Unfolded Structure Research Articles

A base measure of precision for protein stability predictors: structural sensitivity

BackgroundPrediction of the change in fold stability (ΔΔG) of a protein upon mutation is of major importance to protein engineering and screening of disease-causing variants. Many prediction methods can use 3D structural information to predict ΔΔG. While the performance of these methods has been extensively studied, a new problem has arisen due to the abundance of crystal structures: How precise are these methods in terms of structure input used, which structure should be used, and how much does it matter? Thus, there is a need to quantify the structural sensitivity of protein stability prediction methods.ResultsWe computed the structural sensitivity of six widely-used prediction methods by use of saturated computational mutagenesis on a diverse set of 87 structures of 25 proteins. Our results show that structural sensitivity varies massively and surprisingly falls into two very distinct groups, with methods that take detailed account of the local environment showing a sensitivity of ~ 0.6 to 0.8 kcal/mol, whereas machine-learning methods display much lower sensitivity (~ 0.1 kcal/mol). We also observe that the precision correlates with the accuracy for mutation-type-balanced data sets but not generally reported accuracy of the methods, indicating the importance of mutation-type balance in both contexts.ConclusionsThe structural sensitivity of stability prediction methods varies greatly and is caused mainly by the models and less by the actual protein structural differences. As a new recommended standard, we therefore suggest that ΔΔG values are evaluated on three protein structures when available and the associated standard deviation reported, to emphasize not just the accuracy but also the precision of the method in a specific study. Our observation that machine-learning methods deemphasize structure may indicate that folded wild-type structures alone, without the folded mutant and unfolded structures, only add modest value for assessing protein stability effects, and that side-chain-sensitive methods overstate the significance of the folded wild-type structure.

Ultrasound-assisted Maillard reaction of ovalbumin/xylose: The enhancement of functional properties and its mechanism

This study aims to optimize the ultrasound treatment conditions for enhancing the degree of glycation (DG) of ovalbumin (OVA)-xylose conjugates through Maillard reaction and investigate the correlation between DG and functional properties affected by structural changes. The structural and functional properties of classical heating OVA, glycated OVA, ultrasonic treated OVA, and ultrasound-assisted glycated OVA were investigated to explore the interaction mechanism of ultrasound treatment on foaming and emulsifying properties improvement. Results indicated that the ultrasound assistance increased free sulfhydryl content, surface hydrophobicity and particle size of OVA-xylose conjugates, and thus enhancing the surface properties, which were strongly linear correlated with DG under different glycation parameters (pH, xylose/OVA ratio, heating time). Additionally, circular dichroism spectroscopy analysis revealed that ultrasound promoted the conversion of α-helices to β-sheets and unfolded structures, which was consistent with the formation of short amyloid-like aggregates that observed by atomic force microscopy phenomenon. Overall, our study provides new insights into the effects of ultrasound treatment on Maillard-induced protein functional properties enhancement, which may be a new strategy to tune the DG and functionality of protein-saccharide grafts during ultrasound processing.

Improved Processability of Soy Proteins Due to Conformational Controls under a Combination of Chemical and Mechanical Treatments

Conformations of soy proteins in soy protein isolate (SPI) aqueous dispersions determine the processability of the SPI and are affected significantly by pH conditions and the addition of a plasticizer, when mechanical forces are present. In this work, the effect of chemical forces facilitating the physical treatment in modifying the conformational structures of soy proteins was investigated. SPI in a H2O system under extreme pH conditions and a glycerol/H2O system was subjected to a combination of ultrasound and shear (USSH) treatments to increase the processability of soy proteins by conformational denaturation. In the H2O system, the combination of the USSH treatment and different pH conditions provides varied properties of denatured SPI solutions and fabricated SPI–cellophane composite films. In the glycerol/H2O system, with an increased and stabilized viscosity, a higher content of sulfhydryl groups, swelled particle sizes, and unfolded protein structures, glycerol proved to be an efficient structural stabilizing agent assisting the deformation of soy proteins under the USSH treatment. The combinations of the USSH treatment and extreme pH conditions or the glycerol/H2O system proved to be efficient processing methods for increasing the processability of soy proteins as a raw material in products.

Иерархическая классификация географических систем

A hierarchical system is the result of dividing a set of objects into subordinate groups in order from highest to lowest, where each lower level reveals and clarifies the properties of objects at a higher level. There is a difference between the natural hierarchy of geosystems-geochors and the hierarchy of geomers, which leads to taxonomic classification. Theoretical basis for creating a hierarchical classification of geosystems are developed using a conceptual model of geographical cycles of accumulation and removal of factor load on territorial objects of various scales. The cone of chorological and typological connections is considered as the basic metamodel of hierarchical structure. For its research, we use descriptive geometry tools to represent the cone in the vertical and horizontal (plan) projections. The surface and unfolding structures of the cone with sections at different levels reflect the hierarchy. The planned projection in the form of concentric structures is considered as model of the archetype of hierarchy formation. The horological and typological classifications converge in the position “natural zone” as the “parent core” of the type of natural environment, which represents the zonal norm. The concentric model has various interpretations, in particular, it is described as a system of local coordinates, where each coordinate corresponds to the categories of seriality of geosystems, i.e. the degree of their factoral-dynamic variability relatively to zonal geosystems. In the coordinate approach, the classification looks like a ranked set of merons and taxa, where the meron categories are represented by quantum numbers of the coordinate series, and the taxon is a sequence of such numbers of different series (numeric code). The formation of hierarchical classification is based on the triad principle, when the taxon of the upper level is divided into three lower level gradations, which are arranged in a homological series according to the degree of seriality. There is an analogy between the hierarchical structure of the periodic system of chemical elements and the typological classification of geosystems, when the periods of the system of elements correspond to the high-altitude layers and latitudinal zones of geochor placement or hierarchical levels of geomer classification. An unfolding and plan projection of the classification cone of facies for the Prichunsky landscape of the southern taiga of Central Siberia in three basic categories of variability of different levels geomers are presented.

A protein folding robot driven by a self-taught agent

This paper presents a computer simulation of a virtual robot that behaves as a peptide chain of the Hemagglutinin-Esterase protein (HEs) from human coronavirus. The robot can learn efficient protein folding policies by itself and then use them to solve HEs folding episodes. The proposed robotic unfolded structure inhabits a dynamic environment and is driven by a self-taught neural agent. The neural agent can read sensors and control the angles and interactions between individual amino acids. During the training phase, the agent uses reinforcement learning to explore new folding forms that conduce toward more significant rewards. The memory of the agent is implemented with neural networks. These neural networks are noise-balanced trained to satisfy the look for future conditions required by the Bellman equation. In the operating phase, the components merge into a wise up protein folding robot with look-ahead capacities, which consistently solves a section of the HEs protein.

A combinatorial native MS and LC-MS/MS approach reveals high intrinsic phosphorylation of human Tau but minimal levels of other key modifications

Abnormal changes of neuronal Tau protein, such as phosphorylation and aggregation, are considered hallmarks of cognitive deficits in Alzheimer's disease. Abnormal phosphorylation is thought to precede aggregation and therefore to promote aggregation, but the nature and extent of phosphorylation remain ill-defined. Tau contains ∼85 potential phosphorylation sites, which can be phosphorylated by various kinases because the unfolded structure of Tau makes them accessible. However, methodological limitations (e.g. in MS of phosphopeptides, or antibodies against phosphoepitopes) led to conflicting results regarding the extent of Tau phosphorylation in cells. Here we present results from a new approach based on native MS of intact Tau expressed in eukaryotic cells (Sf9). The extent of phosphorylation is heterogeneous, up to ∼20 phosphates per molecule distributed over 51 sites. The medium phosphorylated fraction Pm showed overall occupancies of ∼8 Pi (± 5) with a bell-shaped distribution; the highly phosphorylated fraction Ph had 14 Pi (± 6). The distribution of sites was highly asymmetric (with 71% of all P-sites in the C-terminal half of Tau). All sites were on Ser or Thr residues, but none were on Tyr. Other known posttranslational modifications were near or below our detection limit (e.g. acetylation, ubiquitination). These findings suggest that normal cellular Tau shows a remarkably high extent of phosphorylation, whereas other modifications are nearly absent. This implies that abnormal phosphorylations at certain sites may not affect the extent of phosphorylation significantly and do not represent hyperphosphorylation. By implication, the pathological aggregation of Tau is not likely a consequence of high phosphorylation.

Learning from Failure: Big Data Analysis for Detecting the Patterns of Failure in Innovative Startups.

This article aims at identifying appropriate models for analyzing large datasets to serve a twofold goal: first, to better understand the dynamics impacting innovative startups' performance and their managerial practice and, second, to detect their patterns of failure. Therefore, we investigate the interaction of economic-financial, context, and governance dimensions of 4185 Italian innovative startups created from 2012 to 2015. Once startups have been grouped, we focus only on those that are unsuccessful. Then, failure patterns have been uncovered, integrating the use of factor and cluster analysis, where factor scores for each firm are used to identify a set of homogeneous groups based on clustering methods. The integrated use of those large-dimensional data techniques permits to classify items in rigorous ways and to unfold structures of the data, which are not apparent in the beginning. The analysis suggests that each pattern of failure is a multidimensional construct and, as a consequence can generate different managerial implications. Therefore, an effective handling of failure requires management to use appropriate interventions targeted at the challenges faced by that particular pattern of failure in the age of different firms.

Understanding the lost functionality of ethanol in non-alcoholic beer using sensory evaluation, aroma release and molecular hydrodynamics

Consumer sensory evaluation, aroma release analysis and biophysical protein analysis were used to investigate the effect of ethanol on the release and perception of flavour in beer (lager and stout) at different ethanol levels (0 and 5% ABV). Consumer study results showed no significant differences in orthonasal perception, yet retronasal results showed that 0% lager was perceived as maltier with reduced fruitiness, sweetness, fullness/body and alcohol warming sensation (p < 0.05). Whilst ethanol alone decreases the aroma release regardless of LogP, the presence of α-amylase selectively reduces the headspace concentration of hydrophobic compounds. It was found that ethanol has a subtle inhibitory effect on the binding of hydrophobic compounds to α-amylase, thereby increasing their headspace concentration in the 5% ABV as compared to the 0% beers. This synergistic ethanol * saliva effect is attributed to the changes in the conformation of α-amylase due to ethanol-induced denaturation. It is hypothesised that the partially unfolded protein structures have a lower number of hydrophobic pockets, leading to a lower capacity to entrap hydrophobic aroma compounds. This supports the hypothesis that ethanol * saliva interactions directly impact the sensory and flavour properties of beer, which would provide a basis for further investigations in reformulation of 0% ABV drinks.

Zur temporalen Entfaltung und multimodalen Orchestrierung von konzeptuellen Räumen am Beispiel einer Erzählung

The study presented in this article investigates the temporal unfolding and multimodal orchestration of meaning in a narration. Two aspects are focused on. First, the temporal and multimodal orchestration of conceptual spaces in the entire narrative is described. Five conceptual spaces were identified which were construed by multiple visual-kinesic modalities and speech. Moreover, the study showed that the conceptual spaces are often created simultaneously, which, however, does not lead to communication problems due to the media properties of the modalities involved (see also Schmitt 2005). The second part of the analysis zoomed in onto the phase of the narrative climax in which the multimodal production of the narrative space with role shift dominated. By applying a timeline-annotation procedure for gestures (Müller/Ladewig 2013) a temporally unfolding salience structure (Müller/Tag 2010) could be reconstructed which highlights certain semantic aspects in the creation and flow of multimodal meaning. Thus, specific information “necessary” to understand the climax of the narration was foregrounded and made prominent for a co-participant. By focusing methodically and theoretically on the temporal structure and the interplay of different modalities, the paper offers a further contribution to the current discussion about temporality, dynamics and multimodality of language (Deppermann/Günthner 2015; Müller 2008b).

Meta Learning-Based MIMO Detectors: Design, Simulation, and Experimental Test

Deep neural networks (NNs) have exhibited considerable potential for efficiently balancing the performance and complexity of multiple-input and multiple-output (MIMO) detectors. However, existing NN-based MIMO detectors are difficult to be deployed in practical systems because of their slow convergence speed and low robustness in new environments. To address these issues systematically, we propose a receiver framework that enables efficient online training by leveraging the following simple observation: although NN parameters should adapt to channels, not all of them are channel-sensitive. In particular, we use a deep unfolded NN structure that represents iterative algorithms in signal detection and channel decoding modules as multi layer deep feed forward networks. An expectation propagation (EP) module, called EPNet, is established for signal detection by unfolding the EP algorithm and rendering the damping factors trainable. An unfolded turbo decoding module, called TurboNet, is used for channel decoding. This component decodes the turbo code, where trainable NN units are integrated into the traditional max-log-maximum <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">a posteriori</i> decoding procedure. We demonstrate that TurboNet is robust for channels and requires only one off-line training. Therefore, only a few damping factors in EPNet must be re-optimized online. An online training mechanism based on meta learning is then developed. Here, the optimizer, which is implemented by long short-term memory NNs, is trained to update damping factors efficiently by using a small training set such that they can quickly adapt to new environments. Simulation results indicate that the proposed receiver significantly outperforms traditional receivers and that the online learning mechanism can quickly adapt to new environments. Furthermore, an over-the-air platform is presented to demonstrate the significant robustness of the proposed receiver in practical deployment.

Bovine β-casein binding studies of a Schiff base ligand: fluorescence and circular dichroism approaches.

In this study, a Schiff base derived from a heterocyclic moiety was synthesized and characterized. The in vitro binding behaviour of this ligand with β-casein (β-CN) was investigated using biophysical techniques. For evaluation, thermodynamics variables of interactions between the Schiff base ligand and β-CN, such as fluorescence at different temperatures, were measured. The results showed that the Schiff base ligand possessed considerable associated binding to β-CN and that the procedure was enthalpy driven. The β-CN conformation was also changed to give a further unfolded structure. Fluorescence resonance energy transfer was used to estimate the interval between donor (β-CN) and acceptor (Schiff base ligand). All these experimental results proposed that β-CN might act as carrier protein for the Schiff base ligand to deliver it to the target molecules.

Cu-Doped KCl Unfolded Band Structure and Optical Properties Studied by DFT Calculations.

The unfolded band structure and optical properties of Cu-doped KCl crystals were computed by first principles within the framework of density functional theory, implemented in the ABINIT software program, utilizing pseudopotential approximation and a plane-wave basis set. From a theoretical point of view, Cu substitution into pristine KCl crystals requires calculation by the supercell (SC) method. This procedure shrinks the Brillouin zone, resulting in a folded band structure that is difficult to interpret. To solve this problem and gain insight into the effect of copper ions (Cu+) on electronic properties, the band structure of SC KCl:Cu was unfolded to make a direct comparison with the band structure of the primitive cell (PC) of pristine KCl. To understand the effect of Cu substitution on optical absorption, we calculated the imaginary part of the dielectric function of KCl:Cu through a sum-over-states formalism and broke it down into different band contributions by partially making an iterated cumulative sum (ICS) of selected valence and conduction bands. Consequently, we identified those interband transitions that give rise to the absorption peaks due to the Cu+ ion. These transitions involve valence and conduction bands formed by the Cu-3d and Cu-4s electronic states.

In vitro digestion and cellular antioxidant activity of β-carotene-loaded emulsion stabilized by soy protein isolate-Pleurotus eryngii polysaccharide conjugates

β-Carotene is a natural fat-soluble antioxidant, while the poor oral bioavailability of β-carotene restricts its application for functional foods. To overcome this barrier, a stable oil-in-water emulsion was structured to effectively deliver β-carotene. In this study, soy protein isolate (SPI)-Pleurotus eryngii polysaccharide (PEP) conjugate was prepared by Maillard reaction under controlled wet-heating conditions. β-Carotene was encapsulated in SPI-PEP conjugate-stabilized emulsion and its gastrointestinal behavior and antioxidant activity were assessed in vitro. The results showed that such conjugate with high molecular weight was mainly formed through PEP covalently binding to lysine and cysteine of SPI via C–N. Changes in spatial structure of SPI-PEP conjugate resulted from its decreased tryptophan fluorescence intensity and unfolded protein secondary structure. A decreased surface hydrophobicity and flat surface morphology of SPI-PEP conjugate contributed to its increased water solubility and emulsibility. Additionally, lipid digestion and the formation of mixed micelles were promoted in SPI-PEP conjugate-stabilized emulsion due to its strong steric repulsion, resulting in an improved bioavailability of β-carotene. Such improvement was favorable for β-carotene to relieve tert-butyl hydroperoxide-induced oxidative stress by decreasing reactive oxygen species production and enhancing antioxidant enzyme activities in Caco-2 cells. Our study suggested that Maillard-type protein-polysaccharide conjugates-stabilized emulsions had a potential industry application for the delivery of fat-soluble nutrients.

Conserved tryptophan mutation disrupts structure and function of immunoglobulin domain revealing unusual tyrosine fluorescence.

Immunoglobulin (Ig) domains are the most prevalent protein domain structure and share a highly conserved folding pattern; however, this structural family of proteins is also the most diverse in terms of biological roles and tissue expression. Ig domains vary significantly in amino acid sequence but share a highly conserved tryptophan in the hydrophobic core of this beta-stranded protein. Palladin is an actin binding and bundling protein that has five Ig domains and plays an important role in normal cell adhesion and motility. Mutation of the core tryptophan in one Ig domain of palladin has been identified in a pancreatic cancer cell line, suggesting a crucial role for this sole tryptophan in palladin Ig domain structure, stability, and function. We found that actin binding and bundling was not completely abolished with removal of this tryptophan despite a partially unfolded structure and significantly reduced stability of the mutant Ig domain as shown by circular dichroism investigations. In addition, this mutant palladin domain displays a tryptophan-like fluorescence attributed to an anomalous tyrosine emission at 341 nm. Our results indicate that this emission originates from a tyrosinate that may be formed in the excited ground state by proton transfer to a nearby aspartic acid residue. Furthermore, this study emphasizes the importance of tryptophan in protein structural stability and illustrates how tyrosinate emission contributions may be overlooked during the interpretation of the fluorescence properties of proteins.

Real-time tracking of protein unfolding with time-resolved x-ray solution scattering.

The correct folding of proteins is of paramount importance for their function, and protein misfolding is believed to be the primary cause of a wide range of diseases. Protein folding has been investigated with time-averaged methods and time-resolved spectroscopy, but observing the structural dynamics of the unfolding process in real-time is challenging. Here, we demonstrate an approach to directly reveal the structural changes in the unfolding reaction. We use nano- to millisecond time-resolved x-ray solution scattering to probe the unfolding of apomyoglobin. The unfolding reaction was triggered using a temperature jump, which was induced by a nanosecond laser pulse. We demonstrate a new strategy to interpret time-resolved x-ray solution scattering data, which evaluates ensembles of structures obtained from molecular dynamics simulations. We find that apomyoglobin passes three states when unfolding, which we characterize as native, molten globule, and unfolded. The molten globule dominates the population under the conditions investigated herein, whereas native and unfolded structures primarily contribute before the laser jump and 30 μs after it, respectively. The molten globule retains much of the native structure but shows a dynamic pattern of inter-residue contacts. Our study demonstrates a new strategy to directly observe structural changes over the cause of the unfolding reaction, providing time- and spatially resolved atomic details of the folding mechanism of globular proteins.

Unfolding optical transition weights of impurity materials for first-principles LCAO electronic structure calculations

A method to analyze optical transitions is developed by combining the Kubo-Greenwood formula with the unfolding method to construct an unfolded electronic band structure with optical transition weights, which allows us to investigate how optical transitions are perturbed by imperfections such as impurity, vacancy, and structural distortions. Based on the Kubo-Greenwood formula, we first calculate frequency-dependent optical conductivity based on the first-principles electronic structure calculations using the linear combinations of atomic orbitals. Benefiting from the atomic orbital basis sets, the frequency-dependent optical conductivity can be traced back to their individual components before summations over all of $k$ points and bands. As a result, optical transition weights of the material can be put on the unfolded electronic band structure to show contributions at different $k$ points and bands. This method is especially useful to study the effects of broken symmetry in the optical transitions due to presence of impurities in the materials. As a demonstration, decomposed optical transition weights of a monolayer Si-doped graphene are shown in the electronic band structure.

Gold/alpha-lactalbumin nanoprobes for the imaging and treatment of breast cancer.

Theranostic agents should ideally be renally cleared and biodegradable. Here, we report the synthesis, characterization and theranostic applications of fluorescent ultrasmall gold quantum clusters that are stabilized by the milk metalloprotein alpha-lactalbumin. We synthesized three types of these nanoprobes that together display fluorescence across the visible and near-infrared spectra when excited at a single wavelength through optical colour coding. In live tumour-bearing mice, the near-infrared nanoprobe generates contrast for fluorescence, X-ray computed tomography and magnetic resonance imaging, and exhibits long circulation times, low accumulation in the reticuloendothelial system, sustained tumour retention, insignificant toxicity and renal clearance. An intravenously administrated near-infrared nanoprobe with a large Stokes shift facilitated the detection and image-guided resection of breast tumours in vivo using a smartphone with modified optics. Moreover, the partially unfolded structure of alpha-lactalbumin in the nanoprobe helps with the formation of an anti-cancer lipoprotein complex with oleic acid that triggers the inhibition of the MAPK and PI3K-AKT pathways, immunogenic cell death and the recruitment of infiltrating macrophages. The biodegradability and safety profile of the nanoprobes make them suitable for the systemic detection and localized treatment of cancer.

π-Stacking Driven Aggregation and Folding of Squaramides.

Competing noncovalent interactions play a pivotal role in the folding and assembly of three-dimensional structures, especially in flexible molecules. Calculations using density functional theory reveal that two squaramide rings aggregate to form a slipped antiparallel π-stacked dimer with high propensity. This π-π stacking interaction is used to design foldamers in which the squaramides are tethered by a simple methylene bridge, and consequently, the structure folds on to itself incorporating a "turn" element. The variation in relative energy with respect to change in dihedral angle for these foldamers show that for all the structures two rings are displaced in space and the folding potential is asymmetric, starting from seemingly symmetric molecules. The addition of successive squaramide rings connected with simple methylene bridges leads to the formation of higher-order structures with a "Turn-Stack-Turn" structural motif. The "Turn-Stack-Turn" motif can be used in designing new synthetic foldamers which could potentially mimic closely related biological systems. Further, it was found that the aggregation of the folded structures was energetically favored over the unfolded structures. The present set of calculations are important in light of the fact that these simple methylene bridged squaramide rings present synthetic challenges.

Unfolding Dynamics of a Photoswitchable Helical Peptide

We present an atomistic force field for the azo-moiety of the photoswitchable FK-11-X peptide. We use the parameters to study the unfolding of the peptide through molecular dynamics simulations. The unfolded ensemble contains many different structures, ranging from a partially unfolded peptide to a fully unfolded structure. The averaged computed far-ultraviolet circular dichroism (CD) spectrum of the set of structures, which was simulated using the newly developed force field, agrees well with experiment. The rate of the simulated unfolding process was estimated to have a time constant of 5.80 ± 0.03 ns from the time evolution of the CD spectrum of the peptide, computed from the backbone conformations sampled over 40 simulated trajectories. Our estimated time constant is faster than, but not inconsistent with, previous experimental estimates from time-resolved infrared and optical rotatory dispersion spectroscopy.

Optimization of the stages of unfolding a large-sized space-based reflector

The safety of space flights depends on the reliable and smooth unfolding of large parts of the spacecraft. The process of unfolding the elements of a large-sized space-based reflector is considered. Unfolding structures are used in various spacecraft from satellites to inhabited stations. Due to increased interest in large-sized reflectors, the processes of unfolding are considered specifically for such a system. It is demonstrated that the minimization of oscillations of the unfolding structure is important. The fulfillment of this condition improves the reliability of the system. In the process of bringing the unfolding system into the operation state and after its completion, high stresses arise in the structural elements as a result of impacts from the control organ, as well as the mechanisms of restraint and fixation. As a result, oscillations of the entire satellite can occur, leading to a long period of its inactivity. Algorithms for the correction of the control structure parameters have been developed, which in real time allow solving the optimal control problem in the absence of difficulties in convergence, in contrast to the classical methods of the optimal control theory. To unfold the construction, specific actuators and measuring devices have been selected. The distribution laws of random system parameters have been estimated. A prototype facet of a large-sized reflector has been developed. A method based on the Laplace equation for the membrane has been used for pointwise adjustment of the shape of this prototype.