Amphipathic Environment Research Articles

A novel strategy for partial purification of alkane hydroxylase from P. chrysogenum SNP5 through reconstituting its native membrane into liposome

Integral proteins or enzymes are still challenging to purify into their native state because of their need for an amphipathic environment and cofactors. Alkane hydroxylase (AlkB) is a membrane-bound enzyme that catalyzes the hydroxylation of a range of alkanes that have a broad spectrum of applications. In the current study, a novel approach has been explored for partial purification of alkane hydroxylase (AlkB) in its native state through restructuring the lipid bilayer of Penicilliumchrysogenum SNP5 into a liposome to extend the native and protective environment to AlkB enzyme. Three different methods i.e., reverse-phase evaporation method (RPEM), detergent-based method (DBM), and ethanol injection method (EIM) have been used for reconstituting its native membrane into liposome. On characterizing liposomes through fluorescence imaging, AFM, and particle size analysis, the reverse-phase evaporation method gave the best results based on the size distribution (i.e., 100–300 nm), the morphology of liposomes, and maximum AlkB specific activity (i.e., 140.68 U/mg). The maximum reconstitution efficiency of 29.48% was observed in RPEM followed by 17.3% in DBM and 12.3% in EIM. On the characterization of the purified AlkB, the molecular weight was measured of 44.6 KDa and the thermostability of liposomes synthesized with the RPEM method was obtained maximum at 55 °C. This approach may open a new strategy for the purification of integral enzymes/proteins in their native state in the field of protein purification and its applications in diversified industries.

Bending Elasticity of Phospholipid Bilayers Containing an Amphipathic Peptide with Low Mammalian Cytotoxicity


 
 
 Peptide mimetics imitate natural peptides’ structure but they could be specifically designed to be more selective concerning their toxicity to mammalian cells. In most cases this specificity is due to their ability to form α-helix in amphipathic environment. In addition, the specific activity depends on the ability of final structure to penetrate cell membrane. Being responsible for the cell integrity and compartmentalization, biomembranes also play a major role in cellular processes, in which the membrane deformations are important. In the present study we probe peptide-membrane interactions for a shortened amino acid sequence KLAKLAK-NH2 of an antimicrobial peptide with apoptotic effect. The bending rigidity of model lipid bilayers is measured by flicker spectroscopy of quasispherical unilamellar vesicles monitored and analyzed in phase contrast light microscopy. At high peptide concentrations ∼ 30 μmol/L and peptide-to-lipid total molar ratios ∼ 0.90 bilayer stacking formation is observed. A reduction of the bending constant is reported at peptide-to-lipid total molar ratio ∼ 0.80. The membrane softening indicates peripheral peptide orientation at the lipid bilayer, which is considered a prerequisite for channel formation. Based on KLAKLAK-NH2 effect on the membrane bending elasticity we provide an evaluation of the peptide partition coefficient characterizing its affinity to POPC bilayers. The acquired results might be helpful in efforts to further tailor the pharmacokinetic properties of antimicrobial peptides in combination with strengthened stability towards enzymatic degradation.
 
 

Methods to study phosphoinositide regulation of ion channels.

Ion channel are embedded in the lipid bilayers of biological membranes. Membrane phospholipids constitute a barrier to ion movement, and they have been considered for a long time as a passive environment for channel proteins. Membrane phospholipids, however, do not only serve as a passive amphipathic environment, but they also modulate channel activity by direct specific lipid-protein interactions. Phosphoinositides are quantitatively minor components of biological membranes, and they play roles in many cellular functions, including membrane traffic, cellular signaling and cytoskeletal organization. Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is mainly found in the inner leaflet of the plasma membrane. Its role as a potential ion channel regulator was first appreciated over two decades ago and by now this lipid is a well-established cofactor or regulator of many different ion channels. The past two decades witnessed the steady development of techniques to study ion channel regulation by phosphoinositides with progress culminating in recent cryoEM structures that allowed visualization of how PI(4,5)P2 opens some ion channels. This chapter will provide an overview of the methods to study regulation by phosphoinositides, focusing on plasma membrane ion channels and PI(4,5)P2.

Curved or linear? Predicting the 3-dimensional structure of α-helical antimicrobial peptides in an amphipathic environment.

α-Helical membrane-active antimicrobial peptides (AMPs) are known to act via a range of mechanisms, including the formation of barrel-stave and toroidal pores and the micellisation of the membrane (carpet mechanism). Different mechanisms imply that the peptides adopt different 3D structures when bound at the water-membrane interface, a highly amphipathic environment. Here, an evolutionary algorithm is used to predict the 3D structure of a range of α-helical membrane-active AMPs at the water-membrane interface by optimising amphipathicity. This amphipathic structure prediction (ASP) is capable of distinguishing between curved and linear peptides solved experimentally, potentially allowing the activity and mechanism of action of different membrane-active AMPs to be predicted. The ASP algorithm is accessible via a web interface at http://atb.uq.edu.au/asp/.

Self-Association of Antimicrobial Peptides: A Molecular Dynamics Simulation Study on Bombinin.

Antimicrobial peptides (AMPs) are a diverse group of membrane-active peptides which play a crucial role as mediators of the primary host defense against microbial invasion. Many AMPs are found to be fully or partially disordered in solution and to acquire secondary structure upon interaction with a lipid membrane. Here, we report molecular dynamics simulations studies on the solution behaviour of a specific AMP, bombinin H2. We show that in monomeric form in water solution the peptide is somewhat disordered and preferably adopts a helix-loop-helix conformation. However, when more than a single monomer is placed in the solution, the peptides self-associate in aggregates. Within the aggregate, the peptides provide each other with an amphipathic environment that mimics the water–membrane interface, which allows them to adopt a single-helix structure. We hypothesise that this is the mechanism by which bombinin H2 and, possibly, other small linear AMPs reach the target membrane in a functional folded state and are able to effectively exert their antimicrobial action on it.

Molecular Dynamics Simulations on the Bioactive Molecule of hIAPP22-29 (NFGAILSS) and Rational Drug Design.

This chapter includes information about the structure in equilibrium of the bioactive molecule hIAPP22-29 (NFGAILSS). The experimental structure was derived using X-ray and its 2D NOESY NMR experiments in d 6-DMSO and d-HFIP solvents. This molecule contains eight of the ten amino acids of the 20-29 region of the human islet amyloid polypeptide (hIAPP) often referred as the "amyloidogenic core." Amyloid deposits are well-known to cause as many as 20 pathological neurodegenerative disorders such as Alzheimer, Parkinson, Huntington, and Creutzfeldt-Jakob. The experimental structure was relaxed using molecular dynamics (MD) in simulation boxes consisting in DMSO and HFIP; the latter not provided by the applied software. The calculations were performed in GPUs and supercomputers, and some basic scripting is described for reference. The simulations confirmed the inter- and intramolecular forces that led to an "amyloidogenic core" observed from NOE experiments. The results showed that in DMSO and HFIP environment, Phe is not in spatial proximity with Leu or Ile, and this is consistent with an amyloidogenic core. However, in an amphipathic environment such as the model lipid bilayers, this communication is possible and may influence peptide amyloidogenic properties. The knowledge gained through this study may contribute to the rational drug design of novel peptides or organic molecules acting by modifying preventing amyloidogenic properties of the hIAPP peptide.

Designing Mixed Detergent Micelles for Uniform Neutron Contrast.

Micelle-forming detergents provide an amphipathic environment that mimics lipid bilayers and are important tools used to solubilize and stabilize membrane proteins in solution for in vitro structural investigations. Small-angle neutron scattering (SANS) at the neutron contrast match point of detergent molecules allows observing the signal from membrane proteins unobstructed by contributions from the detergent. However, we show that even for a perfectly average-contrast matched detergent there arises significant core-shell scattering from the contrast difference between aliphatic detergent tails and hydrophilic head groups. This residual signal interferes with interpreting structural data of membrane proteins. This complication is often made worse by the presence of excess empty (protein-free) micelles. We present an approach for the rational design of mixed micelles containing a deuterated detergent analog, which eliminates neutron contrast between core and shell and allows the micelle scattering to be fully contrast-matched to unambiguously resolve membrane protein structure using solution SANS.

Structural characterization of a novel peptide with antimicrobial activity from the venom gland of the scorpion Tityus stigmurus: Stigmurin

A new antimicrobial peptide, herein named Stigmurin, was selected based on a transcriptomic analysis of the Brazilian yellow scorpion Tityus stigmurus venom gland, an underexplored source for toxic peptides with possible biotechnological applications. Stigmurin was investigated in silico, by circular dichroism (CD) spectroscopy, and in vitro. The CD spectra suggested that this peptide interacts with membranes, changing its conformation in the presence of an amphipathic environment, with predominance of random coil and beta-sheet structures. Stigmurin exhibited antibacterial and antifungal activity, with minimal inhibitory concentrations ranging from 8.7 to 69.5μM. It was also showed that Stigmurin is toxic against SiHa and Vero E6 cell lines. The results suggest that Stigmurin can be considered a potential anti-infective drug.

Structure Determination of Membrane Proteins in Their Native Phospholipid Bilayer Environment by Rotationally Aligned Solid-State NMR Spectroscopy

One of the most important topics in experimental structural biology is determining the structures of membrane proteins. These structures represent one-third of all of the information expressed from a genome, distinguished by their locations within the phospholipid bilayer of cells, organelles, or enveloped viruses. Their highly hydrophobic nature and insolubility in aqueous media means that they require an amphipathic environment. They have unique functions in transport, catalysis, channel formation, and signaling. Researchers are particularly interested in G-protein coupled receptors (GPCRs) because they modulate many biological processes, and about half of the approximately 800 of these proteins within the human genome are or can be turned into drug receptors that affect a wide range of diseases. Because of experimental difficulties, researchers have studied membrane proteins using a wide variety of artificial media that mimic membranes, such as mixed organic solvents or detergents. More sophisticated mimics include bilayer discs (bicelles) and the lipid cubic phase (LCP), but both of these contain a very large detergent component, which can disrupt the stability and function of membrane proteins. To have confidence in the resulting structures and their biological functions and to avoid disrupting these delicate proteins, the structures of membrane proteins should be determined in their native environment of liquid crystalline phospholipid bilayers under physiological conditions. This Account describes a recently developed general method for determining the structures of unmodified membrane proteins in phospholipid bilayers by solid-state NMR spectroscopy. Because it relies on the natural, rapid rotational diffusion of these proteins about the bilayer normal, this method is referred to as rotationally aligned (RA) solid-state NMR. This technique elaborates on oriented sample (OS) solid-state NMR, its complementary predecessor. These methods exploit the power of solid-state NMR, which enables researchers to obtain well-resolved spectra from "immobile" membrane proteins in phospholipid bilayers, to separate and measure frequencies that reflect orientations with respect to the bilayer normal, and to make complementary distance measurements. The determination of the structures of several membrane proteins, most prominently the chemokine receptor CXCR1, a 350-residue GPCR, has demonstrated this approach.

Dependence of micelle size and shape on detergent alkyl chain length and head group.

Micelle-forming detergents provide an amphipathic environment that can mimic lipid bilayers and are important tools for solubilizing membrane proteins for functional and structural investigations in vitro. However, the formation of a soluble protein-detergent complex (PDC) currently relies on empirical screening of detergents, and a stable and functional PDC is often not obtained. To provide a foundation for systematic comparisons between the properties of the detergent micelle and the resulting PDC, a comprehensive set of detergents commonly used for membrane protein studies are systematically investigated. Using small-angle X-ray scattering (SAXS), micelle shapes and sizes are determined for phosphocholines with 10, 12, and 14 alkyl carbons, glucosides with 8, 9, and 10 alkyl carbons, maltosides with 8, 10, and 12 alkyl carbons, and lysophosphatidyl glycerols with 14 and 16 alkyl carbons. The SAXS profiles are well described by two-component ellipsoid models, with an electron rich outer shell corresponding to the detergent head groups and a less electron dense hydrophobic core composed of the alkyl chains. The minor axis of the elliptical micelle core from these models is constrained by the length of the alkyl chain, and increases by 1.2–1.5 Å per carbon addition to the alkyl chain. The major elliptical axis also increases with chain length; however, the ellipticity remains approximately constant for each detergent series. In addition, the aggregation number of these detergents increases by ∼16 monomers per micelle for each alkyl carbon added. The data provide a comprehensive view of the determinants of micelle shape and size and provide a baseline for correlating micelle properties with protein-detergent interactions.

A crystal structure of a dimer of the antibiotic ramoplanin illustrates membrane positioning and a potential Lipid II docking interface

The glycodepsipeptide antibiotic ramoplanin A2 is in late stage clinical development for the treatment of infections from Gram-positive pathogens, especially those that are resistant to first line antibiotics such as vancomycin. Ramoplanin A2 achieves its antibacterial effects by interfering with production of the bacterial cell wall; it indirectly inhibits the transglycosylases responsible for peptidoglycan biosynthesis by sequestering their Lipid II substrate. Lipid II recognition and sequestration occur at the interface between the extracellular environment and the bacterial membrane. Therefore, we determined the structure of ramoplanin A2 in an amphipathic environment, using detergents as membrane mimetics, to provide the most physiologically relevant structural context for mechanistic and pharmacological studies. We report here the X-ray crystal structure of ramoplanin A2 at a resolution of 1.4 A. This structure reveals that ramoplanin A2 forms an intimate and highly amphipathic dimer and illustrates the potential means by which it interacts with bacterial target membranes. The structure also suggests a mechanism by which ramoplanin A2 recognizes its Lipid II ligand.

Fluorescence Mapping of Mitochondrial TIM23 Complex Reveals a Water-Facing, Substrate-Interacting Helix Surface

Protein translocation across the mitochondrial inner membrane is mediated by the TIM23 complex. While its central component, Tim23, is believed to form a protein-conducting channel, the regions of this subunit that face the imported protein are unknown. To examine Tim23 structure and environment in intact membranes at high resolution, various derivatives, each with a single, environment-sensitive fluorescent probe positioned at a specific site, were assembled into functional TIM23 complexes in active mitochondria and analyzed by multiple spectral techniques. Probes placed sequentially throughout a transmembrane region that was identified by crosslinking as part of the protein-conducting channel revealed an alpha helix in an amphipathic environment. Probes on the aqueous-facing helical surface specifically underwent spectral changes during protein import, and their accessibility to hydrophilic quenching agents is considered in terms of channel gating. This approach has therefore provided an unprecedented view of a translocon channel structure in an intact, fully operational, membrane-embedded complex.

Structural-dynamical properties of the transmembrane segment VI of the mitochondrial oxoglutarate carrier studied by site directed spin-labeling

Site directed spin-labeling (SDSL) has been used to probe the structural and dynamic features of residues comprising the sixth transmembrane segment of the mitochondrial oxoglutarate carrier. Starting from a functional carrier, where cysteines have been replaced by serines, 18 consecutive residues (from G281 to I298) have been mutated to cysteine and subsequently labeled with a thiol-selective nitroxide probe. The labeled proteins, reconstituted into liposomes, have been assayed for their transport activity and analyzed with continuous-wave electron paramagnetic resonance. Linewidth analysis, that is correlated to local probe mobility, indicates a well defined periodicity of the whole segment from G281 to I298, indicating that it has an alpha-helical structure. Saturation behaviour, in presence of paramagnetic perturbants of different hydrophobicities, allow the definition of the polarity of the individual residues and to assign their orientation with respect to the lipid bilayer or to the water accessible translocation channel. Comparison of the EPR data, homology model and activity data indicate that the segment is made by an alpha helix, accommodated in an amphipathic environment, partially distorted in the middle at the level of L289, probably because of the presence of a proline residue (P291). The C-terminal region of the segment is less restrained and more flexible than the N-terminus.

Phe- d-Leu-Phe- d-Leu-Phe derivatives as formylpeptide receptor antagonists in human neutrophils: cellular and conformational aspects

We synthesized several Phe- d-Leu-Phe- d-Leu-Phe analogues in which tert-butyloxycarbonyl and four different ureido substituents were included at the N-terminal of the peptides, obtained as free acid and methyl-ester derivatives. Their biological action was analysed on human neutrophil responses induced by N-formyl-Met-Leu-Phe (fMLF). Several in vitro assays were carried out: receptor binding, measurement of Ca 2+ intracellular concentration, chemotaxis, superoxide anion production and enzyme release. A conformational investigation, using infrared absorption and circular dichroism, was also performed. Our results demonstrate that the compounds examined prefer an ordered conformation (β-turn) in amphipathic environment, and are able to antagonize the neutrophil functions evoked by fMLF. Moreover, the extent of inhibition of Ca 2+ intracellular enhancement, as well as of superoxide anion production and granule enzyme release, appears related to their affinity toward the formylpeptide receptor. The free acid peptide derivatives appear to be more active antagonists than the methyl-ester ones.

Greater partitioning of small spin labels into interdigitated than into non-interdigitated gel phase bilayers

Partitioning of the small amphipathic spin labels 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO), 4-oxo-2,2,6,6-tetramethylpiperidinyl- N-oxy (TEMPONE), and di-tertiary butyl nitroxide (DTBN) into interdigitated L β I and non-interdigitated L β ′, P β ′, and L α phases was compared. The double chain interdigitated phases examined were 1,2-dipalmitoylphosphatidylcholine (DPPC) in the presence of 2.17 M ethanol, dihexadecylphosphatidylcholine (DHPC), and the complexes of dipalmitoylphosphatidylglycerol (DPPG) with polymyxin B and myelin basic protein. The triple chain mixed interdigitated phase of the asymmetric chain 1-stearoyl-2-caproyl-phosphatidylcholine (18:10-PC) was also examined. The non-interdigitated lipids were DPPC, DPPC in the presence of 0.87 M ethanol, DPPG, and the complex of DPPG with polylysine. Quantitation of the percentage of the membrane-bound spectral contribution in the presence of NiSO 4, used to broaden the aqueous spectral contribution, showed that all three spin labels partitioned into the L β I phase significantly more than into the L β ′ phase. The hyperfine splitting values indicated that all three spin labels were located near the apolar/polar interface in the L β I phase. The amount of TEMPO and DTBN bound to the L β I phase was similar to that in the L α phase but more TEMPONE was bound to the L β I phase than to the L α phase. This is attributed to the greater polarity of TEMPONE, its preference for a polar or amphipathic environment, and the larger volume between lipid head groups at the apolar/polar interface in the L β I phase compared to the other phases. However, TEMPO binding to the mixed interdigitated gel phase of 18:10-PC was no greater than to the non-interdigitated L β ′ phase of DPPC, reflecting the smaller volume at the apolar/polar interface of this triple chain interdigitated bilayer compared to the double chain interdigitated bilayers. Thus interdigitation of the lipid bilayer, whether due to addition of a substance like ethanol, or spontaneous as in DHPC, can cause increased partitioning of other substances into the bilayer, provided that they are small enough to fit into the volume created at the apolar/polar interface. This increased partitioning could contribute to an increased permeability of small molecules across interdigitated bilayers.

Conformation of retro‐bombolitin I in aqueous solution containing surfactant micelles

Bombolitins are five naturally occurring heptadecapeptides acting at the membrane level and able to increase the activity of phospholipase A2. As for other peptides with similar function, the biological activity of bombolitins seems to be mainly due to their ability to form amphipathic helical structures. We synthesized and tested the retro sequence of bombolitin I (retro-bombolitin I). This peptide showed an activity similar to that of the natural sequence and was able to adopt a helical structure in the presence of an amphipathic environment consisting of SDS micelles. The secondary structure of this peptide was fully characterized by CD and nmr spectroscopy.

Change in Target Molecular Size of the Red Beet Plasma Membrane ATPase during Solubilization and Reconstitution

The plasma membrane ATPase from red beet (Beta vulgaris L.) storage tissue associated with either native plasma membrane vesicles, a detergent-solubilized enzyme preparation or reconstituted liposomes was subjected to radiation inactivation analysis to determine if changes in target molecular size occurred with modification of its amphipathic environment. For each preparation of the enzyme, the decline in ATP hydrolytic activity with increasing dose of gamma-ray radiation demonstrated a simple exponential profile indicating the presence of a single target size. Analysis of the radiation inactivation profiles for the plasma membrane associated, solubilized, and reconstituted enzyme revealed target molecular sizes of 225 kilodaltons (kD), 129 kD, and 218 kD, respectively. These results suggest that the plasma membrane associated and reconstituted ATPase preparations consist of enzyme present as a dimer of 100 kD subunits while the solubilized enzyme is present in the monomeric form. These results also indicate that the 100 kD catalytic subunit most likely represents the minimal unit of ATP hydrolytic activity.

Structural studies of bee melittin

The question of how proteins refold in passing from an aqueous phase to an amphipathic environment such as a membrane is beig addressed by a structural study of bee melittin. Melittin is the toxic, main protein of bee venom, and has been shown by others to integrate into natural and synthetic membranes and to lyse a variety of cells. This function is presumably related to its unusual sequence. Except for charges at the N-terminus and at lysine 7, the first 20 residues are largely apolar. In contrast, the last six residues contain four charges and two polar residues.