutant 5aa, whose ultra-simple activation (Gonzalez, C., E. Rosenman, F. Bezanilla, O. Alvarez, and R. Latorre. 2000. J. Gen. Physiol. 115:193–208.) and temporally matched activation and slow inactivation were ideal for these studies. We focused on macroscopic patch current parameters related to elementary channel transitions: maximum slope and delay of current rise, and time constant of current decline. Stretch altered the magnitude of these parameters, but not, or minimally, their voltage dependence. Maximum slope and delay versus voltage with and without stretch as well as current rising phases were well described by expressions derived for an irreversible four-step activation model, indicating there is no separate stretch-activated opening pathway. This model, with slow inactivation added, explains most of our data. From this we infer that the voltage-dependent activation path is inherently stretch sensitive. Simulated currents for schemes with additional activation steps were compared against datasets; this showed that generally, additional complexity was not called for. Because the voltage sensitivities of activation and inactivation differ, it was not possible to substitute depolarization for stretch so as to produce the same overall P_O time course. What we found, however, was that at a given voltage, stretch-accelerated current rise and decline almost identically—normalized current traces with and without stretch could be matched by a rescaling of time. Rate-limitation of the current falling phase by activation was ruled out. We hypothesize, therefore, that stretch-induced bilayer decompression facilitates an in-plane expansion of the protein in both activation and inactivation. Dynamic structural models of this class of channels will need to take into account the inherent mechanosensitivity of voltage-dependent gating.

Size-exclusion high-performance liquid chromatography in the study of the autoassociating antibiotic gramicidin A in micellar milieu

Gramicidin A (gA) is a polypeptide antibiotic which forms dimeric channels specific for monovalent cations in biological membranes. It is a polymorphic molecule that adopts several different conformations, double-stranded (ds) helical dimers (pore conformation) and single-stranded beta-helical dimers (channel conformation). This study investigated the conformational adaptability of gramicidin A when incorporated into micelles as membrane-mimetic model system. Taking advantage of our reported, versatile, size-exclusion high-performance liquid chromatography (SE-HPLC) strategy that allows the separation of double-stranded dimers and monomers, we have quantitatively characterized the conformational transition undergone by the peptide in the micellar milieu. The importance of both hydrophobic/hydrophilic moieties of the amphipaths in the stabilization of concrete conformational species is demonstrated using detergents with different hydrocarbon chain length and/or polar head. SE-HPLC is a valuable, rapid, accurate technique for the structural characterization of hydrophobic autoassociating peptides that work in lipid environments such as biological membranes.

Solid-state 19F-NMR analysis of 19F-labeled tryptophan in gramicidin A in oriented membranes

The response of membrane-associated peptides toward the lipid environment or other binding partners can be monitored by solid-state NMR of suitably labeled side chains. Tryptophan is a prominent amino acid in transmembrane helices, and its (19)F-labeled analogues are generally biocompatible and cause little structural perturbation. Hence, we use 5F-Trp as a highly sensitive NMR probe to monitor the conformation and dynamics of the indole ring. To establish this (19)F-NMR strategy, gramicidin A was labeled with 5F-Trp in position 13 or 15, whose chi(1)/chi(2) torsion angles are known from previous (2)H-NMR studies. First, the alignment of the (19)F chemical shift anisotropy tensor within the membrane was deduced by lineshape analysis of oriented samples. Next, the three principal axes of the (19)F chemical shift anisotropy tensor were assigned within the molecular frame of the indole ring. Finally, determination of chi(1)/chi(2) for 5F-Trp in the lipid gel phase showed that the side chain alignment differs by up to 20 degrees from its known conformation in the liquid crystalline state. The sensitivity gain of (19)F-NMR and the reduction in the amount of material was at least 10-fold compared with previous (2)H-NMR studies on the same system and 100-fold compared with (15)N-NMR.

The structure and function of gramicidin A embedded in interdigitated bilayer

The effects of phase transition from normal to interdigitated lipid bilayer on the function and structure of membrane proteins were studied using linear gramicidin (gramicidin A) as a model. Interdigitated bilayer structure of dipalmitoylphosphatidylglycerol (DPPG) liposomes that was induced by atropine could not be changed notably by intercalating of gramicidin. The K+ transportation of gramicidin in both normal and interdigitated bilayer was assayed by measuring the membrane potential. Results showed that gramicidin in interdigitated bilayer exhibited lower transport capability. Intrinsic fluorescence spectrum of gramicidin in interdigitated bilayer blue-shifted 2.8 nm from the spectrum in normal bilayer, which means that interdigitation provides a more hydrophobic environment for gramicidin. Circular dichroism measurement results indicated that the conformation of gramicidin in interdigitated bilayer is not the typical beta6.3 helix as in the normal bilayer. The results suggested that the interdigitated lipid bilayer might largely affect the structure and function of membrane proteins.

Distinctly different interactions of anesthetic and nonimmobilizer with transmembrane channel peptides

Although it plays no clinical role in general anesthesia, gramicidin A, a transmembrane channel peptide, provides an excellent model for studying the specific interaction between volatile anesthetics and membrane proteins at the molecular level. We show here that a pair of structurally similar volatile anesthetic and nonimmobilizer (nonanesthetic), 1-chloro-1,2,2-trifluorocyclobutane (F3) and 1, 2-dichlorohexafluorocyclobutane (F6), respectively, interacts differently with the transmembrane peptide. With 400 microM gramicidin A in a vesicle suspension of 60 mM phosphatidylcholine-phosphatidylglycerol (PC/PG), the intermolecular cross-relaxation rate constants between (19)F of F3 and (1)H in the chemical shift regions for the indole and backbone amide protons were 0.0106 +/- 0.0007 (n = 12) and 0.0105 +/- 0.0014 (n = 8) s(-1), respectively. No cross-relaxation was measurable between (19)F of F6 and protons in these regions. Sodium transport study showed that with 75 microM gramicidin A in a vesicle suspension of 66 mM PC/PG, F3 increased the (23)Na apparent efflux rate constant from 149.7 +/- 7.2 of control (n = 3) to 191.7 +/- 12.2 s(-1) (n = 3), and the apparent influx rate constant from 182.1 +/- 15.4 to 222.8 +/- 21.7 s(-1) (n = 3). In contrast, F6 had no effects on either influx or efflux rate. It is concluded that the ability of general anesthetics to interact with amphipathic residues near the peptide-lipid-water interface and the inability of nonimmobilizer to do the same may represent some characteristics of anesthetic-protein interaction that are of importance to general anesthesia.

Noncontact dipole effects on channel permeation. II. Trp conformations and dipole potentials in gramicidin A

The four Trp dipoles in the gramicidin A (gA) channel modulate channel conductance, and their side chain conformations should therefore be important, but the energies of different conformations are unknown. A conformational search for the right-handed helix based on molecular mechanics in vacuo yielded 46 conformations within 20 kcal/mol of the lowest energy conformation. The two lowest energy conformations correspond to the solid-state and solution-state NMR conformations, suggesting that interactions within the peptide determine the conformation. For representative conformations, the electrostatic potential of the Trp side chains on the channel axis was computed. A novel application of the image-series method of. Biophys. J. 9:1160-1170) was introduced to simulate the polarization of bulk water by the Trp side chains. For the experimentally observed structures, the CHARm toph19 potential energy (PE) of a cation in the channel center is -1.65 kcal/mol without images. With images, the PE is -1.9 kcal/mol, demonstrating that the images further enhance the direct dipole effect. Nonstandard conformations yielded less favorable PEs by 0.4-1.1 kcal/mol.

Unifying characteristics of sites of anesthetic action revealed by combined use of anesthetics and non-anesthetics

1. The usefulness of nonanesthetics in the study of mechanisms of general anesthesia lies in the possibility to identify the unifying characteristics of molecular sites that are shared by the anesthetics but not by the structurally similar nonanesthetics. 2. In model membranes, pairs of structurally similar anesthetics and nonanesthetics showed distinctly different submolecular distributions. 3. This difference may be the underlying cause for the different anesthetic and nonanesthetic interaction with gramicidin A, a model transmembrane cation channel. 4. Generalization of our findings suggests that the nature of the sites, whether in lipids or proteins, must be neither extremely hydrophilic nor extremely lipophilic, but amphiphilic.

Role of phosphatidylethanolamine lipids in the stabilization of protein-lipid contacts

We have investigated the effect of lipids with phosphatidylethanolamine (PE) head groups on the stabilization of contacts between the tryptophan side chains of gramicidin and the lipid head groups. We initially developed two fluorescence methods that can be correlated to the spontaneous curvature of DOPC/DOPE and DOPC/DOPEme. One is based on bilayer structure and measures the rotational motion of a probe located close to the membrane surface relative to a more deeply-buried probe. The second is based on surface hydration/polarity and measures the emission energy of a polarity-sensitive probe located on the membrane surface. We used these methods to estimate the pseudo-curvature (i.e., curvature obtained by fluorescence measurements) of lipids with dimyristyl chains, and their pressure and temperature dependence. We then investigated the stability of gramicidin tryptophan-lipid contacts in DMPC/DMPE as a function of temperature and pressure. Stability was assessed by tryptophan rotational motion as determined by fluorescence anisotropy, since rotational motion is limited when the indoles are hydrogen bonded to the lipid head groups. The results suggest that the presence of PE lipids destabilizes these contacts due to either their smaller size relative to PC head groups, or their tendency to self-interact. Fluorescence quenching studies support these results.

Species heterogeneity of Gly-11 gramicidin A incorporated into sodium dodecyl sulfate micelles

Evidence is presented for species heterogeneity of the gly-11 analog of gramicidin A incorporated into sodium dodecyl sulfate (SDS) micelles. The evidence for species heterogeneity has been obtained using one-dimensional (1D) 1H NMR spectroscopy. The 1D spectra of the indole NH moiety of tryptophans 9, 13, and 15 show the presence of more than one species. It has been found that the heterogeneity is dependent upon the gly-11/SDS molar ratio. At high SDS concentration (i.e., gly-11/SDS of 3 mM/700 mM) the heterogeneity almost completely disappears. The temperature dependence of these 1H NMR signals suggests that the two species do not interconvert. The results of nuclear Overhauser effect spectroscopy NMR experiments indicate that one species is embedded within the micelle, while the other is nearer the aqueous interface. The importance of side chain interactions with the membrane environment in producing stable, solubilized species of small peptides in SDS micelles is illustrated.

Gramicidin tryptophans mediate formamidinium-induced channel stabilization

Compared with alkali metal cations, formamidinium ions stabilize the gramicidin A channel molecule in monoolein bilayers (Seoh and Busath, 1993a). A similar effect is observed with N-acetyl gramicidin channel molecules in spite of the modified forces at the dimeric junction (Seoh and Busath, 1993b). Here we use electrophysiological measurements with tryptophan-to-phenylalanine-substituted gramicidin analogs to show that the formamidinium-induced channel molecule stabilization is eliminated when the four gramicidin tryptophans are replaced with phenylalanines in gramicidin M-. This suggests that the stabilization is mediated by the tryptophan side chains. Tryptophan residues 9, 13, and 15 must cooperate to produce the effect because replacement of any one of the three with phenylalanine significantly reduces stabilization; replacement of Trp-11 with phenylalanine causes negligible decrease in stabilization. In addition, formamidinium-related current-voltage supralinearity and open-channel noise are absent with gramicidin M-. When the lipid bilayer was formed with monoolein ether rather than monoolein ester, the channel lifetimes were reduced markedly and, at low voltage and relative to those in KCl solution, were decreased by a factor of 2, whereas the open-channel noise was unaffected and the current-voltage relation was only modestly affected. These results suggest that formamidinium modifies the state of the tryptophan side chains, which, in turn, affects channel lifetime, current-voltage supralinearity, and open-channel noise through interactions with water or lipid headgroup atoms including the lipid ester carbonyl.

Motionally restricted tryptophan environments at the peptide-lipid interface of gramicidin channels

The tryptophans in the gramicidin channel play a crucial role in the organization and function of the channel. The localization and dynamics of these tryptophans have been studied using fluorescence spectroscopy, especially utilizing environment-induced effects on the rates of solvent relaxation around these residues in membranes. When incorporated into model membranes of dioleoyl-sn-glycero-3-phosphocholine (DOPC), the tryptophans in the gramicidin channel exhibit a red edge excitation shift (REES) of 6 nm. In addition, fluorescence polarization shows both excitation and emission wavelength dependence. Fluorescence lifetime analysis shows a biexponential decay, corresponding to a short- and a long-lifetime component. The mean lifetime was found to be dependent on both excitation and emission wavelengths. Analysis of time-resolved emission spectra (TRES) shows a heterogeneous environment for the tryptophans consistent with the lifetime information. Taken together, these observations point out the motional restriction experienced by the tryptophans in the gramicidin channel. This is consistent with other studies in which such restrictions are thought to be imposed due to hydrogen bonding between the indole rings of the tryptophans and the neighboring lipid carbonyls. The significance of such organization in terms of functioning of the channel is brought out by the fact that substitution, photodamage, or chemical modification of these tryptophans is known to give rise to channels with conformation and reduced conductivity.

Solvent history dependence of gramicidin-lipid interactions: a Raman and infrared spectroscopic study

We have investigated the interactions between gramicidin and a model membrane composed of one phospholipid, dimyristoylphosphatidylcholine, as a function of the cosolubilization solvent and incubation time used in the sample preparation. Three organic solvents have been used; trifluoroethanol, a mixture of methanol/chloroform (1:1 v/v), and ethanol. Using Fourier transform infrared spectroscopy, we have demonstrated that the conformation adopted by gramicidin in the membrane is dependent upon the cosolubilization solvent used, and, only with trifluoroethanol, it is possible to incorporate gramicidin entirely as a beta 6.3-helix. Moreover, Raman spectroscopy results indicate that the orientation of the tryptophan side chains in gramicidin and their interaction with the hydrocarbon chains and the carbonyl groups of the lipids are also dependent on the cosolubilization solvent. On the other hand, the effect of the incorporation of gramicidin on the thermotropism of the lipid bilayer was found to be dependent upon the conformation of gramicidin in the lipid bilayers.