Deviation from the Residue-Based Linear Free Energy Relationship Reveals a Non-Native Structure in Protein Folding

Multiprobe measurements, such as NMR and hydrogen exchange study, can provide the equilibrium constant K and kinetic rate constant k of the structural changes of a polypeptide on a per-residue basis. We previously found a linear relationship between residue-specific log K values and residue-specific log k values for the two-state topological isomerization of a 27-residue peptide. To test the general applicability of the residue-based linear free energy relationship (rbLEFR), we performed a literature search to collect residue-specific equilibrium and kinetic constants in various exchange processes, including protein folding, coupled folding and binding of intrinsically disordered peptides, and structural fluctuations of folded proteins. The good linearity in a substantial number of log-log plots proved that the rbLFER holds for the structural changes in a wide variety of protein-related phenomena. Protein molecules quickly fold into their native structures and change their conformations smoothly. Theoretical studies and molecular simulations advocate that the physicochemical basis is the consistency principle and the minimal frustration principle: Non-native structures/interactions are absent or minimized along the folding pathway. The linearity of the residue-based free energy relationship demonstrates experimentally the absence of non-native structures in transition states. In this context, the hydrogen exchange study of apomyoglobin folding intermediates is particularly interesting. We found that the residues that deviated from the linear relationship corresponded to the non-native structure, which had been identified by other experiments. The rbLFER provides a unique and practical method to probe the dynamic aspects of the transition states of protein molecules.

On the Possible Spatial Structures of the β – Amyloid.

Spatial models of the β - structures of protein molecules, forming layers of amino acids, in principle, of unlimited length for both antiparallel and parallel conformation have been constructed. It is shown that the simplified flat Pauling models do not reflect the spatial structure of these layers. Using the recently developed theory of higher-dimensional polytopic prismahedrons, models of the volumetric filling of space with amino acid molecules are constructed. The constructed models for the first time mathematically describe the native structures of globular proteins.

Spatial Structures of Fibrillar Proteins

The protein molecules are considerate in the space of the highest dimension with a change in dimension with demand at the conformation of the molecules. It was shown that the widespread quasi-plane model of the Pouling protein structure do not reflect and even contradict the spatial structures of the protein in various conformations. It was found that the linear structures and folded structures of the protein in space of the highest dimension have translational symmetry. The elementary elements of protein translational symmetry were determined, their dimensions were calculated (9 for the linear structures and 23 for folded structures).

Composite systems for medical purposes, created on the basis of hydrophobic silica

Composite systems with certain cytotoxic (AM1/lectin) and adsorption (AM1/gelatin) activity have been developed on the basis of methyl silica and protein molecules – lectin and gelatin. For both types of composites, mechanisms of water binding to the surface and methods of transferring of hydrophobic materials into the aquatic environment have been investigated. The state of interfacial water in air, organic and acid media was studied. It has been found that the presence of a hydrophobic component in composites stabilizes of surface water in a weakly associated state, when a significant part of water molecules does not form hydrogen bonds. Liquid hydrophobic medium enhances this effect, and the strong acid (trifluoroacetic), added to it, promotes the transition of water to a strongly associated state. It has been shown that the redistribution of water in the interparticle intervals of AM1 with protein molecules immobilized on their surface changes under the influence of mechanical loads. Mechanoactivated samples are characterized by the possibility of water penetration into the spaces between the primary particles of methyl silica. It has been shown that immobilization of lectin on the surface of AM1 is accompanied by an increase in the interfacial energy gS from 4.1 to 5.2 J/g. This is due to an increase in the concentration of strongly bound water. If we analyze the changes in the distributions of radii R of the clusters of adsorbed water, we can state that in the water adsorbed by native lectin molecules, there are two main maxima at R = 1 and 3 nm. In the immobilized state, the maximum at R = 1 nm is present in both types of water (of different order), but the second maximum is observed only for more ordered associates.

Shock-Induced Damage Mechanism of Perineuronal Nets

The perineuronal net (PNN) region of the brain’s extracellular matrix (ECM) surrounds the neural networks within the brain tissue. The PNN is a protective net-like structure regulating neuronal activity such as neurotransmission, charge balance, and action potential generation. Shock-induced damage of this essential component may lead to neuronal cell death and neurodegenerations. The shock generated during a vehicle accident, fall, or improvised device explosion may produce sufficient energy to damage the structure of the PNN. The goal is to investigate the mechanics of the PNN in reaction to shock loading and to understand the mechanical properties of different PNN components such as glycan, GAG, and protein. In this study, we evaluated the mechanical strength of PNN molecules and the interfacial strength between the PNN components. Afterward, we assessed the PNN molecules’ damage efficiency under various conditions such as shock speed, preexisting bubble, and boundary conditions. The secondary structure altercation of the protein molecules of the PNN was analyzed to evaluate damage intensity under varying shock speeds. At a higher shock speed, damage intensity is more elevated, and hyaluronan (glycan molecule) is most likely to break at the rigid junction. The primary structure of the protein molecules is least likely to fail. Instead, the molecules’ secondary bonds will be altered. Our study suggests that the number of hydrogen bonds during the shock wave propagation is reduced, which leads to the change in protein conformations and damage within the PNN structure. As such, we found a direct connection between shock wave intensity and PNN damage.

Near-Wall Aggregation of Amyloidogenic Aβ 1-40 Peptide: Direct Observation by the FRET

The formation of amyloid fibrils is one of the variants of the self-organization of polypeptide chains. For the amyloid aggregation, the solution must be oversaturated with proteins. The interface of the liquid (solution) and solid (vessel walls) phases can trigger the adsorption of protein molecules, and the resulting oversaturation can initiate conformational transitions in them. In any laboratory experiment, we cannot exclude the presence of surfaces such as the walls of vessels, cuvettes, etc. However, in many works devoted to the study of amyloid formation, this feature is not considered. In our work, we investigated the behavior of the Aβ 1-40 peptide at the water–glass, water–quartz, and water–plastic interface. We carried out a series of simple experiments and showed that the Aβ 1-40 peptide is actively adsorbed on these surfaces, which leads to a significant interaction and aggregation of peptides. This means that the interface can be the place where the first amyloid nucleus appears. We suggest that this effect may also be one of the reasons for the difficulty of reproducing kinetic data when studying the aggregation of the amyloid of the Aβ 1-40 peptide and other amyloidogenic proteins

The Role of Cations of the Precipitant in the Interaction of Protein Molecules in the Lysozyme Oligomers in Crystallization Solutions

At the moment, the main opinion is that protein crystallization depends mainly on the the precipitant anions, therefore, there have been only few works devoted to the problem of the influence of its cations. Using the molecular dynamics method, we investigated the stability, changes in the compactness and structural transformations of lysozyme dimers and octamers in solutions with different precipitants (LiCl, NaCl, KCl and CuCl2) in order to study the contribution of cations during crystal formation in more detail. As a result, we found that cations have a rather noticeable effect on the behavior of oligomers: the higher the atomic mass of the cation, the greater the changes in the dimers structures during its dynamics and, according to the data of SAXS experiments, the lower the concentration of dimers. However, for octamers, this dependence is more complicated.

Dps protein localization studies in nanostructured silicon matrix by scanning electron microscopy

The present work is related to the microscopic studies of the morphology of the planar and inner part of silicon nanowires arrays before and after immobilization with a natural nanomaterial, Dps protein of bacterial origin. Silicon nanowires were formed by metal-assisted wet chemical etching. To obtain the recombinant protein, Escherichia coli cells were used as excretion strain and purification were carried out using chromatography. The combination of silicon nanowires with protein molecules was carried out by layering at laboratory conditions followed by drying under air. The resulting hybrid material was studied by high-resolution scanning electron microscopy. Studies of the developed surface of the nanowires array were carried out before and after combining with the bioculture. The initial arrays of silicon wireshave a sharp boundaries in the planar part and in the depth of the array, transition layers are not observed. The diameter of the silicon nanowires is about 100 nm, the height is over a micrometer, while the distances between the nanowires are several hundred of nanometers. The pores formed in this way are available for filling with protein during the immobilization of protein.The effectiveness of using the scanning electron microscopy to study the surface morphology of the hybrid material “silicon wires – bacterial protein Dps” has been demonstrated. It is shown that the pores with an extremely developed surface can be combined with a bio-material by deposition deep into cavities. The protein molecules can easily penetrate through whole porous wires matrix array. The obtained results demonstrate the possibility of efficient immobilization of nanoscaled Dps protein molecules into an accessible and controllably developed surface of silicon nanowires.

Mechanisms of modulation of pre-mRNA 3D structural scaffolds for splicing substrate definition

Coordination of different serine-arginine-rich (SR) proteins - a class of critical splicing activators - facilitates recognition of the highly degenerate cognate splice signal sequences against the background sequences. Yet, the mechanistic details of their actions remain unclear. Here we show that cooperative binding of SR proteins to exonic and intronic motifs remodels the pre-mRNA 3D structural scaffold. The scaffold generated by pre-mRNA-specific combinations of different SR proteins in an appropriate stoichiometry is recognized by U1 snRNP. A large excess of U1 snRNP particles displaces the majority of the bound SR protein molecules from the remodeled pre-mRNA. A higher than optimal stoichiometry of SR proteins occludes the binding sites on the pre-mRNA, raising the U1 snRNP levels required for SR protein displacement and potentially impeding spliceosome assembly. This novel step is important for distinguishing the substrate and the non-substrate by U2AF65 - the primary 3' splice site-recognizing factor. Overall, this work elucidates early regulatory steps of mammalian splicing substrate definition by SR proteins.

Single Molecule Measurements of the Accessibility of Molecular Surfaces

An important measure of the conformation of protein molecules is the degree of surface exposure of its specific segments. However, this is hard to measure at the level of individual molecules. Here, we combine single molecule photobleaching (smPB, which resolves individual photobleaching steps of single molecules) and fluorescence quenching techniques to measure the accessibility of individual fluorescently labeled protein molecules to quencher molecules in solution. A quencher can reduce the time a fluorophore spends in the excited state, increasing its photostability under continuous irradiation. Consequently, the photo-bleaching step length would increase, providing a measure for the accessibility of the fluorophore to the solvent. We demonstrate the method by measuring the bleaching step-length increase in a lipid, and also in a lipid-anchored peptide (both labelled with rhodamine-B and attached to supported lipid bilayers). The fluorophores in both molecules are expected to be solvent-exposed. They show a near two-fold increase in the step length upon incubation with 5 mM tryptophan (a quencher of rhodamine-B), validating our approach. A population distribution plot of step lengths before and after addition of tryptophan show that the increase is not always homogenous. Indeed there are different species present with differential levels of exposure. We then apply this technique to determine the solvent exposure of membrane-attached N-terminus labelled amylin (h-IAPP, an amyloid associated with Type II diabetes) whose interaction with lipid bilayers is poorly understood. hIAPP shows a much smaller increase of the step length, signifying a lower level of solvent exposure of its N-terminus. Analysis of results from individual molecules and step length distribution reveal that there are at least two different conformers of amylin in the lipid bilayer. Our results show that our method (“Q-SLIP”, Quenching-induced Step Length increase in Photobleaching) provides a simple route to probe the conformational states of membrane proteins at a single molecule level.