Stages Of Folding Research Articles

Determining the function of ripening associated genes and biochemical changes during tomato (Solanum lycopersicum L.) fruit maturation.

This article examines biochemical alterations and gene expression changes during tomato fruit physiology. The chroma index increases from mature green (41.27) to red ripe (48.36) stages, and the texture softens from mature green (43.56 N) to red ripe (24.75 N). Reducing sugar and total carotenoid levels rise at the red ripe stage. Free radical content was elevated in the early stages (7nM) of ripening and declined at the later stages (4nM). The specific activity of α-mannosidase and β-N-acetyl hexosaminidase was high at the breaker (0.077 & 0.075 U/mg, respectively) stages, while polygalacturonase activity was high at red ripe (1.173 U/mg) stage. qPCR experiments revealed that the α-mannosidase was upregulated during the breaker (1.2 fold) stages of tomato ripening, the β-N-acetyl Hexosaminidase was upregulated throughout the breaker (2 fold), and pink (1.2 fold) stages of tomato ripening, and the β-xylosidase was upregulated significantly during the breaker stage (3.9 fold) of tomato ripening. The current findings revealed that the α-Mannosidase (0.77), β-N-acetylhexosaminidase (0.99), xylosidase (0.85), ethylene-responsive factors (0.86), aminocylco propane carboxylic oxidase (0.90), and pectin methylesterase (0.83), were significantly associated with textural softening. Polygalacturonase (0.75) positively correlated to reducing sugar formation, aminocylco propane carboxylic synthase 4 (0.96) expression correlates with chroma changes during tomato fruit ripening. These correlations illustrate the complex interplay between gene expression and the physical and biochemical changes occurring during tomato fruit ripening.

Enhancing augmented reality with machine learning for hands-on origami training

This research explores integrating augmented reality (AR) with machine learning (ML) to enhance hands-on skill acquisition through origami folding. We developed an AR system using the YOLOv8 model to provide real-time feedback and automatic validation of each folding step, offering step-by-step guidance to users. A novel approach to training dataset preparation was introduced, which improves the accuracy of detecting and assessing origami folding stages. In a formative user study involving 16 participants tasked with folding multiple origami models, the results revealed that while the ML-driven feedback increased task completion times, it also made participants feel more confident throughout the folding process. However, they also reported that the feedback system added cognitive load, slowing their progress, though it provided valuable guidance. These findings suggest that while ML-supported AR systems can enhance the user experience, further optimization is required to streamline the feedback process and improve efficiency in complex manual tasks.

Importance of Secondary Structure Data in Large Scale Protein Modeling Using Low-Resolution SURPASS Method.

Secondary structure elements, such as alpha helices and beta strands, play a fundamental role in defining the overall fold of a protein. Leveraging secondary structure information is essential for encoding the structural features in coarse-grained protein models. Such models simplify the representation of amino acid residues, thereby reducing computational complexity. By incorporating accurate (even if only partial) secondary structure data, the models can efficiently search for the native conformation of proteins and preserve the core structural motifs across extended time frames. Here, the pivotal role of (predicted) secondary structure data in the coarse-grained modeling of protein tertiary and quaternary structures, along with their long-time dynamics, is investigated. Computational simulations of large protein systems using a low-resolution SURPASS model were performed. These case studies demonstrate the sufficiency of predicted secondary structure data in an accurate fold assembly. It leads to a realistic depiction of long-time dynamics in the recorded pseudo-trajectories by employing the Monte Carlo dynamics sampling schema, based on a long random sequence of local conformational modifications. This approach may provide a powerful tool for investigating the critical stages of protein folding. Future combination with knowledge-based potentials derived using machine learning techniques offers exciting opportunities to unravel the underlying mechanisms of biological processes in a variety of molecular complexes.

Insights into the Allosteric Regulation of Human Hsp90 Revealed by NMR Spectroscopy.

Human heat shock protein 90 (Hsp90) is one of the most important chaperones that play a role in the late stages of protein folding. Errors in the process of the chaperone cycle can lead to diseases such as cancer and neurodegenerative diseases. Therefore, the activity of Hsp90 must be carefully regulated. One of the possibilities is allosteric regulation by its natural allosteric modulators-nucleotides, co-chaperones and client proteins-and synthetic small-molecule allosteric modulators, such as those targeting the middle domain or the C-terminal domain (CTD) of Hsp90. Since no experimentally determined structure of a small-molecule allosteric modulator bound to the CTD of human Hsp90 has yet been obtained, the challenge for a structure-based design of allosteric modulators remains. Solution nuclear magnetic resonance (NMR) spectroscopy could be utilized to overcome these problems. The main aim of this review article is to discuss how solution NMR techniques, especially protein-based, and the advanced isotope labeling of proteins have been used to investigate the allosteric regulation of the cytosolic isoforms of human Hsp90 with allosteric modulators. This article provides the basis for planning future NMR experiments, with the aim of gaining insights into allosteric sites and the mechanisms of allosteric regulation.

Exploring Compactness and Dynamics of Apomyoglobin.

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) approach has become a valuable analytical complement to traditional methods. HDX-MS allows the identification of dynamic surfaces in proteins. We have shown that the introduction of various mutations into the amino acid sequence of whale apomyoglobin (apoMb) leads to a change in the number of exchangeable hydrogen atoms, which is associated with a change in its compactness in the native-like condition. Thus, amino acid substitutions V10A, A15S, P120G, and M131A result in an increase in the number of exchangeable hydrogen atoms at the native-like condition, while the mutant form A144S leads to a decrease in the number of exchangeable hydrogen atoms. This may be due to a decrease and increase in the compactness of apoMb structure compared to the wild-type apoMb, respectively. The L9F and L9E mutations did not affect the compactness of the molecule compared to the wild type. We have demonstrated that V10A and M131A substitutions lead to the maximum and large increase correspondently in the average number of exchangeable hydrogen atoms for deuterium, since these substitutions lead to the loss of contacts between important parts of myoglobin structure: helices A, G, and H, which are structured at the early stage of folding.

War memorials in Tyumen in 1967–1987 (materials of the GBUTO GASPITO): formation, preservation and use

One of the significant periods of Russian history is the Great Patriotic War. In order to immortalize the events of 1941–1945, a war-memorial landscape was formed in many Soviet cities. The main stage of folding of commemorative signs into a single complex was carried out during the Brezhnev era. Memorials can rightfully be considered the dominants of the Tyumen ensemble of “military” monuments. The purpose of the article is to identify the problems associated with the process of formation, preservation and use of Tyumen war memorials in 1967–1987. The work is based on the documents from State Archive of Social and Political History of the Tyumen Region. The article examines the Tyumen war memorial located on the “Memory” square, which includes a cultural heritage site of regional significance, the historical monument “Mass grave of Soviet soldiers who died from wounds in hospitals in Tyumen during the Great Patriotic War in 1941–1945” and “Monument at the site of the mass grave of those who died from wounds in hospitals in Tyumen”, as well as the complex located on the Historical square, including the “Monument to the fallen soldiers of the Great Patriotic War of 1941–1945”. The methodology of the work is based on the principles of objectivity and historicism, comparative and descriptive methods of research are applied. The article presents the dynamics and peculiarities of construction of Tyumen war memorials. The role of the City society for the protection of monuments in the implementation of programs aimed at their creation is noted. The question of using the objects as a means of forming the identity and collective memory of the citizens is touched upon. Special attention is paid to the problems associated with the implementation of state and public activities aimed at the preservation of the objects in question. The conclusions obtained concretise the results of the work of researchers who have addressed the study of the history of the formation of war memorials in Soviet Russia. Consideration of the process of transformation of Tyumen war memorials carried out by the city authorities at present requires a separate study.

Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.

Guanine quadruplexes (GQs) play crucial roles in various biological processes, and understanding their folding pathways provides insight into their stability, dynamics, and functions. This knowledge aids in designing therapeutic strategies, as GQs are potential targets for anticancer drugs and other therapeutics. Although experimental and theoretical techniques have provided valuable insights into different stages of the GQ folding, the structural complexity of GQs poses significant challenges, and our understanding remains incomplete. This study introduces a novel computational protocol for folding an entire GQ from single-strand conformation to its native state. By combining two complementary enhanced sampling techniques, we were able to model folding pathways, encompassing a diverse range of intermediates. Although our investigation of the GQ free energy surface (FES) is focused solely on the folding of the all-anti parallel GQ topology, this protocol has the potential to be adapted for the folding of systems with more complex folding landscapes.

Study on the folding damage mechanism of SiC fiber braided fabric based on synchrotron radiation CT and finite-element analysis

Silicon carbide (SiC) fiber exhibits high strength, thermal resistance, and chemical stability, but its insufficient flexural strength renders it unsuitable for use in flexible structural materials. In this study, the microstructure evolution and damage mechanisms of SiC fiber braided fabric were investigated at different braiding angles and folding stages using synchrotron micro computed tomography (µ-CT) and finite-element analysis. Results from synchrotron radiation CT scans indicate that, with an increase in the number of folding cycles, both fiber surface fractures and slippage gradually increased, leading to a looser internal structure and diminished fiber continuity. The SiC fiber braided fabric at 37.8° was predominantly influenced by the folding behavior, exhibiting a higher frequency of fiber breakages. Conversely, the 43.1° SiC fiber braided fabric was primarily affected by inter-bundle abrasion, resulting in looser fiber bundles and increased slippage. In the case of the 41.2° SiC fiber braided fabric, under the combined effects of friction and folding, the highest occurrences of fiber slippage and breakages were observed. Finite-element simulation results reveal that the stress at the folding site of the 40° braided fabric was higher than those of the 45° and 50° braided fabrics, confirming the experimental conclusion that the folding resistance of SiC fiber fabrics is poorest at a braiding angle of around 41° to 42°. This research is of significant importance for a deeper understanding of the folding performance and damage behavior of SiC fiber braided fabric, providing valuable insights for further optimizing material design and applications.

Native β-barrel substrates pass through two shared intermediates during folding on the BAM complex.

The assembly of β-barrel proteins into membranes is mediated by the evolutionarily conserved β-barrel assembly machine (BAM) complex. In Escherichia coli, BAM folds numerous substrates which vary considerably in size and shape. How BAM is able to efficiently fold such a diverse array of β-barrel substrates is not clear. Here, we develop a disulfide crosslinking method to trap native substrates in vivo as they fold on BAM. By placing a cysteine within the luminal wall of the BamA barrel as well as in the substrate β-strands, we can compare the residence time of each substrate strand within the BamA lumen. We validated this method using two defective, slow-folding substrates. We used this method to characterize stable intermediates which occur during folding of two structurally different native substrates. Strikingly, these intermediates occur during identical stages of folding for both substrates: soon after folding has begun and just before folding is completed. We suggest that these intermediates arise due to barriers to folding that are common between β-barrel substrates, and that the BAM catalyst is able to fold so many different substrates because it addresses these common challenges.

On the Nature of the Kharamatolou Structure and the Ratio of the Amount of Ultramafic Rocks of the Voykar-Synya Massif to That of the Ray-Iz Massif, Polar Urals

There have been petrographic, geochemical, geochronological (Rb-Sr, Ar-Ar) and isotopic (Sm-Nd) studies done on the metamorphic formations of the Kharamatolou structure of the Polar Urals, which were usually assigned to the Precambrian. The temperatures of metamorphism have been shown to range from 450 to 626 °C, and the pressures – from 3.7–9.1 kbar once PT-conditions reached the amphibolite facies. The amphibolites of the Kharamatolou formation are geochemically divided into two groups. According to the distribution spectra of lanthanides and Nd isotope composition, one group has the characteristics similar to depleted N-MORB basalts εNd(0)=+7.0, and another group – those similar to moderately enriched E-MORB basalts εNd(0)=+(4.5–2.4). It has been found that the Kharamatolou structure is probably composed of the Early to Middle Paleozoic continental rise deposit of the Russian Platform, which passed the main stage of folding and metamorphism in the Late Devonian (Rb-Sr, 366±11 Ma). The gabbro-ultrabasic Ray-Iz and Voykar-Synya massifs have been shown to be one during most of their Pre-Triassic history. Now these ultrabasite massifs are separated by the young (Triassic) Kharamatolou uplift which is an erosive-tectonic semi-window where ultrabasic rocks of the Polar-Ural belt are exposed at the base of the thrust fault. The Kharamatolou structure is one of the transverse uplifts of the Urals which probably resulted from the Middle to Late Triassic compression therealong. As a result of the Middle to Late Triassic uplift of the Haramatolou metamorphites, the overlying ultrabasites were washed away by erosion. The mélange serpentinites observed in the center of the Kharamatolou structure are uneroded remnants of the link that once existed between the Ray-Iz and Voikar-Synya massifs. This significantly increases the metallogenic potential of the Voikar-Synya massif, as the Ray-Iz hosts the largest known chromite deposits in Russia.

Inside of the burst-phase intermediate of a protein folding. Hydration of hydrophobic groups

The thermal effect of the formation of the "burst-phase" folding intermediate has been studied using a titration calorimeter. It is shown that, unlike the total thermal effect of native structure formation, it can be both positive and negative depending on the temperature. The reasons for this paradoxical behavior are analyzed. A conclusion is drawn about the leading role of dehydration of non-polar groups in the first stage of folding.

An ATP13A1-assisted topogenesis pathway for folding multi-spanning membrane proteins

Many multi-spanning membrane proteins contain poorly hydrophobic transmembrane domains (pTMDs) protected from phospholipid in mature structure. Nascent pTMDs are difficult for translocon to recognize and insert. How pTMDs are discerned and packed into mature, muti-spanning configuration remains unclear. Here, we report that pTMD elicits a post-translational topogenesis pathway for its recognition and integration. Using six-spanning protein adenosine triphosphate-binding cassette transporter G2 (ABCG2) and cultured human cells as models, we show that ABCG2's pTMD2 can pass through translocon into the endoplasmic reticulum (ER) lumen, yielding an intermediate with inserted yet mis-oriented downstream TMDs. After translation, the intermediate recruits P5A-ATPase ATP13A1, which facilitates TMD re-orientation, allowing further folding and the integration of the remaining lumen-exposed pTMD2. Depleting ATP13A1 or disrupting pTMD-characteristic residues arrests intermediates with mis-oriented and exposed TMDs. Our results explain how a "difficult" pTMD is co-translationally skipped for insertion and post-translationally buried into the final correct structure at the late folding stage to avoid excessive lipid exposure.

Paleostress Analysis Using Fracture Data, a Case Study of Kewa Charmula Anticline, Kurdistan Region, Northeastern Iraq

Fracture analysis was carried out through three adjacent traverses. The study area is considered a part of the Arabian Plate and geologically falls within the boundary between the Low Folded Zone and the High Folded Zone of the Western Zagros Fold-Thrust Belt in the Iraqi Kurdistan Region. Five formations are cropped out in this anticline, extending from the Late Oligocene up to the Late Miocene – Pliocene. Those formations are (Anah, Jeribe, Fatha, Injana, and Mukdadiya). In addition, identify an Oligocene unit the Kirkuk Group, represented by the (Anah Fn.) that no other studies have previously referred to, in addition, to observing the Jeribe Formation along Tilyan Gorge. About 350 fracture planes were measured for the study and classified into sets and systems concerning their relations to the three mutually perpendicular geometrical axes (tectonic axes). Tension sets are (ac), which are formed by extension along the fold axis accompanying direct compression perpendicular to the fold trend, whereas the (bc) set is supposed to be the product of relaxation that motivated the primary compressional stress. The shear systems are each of hk0, h0l, and 0kl developed successively during direct compression and subsequent relaxation episodes of each tectonic stress. The results of the paleostress analyses showed that there is a general coincidence in the direction of the major stress axis (σ1) and the minor stress axis (σ3), which were derived from the joints (fracture planes). Joints are presented as sets and systems. The analysis of joint attitudes revealed that the joints might be due to the influence of the main horizontal compression paleostress in the direction NE – SW that is responsible for folding, or they might be caused by the stretching of the outer arc for the folded layers. According to field observations and paleostress studies, the region experienced four stress stages. The first is a main compressive tectonic phase in the NE – SW direction. The second phase is the second compressive tectonic stress in the direction NW – SE. The third was a NE – SW extension tectonic phase that originated during the final uplift stage of folding and it is representative of the major fold trend. The fourth is the NW – SE extension face considered as the extension stress connected to the principal NE – SW compressive stress.

The Mechanism of Folding of Human Frataxin in Comparison to the Yeast Homologue – Broad Energy Barriers and the General Properties of the Transition State

The funneled energy landscape theory suggests that the folding pathway of homologous proteins should converge at the late stages of folding. In this respect, proteins displaying a broad energy landscape for folding are particularly instructive, allowing inferring both the early, intermediate and late stages of folding. In this paper we explore the folding mechanisms of human frataxin, an essential mitochondrial protein linked to the neurodegenerative disorder Friedreich's ataxia. Building upon previous studies on the yeast homologue, the folding pathway of human frataxin is thoroughly examined, revealing a mechanism implying the presence of a broad energy barrier, reminiscent of the yeast counterpart. Through an extensive site-directed mutagenesis, we employed a Φ -value analysis to map native-like contacts in the folding transition state. The presence of a broad energy barrier facilitated the exploration of such contacts in both early and late folding events. We compared results from yeast and human frataxin providing insights into the impact of native topology on the folding mechanism and elucidating the properties of the underlying free energy landscape. The findings are discussed in the context of the funneled energy landscape theory of protein folding.

Dynamic physical-geological model of complex folding according to paleomagnetic data

The purpose of the study is to evaluate the possibility of using the mathematical apparatus of spatial rotations to solve the determination issues of the nature and age of natural remanent magnetization vectors under complex tectonic dislocations of rocks manifested in the areas of modern folded structures of platform framing. Dynamic physical-geological models are shown to be useful when forming complex tectonic-magmatic systems. Mathematical (computer) modeling in comparison with other methods of studying geological processes features higher accuracy, cost-effectiveness and unambiguity of data interpretation in achieving the set goal. On the basis of dynamic physical-geological model of complex folding, an algorithm is developed and the results of mathematical modeling of natural remanent magnetization vectors are given for solving direct and inverse problems on correct application of the fold test under complex rock deformations. The dynamic physical-geological model of complex folded structure formation shows that the characteristic natural remanent magnetization vectors identified in laboratory experiments on demagnetization can be used to determine their age relative to the folding stages, and, depending on this, fully or partially restore the number, sequence and direction of tectonic dislocations. This will enable us to solve the mineralogenic and geodynamic problems of folded region development more effectively on the basis of paleomagnetic data.

Nonlinear wrap-folding of membranes with predefined creases and seams

Nonlinear wrap-folding of membranes with predefined creases and seams

Cardiac competence of the paraxial head mesoderm fades concomitant with a shift towards the head skeletal muscle programme

The vertebrate head mesoderm provides the heart, the great vessels, some smooth and most head skeletal muscle, in addition to parts of the skull. It has been speculated that the ability to generate cardiac and smooth muscle is the evolutionary ground-state of the tissue. However, whether indeed the entire head mesoderm has generic cardiac competence, how long this may last, and what happens as cardiac competence fades, is not clear. Bone morphogenetic proteins (Bmps) are known to promote cardiogenesis. Using 41 different marker genes in the chicken embryo, we show that the paraxial head mesoderm that normally does not engage in cardiogenesis has the ability to respond to Bmp for a long time. However, Bmp signals are interpreted differently at different time points. Up to early head fold stages, the paraxial head mesoderm is able to read Bmps as signal to engage in the cardiac programme; the ability to upregulate smooth muscle markers is retained slightly longer. Notably, as cardiac competence fades, Bmp promotes the head skeletal muscle programme instead. The switch from cardiac to skeletal muscle competence is Wnt-independent as Wnt caudalises the head mesoderm and also suppresses Msc-inducing Bmp provided by the prechordal plate, thus suppressing both the cardiac and the head skeletal muscle programmes. Our study for the first time suggests a specific transition state in the embryo when cardiac competence is replaced by skeletal muscle competence. It sets the stage to unravel the cardiac-skeletal muscle antagonism that is known to partially collapse in heart failure.

Influence of Mg2+ Distribution on the Stability of Folded States of the Twister Ribozyme Revealed Using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced Sampling.

Metal ions, particularly magnesium ions (Mg2+), play a role in stabilizing the tertiary structures of RNA molecules. Theoretical models and experimental techniques show that metal ions can change RNA dynamics and how it transitions through different stages of folding. However, the specific ways in which metal ions contribute to the formation and stabilization of RNA's tertiary structure are not fully understood at the atomic level. Here, we combined oscillating excess chemical potential Grand Canonical Monte Carlo (GCMC) and metadynamics to bias toward the sampling of unfolded states using reaction coordinates generated by machine learning allowing for examination of Mg2+-RNA interactions that contribute to stabilizing folded states of the pseudoknot found in the Twister ribozyme. GCMC is used to sample diverse ion distributions around the RNA with deep learning applied to iteratively generate system-specific reaction coordinates to maximize conformational sampling during metadynamics simulations. Results from 6 μs simulations performed on 9 individual systems indicate that Mg2+ ions play a crucial role in stabilizing the three-dimensional (3D) structure of the RNA by stabilizing specific interactions of phosphate groups or phosphate groups and bases of neighboring nucleotides. While many phosphates are accessible to interactions with Mg2+, it is observed that multiple, specific interactions are required to sample conformations close to the folded state; coordination of Mg2+ at individual specific sites facilitates sampling of folded conformations though unfolding ultimately occurs. It is only when multiple specific interactions occur, including the presence of specific inner-shell cation interactions linking two nucleotides, that conformations close to the folded state are stable. While many of the identified Mg2+ interactions are observed in the X-ray crystal structure of Twister, the present study suggests two new Mg2+ ion sites in the Twister ribozyme that contribute to stabilization. In addition, specific interactions with Mg2+ are observed that destabilize the local RNA structure, a process that may facilitate the folding of RNA into its correct structure.

Pathway and mechanism of tubulin folding mediated by TRiC/CCT along its ATPase cycle revealed using cryo-EM

The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate substrate of TRiC. Here, we present an ensemble of cryo-EM structures of endogenous human TRiC throughout its ATPase cycle, with three of them revealing endogenously engaged tubulin in different folding stages. The open-state TRiC-tubulin-S1 and -S2 maps show extra density corresponding to tubulin in the cis-ring chamber of TRiC. Our structural and XL-MS analyses suggest a gradual upward translocation and stabilization of tubulin within the TRiC chamber accompanying TRiC ring closure. In the closed TRiC-tubulin-S3 map, we capture a near-natively folded tubulin—with the tubulin engaging through its N and C domains mainly with the A and I domains of the CCT3/6/8 subunits through electrostatic and hydrophilic interactions. Moreover, we also show the potential role of TRiC C-terminal tails in substrate stabilization and folding. Our study delineates the pathway and molecular mechanism of TRiC-mediated folding of tubulin along the ATPase cycle of TRiC, and may also inform the design of therapeutic agents targeting TRiC-tubulin interactions.

Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from S. aureus.

Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and proteins' folding, modification and binding, with the involvement of numerous RNAses, helicases, GTPases, chaperones, RNA, protein-modifying enzymes, and assembly factors. One such assembly factor involved in bacterial 30S subunit maturation is ribosomal binding factor A (RbfA). In this study, we present the crystal (determined at 2.2 Å resolution) and NMR structures of RbfA as well as the 2.9 Å resolution cryo-EM reconstruction of the 30S-RbfA complex from Staphylococcus aureus (S. aureus). Additionally, we show that the manner of RbfA action on the small ribosomal subunit during its maturation is shared between bacteria and mitochondria. The obtained results clarify the function of RbfA in the 30S maturation process and its role in ribosome functioning in general. Furthermore, given that S. aureus is a serious human pathogen, this study provides an additional prospect to develop antimicrobials targeting bacterial pathogens.