High-resolution structures and orientations of antimicrobial peptides piscidin 1 and piscidin 3 in fluid bilayers reveal tilting, kinking, and bilayer immersion.

While antimicrobial peptides (AMPs) have been widely investigated as potential therapeutics, high-resolution structures obtained under biologically relevant conditions are lacking. Here, the high-resolution structures of the homologous 22-residue long AMPs piscidin 1 (p1) and piscidin 3 (p3) are determined in fluid-phase 3:1 phosphatidylcholine/phosphatidylglycerol (PC/PG) and 1:1 phosphatidylethanolamine/phosphatidylglycerol (PE/PG) bilayers to identify molecular features important for membrane destabilization in bacterial cell membrane mimics. Structural refinement of (1)H-(15)N dipolar couplings and (15)N chemical shifts measured by oriented sample solid-state NMR and all-atom molecular dynamics (MD) simulations provide structural and orientational information of high precision and accuracy about these interfacially bound α-helical peptides. The tilt of the helical axis, τ, is between 83° and 93° with respect to the bilayer normal for all systems and analysis methods. The average azimuthal rotation, ρ, is 235°, which results in burial of hydrophobic residues in the bilayer. The refined NMR and MD structures reveal a slight kink at G13 that delineates two helical segments characterized by a small difference in their τ angles (<10°) and significant difference in their ρ angles (~25°). Remarkably, the kink, at the end of a G(X)4G motif highly conserved among members of the piscidin family, allows p1 and p3 to adopt ρ angles that maximize their hydrophobic moments. Two structural features differentiate the more potent p1 from p3: p1 has a larger ρ angle and less N-terminal fraying. The peptides have comparable depths of insertion in PC/PG, but p3 is 1.2 Å more deeply inserted than p1 in PE/PG. In contrast to the ideal α-helical structures typically assumed in mechanistic models of AMPs, p1 and p3 adopt disrupted α-helical backbones that correct for differences in the amphipathicity of their N- and C-ends, and their centers of mass lie ~1.2-3.6 Å below the plane defined by the C2 atoms of the lipid acyl chains.

Single tryptophan and tyrosine comparisons in the N-terminal and C-terminal interface regions of transmembrane GWALP peptides.

Hydrophobic membrane-spanning helices often are flanked by interfacial aromatic or charged residues. In this paper, we compare the consequences of single Trp → Tyr substitutions at each interface for the properties of a defined transmembrane helix in the absence of charged residues. The choice of molecular framework is critical for these single-residue experiments because the presence of "too many" aromatic residues (more than one at either membrane-water interface) introduces excess dynamic averaging of solid state NMR observables. To this end, we compare the outcomes when changing W(5) or W(19), or both of them, to tyrosine in the well-characterized transmembrane peptide acetyl-GGALW(5)(LA)6LW(19)LAGA-amide ("GWALP23"). By means of solid-state (2)H and (15)N NMR experiments, we find that Y(19)GW(5)ALP23 displays similar magnitudes of peptide helix tilt as Y(5)GW(19)ALP23 and responds similarly to changes in bilayer thickness, from DLPC to DMPC to DOPC. The presence of Y(19) changes the azimuthal rotation angle ρ (about the helix axis) to a similar extent as Y(5), but in the opposite direction. When tyrosines are substituted for both tryptophans to yield GY(5,19)ALP23, the helix tilt angle is again of comparable magnitude, and furthermore, the preferred azimuthal rotation angle ρ is relatively unchanged from that of GW(5,19)ALP23. The extent of dynamic averaging increases marginally when Tyr replaces Trp. Yet, importantly, all members of the peptide family having single Tyr or Trp residues near each interface exhibit only moderate and not highly extensive dynamic averaging. The results provide important benchmarks for evaluating conformational and dynamic control of membrane protein function.

Properties of membrane-incorporated WALP peptides that are anchored on only one end.

Peptides of the "WALP" family, acetyl-GWW(LA)(n)LWWA-[ethanol]amide, have proven to be opportune models for investigating lipid-peptide interactions. Because the average orientations and motional behavior of the N- and C-terminal Trp (W) residues differ, it is of interest to investigate how the positions of the tryptophans influence the properties of the membrane-incorporated peptides. To address this question, we synthesized acetyl-GGWW(LA)(n)-ethanolamide and acetyl-(AL)(n)WWG-ethanolamide, in which n = 4 or 8, which we designate as "N-anchored" and "C-anchored" peptides, respectively. Selected (2)H or (15)N labels were incorporated for solid-state nuclear magnetic resonance (NMR) spectroscopy. These peptides can be considered "half"-anchored WALP peptides, having only one pair of interfacial Trp residues near either the amino or the carboxyl terminus. The hydrophobic lengths of the (n = 8) peptides are similar to that of WALP23. These longer half-anchored WALP peptides incorporate into lipid bilayers as α-helices, as reflected in their circular dichroism spectra. Solid-state NMR experiments indicate that the longer peptide helices assume defined transmembrane orientations with small non-zero average tilt angles and moderate to high dynamic averaging in bilayer membranes of 1,2-dioleoylphosphatidylcholine, 1,2-dimyristoylphosphatidylcholine, and 1,2-dilauroylphosphatidylcholine. The intrinsically small apparent tilt angles suggest that interactions of aromatic residues with lipid headgroups may play an important role in determining the magnitude of the peptide tilt in the bilayer membrane. The shorter (n = 4) peptides, in stark contrast to the longer peptides, display NMR spectra that are characteristic of greatly reduced motional averaging, probably because of peptide aggregation in the bilayer environment, and CD spectra that are characteristic of ß-structure.

Proline kink angle distributions for GWALP23 in lipid bilayers of different thicknesses.

By using selected (2)H and (15)N labels, we have examined the influence of a central proline residue on the properties of a defined peptide that spans lipid bilayer membranes by solid-state nuclear magnetic resonance (NMR) spectroscopy. For this purpose, GWALP23 (acetyl-GGALW(5)LALALALALALALW(19)LAGA-ethanolamide) is a suitable model peptide that employs, for the purpose of interfacial anchoring, only one tryptophan residue on either end of a central α-helical core sequence. Because of its systematic behavior in lipid bilayer membranes of differing thicknesses [Vostrikov, V. V., et al. (2010) J. Biol. Chem. 285, 31723-31730], we utilize GWALP23 as a well-characterized framework for introducing guest residues within a transmembrane sequence; for example, a central proline yields acetyl-GGALW(5)LALALAP(12)ALALALW(19)LAGA-ethanolamide. We synthesized GWALP23-P12 with specifically placed (2)H and (15)N labels for solid-state NMR spectroscopy and examined the peptide orientation and segmental tilt in oriented DMPC lipid bilayer membranes using combined (2)H GALA and (15)N-(1)H high-resolution separated local field methods. In DMPC bilayer membranes, the peptide segments N-terminal and C-terminal to the proline are both tilted substantially with respect to the bilayer normal, by ~34 ± 5° and 29 ± 5°, respectively. While the tilt increases for both segments when proline is present, the range and extent of the individual segment motions are comparable to or smaller than those of the entire GWALP23 peptide in bilayer membranes. In DMPC, the proline induces a kink of ~30 ± 5°, with an apparent helix unwinding or "swivel" angle of ~70°. In DLPC and DOPC, on the basis of (2)H NMR data only, the kink angle and swivel angle probability distributions overlap those of DMPC, yet the most probable kink angle appears to be somewhat smaller than in DMPC. As has been described for GWALP23 itself, the C-terminal helix ends before Ala(21) in the phospholipids DMPC and DLPC yet remains intact through Ala(21) in DOPC. The dynamics of bilayer-incorporated, membrane-spanning GWALP23 and GWALP23-P12 are less extensive than those observed for WALP family peptides that have more than two interfacial Trp residues.

Tyrosine replacing tryptophan as an anchor in GWALP peptides.

Synthetic model peptides have proven useful for examining fundamental peptide-lipid interactions. A frequently employed peptide design consists of a hydrophobic core of Leu-Ala residues with polar or aromatic amino acids flanking each side at the interfacial positions, which serve to "anchor" a specific transmembrane orientation. For example, WALP family peptides (acetyl-GWW(LA)(n)LWWA-[ethanol]amide), anchored by four Trp residues, have received particular attention in both experimental and theoretical studies. A recent modification proved successful in reducing the number of Trp anchors to only one near each end of the peptide. The resulting GWALP23 (acetyl-GGALW(5)(LA)(6)LW(19)LAGA-[ethanol]amide) displays reduced dynamics and greater sensitivity to lipid-peptide hydrophobic mismatch than traditional WALP peptides. We have further modified GWALP23 to incorporate a single tyrosine, replacing W(5) with Y(5). The resulting peptide, Y(5)GWALP23 (acetyl-GGALY(5)(LA)(6)LW(19)LAGA-amide), has a single Trp residue that is sensitive to fluorescence experiments. By incorporating specific (2)H and (15)N labels in the core sequence of Y(5)GWALP23, we were able to use solid-state NMR spectroscopy to examine the peptide orientation in hydrated lipid bilayer membranes. The peptide orients well in membranes and gives well-defined (2)H quadrupolar splittings and (15)N/(1)H dipolar couplings throughout the core helical sequence between the aromatic residues. The substitution of Y(5) for W(5) has remarkably little influence on the tilt or dynamics of GWALP23 in bilayer membranes of the phospholipids DOPC, DMPC, or DLPC. A second analogue of the peptide with one Trp and two Tyr anchors, Y(4,5)GWALP23, is generally less responsive to the bilayer thickness and exhibits lower apparent tilt angles with evidence of more extensive dynamics. In general, the peptide behavior with multiple Tyr anchors appears to be quite similar to the situation when multiple Trp anchors are present, as in the original WALP series of model peptides.

Amphipathic antimicrobial piscidin in magnetically aligned lipid bilayers.

The amphipathic antimicrobial peptide piscidin 1 was studied in magnetically aligned phospholipid bilayers by oriented-sample solid-state NMR spectroscopy. (31)P NMR and double-resonance (1)H/(15)N NMR experiments performed between 25 °C and 61 °C enabled the lipid headgroups as well as the peptide amide sites to be monitored over a range of temperatures. The α-helical peptide dramatically affects the phase behavior and structure of anionic bilayers but not those of zwitterionic bilayers. Piscidin 1 stabilizes anionic bilayers, which remain well aligned up to 61 °C when piscidin 1 is on the membrane surface. Two-dimensional separated-local-field experiments show that the tilt angle of the peptide is 80 ± 5°, in agreement with previous results on mechanically aligned bilayers. The peptide undergoes fast rotational diffusion about the bilayer normal under these conditions, and these studies demonstrate that magnetically aligned bilayers are well suited for structural studies of amphipathic peptides.

On the combined analysis of ²H and ¹5N/¹H solid-state NMR data for determination of transmembrane peptide orientation and dynamics.

The dynamics of membrane-spanning peptides have a strong affect on the solid-state NMR observables. We present a combined analysis of ²H-alanine quadrupolar splittings together with ¹5N/(1)H dipolar couplings and ¹5N chemical shifts, using two models to treat the dynamics, for the systematic evaluation of transmembrane peptides based on the GWALP23 sequence (acetyl-GGALW(LA)6LWLAGA-amide). The results indicate that derivatives of GWALP23 incorporating diverse guest residues adopt a range of apparent tilt angles that span 5°-35° in lipid bilayer membranes. By comparing individual and combined analyses of specifically ²H- or ¹5N-labeled peptides incorporated in magnetically or mechanically aligned lipid bilayers, we examine the influence of data-set size/identity, and of explicitly modeled dynamics, on the deduced average orientations of the peptides. We conclude that peptides with small apparent tilt values (<∼10°) can be fitted by extensive families of solutions, which can be narrowed by incorporating additional ¹5N as well as ²H restraints. Conversely, peptides exhibiting larger tilt angles display more narrow distributions of tilt and rotation that can be fitted using smaller sets of experimental constraints or even with ²H or ¹5N data alone. Importantly, for peptides that tilt significantly more than 10° from the bilayer-normal, the contribution from rigid body dynamics can be approximated by a principal order parameter.

1H-13C separated local field spectroscopy of uniformly 13C labeled peptides and proteins.

By incorporating homonuclear decoupling on both the (1)H and (13)C channels it is feasible to obtain high-resolution two-dimensional separated local field spectra of peptides and proteins that are 100% labeled with (13)C. Dual-PISEMO (Polarization Inversion Spin Exchange Modulated Observation) can be performed as a conventional two-dimensional experiment, or with windowed detection as a one-dimensional experiment that offers flexibility as a building block for shiftless and other multidimensional triple-resonance experiments with the inclusion of (15)N irradiation. The triple-resonance MAGC probe used to perform these experiments at 500 MHz is described.

Probes for high field solid-state NMR of lossy biological samples.

In solid-state NMR hydrated samples of biopolymers are susceptible to radio frequency heating and have a significant impact on probe tuning frequency and performance parameters such as sensitivity. These considerations are increasingly important as magnetic field strengths increase with improved magnet technology. Recent developments in the design, construction, and performance of probes for solid-state NMR experiments on stationary lossy biological samples at high magnetic fields are reviewed.

A Modified Alderman-Grant Coil makes possible an efficient cross-coil probe for high field solid-state NMR of lossy biological samples.

The design, construction, and performance of a cross-coil double-resonance probe for solid-state NMR experiments on lossy biological samples at high magnetic fields are described. The outer coil is a Modified Alderman-Grant Coil (MAGC) tuned to the (1)H frequency. The inner coil consists of a multi-turn solenoid coil that produces a B(1) field orthogonal to that of the outer coil. This results in a compact nested cross-coil pair with the inner solenoid coil tuned to the low frequency detection channel. This design has several advantages over multiple-tuned solenoid coil probes, since RF heating from the (1)H channel is substantially reduced, it can be tuned for samples with a wide range of dielectric constants, and the simplified circuit design and high inductance inner coil provides excellent sensitivity. The utility of this probe is demonstrated on two electrically lossy samples of membrane proteins in phospholipid bilayers (bicelles) that are particularly difficult for conventional NMR probes. The 72-residue polypeptide embedding the transmembrane helices 3 and 4 of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) (residues 194-241) requires a high salt concentration in order to be successfully reconstituted in phospholipid bicelles. A second application is to paramagnetic relaxation enhancement applied to the membrane-bound form of Pf1 coat protein in phospholipid bicelles where the resistance to sample heating enables high duty cycle solid-state NMR experiments to be performed.

A strip-shield improves the efficiency of a solenoid coil in probes for high-field solid-state NMR of lossy biological samples.

A strip-shield inserted between a high inductance double-tuned solenoid coil and the glass tube containing the sample improves the efficiency of probes used for high-field solid-state NMR experiments on lossy aqueous samples of proteins and other biopolymers. A strip-shield is a coil liner consisting of thin copper strips layered on a PTFE (polytetrafluoroethylene) insulator. With lossy samples, the shift in tuning frequency is smaller, the reduction in Q, and RF-induced heating are all significantly reduced when the strip-shield is present. The performance of 800MHz (1)H/(15)N and (1)H/(13)C double-resonance probes is demonstrated on aqueous samples of membrane proteins in phospholipid bilayers.

Comparison of "Polarization inversion with spin exchange at magic angle" and "geometric analysis of labeled alanines" methods for transmembrane helix alignment.

Using the model alpha-helical peptide acetyl-GGALW5LALALALALALALW19LAGA-ethanolamide ("GWALP23"), we have compared the polarization inversion with spin exchange at magic angle method and geometric analysis of labeled alanines method for estimating the transmembrane helix orientation. For GWALP23 in bilayers of a short lipid, dilauroylphosphatidylcholine, we find general agreement between the two methods, with a static helix tilt of about 11degrees-13degrees with respect to the bilayer normal.

An efficient (1)H/(31)P double-resonance solid-state NMR probe that utilizes a scroll coil.

The construction and performance of a scroll coil double-resonance probe for solid-state NMR on stationary samples is described. The advantages of the scroll coil at the high resonance frequencies of (1)H and (31)P include: high efficiency, minimal perturbations of tuning by a wide range of samples, minimal RF sample heating of high dielectric samples of biopolymers in aqueous solution, and excellent RF homogeneity. The incorporation of a cable tie cinch for mechanical stability of the scroll coil is described. Experimental results obtained on a Hunter Killer Peptide 1 (HKP1) interacting with phospholipid bilayers of varying lipid composition demonstrate the capabilities of this probe on lossy aqueous samples.

Triple resonance experiments for aligned sample solid-state NMR of (13)C and (15)N labeled proteins.

Initial steps in the development of a suite of triple-resonance (1)H/(13)C/(15)N solid-state NMR experiments applicable to aligned samples of (13)C and (15)N labeled proteins are described. The experiments take advantage of the opportunities for (13)C detection without the need for homonuclear (13)C/(13)C decoupling presented by samples with two different patterns of isotopic labeling. In one type of sample, the proteins are approximately 20% randomly labeled with (13)C in all backbone and side chain carbon sites and approximately 100% uniformly (15)N labeled in all nitrogen sites; in the second type of sample, the peptides and proteins are (13)C labeled at only the alpha-carbon and (15)N labeled at the amide nitrogen of a few residues. The requirement for homonuclear (13)C/(13)C decoupling while detecting (13)C signals is avoided in the first case because of the low probability of any two (13)C nuclei being bonded to each other; in the second case, the labeled (13)C(alpha) sites are separated by at least three bonds in the polypeptide chain. The experiments enable the measurement of the (13)C chemical shift and (1)H-(13)C and (15)N-(13)C heteronuclear dipolar coupling frequencies associated with the (13)C(alpha) and (13)C' backbone sites, which provide orientation constraints complementary to those derived from the (15)N labeled amide backbone sites. (13)C/(13)C spin-exchange experiments identify proximate carbon sites. The ability to measure (13)C-(15)N dipolar coupling frequencies and correlate (13)C and (15)N resonances provides a mechanism for making backbone resonance assignments. Three-dimensional combinations of these experiments ensure that the resolution, assignment, and measurement of orientationally dependent frequencies can be extended to larger proteins. Moreover, measurements of the (13)C chemical shift and (1)H-(13)C heteronuclear dipolar coupling frequencies for nearly all side chain sites enable the complete three-dimensional structures of proteins to be determined with this approach.

Solid-state NMR investigation of sodium nucleotide complexes.

Solid-state NMR has been used to analyze the chemical environments of sodium sites in powdered crystalline samples of sodium nucleotide complexes. Three of the studied complexes have been previously characterized structurally by crystallography (disodium deoxycytidine-5'-monophosphate heptahydrate, disodium deoxyuridine-5'-monophosphate pentahydrate and disodium adensoine-5'-triphosphate trihydrate). For these salts, the nuclear quadrupole coupling parameters measured by (23)Na multiple-quantum magic-angle-spinning NMR could be readily correlated with sodium ion coordination environments. Furthermore, two complexes that had not been previously characterized structurally, disodium uridine-3'-monophosphate and a disodium uridine-3'-monophosphate/disodium uridine-2'-monophosphate mix, were identified by solid-state NMR. A spectroscopic assignment of the four sites of an additional salt, disodium adensoine-5'-triphosphate trihydrate, is also presented and discussed within the context of creating a general approach for the spectroscopic assignment of multiple sites in sodium nucleotide complexes.

SPINAL modulated decoupling in high field double- and triple-resonance solid-state NMR experiments on stationary samples.

Continuous wave irradiation has limited bandwidth for heteronuclear 1H decoupling at high fields and for 13C decoupling in 1H/13C/15N triple-resonance experiments. SPINAL-16 modulation is shown to improve the efficiency of 1H and 13C heteronuclear decoupling on single crystals of peptides and on magnetically aligned samples of membrane proteins in bicelles, which is of particular importance because aqueous samples of biomolecules are lossy at high fields, which limits the strengths of the RF fields that can be applied.

Separate-local-field NMR spectroscopy on half-integer quadrupolar nuclei.

New approaches to the characterization of resonances in the solid-state NMR spectroscopy of half-integer quadrupolar nuclei are explored, on the basis of the acquisition of heteronuclear separate-local-field spectra on rotating solids. In their two-dimensional version, these experiments correlate for each chemical site a second-order quadrupolar MAS powder pattern with the dipolar MAS sideband pattern to nearby heteronuclei. As 3D NMR sequences, such 2D anisotropic correlation spectra become separated for inequivalent chemical sites along a third, isotropic dimension. Extending in such manner separate-local-field NMR approaches to quadrupoles facilitates the assignment of inequivalent resonances to specific structural environments, and provides new tools for the investigation of dynamics in solids. Details about these 2D and 3D NMR experiments are given, and their application is illustrated with 1H-23Na recoupling experiments on mononucleotides possessing multiple bound cations.

59Co solid-state NMR as a new probe for elucidating metal binding in polynucleotides.

Although magnesium fulfills several essential biochemical roles, direct studies on this ion are complicated by its unfavorable spectroscopic characteristics. This contribution explores the possibility of monitoring magnesium-nucleic acid binding via a combination of [Co(NH3)6]3+ as surrogate for [Mg(H2O)6]2+, and of high-resolution solid-state 59Co NMR as a spectroscopic probe. Such strategy quenches fast cationic exchanges between bound and free states, while exploiting the superior NMR properties of the 59Co spin. Experiments on relatively small amounts of tRNA can then discern resonances corresponding to different metal binding environments. These characterizations were assisted by studies on model compounds and by multinuclear 31P-59Co recoupling experiments.

Structural analysis of metal ion ligation to nucleotides and nucleic acids using pulsed EPR spectroscopy.

Metal ions play key structural and functional roles in many nucleic acid systems, particularly as required cofactors for many catalytic RNA molecules (ribozymes). We apply the pulsed EPR technologies of electron spin-echo envelope modulation and electron spin-echo-electron nuclear double resonance to the structural analysis of the paramagnetic metal ion Mn(II) bound to nucleotides and nucleic acids. We demonstrate that pulsed EPR, supplemented with specific isotope labeling, can characterize ligation to nucleotide base nitrogens, outer-sphere interactions with phosphate groups, distances to sites of specific (2)H atom labels, and the hydration level of the metal ion. These techniques allow a comprehensive structural analysis of the mononucleotide model system MnGMP. Spectra of phenylalanine-specific transfer RNA from budding yeast and of the hammerhead ribozyme demonstrate the applicability of the methods to larger, structured RNA systems. This suite of experiments opens the way to detailed structural characterization of specifically bound metal ions in a variety of ribozymes and other nucleic acids of biological interest.

Probing the Molecular Geometry of Five-Coordinate Vanadyl Complexes with Pulsed ENDOR.

The pulsed electron paramagnetic resonance (EPR) technique of (51)V electron spin echo-electron nuclear double resonance (ESE-ENDOR) has been used to measure the nuclear quadrupole coupling constants of a series of five-coordinate vanadyl complexes containing Schiff base ligands with geometries ranging from distorted square pyramidal to distorted trigonal bipyramidal. Vanadium nuclear quadrupole coupling constants are sensitive to the coordination geometry of the vanadyl ion, and thus sensitive to the structural distortions within this series of complexes. (51)V ESE-ENDOR has been shown to be a probe of the coordination geometry of vanadyl complexes. Such a spectroscopic probe should prove useful in the investigation of vanadyl of unknown coordination geometry, such as may be found in the interaction of the vanadyl ion with biomolecules.