Andrei Filippov

A Hexameric Peptide Barrel as Building Block of Amyloid‐β Protofibrils

Oligomeric and protofibrillar aggregates formed by the amyloid-β peptide (Aβ) are believed to be involved in the pathology of Alzheimers disease. Central to Alzheimer pathology is also the fact that the longer Aβ42 peptide is more prone to aggregation than the more prevalent Aβ40 . Detailed structural studies of Aβ oligomers and protofibrils have been impeded by aggregate heterogeneity and instability. We previously engineered a variant of Aβ that forms stable protofibrils and here we use solid-state NMR spectroscopy and molecular modeling to derive a structural model of these. NMR data are consistent with packing of residues 16 to 42 of Aβ protomers into hexameric barrel-like oligomers within the protofibril. The core of the oligomers consists of all residues of the central and C-terminal hydrophobic regions of Aβ, and hairpin loops extend from the core. The model accounts for why Aβ42 forms oligomers and protofibrils more easily than Aβ40 .

Hydrogen Bonding in Alzheimer’s Amyloid‐β Fibrils Probed by 15N{17O} REAPDOR Solid‐State NMR Spectroscopy

An exclusive label: 15N{17O} REAPDOR NMR was used to validate intermolecular C17O⋅⋅⋅H15N hydrogen bonding in Ac-Aβ(16–22)-NH2 (see scheme) and Aβ(11–25) amyloid fibrils, which are associated with Alzheimers disease, by selectively labeling them with 17O and 15N. This method was effective for confirming the structure of these fibrils, and could be useful for a number of other biological samples.

High-resolution NMR structure of the antimicrobial peptide protegrin-2 in the presence of DPC micelles

AbstractPG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-α-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, since the dimer can be regarded as the primary unit for assembly into the ordered aggregates. It was supposed that only 12 residues (RGGRL-CYCRR-RFCVC-V) are needed to endow protegrin molecules with strong antibacterial activity and that at least four additional residues are needed to add potent antifungal properties. Thus, the 16-residue protegrin (PG-2) represents the minimal structure needed for broad-spectrum antimicrobial activity encompassing bacteria and fungi. As the peptide conformation and peptide-to-membrane binding properties are very sensitive to single amino acid substitutions, the solution structure of PG-2 in solution and in a membrane mimicking environment are crucial. In order to find evidence if the oligomerization state of PG-1 in a lipid environment will be the same or not for another protegrins, we investigate in the present work the PG-2 NMR solution structure in the presence of perdeuterated DPC micelles. The NMR study reported in the present work indicates that PG-2 form a well-defined structure (PDB: 2MUH) composed of a two-stranded antiparallel β-sheet when it binds to DPC micelles.

Aggregation of amyloid Aβ(1–40) peptide in perdeuterated 2,2,2-trifluoroethanol caused by ultrasound sonication

Ultrasound sonication of protein and peptide solutions is routinely used in biochemical, biophysical, pharmaceutical and medical sciences to facilitate and accelerate dissolution of macromolecules in both aqueous and organic solvents. However, the impact of ultrasound waves on folding/unfolding of treated proteins, in particular, on aggregation kinetics of amyloidogenic peptides and proteins is not understood. In this work, effects of ultrasound sonication on the misfolding and aggregation behavior of the Alzheimers Aβ(1–40)‐peptide is studied by pulsed‐field gradient (PFG) spin–echo diffusion NMR and UV circular dichroism (CD) spectroscopy. Upon simple dissolution of Aβ(1–40) in perdeuterated trifluoroethanol, CF3‐CD2‐OD (TFE‐d3), the peptide is present in the solution as a stable monomer adopting α‐helical secondary structural motifs. The self‐diffusion coefficient of Aβ(1–40) monomers in TFE‐d3 was measured as 1.35 × 10−10 m2 s−1, reflecting its monomeric character. However, upon ultrasonic sonication for less than 5 min, considerable populations of Aβ molecules (ca 40%) form large aggregates as reflected in diffusion coefficients smaller than 4.0 × 10−13 m2 s−1. Sonication for longer times (up to 40 min in total) effectively reduces the fraction of these aggregates in 1H PFG NMR spectra to ca 25%. Additionally, absorption below 230 nm increased significantly upon sonication treatment, an observation, which also clearly confirms the ongoing aggregation process of Aβ(1–40) in TFE‐d3. Surprisingly, upon ultrasound sonication only small changes in the peptide secondary structure were detected by CD: the peptide molecules mainly adopt α‐helical motifs in both monomers and aggregates formed upon sonication. Copyright

Lateral diffusion in sphingomyelin bilayers

Sphingomyelin (SM) is an important lipid of eukaryotic cellular membranes and neuronal tissues. We studied lateral diffusion in macroscopically oriented bilayers of synthetic palmitoylsphingomyelin (PSM) and natural sphingomyelins of egg yolk (eSM), bovine brain (bSM) and bovine milk (mSM) by pulsed field gradient NMR (PFG NMR) in the temperature range 45–60 °C. We found that the mean values of lateral diffusion coefficients (LDCs) of SMs are 1.9‐fold lower compared with those of dipalmitoylphosphatidylcholine (DPPC), which is similar in molecular structure. This discrepancy could be explained by the characteristics of intermolecular SM interactions. The LDCs of different SMs differ: egg SM is most similar to PSM; both of them have a 10% higher LDC value compared with the other two natural SMs. Besides, all natural SMs show a complicated form of the spin‐echo diffusion decay (DD), which is an indicator of a distribution of LDC values in bilayers. This peculiarity is explained by the broad distributions of hydrocarbon chain lengths of the natural SMs studied here, especially mSM and bSM. We confirmed the relationship between chain length and LDC in the bilayers by computer analysis of a set of 1H NMR spectra obtained by scanning the value of the pulsed field gradient. There is a correlation between lower LDC values and SM molecules with longer acyl chains. The most probable mechanisms by which long‐chain SM molecules decrease their lateral diffusion relative to the average value are protrusion into the other side of the bilayer or lateral separation into areas that diverge with their LDCs. Copyright

Amyloid Hydrogen Bonding Polymorphism Evaluated by 15N{17O}REAPDOR Solid-State NMR and Ultra-High Resolution Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

A combined approach, using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and solid-state NMR (Nuclear Magnetic Resonance), shows a high degree of polymorphism exhibited by Aβ species in forming hydrogen-bonded networks. Two Alzheimers Aβ peptides, Ac-Aβ(16-22)-NH2 and Aβ(11-25), selectively labeled with (17)O and (15)N at specific amino acid residues were investigated. The total amount of peptides labeled with (17)O as measured by FTICR-MS enabled the interpretation of dephasing observed in (15)N{(17)O}REAPDOR solid-state NMR experiments. Specifically, about one-third of the Aβ peptides were found to be involved in the formation of a specific >C═(17)O···H-(15)N hydrogen bond with their neighbor peptide molecules, and we hypothesize that the rest of the molecules undergo ± n off-registry shifts in their hydrogen bonding networks.

Self‐diffusion and interactions in mixtures of imidazolium bis(mandelato)borate ionic liquids with polyethylene glycol: 1H NMR study

We used 1H nuclear magnetic resonance pulsed‐field gradient to study the self‐diffusion of polyethylene glycol (PEG) and ions in a mixture of PEG and imidazolium bis(mandelato)borate ionic liquids (ILs) at IL concentrations from 0 to 10 wt% and temperatures from 295 to 370 K. PEG behaves as a solvent for these ILs, allowing observation of separate lines in 1H NMR spectra assigned to the cation and anion as well as to PEG. The diffusion coefficients of PEG, as well as the imidazolium cation and bis(mandelato)borate (BMB) anion, differ under all experimental conditions tested. This demonstrates that the IL in the mixture is present in at least a partially dissociated state, while the lifetimes of the associated states of the ions and ions with PEG are less than ~30 ms. Generally, increasing the concentration of the IL leads to a decrease in the diffusion coefficients of PEG and both ions. The diffusion coefficient of the anion is less than that of the cation; the molecular mass dependence of diffusion of ions can be described by the Stokes–Einstein model. NMR chemical shift alteration analysis showed that the presence of PEG changes mainly the chemical shifts of protons belonging to imidazole ring of the cation, while chemical shifts of protons of anions and PEG remain unchanged. This demonstrated that the imidazolium cation interacts mainly with PEG, which most probably occurs through the oxygen of PEG and the imidazole ring. The BMB anion does not strongly interact with PEG, but it may be indirectly affected by PEG through interaction with the cation, which directly interacts with PEG. Copyright

Effect of Curcumin on Lateral Diffusion of Phosphatidylcholines in Saturated and Unsaturated Bilayers

Curcumin, a dietary polyphenol, is a natural spice with preventive and therapeutic potential for neurodegenerative diseases such as Alzheimers and Parkinsons diseases. Curcumin possesses a spectrum of antioxidant, anti-inflammatory, anticarcinogenic, and antimutagenic properties. Because of this broad spectrum of pharmacological activity, it has been suggested that, like cholesterol, curcumin exerts its effect on a rather basic biological level, such as on lipid bilayers of biomembranes. The effect of curcumin on translational mobility of lipids in biomembranes has not yet been studied. In this work, we used (1)H NMR diffusometry to explore lateral diffusion in planar-oriented bilayers of dimyristoylphosphatidylcholine (DMPC) and dioleoylphosphatidylcholine (DOPC) at curcumin concentrations of up to 40 mol % and in the temperature range of 298-333 K. The presence of curcumin at much lower concentrations (∼7 mol %) leads to a decrease in the lateral diffusion coefficient of DOPC by a factor of 1.3 at lower temperatures and by a factor of 1.14 at higher temperatures. For DMPC, the diffusion coefficient decreases by a factor of 1.5 at lower temperatures and by a factor of 1.2 at higher temperatures. Further increasing the curcumin concentration has no effect. Comparison with cholesterol showed that curcumin and cholesterol influence lateral diffusion of lipids differently. The effect of curcumin is determined by its solubility in lipid bilayers, which is as low as 10 mol % that is much less than that of cholesteroĺs 66 mol %.

Insights into the effect of CO2 absorption on the ionic mobility of ionic liquids

We investigate a comparative effect of CO2 absorption on the ionic mobility of two choline based ionic liquids comprising two different anions such as threonine and imidazole. The synthesized ionic liquids were characterized using 1H and 13C NMR and other spectroscopic techniques. By keeping a common cation and changing the anion from threonine to imidazole both the viscosity and density reduced drastically. We found that [N1,1,6,2OH][Imi] exhibits the highest CO2 capture capacity at 20 °C of 5.27 mol of CO2 per kg of ionic liquid (1.27 mol of CO2 per mol of ionic liquid, 23.26 wt% of CO2) whereas [N1,1,6,2OH][Threo] exhibits 3.6 mol of CO2 per kg of ionic liquid (1.05 mol of CO2 per mol of ionic liquid, 15.87 wt% of CO2). The activation energy for diffusion is calculated using the Vogel-Fulcher-Tamman (VFT) equation in the form of diffusivity. It was found that the activation energy for the diffusion of [N1,1,6,2OH][Threo] is ∼10 times higher than that of [N1,1,6,2OH][Imi]. 1H diffusion NMR data revealed that the diffusivity of [N1,1,6,2OH][Imi] is increased after CO2 absorption whereas a decrease in diffusivity was observed in the case of [N1,1,6,2OH][Threo]. This anomalous behavior of [N1,1,6,2OH][Imi] was further explained by using DFT calculations.

Micelle structure and molecular self-diffusion in isononylphenol ethoxylate–water systems

The structure and dynamic properties of micellar solutions of nonionic surfactants of a series of isononylphenol ethoxylates, C9H19C6H4O(C2H4O)nH (where n = 6,8,9,10, and 12), were studied by NMR diffusometry, dynamic light scattering, and viscosimetry. The sizes of the micelles were determined for different surfactants and at different surfactant concentrations. The numbers of water molecules bound by a micelle and by one oxyethylene group of the surfactant were estimated. Copyright