Interaction of N-terminal peptide analogues of the Na+,K+-ATPase with membranes

Electrostatic switch mechanisms of membrane protein trafficking and regulation

Lipid-protein interactions are normally classified as either specific or general. Specific interactions refer to lipid binding to specific binding sites within a membrane protein, thereby modulating the protein's thermal stability or kinetics. General interactions refer to indirect effects whereby lipids affect membrane proteins by modulating the membrane's physical properties, e.g., its fluidity, thickness, or dipole potential. It is not widely recognized that there is a third distinct type of lipid-protein interaction. Intrinsically disordered N- or C-termini of membrane proteins can interact directly but nonspecifically with the surrounding membrane. Many peripheral membrane proteins are held to the cytoplasmic surface of the plasma membrane via a cooperative combination of two forces: hydrophobic anchoring and electrostatic attraction. An acyl chain, e.g., myristoyl, added post-translationally to one of the protein's termini inserts itself into the lipid matrix and helps hold peripheral membrane proteins onto the membrane. Electrostatic attraction occurs between positively charged basic amino acid residues (lysine and arginine) on one of the protein's terminal tails and negatively charged phospholipid head groups, such as phosphatidylserine. Phosphorylation of either serine or tyrosine residues on the terminal tails via regulatory protein kinases allows for an electrostatic switch mechanism to control trafficking of the protein. Kinase action reduces the positive charge on the protein's tail, weakening the electrostatic attraction and releasing the protein from the membrane. A similar mechanism regulates many integral membrane proteins, but here only electrostatic interactions are involved, and the electrostatic switch modulates protein activity by altering the stabilities of different protein conformational states.

Involvement of the alpha-subunit N-terminus in the mechanism of the Na+,K+-ATPase

Previous studies have shown that cytoplasmic K+ release and the associated E2 → E1 conformational change of the Na+,K+-ATPase is a major rate-determining step of the enzyme's ion pumping cycle and hence a prime site of acute regulatory intervention. From the ionic strength dependence of the enzyme's distribution between the E2 and E1 states, it has also been found that E2 is stabilized by an electrostatic attraction. Any disruption of this electrostatic attraction would, thus, have profound effects on the rate of ion pumping. The aim of this paper is to identify the location of this interaction. Using enhanced-sampling molecular dynamics simulations with a predicted N-terminal structure added to the X-ray crystal structure of the Na+,K+-ATPase, a previously postulated salt bridge between Lys32 and Glu233 (rat sequence numbering) of the enzyme's α-subunit can be excluded. The residues never approach closely enough to form a salt bridge. In contrast, strong interactions with anionic lipid head groups were seen. To investigate the possibility of a protein-lipid interaction experimentally, the surface charge density of Na+,K+-ATPase-containing membrane fragments was estimated from zeta potential measurements to be 0.019 (± 0.001) C m-2. This is in good agreement with the charge density previously determined to be responsible for stabilization of the E2 state of 0.023 (± 0.009) C m-2 and the membrane charge density estimated here from published electron-microscopic images of 0.018C m-2. The results are, therefore, consistent with an interaction of the Na+,K+-ATPase α-subunit N-terminus with negatively-charged lipid head groups of the neighbouring cytoplasmic membrane surface as the origin of the electrostatic interaction stabilising the E2 state.

Order-disorder transitions of cytoplasmic N-termini in the mechanisms of P-type ATPases

Membrane protein structure and function are modulated via interactions with their lipid environment. This is particularly true for integral membrane pumps, the P-type ATPases. These ATPases play vital roles in cell physiology, where they are associated with the transport of cations and lipids, thereby generating and maintaining crucial (electro-)chemical potential gradients across the membrane. Several pumps (Na⁺, K⁺-ATPase, H⁺, K⁺-ATPase and the plasma membrane Ca²⁺-ATPase) which are located in the asymmetric animal plasma membrane have been found to possess polybasic (lysine-rich) domains on their cytoplasmic surfaces, which are thought to act as phosphatidylserine (PS) binding domains. In contrast, the sarcoplasmic reticulum Ca²⁺-ATPase, located within an intracellular organelle membrane, does not possess such a domain. Here we focus on the lysine-rich N-termini of the plasma-membrane-bound Na⁺, K⁺- and H⁺, K⁺-ATPases. Synthetic peptides corresponding to the N-termini of these proteins were found, via quartz crystal microbalance and circular dichroism measurements, to interact via an electrostatic interaction with PS-containing membranes, thereby undergoing an increase in helical or other secondary structure content. As well as influencing ion pumping activity, it is proposed that this interaction could provide a mechanism for sensing the lipid asymmetry of the plasma membrane, which changes drastically when a cell undergoes apoptosis, i.e. programmed cell death. Thus, polybasic regions of plasma membrane-bound ion pumps could potentially perform the function of a "death sensor", signalling to a cell to reduce pumping activity and save energy.

Molecular Dynamics Simulation of Small Molecules Interacting with Biological Membranes

Cell membranes protect and compartmentalise cells and their organelles. The semi-permeable nature of these membranes controls the exchange of solutes across their structure. Characterising the interaction of small molecules with biological membranes is critical to understanding of physiological processes, drug action and permeation, and many biotechnological applications. This review provides an overview of how molecular simulations are used to study the interaction of small molecules with biological membranes, with a particular focus on the interactions of water, organic compounds, drugs and short peptides with models of plasma cell membrane and stratum corneum lipid bilayers. This review will not delve on other types of membranes which might have different composition and arrangement, such as thylakoid or mitochondrial membranes. The application of unbiased molecular dynamics simulations and enhanced sampling methods such as umbrella sampling, metadynamics and replica exchange are described using key examples. This review demonstrates how state-of-the-art molecular simulations have been used successfully to describe the mechanism of binding and permeation of small molecules with biological membranes, as well as associated changes to the structure and dynamics of these membranes. The review concludes with an outlook on future directions in this field.

Wear Resistant Nanocomposites Based on Biomedical Grade UHMWPE Paraffin Oil and Carbon Nano-Filler: Preliminary Biocompatibility and Antibacterial Activity Investigation

In the present paper, we investigate the effectiveness of nanocomposites (composed of ultra-high molecular weight polyethylene (UHMWPE) mixed with carbon nano-filler (CNF) and medical grade paraffin oil (PO), from the biological point of view. Wear measurements were carried out without (air) and with lubricant (distilled water, natural, and artificial lubricant), and antibacterial activity and cytotoxicity were evaluated. The results highlighted that the presence of CNF is important in the nanocomposite formulation because it reduces the wear rate and prevents oxidative degradation during its processing. An amount of 1.0 wt % of CNF is best because it reaches the optimal distribution within the polymeric matrix, resulting in the best wear resistant, bio-active, and anti-bacterial nanocomposite among all investigated samples.

Use of the Sol–Gel Method for the Preparation of Coatings of Titanium Substrates with Hydroxyapatite for Biomedical Application

Hydroxyapatite (HA) was coated onto the surface of commercially pure titanium grade 4 (a material generally used for implant application) by a dip coating method using HA sol. Hydroxyapatite sol was synthesized via sol–gel using Ca(NO3)2∙4H2O and P2O5 as precursors. The surface of the HA coating was homogeneous, as determined by scanning electron microscopy (SEM), attenuated total reflectance Fourier transform infrared (ATR-FTIR), and X-ray diffraction (XRD), which allowed the materials to be characterized. The bioactivity of the synthesized materials and their efficiency for use as future bone implants was confirmed by observing the formation of a layer of hydroxyapatite on the surface of the samples soaked in a fluid simulating the composition of human blood plasma. To verify the biocompatibility of the obtained biomaterial, fibroblasts were grown on a glass surface and were tested for viability after 24 h. The results of the WST-8 analysis suggest that the HA systems, prepared by the sol–gel method, are most suitable for modifying the surface of titanium implants and improving their biocompatibility.

FT-IR Characterization of Antimicrobial Hybrid Materials through Sol-Gel Synthesis

Silica/polycaprolactone and titania/polycaprolactone hybrid organic/inorganic amorphous composites were prepared via a sol-gel method starting from a multi-element solution containing tetramethyl orthosilicate (TMOS) or titanium butoxide (TBT), polycaprolactone (PCL), water and methylethylketone (MEK). The molecular structure of the crosslinked network was based on the presence of the hydrogen bonds between organic/inorganic elements as confirmed by Fourier Transform Infra-Red (FT-IR) analysis. In particular, the structure of crosslinked network was realized by hydrogen bonds between the X-OH (X = Si or Ti) group (H donator) in the sol-gel intermediate species and ester groups (H-acceptors) in the repeating units of the polymer. The morphology of the hybrid materials; pore size distribution, elemental homogeneity and surface features, was studied by scanning electron microscopy/energy dispersive spectroscopy (SEM/EDS) and by atomic force microscopy (AFM). The bioactivity of the synthesized hybrid materials was confirmed by observing the formation of a layer of hydroxyapatite (HAP) on the surface of the samples soaked in a simulated body fluid. The antimicrobial behavior of synthetized hybrids was also assessed against Escherichia coli bacteria. In conclusion, the prepared hybrid materials are proposed for use as future bone implants.

New SiO2/Caffeic Acid Hybrid Materials: Synthesis, Spectroscopic Characterization, and Bioactivity

The sol–gel route represents a valuable technique to obtain functional materials, in which organic and inorganic members are closely connected. Herein, four hybrid materials, containing caffeic acid entrapped in a silica matrix at 5, 10, 15, and 20 wt.%, were synthesized and characterized through Fourier-Transform Infrared (FT-IR) and Ultraviolet-Visible (UV–Vis) spectroscopy. FT-IR analysis was also performed to evaluate the ability to induce the hydroxyapatite nucleation. Despite some structural changes occurring on the phenol molecular skeleton, hybrid materials showed scavenging properties vs. 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and 2,2′-azinobis-(3-ethylbenzothiazolin-6-sulfonic acid) radical cation (ABTS•⁺), which was dependent on the tested dose and on the caffeic acid wt.%. The SiO₂/caffeic acid materials are proposed as valuable antibacterial agents against Escherichia coli and Enterococcus faecalis.

Polarity of the ATP binding site of the Na+,K+-ATPase, gastric H+,K+-ATPase and sarcoplasmic reticulum Ca2+-ATPase

A fluorescence ratiometric method utilizing the probe eosin Y is presented for estimating the ATP binding site polarity of P-type ATPases in different conformational states. The method has been calibrated by measurements in a series of alcohols and tested using complexation of eosin Y with methyl-β-cyclodextrin. The results obtained with the Na⁺,K⁺-, H⁺,K⁺- and sarcoplasmic reticulum Ca²⁺-ATPases indicate that the ATP binding site, to which eosin is known to bind, is significantly more polar in the case of the Na⁺,K⁺- and H⁺,K⁺-ATPases compared to the Ca²⁺-ATPase. This result was found to be consistent with docking calculations of eosin with the E2 conformational state of the Na⁺,K⁺-ATPase and the Ca²⁺-ATPase. Fluorescence experiments showed that eosin binds significantly more strongly to the E1 conformation of the Na⁺,K⁺-ATPase than the E2 conformation, but in the case of the Ca²⁺-ATPase both fluorescence experiments and docking calculations showed no significant difference in binding affinity between the two conformations. This result could be due to the fact that, in contrast to the Na⁺,K⁺- and H⁺,K⁺-ATPases, the E2-E1 transition of the Ca²⁺-ATPase does not involve the movement of a lysine-rich N-terminal tail which may affect the overall enzyme conformation. Consistent with this hypothesis, the eosin affinity of the E1 conformation of the Na⁺,K⁺-ATPase was significantly reduced after N-terminal truncation. It is suggested that changes in conformational entropy of the N-terminal tail of the Na⁺, K⁺- and the H⁺,K⁺-ATPases during the E2-E1 transition could affect the thermodynamic stability of the E1 conformation and hence its ATP binding affinity.

Penetration of phospholipid membranes by poly-l-lysine depends on cholesterol and phospholipid composition

Clusters of positively-charged basic amino acid residues, particularly lysine, are known to promote the interaction of many peripheral membrane proteins with the cytoplasmic surface of the plasma membrane via electrostatic interactions. In this work, cholesterol's effects on the interaction between lysine residues and membranes have been studied. Using poly-l-lysine (PLL) and vesicles as models to mimic the interaction between lysine-rich protein domains and the plasma membrane, light scattering measurements indicated cholesterol enhanced the electrostatic interaction through indirectly affecting the negatively charged phospholipid dioleoylphosphatidylserine, DOPS. Addition of PLL to lipid vesicles containing DOPS showed an initial increase in static light scattering (SLS), attributed to binding of PLL to the vesicle surface, followed by a slower continuously declining SLS signal, which, from comparison with fluorescent dye leakage studies could be attributed to vesicle lysis. Although electrostatic interactions between PLL and the membrane were not necessary for penetration to occur, cholesterol promoted membrane disruption of negatively charged vesicles, possibly by increasing the electrostatic interactions between PLL and the membrane. In contrast, cholesterol lowered the susceptibility of uncharged vesicles (formed using dioleoylphosphatidylcholine, DOPC) to PLL penetration. This can be explained by the absence of electrostatic interactions and cholesterol's known ability to increase membrane thickness and mechanical strength. Thus, the ability of cationic peptides to penetrate membranes including cholesterol is likely to depend on the membrane's PS:PC ratio.

General and specific interactions of the phospholipid bilayer with P-type ATPases

Protein structure and function are modulated via interactions with their environment, representing both the surrounding aqueous media and lipid membranes that have an active role in shaping the structural topology of membrane proteins. Compared to a decade ago, there is now an abundance of crystal structural data on membrane proteins, which together with their functional studies have enhanced our understanding of the salient features of lipid-protein interactions. It is now important to recognize that membrane proteins are regulated by both (1) general lipid-protein interactions, where the general physicochemical properties of the lipid environment affect the conformational flexibility of a membrane protein, and (2) by specific lipid-protein interactions, where lipid molecules directly interact via chemical interactions with specific lipid-binding sites located on the protein. However, due to local differences in membrane composition, thickness, and lipid packing, local membrane physical properties and hence the associated lipid-protein interactions also differ due to membrane location, even for the same protein. Such a phenomenon has been shown to be true for one family of integral membrane ion pumps, the P2-type adenosine triphosphatases (ATPases). Despite being highly homologous, individual members of this family have distinct structural and functional activity and are an excellent candidate to highlight how the local membrane physical properties and specific lipid-protein interactions play a vital role in facilitating the structural rearrangements of these proteins necessary for their activity. Hence in this review, we focus on both the general and specific lipid-protein interactions and will mostly discuss the structure-function relationships of the following P2-type ATPases, Na⁺,K⁺-ATPase (NKA), gastric H⁺,K⁺-ATPase (HKA), and sarco(endo)plasmic reticulum Ca²⁺-ATPase (SERCA), in concurrence with their lipid environment.

Emerging Diversity in Lipid-Protein Interactions

Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein functions. Experimental and computational advances are converging in a rapidly expanding research area of lipid-protein interactions. Experimentally, the database of high-resolution membrane protein structures is growing, as are capabilities to identify the complex lipid composition of different membranes, to probe the challenging time and length scales of lipid-protein interactions, and to link lipid-protein interactions to protein function in a variety of proteins. Computationally, more accurate membrane models and more powerful computers now enable a detailed look at lipid-protein interactions and increasing overlap with experimental observations for validation and joint interpretation of simulation and experiment. Here we review papers that use computational approaches to study detailed lipid-protein interactions, together with brief experimental and physiological contexts, aiming at comprehensive coverage of simulation papers in the last five years. Overall, a complex picture of lipid-protein interactions emerges, through a range of mechanisms including modulation of the physical properties of the lipid environment, detailed chemical interactions between lipids and proteins, and key functional roles of very specific lipids binding to well-defined binding sites on proteins. Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein interactions.

Coating of Titanium Substrates with ZrO2 and ZrO2-SiO2 Composites by Sol-Gel Synthesis for Biomedical Applications: Structural Characterization, Mechanical and Corrosive Behavior

The use of metallic materials as implants presents some major drawbacks, such as their harmful effects on the living organism, especially those induced by corrosion. To overcome this problem, the implant surface of titanium implants can be improved using a coating of bioactive and biocompatible materials. The aim of this work is the synthesis of SiO2/ZrO2 composites with different percentages of zirconia matrix (20, 33 and 50 wt.%), by the sol-gel method to coat commercial Grade 4 titanium disks using a dip coater. Attenuated total reflectance Fourier transform infrared (ATR/FTIR) spectroscopy was used to evaluate the interactions between the inorganic matrices. Furthermore, the mechanical properties and corrosive behavior of the SiO2/ZrO2 coatings were evaluated as a function of the ZrO2 content. The bioactive properties of the substrate coated with different composites were evaluated using simulated body fluid (SBF). The antibacterial activity was tested against gram-negative and gram-positive Escherichia coli and Enterococcus faecalis, respectively, to assess the release of toxic products from the different composites and to evaluate the possibility of using them in the biomedical field.

Sol⁻Gel Synthesis of Silica-Based Materials with Different Percentages of PEG or PCL and High Chlorogenic Acid Content

Implanted biomedical devices can induce adverse responses in the human body, which can cause failure of the implant-referred to as implant failure. Early implant failure is induced numerous factors, most importantly, infection and inflammation. Natural products are, today, one of the main sources of new drug molecules due to the development of pathogenic bacterial strains that possess resistance to more antibiotics used currently in various diseases. The aim of this work is the sol⁻gel synthesis of antibacterial biomedical implants. In the silica matrix, different percentages (6, 12, 24, 50 wt %) of polyethylene glycol (PEG) or poly(ε-caprolactone) (PCL) were embedded. Subsequently, the ethanol solutions with high amounts of chlorogenic acid (CGA 20 wt %) were slowly added to SiO₂/PEG and SiO₂/PCL sol. The interactions among different organic and inorganic phases in the hybrid materials was studied by Fourier transform infrared (FTIR) spectroscopy. Furthermore, the materials were soaked in simulated body fluid (SBF) for 21 days and the formation of a hydroxyapatite layer on their surface was evaluated by FTIR and XRD analysis. Finally, Escherichia coli and Pseudomonas aeruginosa were incubated with several hybrids, and the diameter of zone of inhibition was observed to assessment the potential antibacterial properties of the hybrids.

Chlorogenic Acid Entrapped in Hybrid Materials with High PEG Content: A Strategy to Obtain Antioxidant Functionalized Biomaterials?

The formation of pro-oxidant species after implantation of biomaterials could be responsible for the failure of the implant itself, because of oxidative stress-induced damage. In this work, the SiO₂/polyethylene glycol (PEG)/chlorogenic acid (CGA) hybrids synthesized by the sol⁻gel method with 50 wt% of the polymer and different amounts of CGA (5, 10, 15 and 20 wt%) were studied. The hybrids soaked in simulated body fluid (SBF) showed the formation of hydroxyapatite layers on their surface, suggesting that the hybrids are bioactive. Their radical scavenging capacity towards DPPH· and ABTS·+ (2,2'-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid), evaluated at three different doses (0.5, 1 and 2 mg), showed probe- and dose-dependent behavior. In addition, the antioxidant properties of CGA were not affected by the presence of high amounts of the polymer. The in vitro biocompatibility in three cell lines (NIH 3T3, HaCaT and SH-SY5Y) was assessed by using the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. Apart from SH-SY5Y, the cell viability-expressed as mitochondrial redox activity percentage of cells directly exposed to powders-and morphology was not affected, suggesting that the hybrids have the ability to interfere and act selectively against tumor cells. The antibacterial properties of the different materials against Escherichia coli and Enterococcus faecalis were affected by different amounts of the natural antioxidant component.

Influence of the Heat Treatment on the Particles Size and on the Crystalline Phase of TiO₂ Synthesized by the Sol-Gel Method

Titanium biomaterials’ response has been recognized to be affected by particles size, crystal structure, and surface properties. Chemical and structural properties of these nanoparticle materials are important, but their size is the key aspect. The aim of this study is the synthesis of TiO₂ nanoparticles by the sol-gel method, which is an ideal technique to prepare nanomaterials at low temperature. The heat treatment can affect the structure of the final product and consequently its biological properties. For this reason, the chemical structure of the TiO₂ nanoparticles synthesized was investigated after each heat treatment, in order to evaluate the presence of different phases formed among the nanoparticles. FTIR spectroscopy and XRD have been used to evaluate the different structures. The results of these analyses suggest that an increase of the calcination temperature induces the formation of mixed-crystalline-phases with different content of anatase and rutile phases. The results obtained by SEM measurements suggest that an increase in the particles size accompanied by a noticeable aggregation of TiO₂ nanoparticles is due to high temperatures achieved during the thermal treatments and confirmed the presence of different content of the two crystalline phases of titanium dioxide.

Drug Release of Hybrid Materials Containing Fe(II)Citrate Synthesized by Sol-Gel Technique

The use of oral iron integration is commonly recommended for the treatment of iron deficiency, nevertheless the diagnosis and treatment of this disease could clearly be improved. The aim of this work was the synthesis of therapeutic systems, iron (II) based, by sol-gel method. In an SiO₂ matrix, we embedded different weight percentages of polyethylene glycol (PEG6, 12, 24 wt%) and ferrous citrate (Fe(II)C5, 10, 15 wt%) for drug delivery applications. Fourier Transform Infrared (FTIR) spectroscopy was used to study the interactions among different components in the hybrid materials. Release kinetics in a simulated body fluid (SBF) were investigated and the amount of Fe2+ released was detected by Ultraviolet⁻Visible spectroscopy (UV-VIS) after reaction with ortho-phenantroline. Furthermore, the biological characterization was carried out. The bioactivity of the synthesized hybrid materials was evaluated by the formation of a layer of hydroxyapatite on the surface of samples soaked in SBF using FTIR spectroscopy. Finally, also, the potential antibacterial properties of the different materials against two different bacteria, E. coli and P. aeruginosa, were investigated.

Evolutionary Analysis of the Lysine-Rich N-terminal Cytoplasmic Domains of the Gastric H+,K+-ATPase and the Na+,K+-ATPase

The catalytic α-subunits of both the Na⁺,K⁺-ATPase and the gastric H⁺,K⁺-ATPase possess lysine-rich N-termini which project into the cytoplasm. Due to conflicting experimental results, it is currently unclear whether the N-termini play a role in ion pump function or regulation, and, if they do, by what mechanism. Comparison of the lysine frequencies of the N-termini of both proteins with those of all of their extramembrane domains showed that the N-terminal lysine frequencies are far higher than one would expect simply from exposure to the aqueous solvent. The lysine frequency was found to vary significantly between different vertebrate classes, but this is due predominantly to a change in N-terminal length. As evidenced by a comparison between fish and mammals, an evolutionary trend towards an increase of the length of the N-terminus of the H⁺,K⁺-ATPase on going from an ancestral fish to mammals could be identified. This evolutionary trend supports the hypothesis that the N-terminus is important in ion pump function or regulation. In placental mammals, one of the lysines is replaced by serine (Ser-27), which is a target for protein kinase C. In most other animal species, a lysine occupies this position and hence no protein kinase C target is present. Interaction with protein kinase C is thus not the primary role of the lysine-rich N-terminus. The disordered structure of the N-terminus may, via increased flexibility, facilitate interaction with another binding partner, e.g. the surrounding membrane, or help to stabilise particular enzyme conformations via the increased entropy it produces.

Sol-Gel Synthesis, Spectroscopic and Thermal Behavior Study of SiO₂/PEG Composites Containing Different Amount of Chlorogenic Acid

In this work, new phenol-based materials have been synthesized by the sol-gel method, in which different amounts of the phenolic antioxidant chlorogenic acid (CGA) (from 5 wt % to 20 wt %) were embedded in two different silica matrices: pure silica and silica-based hybrids materials, containing 50 wt % of polyethylene glycol (PEG). The incorporation of CGA in different sol-gel matrices might protect them from degradation, which could cause the loss of their properties. The two series of materials were chemically characterized by Fourier transform infrared (FTIR) spectroscopy. In addition, the thermal behavior of both series of materials containing CGA was studied by thermogravimetry under both air and inert N₂ flowing gas atmosphere. The bioactivity was evaluated by soaking the synthesized hybrids in a simulated body fluid, showing that the bioactivity of the silica matrix is not modified by the presence of PEG and CGA.