The Coarse-Grained (CG) molecular dynamics (MD) simulations were used to simulate the structural behavior of biological membranes. The CG MD simulated models cover the different membrane lipidic vesicle systems with amyloid peptides and/or cholesterol and melatonin molecules. The CG MD technique allows one to considerable extend the accessible size and time in simulations of biological systems such as lipid bilayers, big vesicles, filaments, etc, containing several hundred thousand up to multi-million particles. The structural properties of model lipid membranes (spherical-like vesicles) were studied and MD simulation data were correlated with the experimental ones (the neutron scattering in particular). The molecular systems were designed and studied to associate the experimental and model studies with the nature of the mechanisms of occurrence of Alzheimer’s disease. Under certain conditions the amyloid beta oligomer can undergo an incorrect conformational rearrangement leading to the transition of “normal” soluble peptides into a toxic conformation, while causing the formation of filamentous aggregates – insoluble rigid fibrils of large sizes, that are a sign of the disease. However, the toxic effect, which has a destructive effect on the nerve cells of the brain, is possessed already by isolated misfolded peptides born in the cell membrane.

We have studied the effect of calcium ions (Ca 2 + ) at various concentrations on the structure of lipid vesicles in the presence of amyloid-beta peptide A beta (25-35). In particular, we have investigated the influence of calcium ions on the formation of recently documented bicelle-like structures (BLSs) emerged as a result of A beta (25-35) triggered membrane disintegration. First, we have shown by using small-angle X-ray and neutron scattering that peptide molecules rigidify the lipid bilayer of gel phase DPPC unilamellar vesicles (ULVs), while addition of the calcium ions to the system hinders this effect of A beta (25-35). Secondly, the A beta (25-35) demonstrates a critical peptide concentration at which the BLSs reorganize from ULVs due to heating and cooling the samples through the lipid main phase transition temperature ( T m ). However, addition of calcium ions does not affect noticeably the A beta- induced formation of BLSs and their structural parameters, though the changes in peptide's secondary structure, e.g. the increased alpha-helix fraction, has been registered by circular dichroism spectroscopy. Finally, according to 31 P nuclear magnetic resonance (NMR) measurements, calcium ions do not affect the lipid-peptide arrangement in BLSs and their ability to align in the magnetic field of NMR spectrometer. The influences of various concentrations of calcium ions on the lipid-peptide interactions may prove biologically important because their local concentrations vary widely in in-vivo conditions. In the present work, calcium ions were investigated as a possible tool aimed at regulating the lipid-peptide interactions that demonstrated the disruptive effect of A beta (25-35) on lipid membranes.

Studies of proteins, found in one of the most stress-resistant animals tardigrade Ramazzottius varieornatus, aim to reveal molecular principles of extreme tolerance to various types of stress and developing applications based on them for medicine, biotechnology, pharmacy, and space research. Tardigrade DNA/RNA-binding damage suppressor protein (Dsup) reduces DNA damage caused by reactive oxygen spices (ROS) produced upon irradiation and oxidative stresses in Dsup-expressing transgenic organisms. This work is focused on the determination of structural features of Dsup protein and Dsup-DNA complex, which refines details of protective mechanism. For the first time, intrinsically disordered nature of Dsup protein with highly flexible structure was experimentally proven and characterized by the combination of small angle X-ray scattering (SAXS) technique, circular dichroism spectroscopy, and computational methods. Low resolution models of Dsup protein and an ensemble of conformations were presented. In addition, we have shown that Dsup forms fuzzy complex with DNA.

Our complementary experimental data and molecular dynamics (MD) simulations results reveal the structure of previously observed lipid bicelle-like structures (BLSs) formed in the presence of amyloid-beta peptide Aβ(25-35) below the main phase transition temperature (Tm) of saturated phosphatidylcholine lipids and small unilamellar vesicles (SUVs) above this temperature. First, we show by using solid-state 31P nuclear magnetic resonance (NMR) spectroscopy that our BLSs being in the lipid gel phase demonstrate magnetic alignment along the magnetic field of NMR spectrometer and undergo a transition to SUVs in the lipid fluid phase when heated through the Tm. Secondly, thanks to the BLS alignment we present their lipid structure. Lipids are found located not only in the flat bilayered part but also around its perimeter, which is corroborated by the results of coarse-grained (CG) MD simulations. Finally, peptides appear to mix randomly with lipids in SUVs while assuming predominantly unordered secondary structures revealed by circular dichroism (CD), Raman spectroscopy, and all-atom MD simulations. Importantly, the former is changing little when the system undergoes morphological transitions between BLSs and SUVs. Our structural results then offer a platform for studying and understanding mechanisms of morphological transformations caused by the disruptive effect of amyloid-beta peptides on the lipid bilayer.

Small-angle scattering makes it possible to solve structural biology problems without special sample preparation, which is typical for such methods as X-ray diffraction on protein crystals or cryoelectronic microscopy of proteins. This review provides examples of using small-angle scattering to solve biological problems. It is proposed to introduce into practice the use of small-angle scattering as a method of quality control of the assembly of proteins and protein complexes, as well as testing the identity of the structural organization of biological objects in the native state in prepared samples before measurements by X-ray diffraction or cryo-electron microscopy. The possibilities of the YUMO small-angle neutron scattering spectrometer on the IBR-2 pulse reactor (Laboratory of Neutron Physics of the Joint Institute for Nuclear Research, Dubna, Russia) for solving a wide range of problems, including in biophysics, structural biology, and biotechnology are shown. The main results of studies of various biological systems using small-angle neutron scattering at the YUMO installation are considered. The possibilities of developing methods of structural biology using small-angle scattering, including protein crystallization, are shown.

We have studied by means of small angle neutron scattering and diffraction, and molecular dynamics simulations the effect of lipid membrane fluidity on the amyloid-beta peptide interactions with the membrane. These interactions have been discovered previously to trigger the reorganization of model membranes between unilamellar vesicles and planar membranes (bicelle-like structures) during the lipid phase transition. The morphology changes were taking place in rigid membranes prepared of fully saturated lipids and were proposed to play a role in the onset of amyloid related disorders. We show in this study that the replacement of fully saturated lipids by more fluid mono-unsaturated lipids eliminates the mentioned morphology changes, most likely due to the absence of phase transition within the temperature range investigated. We have therefore controlled the membrane rigidity also while ensuring the presence of membrane phase transition within the biologically relevant temperatures. It was done by the addition of melatonin and/or cholesterol to the initial membranes made of saturated lipids. Small angle neutron scattering experiments performed over a range of cholesterol and melatonin concentrations show their distinctive effects on the local membrane structure only. The cholesterol for example affects the membrane curvature such that spontaneously formed unilamellar vesicles are of much larger sizes than those formed by the neat lipid membranes or membranes with melatonin added. The temperature dependent experiments, however, reveal no influence on the previously discovered membrane breakage whether cholesterol or melatonin have been added.

Ferritin is a vital protein complex responsible for storing iron in almost all living organisms. It plays a crucial role in various metabolic pathways, inflammation processes, stress response, and pathogenesis of cancer and neurodegenerative diseases. In this review we discuss the role of ferritin in diseases, cellular iron regulation, its structural features, and its role in biotechnology. We also show that molecular mechanisms of ferritin self-assembly are key for a number of biotechnological and pharmaceutical applications. The assembly pathways strongly depend on the interface context of ferritin monomers and the stability of its different intermediate oligomers. To date, several schemes of self-assembly kinetics have been proposed. Here, we compare different self-assembly mechanisms and discuss the possibility of self-assembly control by switching between deadlock intermediate states.

Amyloid-β peptide interactions with model lipid membranes have been studied by means of small angle neutron scattering and molecular dynamics simulations. These interactions had been indicated recently as an origin of the membrane structure reorganizations between spherical small unilamellar vesicles and planar bicelle-like structures. In present work, we investigate the influence of charge on the peptide-triggered morphological changes by introducing the anionic lipid DMPS to the underlying DMPC membrane. Changes to the membrane thickness and the overall membrane structure with and without Aβ25-35 incorporated have been investigated over a wide range of temperatures. Our results document the previously reported morphological reformations between bicelle-like structures present in gel phase and small unilamellar vesicles present in fluid phase to be independent from the charge existence in the system.

Despite remarkable progress, mainly due to the development of LCP and ‘bicelle’ crystallization, lack of structural information remains a bottleneck in membrane protein (MP) research. A major reason is the absence of complete understanding of the mechanism of crystallization. Here we present small-angle scattering studies of the evolution of the “bicelle” crystallization matrix in the course of MP crystal growth. Initially, the matrix corresponds to liquid-like bicelle state. However, after adding the precipitant, the crystallization matrix transforms to jelly-like state. The data suggest that this final phase is composed of interconnected ribbon-like bilayers, where crystals grow. A small amount of multilamellar phase appears, and its volume increases concomitantly with the volume of growing crystals. We suggest that the lamellar phase surrounds the crystals and is critical for crystal growth, which is also common for LCP crystallization. The study discloses mechanisms of “bicelle” MP crystallization and will support rational design of crystallization.

Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis ( Np SRII– Np HtrII) was performed. The influence of the polydispersity of Np SRII– Np HtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.

Alzheimer's disease is a neurodegenerative brain disease, where pathological hallmarks are senile plaques consisting primarily of amyloid-beta peptides. The investigations, however, point out not only the importance of physico-chemical properties of peptides themselves, but the membranes as the targeting environment as well. Commensurately, the interrogation approaches are required to focus on these systems at various length scales ranging from the submolecular and molecular levels relevant to the structures of peptides and/or membrane lipids locally, to the supermolecular levels covering the aggregates and large structures ensuing from the peptide-membrane interactions. In this chapter, we are summarizing the previous studies that look at complex model and biological membranes using a variety of experimental and theoretical methods based on, or complementing, the scattering techniques. We attempt to examine the effects modulated by the presence of Aβ peptides, and more importantly to determine the modes of interaction between membranes and peptides.

The amyloid-beta peptide (Aβ) is considered a key factor in Alzheimer's disease (AD) ever since the discovery of the disease. The understanding of its damaging influence has however shifted recently from large fibrils observed in the inter-cellular environment to the small oligomers interacting with a cell membrane. We studied the effect of temperature on the latter interactions by evaluating the structural characteristics of zwitterionic phosphatidylcholine (PC) membranes with incorporated Aβ 25–35 peptide. By means of small angle neutron scattering (SANS), we have observed for the first time a spontaneous reformation of extruded unilamellar vesicles (EULVs) to discoidal bicelle-like structures (BLSs) and small unilamellar vesicles (SULVs). These changes in the membrane self-organization happen during the thermodynamic phase transitions of lipids and only in the presence of the peptide. We interpret the dramatic changes in the membrane's overall shape with parallel changes in its thickness as the Aβ 25–35 triggered membrane damage and a consequent reorganization of its structure. The suggested process is consistent with an action of separate peptides or small size peptide oligomers rather than the result of large Aβ fibrils.

Two-component systems (TCS) are widespread signaling systems present in all domains of life. TCS typically consist of a signal receptor/transducer and a response regulator. The receptors (histidine kinases, chemoreceptors and photoreceptors) are often embedded in the membrane and have a similar modular structure. Chemoreceptors were shown to function in highly ordered arrays, with trimers of dimers being the smallest functional unit. However, much less is known about photoreceptors. Here, we use small-angle scattering (SAS) to show that detergent-solubilized sensory rhodopsin II in complex with its cognate transducer forms dimers at low salt concentration, which associate into trimers of dimers at higher buffer molarities. We then fit an atomistic model of the whole complex into the SAS data. The obtained results suggest that the trimer of dimers is "tripod"-shaped and that the contacts between the dimers occur only through their cytoplasmic regions, whereas the transmembrane regions remain unconnected.

The structure and dynamics of membranes depend on many external and internal factors that in turn determine their biological functions. One of the widely accepted and studied characteristics of biomembranes is their fluidity. We research a simple system with variable fluidity tweakable via its composition. The addition of cholesterol is employed to increase the order of lipid chains, thus decreasing the membrane fluidity, while melatonin is shown to elevate the chain disorder, thus also the membrane fluidity. We utilize the densitometric measurements to show a shift of studied systems closer or further from the gel-to-fluid phase transition. The structural changes represented by changes to membrane thickness are evaluated from small angle neutron scattering. Finally, we look at the ability of the two additives to control the interactions between membrane and amyloid-beta peptides. Our results suggest that fluidizing effect of melatonin can promote an insertion of peptide within the membrane interior. Intriguingly, the latter structure relates possibly to an Alzheimer's disease preventing mechanism postulated in the case of melatonin.

The Alzheimer's disease (AD) is a conformational disease caused by the formation of senile plaques, consisting primarily of Amyloid-beta peptides. The crucial role in this process at its pre-clinical stage is likely imparted by peptide-membrane interactions. The experimental data suggest several intriguing structural properties of biomimetic membranes that modulate such interactions. First, it is their sensitivity to the charge present in the surrounding environment. The structure of membranes changes for example with increasing concentration of ions, which appears to be an effect born by peculiar properties of ions and lipid themselves. Interestingly, the differences in lipid interactions with ions have been linked to the hydration properties of the ions. A plausible mechanism of action in the case of many membrane additives seems to be in shifting the water encroachment the way that bilayers absorb more or less water molecules - one of the smallest and often neglected biomolecule. The hydration interactions appear to determine also the location of membrane constituents, such as cholesterol. Moreover, cholesterol increases the order of lipid hydrocarbon chains while increasing the stiffness of membrane, in the contrary to the fluidizing effect of melatonin. Both of the latter effects have been correlated recently with the development of AD. Although a complete understanding of the physicochemical processes taking place in biomembranes is not established fully, the understanding of lipid bilayer elasto-mechanical properties provides a foundation for better insights into the structure-function relationships that most certainly take place in complex biomembrane systems.

The supramolecular organization of the visual pigment rhodopsin in the photoreceptor membrane remains contentious. Specifically, whether this G protein-coupled receptor functions as a monomer or dimer remains unknown, as does the presence or absence of ordered packing of rhodopsin molecules in the photoreceptor membrane. Completely opposite opinions have been expressed on both issues. Herein, using small-angle neutron and X-ray scattering approaches, we performed a comparative analysis of the structural characteristics of the photoreceptor membrane samples in buffer, both in the outer segment of photoreceptor cells, and in the free photoreceptor disks. The average distance between the centers of two neighboring rhodopsin molecules was found to be ~5.8 nm in both cases. The results indicate an unusually high packing density of rhodopsin molecules in the photoreceptor membrane, but molecules appear to be randomly distributed in the membrane without any regular ordering.