Effects of the incorporation of CHAPS into SDS micelles on neuropeptide-micelle binding: separation of the role of electrostatic interactions from hydrophobic interactions

Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials

Label-free methods to obtain hydrodynamic size from diffusion measurements are desirable in environments that contain multiple macromolecular species at a high total concentration: one example is the crowded cellular environment. In complex, multi-species macromolecular environments - in this article, we feature aqueous systems involving polymers, surfactants and proteins - the link between dynamics and size is harder to unpack due to macromolecular crowding and confinement. In this review, we demonstrate that the pulsed-field gradient NMR technique, with its spectral separation of different chemical components, is ideal for studying the dynamics of the entire system simultaneously and without labelling, in a wide range of systems. The simultaneous measurement of the dynamics of multiple components allows for internal consistency checks and enables quantitative statements about the link between macromolecular dynamics, size, complex formation and crowding in soft materials.

The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids

Anionic and zwitterionic micelles are often used as simple models for the lipids found in bacterial and mammalian cell membranes to investigate antimicrobial peptide-lipid interactions. In our laboratory we have employed a variety of 1D, 2D, and diffusion ordered (DOSY) NMR experiments to investigate the interactions of antimicrobial peptides containing unnatural amino acids with SDS and DPC micelles. Complete assignment of the proton spectra of these peptides is prohibited by the incorporation of a high percentage of unnatural amino acids which don't contain amide protons into the backbone. However preliminary assignment of the TOCSY spectra of compound 23 in the presence of both micelles indicated multiple conformers are present as a result of binding to these micelles. Chemical Shift Indexing agreed with previously collected CD spectra that indicated on binding to SDS micelles compound 23 adopts a mixture of α-helical structures and on binding to DPC micelles this peptide adopts a mixture of helical and β-turn/sheet like structures. DOSY NMR experiments also indicated that the total positive charge and the relative placement of that charge at the N-terminus or C-terminus are important in determining the mole fraction of the peptide that will bind to the different micelles. DOSY and (1) H-NMR experiments indicated that the length of Spacer #1 plays a major role in defining the binding conformation of these analogs with SDS micelles. Results obtained from molecular simulations studies of the binding of compounds 23 and 36 with SDS micelles were consistent with the observed NMR results.

Spectroscopic investigations of the binding mechanisms between antimicrobial peptides and membrane models of Pseudomonas aeruginosa and Klebsiella pneumoniae

CD spectroscopy was used to investigate the interactions of a series of synthetic AMPs with LPS isolated from Pseudomonas aeruginosa and Klebsiella pneumoniae, as well as with various phospholipids to better approximate the chemical composition of the membranes of these two strains of Gram-negative bacteria. This investigation was conducted in order to probe how the contributions of key physicochemical properties of an AMP vary in different regions of the membranes of these two bacteria. The conclusions from this study are as follows. (1) The binding interactions between the AMP and the membranes are defined by the complementarity of delocalization of positive charge density of the basic amino side chains (i.e., electrostatics), molecular flexibility of the peptide backbone, and overall hydrophobicity. (2) The binding interactions of these AMPs to LPS seem to be predominantly with the lipid A region of the LPS. (3) Incorporation of phospholipids into the LPS containing SUVs resulted in dramatic changes in the conformational equilibrium of the bound AMPs. (4) For the LPS-phospholipid models of Pseudomonas aeruginosa, delocalization of the side chain positive charge plays a major role in determining the number of conformers that contribute to the binding conformational equilibrium. This relationship was not observed for the models of the outer and inner membranes of Klebsiella pneumoniae.

Application of unnatural amino acids to the de novo design of selective antibiotic peptides

Because of their unique mechanism of cytotoxicity against bacteria and other microorganisms, antimicrobial peptides have received a great deal of attention as possible therapeutic agents. Incorporation of unnatural amino acids into the peptide sequences has the potential to improve the organism selectivity and potency of these peptides as well as increase their metabolic stability. This protocol outlines the logic used to selectively incorporate unnatural amino acid into a peptide sequence in an attempt to obtain peptides with increased therapeutic potential as antibiotic agents.

Lung surfactant protein A (SP-A) interactions with model lung surfactant lipids and an SP-B fragment

Surfactant protein A (SP-A) is the most abundant protein component of lung surfactant, a complex mixture of proteins and lipids. SP-A performs host defense activities and modulates the biophysical properties of surfactant in concerted action with surfactant protein B (SP-B). Current models of lung surfactant mechanism generally assume SP-A functions in its octadecameric form. However, one of the findings of this study is that when SP-A is bound to detergent and lipid micelles that mimic lung surfactant phospholipids, it exists predominantly as smaller oligomers, in sharp contrast to the much larger forms observed when alone in water. These investigations were carried out in sodium dodecyl sulfate (SDS), dodecylphosphocholine (DPC), lysomyristoylphosphatidylcholine (LMPC), lysomyristoylphosphatidylglycerol (LMPG), and mixed LMPC + LMPG micelles, using solution and diffusion nuclear magnetic resonance (NMR) spectroscopy. We have also probed SP-A’s interaction with Mini-B, a biologically active synthetic fragment of SP-B, in the presence of micelles. Despite variations in Mini-B’s own interactions with micelles of different compositions, SP-A is found to interact with Mini-B in all micelle systems and perhaps to undergo a further structural rearrangement upon interacting with Mini-B. The degree of SP-A–Mini-B interaction appears to be dependent on the type of lipid headgroup and is likely mediated through the micelles, rather than direct binding.

Structure of chemokine-derived antimicrobial Peptide interleukin-8alpha and interaction with detergent micelles and oriented lipid bilayers

Interleukin-8alpha (IL-8alpha) is an antimicrobial peptide derived from the chemokine IL-8. Solution NMR was used to determine the atomic-resolution structure of IL-8alpha in SDS micelles. Solid-state NMR and tryptophan fluorescence were used to probe the interaction of IL-8alpha with model membranes. The peptide interacted differently with anionic versus purely zwitterionic micelles or bilayers. Tryptophan fluorescence demonstrated a deeper position of Trp4 in SDS micelles and POPC/POPG bilayers compared to pure POPC bilayers, consistent with (2)H order parameters, which also indicated a deeper position of the peptide in POPC/POPG bilayers compared to POPC bilayers. Paramagnetic probe data showed that IL-8alpha was situated roughly parallel to the SDS micelle surface, with a slight tilt that positioned the N-terminus more deeply in the micelle compared to the C-terminus. (15)N solid-state NMR spectra indicated a similar, nearly parallel position for the peptide in POPC/POPG bilayers. (31)P and (2)H solid-state NMR demonstrated that the peptide did not induce the formation of any nonlamellar phases and did not significantly disrupt bilayer orientation in aligned model membranes composed of POPC or POPC and POPG.

Effect of micelle interface on the binding of anticoccidial PW2 peptide

PW2 is an anticoccidial peptide active against Eimeria acervulina and Eimeria tenella. We determined the structure of PW2 in dodecylphosphocholine micelles. The structure showed two distinct regions: an amphipathic N-terminal 3(10) helix and an aromatic region containing WWR interface-binding motif. The aromatic region acted as a scaffold of the protein in the interface and shared the same structure in both DPC and SDS micelles. N-terminal helix interacted with DPC but not with SDS interface. Chemical shift change was slow when SDS was added to PW2 in DPC and fast when DPC was added to PW2 in SDS, indicating that interaction with DPC micelles was kinetically more stable than with SDS micelles. Also, DPC interface was able to accommodate PW2, but it maintained the conformational arrangement in the aromatic region observed for SDS micelles. This behavior, which is different from that observed for other antimicrobial peptides with WWR motif, may be associated with the absence of PW2 antibacterial activity and its selectivity for Eimeria parasites.

De Novo Design of Selective Antibiotic Peptides by Incorporation of Unnatural Amino Acids

The evolution of drug-resistant bacteria is one of the most critical problems facing modern medicine and requires the development of new drugs that exhibit their antibacterial activity via novel mechanisms of action. One potential source of new drugs could be the naturally occurring peptides that exhibit antimicrobial activity via membrane disruption. To develop antimicrobial peptides exhibiting increased potency and selectivity against Gram positive, Gram negative, and Mycobacterium bacteria coupled with reduced hemolytic activity, peptides containing unnatural amino acids have been designed, synthesized, and evaluated. These compounds were designed on the basis of the electrostatic surface potential maps derived from the NMR determined SDS and DPC micelle-bound conformations of (Ala8,13,18)magainin-2 amide. Unnatural amino acids were incorporated into the polypeptide backbone to control the structural and physicochemical properties of the peptides to introduce organism selectivity and potency. The methods and results of this investigation are described below.

A pulsed field gradient NMR diffusion investigation of enkephalin peptide-sodium dodecyl sulfate micelle association

Pulsed field gradient NMR (PFG-NMR) diffusion experiments were used to investigate the binding of leucine and methionine enkephalin peptides to anionic sodium dodecyl sulfate (SDS) micelles. The study was undertaken to investigate the mechanism of interaction between enkephalin peptides and SDS micelles and to determine if NMR-derived association constants, K(eq), can predict the elution order in electrokinetic chromatography (EKC). In EKC, peptides are separated on the basis of their interactions with micelles. The Leu-enkephalin peptide-micelle association constant increased from 130 +/- 8 to 1459 +/- 57 and 1744 +/- 64 M(-1), respectively, when an Arg or Lys was added to the C-terminus. The association constant of Leu-enkephalinamide was approximately equal to that of Leu-enkephalin-Arg. Substitution of Phe4 with a Trp or Gly2 with an Ala in the Leu-enkephalin peptides also increased the micelle binding affinity. These results confirm that the interaction of Leu-enkephalin peptides with SDS micelles is largely electrostatic and that the non-polar amino acid side chains interact with the hydrophobic micelle core. The peptide-micelle association constants for the cationic Met-enkephalin peptides were also greater than their zwitterionic counterparts. For example, the Met-enkephalin K(eq) value was 162 +/- 9 M(-1), while the association constants for Met-enkephalin-Arg, Met-enkephalin-Lys, and Met-enkephalinamide were, respectively, 674 +/- 31, 426 +/- 23, and 453 +/- 27 M(-1). In both Met-enkephalin and Met-enkephalinamide, replacing Gly2 with an Ala did not significantly increase the association constant. These results confirm that with the Met-enkephalin peptides, there was little or no interaction of the amino acid side chains with the micelle core. For both the Leu-enkephalin and Met-enkephalin peptides, the association constants were consistent with EKC results, in that the peptides with smaller K(eq) values were found to elute before those with larger association constants.

NMR Conformational Analyses on (des-bromo) Neuropeptide B [1–23] and Neuropeptide W [1–23]: The Importance of α-helices, a Cation-π Interaction and a β-Turn

The preferred conformations of the orphan G-protein coupled receptor agonists (des-bromo) neuropeptide B [1-23] and neuropeptide W [1-23], referred to as NPB and NPW, have been determined by (1)H NMR, CD, and molecular modeling. The sequences of NPB and NPW are WYKPAAGHSSYSVGRAAGLLSGL and WYKHVASPRYHTVGRAAGLLMGL, respectively. These are hypothalamic peptides that exert their biological actions on GPR7 and GPR8 receptors. Micellar solutions using the membrane mimetic, sodium dodecylsulphate-d(25) (SDS), were used to mimic a physiological environment for the peptides. The secondary structure of NPB consists of a type II beta-turn involving residues Lys(3) to Ala(6). The C-terminal region of NPB exists in a conformational equilibrium between different secondary structures, including an alpha-helix from residues Arg(15) to Ser(21), and a 3(10)-helix from residues Ser(12) to Ser(21). The N-terminus of NPW exhibits a cation-pi interaction between the Lys(3) side chain and the quadrupole moment of the Trp(1) indole group. At the C-terminus of NPW, a well-defined alpha-helical conformation exists from Arg(15) to Met(21). As NPB and NPW have 91% sequence homology from residues Val(13) to Leu(23), with only residue 21 differing between the two peptides, the similar C-terminal secondary structures of these two peptides are consistent with the sequences. This is supported by the similar CD spectra. The different secondary structures at the N-termini for NPB and NPW point to the importance of the N-terminus in receptor binding. This is consistent with the work of Fujii et al. [J. Biol. Chem. 277, 34010-34016 (2002)] who observed that iodination of the NPB Tyr(2) resulted in decreased agonistic activity at GPR7. In addition, Tanaka et al. [Proc. Natl. Acad. Sci. USA 100, 6251-6256 (2003)] showed that deletion of Trp(1) from NPB or NPW drastically decreased activity at GPR7 for NPB and GPR7 and GPR8 for NPW. Therefore, we postulate that the N-terminus is involved in membrane recognition and receptor binding.

Water-soluble complexes from random copolymer and oppositely charged surfactant. 2. Complexes of poly(ethylene glycol)-based cationic random copolymer and bile salts

The complexes formed between the positively charged random copolymers (RCPs) of methoxy-poly(ethylene glycol) monomethacrylate (MePEGMA) and (3-(methacryloylamino)propyl)trimethylammonium chloride (MAPTAC) with oppositely charged biosurfactants (bile salts) were studied using turbidimetric titration, steady-state fluorescence, dynamic light scattering, and electron microscopy. Studies showed that the complexes of the RCPs of MAPTAC and MePEGMA with less than 68 mol % of PEG content precipitate in water, whereas the complexes of the copolymer with 89 and 94 mol % of PEG content do not precipitate in the entire range of composition of the mixture including stoichiometric compositions when the electroneutral complexes are formed. The complexes with true hydrophobic domains, which are a prerequisite characteristic to serve as a carrier, can be obtained at much lower concentration than the critical micelle concentration of the corresponding surfactant. For a particular surfactant, hydrophobic domains are obtained at lower Z-/+ for the random copolymer with lower PEG content. The hydrodynamic radii of these complexes vary over a range of 20-35 nm. Overall results reveal that these complexes are qualitatively similar to the polyion complex micelles or block ionomer complexes obtained from the block copolymers and oppositely charged surfactants. As the surfactants used in this study are biocompatible, we hope that these soluble particles will be promising vectors in the field of drug delivery.

A multidimensional 1H NMR investigation of the conformation of methionine-enkephalin in fast-tumbling bicelles

Enkephalins are pentapeptides found in the central nervous system. It is believed that these neuropeptides interact with the nerve cell membrane to adopt a conformation suitable for their binding to an opiate receptor. In this work, we have determined the three-dimensional structure of methionine-enkephalin (Menk) in fast-tumbling bicelles using multidimensional (1)H NMR. Bicelles were selected as model membranes because both their bilayer organization and composition resemble those of natural biomembranes. The effect of the membrane composition on the peptide conformation was explored using both zwitterionic (PC bicelles) and negatively charged bicelles (Bic/PG). Pulsed field gradient experiments allowed the determination of the proportion of Menk bound to the model membranes. Approximately 60% of the water-soluble enkephalin was found to associate to the bicellar systems. Structure calculations from torsion angle and NOE-based distance constraints suggest the presence of both micro - and delta-selective conformers of Menk in each system and slightly different conformers in PC bicelles and Bic/PG. As opposed to previous studies of enkephalins in membrane mimetic systems, our results show that these opiate peptides could adopt several conformations in a membrane environment, which is consistent with the flexibility and poor selectivity of enkephalins.

PFG-NMR Investigations of the Binding of Cationic Neuropeptides to Anionic and Zwitterionic Micelles

The mechanism by which peptides bind to micelles is believed to be a two-phase process, involving (i). initial electrostatic interactions between the peptide and micelle surface, followed by (ii). hydrophobic interactions between peptide side chains and the micelle core. To better characterize the electrostatic portion of this process, a series of pulse field gradient nuclear magnetic resonance (PFG-NMR) spectroscopic experiments were conducted on a group of neuropeptides with varying net cationic charges (+1 to +3) and charge location to determine both their diffusion coefficients and partition coefficients when in the presence of detergent micelles. Two types of micelles were chosen for the study, namely anionic sodium dodecylsulfate (SDS) and zwitterionic dodecylphosphocholine (DPC) micelles. Results obtained from this investigation indicate that in the case of the anionic SDS micelles, peptides with a larger net positive charge bind to a greater extent than those with a lesser net positive charge (bradykinin > substance P > neurokinin A > Met-enkephalin). In contrast, when in the presence of zwitterionic DPC micelles, the degree of mixed-charge nature of the peptide affects binding (neurokinin A > substance P > Met-enkephalin > bradykinin). Partition coefficients between the peptides and the micelles follow similar trends for both micelle types. Diffusion coefficients for the peptides in SDS micelles, when ranked from largest to smallest, follow a trend where increasing net positive charge results in the smallest diffusion coefficient: Met-enkephalin > neurokinin A > bradykinin > substance P. Diffusion coefficients when in the presence of DPC micelles, when ranked from largest to smallest, follow a trend where the presence of negatively-charged side chains results in the smallest diffusion coefficient: bradykinin > Met-enkephalin > substance P > neurokinin A.