Hydrophobic mismatch in gramicidin A'/lecithin systems

Getting membrane proteins on and off the shuttle bus between the endoplasmic reticulum and the Golgi complex

Secretory proteins exit the endoplasmic reticulum (ER) in coat protein complex II (COPII)-coated vesicles and then progress through the Golgi complex before delivery to their final destination. Soluble cargo can be recruited to ER exit sites by signal-mediated processes (cargo capture) or by bulk flow. For membrane proteins, a third mechanism, based on the interaction of their transmembrane domain (TMD) with lipid microdomains, must also be considered. In this Commentary, I review evidence in favor of the idea that partitioning of TMDs into bilayer domains that are endowed with distinct physico-chemical properties plays a pivotal role in the transport of membrane proteins within the early secretory pathway. The combination of such self-organizational phenomena with canonical intermolecular interactions is most likely to control the release of membrane proteins from the ER into the secretory pathway.

Self-assembled, cation-selective ion channels from an oligo(ethylene glycol) derivative of benzothiazole aniline

This paper describes the spontaneous formation of well-defined pores in planar lipid bilayers from the self-assembly of a small synthetic molecule that contains a benzothiazole aniline (BTA) group attached to a tetra-ethylene glycol (EG4) moiety. Macroscopic and single-channel current recordings suggest that these pores are formed by the assembly of four BTA-EG4 monomers with an open pore diameter that appears similar to the one of gramicidin pores (~0.4 nm). The single-channel conductance of these pores is modulated by the pH of the electrolyte and has a minimum at pH~3. Self-assembled pores from BTA-EG4 are selective for monovalent cations and have long open channel lifetimes on the order of seconds. BTA-EG4 monomers in these pores appear to be arranged symmetrically across both leaflets of the bilayer, and spectroscopy studies suggest that the fluorescent BTA group is localized inside the lipid bilayers. In terms of biological activity, BTA-EG4 molecules inhibited growth of gram-positive Bacillus subtilis bacteria (IC50~50 μM) and human neuroblastoma SH-SY5Y cells (IC50~60 μM), while they were not toxic to gram-negative Escherichia coli bacteria at a concentration up to 500 μM. Based on these properties, this drug-like, synthetic, pore-forming molecule with a molecular weight below 500 g mol(-1) might be appealing as a starting material for development of antibiotics or membrane-permeating moieties for drug delivery. From a biophysical point of view, long-lived, well-defined ion-selective pores from BTA-EG4 molecules offer an example of a self-assembled synthetic supramolecule with biological function.

Molecular resolution imaging of an antibiotic peptide in a lipid matrix

In this work, we show molecular resolution scanning tunneling microscopy (STM) images of gramicidin, a model antibacterial peptide, inserted into a phospholipid matrix. The resolution of the images is superior to that obtained in previous attempts to image gramicidin in a lipid environment using atomic force microscopy (AFM). This breakthrough has allowed visualization of individual peptide molecules surrounded by lipid molecules. We have observed several important features: the peptide molecules do not aggregate, the peptide molecules adopt a single conformation corresponding to a specific ion channel form, and the lipid molecules adjacent to the peptide molecules are systematically longer than those in the lipid matrix. These results constitute a new approach to obtain structural characteristics of antibiotic peptides in lipid assemblies that is necessary for the understanding of their biological activity.

A physical chemist's expedition to explore the world of membrane proteins

Despite growing up amid humble surroundings, I ended up receiving an excellent education at the University of California at Berkeley and postdoctoral training at Harvard. My academic career at Caltech was shaped by serendipity, inspirational colleagues, and a stimulating research environment, as well as smart, motivated students and postdocs who were willing to join my search for molecular understanding of complex biological systems. From chemical physics I allowed my research to evolve, beginning with the application of NMR to investigate the base stacking of nucleic acid bases in solution, the dynamic structure of membranes, and culminating with the use of various forms of spectroscopy to elucidate the structure and function of membrane proteins and the early kinetic events in protein folding. The journey was a biased random walk driven by my own intellectual curiosity and instincts and by the pace at which I learned biochemistry from my students and postdocs, my colleagues, and the literature and through osmosis during seminars and scientific meetings.

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.

Modulation of gramicidin channel conformation and organization by hydrophobic mismatch in saturated phosphatidylcholine bilayers

The matching of hydrophobic lengths of integral membrane proteins and the surrounding lipid bilayer is an important factor that influences both structure and function of integral membrane proteins. The ion channel gramicidin is known to be uniquely sensitive to membrane properties such as bilayer thickness and membrane mechanical properties. The functionally important carboxy terminal tryptophan residues of gramicidin display conformation-dependent fluorescence which can be used to monitor gramicidin conformations in membranes [S.S. Rawat, D.A. Kelkar, A. Chattopadhyay, Monitoring gramicidin conformations in membranes: a fluorescence approach, Biophys. J. 87 (2004) 831-843]. We have examined the effect of hydrophobic mismatch on the conformation and organization of gramicidin in saturated phosphatidylcholine bilayers of varying thickness utilizing the intrinsic conformation-dependent tryptophan fluorescence. Our results utilizing steady state and time-resolved fluorescence spectroscopic approaches, in combination with circular dichroism spectroscopy, show that gramicidin remains predominantly in the channel conformation and gramicidin tryptophans are at the membrane interfacial region over a range of mismatch conditions. Interestingly, gramicidin conformation shifts toward non-channel conformations in extremely thick gel phase membranes although it is not excluded from the membrane. In addition, experiments utilizing self quenching of tryptophan fluorescence indicate peptide aggregation in thicker gel phase membranes.

Application of the out-of-phase absorption mode to separating overlapping EPR signals with different T1 values

The use of 90 degrees-out-of-phase first-harmonic absorption (V1'-) EPR to resolve the spectra from nitroxide spin labels with differing T1-relaxation times is described. Non-linear V1'-EPR spectra recorded under moderate saturation have sharper lines compared with the in-phase V1-EPR spectra, and amplitudes that preferentially enhance components with longer T1-relaxation. Discrimination between V1'-spectral components can be increased further by means of selective paramagnetic relaxation enhancement agents. Examples are given of biophysical applications to double labelling in single-component membranes and phase separation in two-component membranes, to lipid-peptide complexes, and to binding of spin-labelled reagents. It is concluded that optimal resolution in V1'-EPR spectroscopy is obtained at relatively low Zeeman modulation frequencies (20-30 kHz) and moderate saturation (H1 approximately 0.2-0.3 G).

Gramicidin A channels switch between stretch activation and stretch inactivation depending on bilayer thickness

The patch clamp-liposome technique was used to examine the stretch sensitivity of a model membrane ion channel, gramicidin A, in membrane patches of different bilayer thickness. We found that small changes in phospholipid acyl chain length (i.e., PC-20 to PC-18) can switch gramicidin A from a stretch-activated to a stretch-inactivated channel. The demonstration that subnanometer changes in bilayer thickness can reverse the response polarity of a model channel has implications for other signaling proteins that may experience local changes in bilayer thickness as a consequence of dynamic targeting to lipid microdomains, electrocompression, or chemical modification of the bilayer.

Peptide influences on lipids

The extent to which the length of the membrane-spanning part of intrinsic membrane proteins matches the hydrophobic thickness of the lipid bilayer may be an important factor in determining membrane structure and function. To gain insight into the consequences of hydrophobic mismatch on a molecular level, we have carried out systematic studies on well-defined peptide-lipid complexes. As model peptides we have chosen gramicidin A and a series of artificial hydrophobic alpha-helical transmembrane peptides that resemble the gramicidin channel. These peptides consist of a hydrophobic stretch of alternating leucine and alanine residues with variable length, flanked by tryptophan residues. Using wide-line NMR techniques, we have investigated the interaction of these peptides with the bilayer-forming diacyl phosphatidylcholines and with phospholipids which by themselves have a tendency to form non-bilayer structures. We have shown that hydrophobic mismatch leads to systematic changes of the bilayer thickness and that it can even change the macroscopic organization of the lipids. The type of lipid organization induced by the peptides and the efficiency of the various processes depend on the properties of the lipids and on the precise extent of mismatch.

Electron-spin resonance study of aggregation of gramicidin in dipalmitoylphosphatidylcholine bilayers and hydrophobic mismatch

The effect of aggregation of gramicidin A' (GA) on the phase structure of dipalmitoylphosphatidylcholine (DPPC) multilamellar vesicles was studied by cw-ESR using a chain-labeled lipid (16PC) at temperatures between 30 degrees and 45 degreesC that span the main phase transition of DPPC. Boundary lipids were observed only in dispersions with GA/DPPC molar ratios >1:15, where GA aggregates. Detailed fits by nonlinear least squares (NLLS) methods are consistent with the boundary lipid being characterized by a large negative order parameter ( approximately -0.4), indicative of a dynamic bending of the end of the acyl chain, and a substantially reduced motion, about an order of magnitude slower than that of the bulk lipid. The NLLS analysis compares favorably with a recent two-dimensional Fourier transform ESR study on DPPC/GA vesicles, which accurately discerned the bulk lipid. The detailed ESR observables are discussed in terms of the ordering effect of GA at low concentration of GA, the dissociation of the GA channel and the dynamic bending of the end chain segment of boundary lipid at high concentration of GA, and of HII phase formation induced by GA. It is suggested that these phenomena can be interpreted in terms of the combined effects of partial dehydration of the lipid headgroup by the GA and of the hydrophobic mismatch between GA and DPPC molecules. Substantial hysteresis is observed for heating versus cooling cycles, but only for a GA/DPPC molar ratio >1:15. This is consistent with the aggregation of GA molecules at high concentrations.

Comparison between the dynamics of lipid/gramicidin A systems in the lamellar and hexagonal phases: a solid-state 13C NMR study

We have investigated the effect of gramicidin A on the dynamics of two model membranes: dimyristoylphosphatidylcholine (DMPC) in the lamellar phase at a lipid-to-peptide molar ratio of 10:1 and dioleoylphosphatidylcholine (DOPC) in the hexagonal HII phase at a lipid-to-peptide molar ratio of 5:1. Natural abundance 13C nuclear magnetic resonance (NMR) spectroscopy was used in combination with magic angle spinning to increase the spectral resolution, therefore allowing the different regions of the lipid bilayers to be investigated from the same spectra. 31P NMR was also used to detect and confirm the formation of the DOPC HII phase in the presence of gramicidin A. In order to examine the effect of gramicidin A on both the fast and slow motions of DMPC and DOPC, the 1H spin-lattice relaxation times in the laboratory frame (HT1) as well as the 1H spin-lattice relaxation times in the rotating frame (HT1rho) were calculated for each resolved protonated lipid resonance in the 13C spectra. For both DMPC and DOPC, we found that the presence of gramicidin A does not significantly affect the fast motions of the lipid acyl chains but increases slightly the fast motions of the polar head group. However, the HT1rho are significantly decreased, this effect being more pronounced for DOPC most likely due to a decrease in the rate of the lipid lateral diffusion.

Hydrophobic mismatch between proteins and lipids in membranes

This review addresses the possible consequences of a mismatch in length between the hydrophobic part of membrane-spanning proteins and the hydrophobic bilayer thickness for membrane structure and function. Overviews are given first of the results of studies in defined model systems. These studies address effects of mismatch on protein activity, stability, orientation, aggregational state, localization, and conformation. With respect to the lipids, effects of mismatch are discussed on lipid chain order, phase transition temperature, lipid phase behavior, and microdomain formation. From these studies, it is concluded that hydrophobic mismatch can strongly affect protein and lipid organization, but that the precise consequences depend on the individual properties of the proteins and lipids. Examples of these properties include the propensity of lipids to form non-lamellar structures, the amino acid composition of the hydrophobic transmembrane segments of the proteins, the nature of the membrane anchoring residues, and the number of transmembrane helices. Finally, the effects of mismatch in biological membranes are discussed and its possible consequences for functional membrane processes, such as protein sorting, protein insertion, and regulation of bilayer thickness.

Influence of membrane-spanning alpha-helical peptides on the phase behavior of the dioleoylphosphatidylcholine/water system

The effect of solubilized hydrophobic peptides on the phase behavior of dioleoylphosphatidylcholine (DOPC)/water system was studied by 2H- and 31P-NMR spectroscopy and by x-ray diffraction, and partial phase diagrams were constructed. The utilized peptides were HCO-AWW(LA)5WWA-NHCH2CH2OH (WALP16), which is an artificial peptide designed to resemble a transmembrane part of a membrane protein; and VEYAGIALFFVAAVLTLWSMLQYLSAAR (Pgs peptide E), a peptide that is identical to one of the putative transmembrane segments of the membrane-associated protein phosphatidylglycerophosphate synthase (Pgs) in Escherichia coli. Circular dichroism spectroscopy suggests that both peptides are mostly alpha-helical in DOPC vesicles. The most striking features in the phase diagram of the WALP16/DOPC/water system are 1) a single lamellar liquid crystalline (L alpha) phase forms only at very low peptide concentrations. 2) At low water content and above a peptide/lipid molar ratio of approximately 1:75 a reversed hexagonal liquid crystalline (H[II]) phase coexists with an L alpha phase, while in excess water this phase forms at a peptide/lipid molar ratio of approximately 1:25. 3) At peptide/lipid ratios > or =1:6 a single H(II) phase is stable. Also, the Pgs peptide E strongly affects the phase behavior, and a single L alpha phase is only found at low peptide concentrations (peptide/lipid molar ratios <1:50), and water concentrations <45% (w/w). Higher peptide content results in coexistence of L alpha and isotropic phases. Generally, the fraction of the isotropic phase increases with increasing temperature and water concentration, and at 80% (w/w) water content only a single isotropic phase is stable at 55 degrees C. Thus, both peptides were found to be able to induce nonlamellar phases, although different in structure, in the DOPC/water system. The phase transitions, the extensions of the one-phase regions, and the phase structures observed for the two systems are discussed in terms of the molecular structure of the two peptides and the matching between the hydrophobic lengths of the peptides and the bilayer thickness of DOPC.

Membrane packing geometry of diphytanoylphosphatidylcholine is highly sensitive to hydration: phospholipid polymorphism induced by molecular rearrangement in the headgroup region

Diphytanoylphosphatidylcholine (DPhPC) has often been used in the study of protein-lipid interaction and membrane channel activity, because of the general belief that it has high bilayer stability, low ion leakage, and fatty acyl packing comparable to that of phospholipid bilayers in the liquid-crystalline state. In this solid-state 31P and 2H NMR study, we find that the membrane packing geometry and headgroup orientation of DPhPC are highly sensitive to the temperature studied and its water content. The phosphocholine headgroup of DPhPC starts to change its orientation at a water content as high as approximately 16 water molecules per lipid, as evidenced by hydration-dependent 2H NMR study at room temperature. In addition, a temperature-induced structural transition in the headgroup orientation is detected in the temperature range of approximately 20-60 degrees C for lipids with approximately 8-11 water molecules per DPhPC. Dehydration of the lipid by one more water molecule leads to a nonlamellar, presumably cubic, phase formation. The lipid packing becomes a hexagonal phase at approximately 6 water molecules per lipid. A phase diagram of DPhPC in the temperature range of -40 degrees C to 80 degrees C is thus constructed on the basis of NMR results. The newly observed hydration-dependent DPhPC lipid polymorphism emphasizes the importance of molecular packing in the headgroup region in modulating membrane structure and protein-induced pore formation of the DPhPC bilayer.

Structure, energetics, and dynamics of lipid-protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer

The microscopic details of lipid-protein interactions are examined using molecular dynamics simulations of the gramicidin A channel embedded in a fully hydrated dimyristoyl phosphatidylcholine (DMPC) bilayer. A novel construction protocol was used to assemble the initial configurations of the membrane protein complex for the simulations. Three hundred systems were constructed with different initial lipid placement and conformations. Seven systems were simulated with molecular dynamics. One system was simulated for a total of 600 psec, four were simulated for 300 psec, and two for 100 psec. Analysis of the resulting trajectories shows that the bulk solvent-membrane interface region is much broader than traditionally pictured in simplified continuum theories: its width is almost 15 angstroms. In addition, lipid-protein interactions are far more varied, both structurally and energetically, than is usually assumed: the total interaction energy between the gramicidin A and the individual lipids varies from 0 to -50 kcal/mol. The deuterium quadrupolar splittings of the lipid acyl chains calculated from the trajectories are in good agreement with experimental data. The lipid chains in direct contact with the GA are ordered but the effect is not uniform due to the irregular surface of the protein. Energy decompositions shows that the most energetically favorable interactions between lipid and protein involve nearly equal contributions from van der Waals and electrostatic interactions. The tryptophans, located near the bulk-membrane interface, appear to be particularly important in mediating both hydrogen bonding interactions with the lipid glycerol backbone and water and also in forming favorable van der Waals contacts with the hydrocarbon chains. In contrast, the interactions of the leucine residues with the lipids, also located near the interface, are dominated by van der Waals interactions with the hydrocarbon lipid chains.

Monte Carlo studies of a model for lipid-gramicidin A bilayers

This paper presents results of Monte Carlo simulations of a full bilayer of 200 lipid chains and one gramicidin A dimer. Simulations are described for systems with lipid chains of 14, 16, and 18 carbons, respectively. Using accepted potential functions to calculate interactions between all non-hydrogen atoms a Monte Carlo configuration sampling is generated from which order parameter profiles are calculated and specific configurations are displayed. Results are compared with experimental data for lipid-gramicidin bilayers.

Deuteron nuclear magnetic resonance study of the dynamic organization of phospholipid/cholesterol bilayer membranes: molecular properties and viscoelastic behavior

The influence of cholesterol on the dynamic organization of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayers was studied by deuteron nuclear magnetic resonance (2H NMR) using unoriented and macroscopically aligned samples. Analysis of the various temperature- and orientation-dependent experiments were performed using a comprehensive NMR model based on the stochastic Liouville equation. Computer simulations of the relaxation data obtained from phospholipids deuterated at the 6-, 13- and 14-position of the sn-2 chain and cholesterol labeled at the 3 alpha-position of the rigid steroid ring system allowed the unambiguous assignment of the various motional modes and types of molecular order present in the system. Above the phospholipid gel-to-liquid-crystalline phase transition, TM, 40 mol % cholesterol was found to significantly increase the orientational and conformational order of the phospholipid with substantially increased trans populations even at the terminal sn-2 acyl chain segments. Lowering the temperature continuously increases both inter- and intramolecular ordering, yet indicates less ordered chains than found for the pure phospholipid in its paracrystalline gel phase. Trans-gauche isomerization rates on all phospholipid alkyl chain segments are slowed down by incorporated cholesterol to values characteristic of gel-state lipid. However, intermolecular dynamics remain fast on the NMR time scale up to 30 K below TM, with rotational correlation times tau R parallel for DMPC ranging from 10 to 100 ns and an activation energy of ER = 35 kJ/mol. Below 273 K a continuous noncooperative condensation of both phospholipid and cholesterol is observed in the mixed membranes, and at about 253 K only a motionally restricted component is left, exhibiting slow fluctuations with correlation times of tau R perpendicular greater than 1 microsecond. In the high-temperature region (T greater than TM), order director fluctuations are found to constitute the dominant transverse relaxation process. Analysis of these collective lipid motions provides the viscoelastic parameters of the membranes. The results (T = 318 K) show that cholesterol significantly reduces the density of the cooperative motions by increasing the average elastic constant of the membrane from K = 1 x 10(-11) N for the pure phospholipid bilayers to K = 3.5 x 10(-11) N for the mixed system.