Folding Time Research Articles

Electrochemistry of Protein Electron Transfer

Protein fold and slow relaxation times impose constraints on configurations sampled by the protein. Incomplete sampling leads to the violation of fluctuation-dissipation relations underlying the traditional theories of electron transfer. The effective reorganization energy of electron transfer is strongly reduced thus leading to lower barriers and faster rates (catalytic effect). Electrochemical kinetic measurements support low activation barriers for protein electron transfer. The distance dependence of the rate constant displays a crossover from a plateau at short distances to a long-distance exponential decay. The transition between these two regimes is controlled by the protein dynamics.

Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology.

Although a large percentage of eukaryotic proteomes consist of proteins with multiple domains, not much is known about their assembly mechanism, especially those with intricate native state architectures. Some have a complex topology in which the structural elements along the sequence are interwoven in such a manner that the domains cannot be separated by cutting at any location along the sequence. Such proteins are multiply connected multidomain proteins (MMPs) with the three-domain (NMP, LID, and CORE) phosphotransferase enzyme adenylate kinase (ADK) being an example. We devised a coarse-grained model to simulate ADK folding initiated by changing either the temperature or guanidinium chloride (GdmCl) concentration. The simulations reproduce the experimentally measured melting temperatures (associated with two equilibrium transitions), FRET efficiency as a function of GdmCl concentration, and the folding times quantitatively. Although the NMP domain orders independently, cooperative interactions between the LID and the CORE domains are required for complete assembly of the enzyme. Kinetic simulations show that, on the collapse time scale, multiple interconnected metastable states are populated, attesting to the folding heterogeneity. The network of kinetically connected states reveals that the CORE domain folds only after the NMP and LID domains, reflecting the interwoven nature of the chain topology.

Enhanced in-plane thermal conductivity of PP composites with high orientation and rational layered distribution of BNNS

Thermally conductive polymeric materials have attracted great interest from academia and industry for several decades. Herein, we report a facile method to fabricate BNNS/PP composites with excellent properties, especially the in-plane thermal conductivity. SEM and XRD results show the orderly dispersion and high orientation of BNNS along the in-plane direction. Attractively, the in-plane thermal conductivity of BNNS/PP composites after 20 times of folding and hot pressing is dramatically improved to 4.08 W/mk at a BNNS content of only 19.1 vol%, which is 20 times higher than that of pure PP and 480% higher than that of single hot pressing composite at the same filler content. In addition, The Hashin-Shtrikman (HS) model and finite element simulations are introduced to interpret the improvement of in-plane thermal conductivity of BNNS/PP composites after repeated hot pressing. Meanwhile, the influence of parallel orientation and layered distribution of BNNS on the mechanical and dielectric properties of BNNS/PP composites has been investigated. This facile method presents a novel approach to design and fabricate polymer composites with excellent in-plane thermal conductivity.

Lung Allocation Revisions Removing the DSA as First Zone of Offering Correlated with Decreased Wait List Mortality

<h3>Purpose</h3> In November 2017 the lung allocation scheme was revised to eliminate DSA as the first geographic region for organ offers in attempt to minimize disparities in organ availability. This study was conducted to determine what impact allocation revisions had on waitlist time disparities and waitlist mortality in the United States. <h3>Methods</h3> The SRTR database was queried to determine waitlist times for all lung transplant recipients in the PRE era (Jan 2014 - Nov 2017) compared to the POST era (Dec 2017 - Feb 2021). Waitlist times were stratified into LAS quintiles. Transplant volumes were determined for each DSA in the PRE and POST eras. Waitlist mortality was determined in the PRE and POST eras. <h3>Results</h3> In the PRE era, waitlist times differed significantly between DSAs for each LAS quintile (p < 0.001) with greater than 10 fold differences for each LAS category between DSAs with the shortest and longest waitlist times. In the POST era, 10 fold waitlist time differences persisted between DSAs for each LAS category (p < 0.001) although ranking of DSAs by waitlist times changed. The number of annual transplants remained constant. Six DSAs performed at least 10 fewer transplants annually in the POST era compared to the PRE while seven DSAs performed at least 10 more. In the POST era, fewer patients in the first and fourth LAS quintiles received transplant while greater numbers of patients in the third and fifth quintiles received transplants. Patients delisted for mortality or condition deterioration decreased from 23.5% in the PRE to 20.1% in the POST eras (p<0.001). <h3>Conclusion</h3> Removing DSA as the first zone for donor lung allocation correlated with decreased waitlist mortality, but it remains unclear whether the UNOS policy change contributed to this reduced waitlist mortality.

Pyrene Excimer Formation (PEF) and Its Application to the Study of Polypeptide Dynamics.

This Perspective describes how the fluorescence blob model (FBM) has been developed and applied over the past 30 years to characterize the long-range backbone dynamics (LRBD) of polymers in solution. In these experiments, the polymers are randomly labeled with the dye pyrene, which forms an excimer upon the encounter between an excited and a ground-state pyrenyl label inside a finite subvolume of the polymer coil referred to as a blob representing the volume probed by the excited pyrene. By compartmentalizing the polymer coil into a cluster of identical blobs, FBM analysis of the fluorescence decays acquired with the polymers yields the number Nblob of structural units inside a blob. Since a flexible or rigid backbone will result in an Nblob that is either large or small, Nblob can be used as a measure of the flexibility of a given polymer. After having established that these experiments based on pyrene excimer formation (PEF) yielded quantitative information about the LRBD of a variety of polymers in solution, control experiments were carried out to characterize the effects that different molecular variables, such as the side-chain size (SCS) of a structural unit or the length of the linker connecting pyrene to the polymeric backbone, had on the parameters retrieved with the FBM. At this point, the FBM was applied to study the LRBD of polypeptides prepared from racemic mixtures of amino acids (aa's). These studies led to the establishment of simple rules that could be developed into mathematical equations to describe the LRBD of polypeptides. The Nblob values retrieved from the FBM analysis of the fluorescence decays acquired with the pyrene-labeled polypeptides could then be employed to predict the total conformational search time (τtcs) of any polypeptide based on their sequence. Strong correlations were found between the predicted τtcs and the experimental folding times of 145 proteins. The good quality of these correlations suggests that the blob-based approach described in this report might represent an interesting mathematical means for studying protein folding.

Inkjet‐Printed, Flexible Full‐Color Photoluminescence‐Type Color Filters for Displays

Photoluminescence‐type color filters (PLCFs) are supposed to offer vivid colors and higher power efficiency for modern displays by removing absorption losses of the conventional color filters (CFs). Inkjet printing (IJP) is a versatile and low‐cost method to pattern color converters. But uniformity of the patterns is a big concern. Poor photoluminescence stability is also problematic, especially for the perovskite nanoparticles (PNPs) and quantum color converters. Herein, a porous polymer film (PF) is deployed as a template for IJP. The capillary effect of sub‐micron pores in the PF modifies the rheological process of ink spreading that eliminates the coffee‐ring effect and simultaneously provides photoluminescence (PL) stability. A high‐quality green PNP, and red quantum rod (QR) based CF array onto the PF is successfully printed. A liquid crystal display (LCD) deploying this full‐color PF CFs is demonstrated. Color gamut of the device could reach 96.9% of BT2020. The PF CFs show good PL stability for more than 218 days. Furthermore, the fabricated PF CFs possess great flexibility, and any chromaticity and brightness change after 10 000 times of folding were not observed. Thus, the proposed CF using the PF is highly suitable for flexible display and photonics components.

In Situ Monitoring of DNA-Hg2+ Binding Reaction within Confined Nanospace of Metamaterial Nanochannel by Plasmon-Enhanced Raman Scattering.

Nanochannel-based plasmon-enhanced Raman scattering (PERS) substrates can simulate biological environments, revealing the recognition and conformation information on biomolecules in confined spaces. In this work, a metamaterial nanochannel-based PERS platform was constructed for highly sensitive analysis of DNA recognition to Hg2+ with the lowest Hg2+ concentration down to 1.0 pM. The established platform enables in situ monitoring of the thermodynamics and kinetics of DNA-Hg2+ recognition reaction in a confined nanospace. The recognition reaction in a nanospace shows good reversibility and specificity, and the isotherm follows well the Freundlich adsorption model. Compared to its folding on a rough Au nanofilm, the folding time of ssDNA-Rox decorated in nanochannels is remarkably increased, and the folding process can be tuned through varying the pore size and ionic strength. The presented PERS platform is promising for studying biomolecule-ion binding events and biomolecule conformation change under nanochannel-confined conditions.

Magnetic tweezers to observe the ultrafast downhill folding of a protein in the millisecond and nanometer scale

Recent advances in magnetic tweezers set them as a promising tool to unveil the dynamics of proteins and nucleic acids by means of hours to days-long stable constant force experiments. Archetypal folds play a crucial role in our means to uncover the intricacies of protein folding. One prominent case is the λ-phage cI transcription repressor fragment λ6-85; a five-helix bundle protein were single point mutations shift its folding time from fast 200 μs to ultrafast downhill-like 2.3 μs kinetics. Can we resolve ultrafast kinetics with the milliseconds time-resolution of the magnetic tweezers? Here, we report the observation of ultrafast protein folding in magnetic tweezers.

Preparation of O-HACC/HEC-acrylate emulsion and its application in paper protection

Abstract To enhance the strength of paper cultural relics and prolong the life of paper cultural relics, it is an urgent need to prepare new material for preservation and protection of paper. In this paper, chitosan quaternary ammonium salt/HEC-acrylate was synthesized with O-hydroxypropyl trimethyl quaternary ammonium salt chitosan (O-HACC) and Hydroxyethyl Cellulose (HEC)-acrylate emulsion, the synthesized materials has multiple functions, such as deacidification, reinforcement, anti-mildew and antibacterial etc. The synthesized new materials were applied on paper, and their protective effect was evaluated by testing the mechanical and optical properties and antibacterial properties of the paper. The results showed that when the mass concentration of O-HACC was 0.6 %, the tensile strength, folding times and tearing strength of the paper coated with protective solution were improved to a certain extent, while the optical properties and appearance of the paper remained basically unchanged. Meanwhile, the paper also had certain anti-mildew and bacterial resistance.

Three-Dimensional hybrid structure loader type flexible supercapacitor based on Polyvinyl alcohol gel and Acetylene black

In order to overcome the structural drawbacks of layered electrodes in flexible supercapacitors, the construction of an electrode frame with high adaptability for the loading of different active materials makes the production of flexible supercapacitors simpler and more accurate. Herein, a novel loader type flexible supercapacitor with three-dimensional hybrid structure is built. In our design, the acetylene black and active material are enriched in the polyvinyl alcohol matrix, and the three-dimensional conductive network that can load different active material is formed. The active material can be selected on demand. The basic electrode (also a loader) formed by polyvinyl alcohol and acetylene black is an electronic conductor (∼1 Scm−1) with good electrochemical and mechanical performance. By loading active materials in this basic electrode, more powerful flexible electrodes can be built easily and accurately with the same steps according to the designed proportion. Electrodes constructed according to this method deliver nonnegligible surface capacity (e.g. 1.1 Fcm−2 in surface capacitance, polyaniline/carbon nanotube composite as active materials) with good response, rate performance, excellent durability (10000 times of charge-discharge), and good foldability (1000 times of folding). This pattern of carrier type electrodes provides a simple and universal strategy for manufacturing flexible supercapacitors.

The Surprising Benefits of Hysteresis in Unlimited Sampling: Theory, Algorithms and Experiments

The Unlimited Sensing Framework (USF) was recently introduced to overcome the sensor saturation bottleneck in conventional digital acquisition systems. At its core, the USF converts a continuous-time high-dynamic-range (HDR) signal into folded, low-dynamic-range, modulo samples and allows the recovery of the HDR signal via algorithmic unfolding. In hardware, however, implementing ideal modulo folding requires careful calibration, analog design and high precision. At the interface of theory and practice, this paper explores a computational sampling strategy that relaxes strict hardware requirements via a novel, mathematically guaranteed reconstruction. We start with a generalized model for USF with two new parameters modeling <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">hysteresis</i> and <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">folding transients</i> in addition to the modulo threshold. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Hysteresis</i> accounts for mismatches between the reset threshold and the amplitude displacement at the folding time and the <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">folding transient</i> is a continuous transition period in the implementation of a reset. Both these effects are motivated by our hardware experiments and also occur in previous, domain-specific applications. We show that hysteresis is beneficial for USF and leverage it to derive the first recovery guarantees in the context of our generalized USF model for a certain sampling rate regime. Additionally, we show how the sampling rate requirement can be greatly reduced via a direct generalization of the proposed recovery. Our theoretical work is corroborated by hardware experiments with a hysteresis enabled, modulo ADC testbed comprising off-the-shelf electronic components. Thus, by capitalizing on a collaboration between hardware and algorithms, our paper enables an end-to-end pipeline for HDR sampling allowing more flexible hardware implementations.

The combined effect of inorganic salt and ionic liquid in pretreatment on enzymatic saccharification of rice straw

The pretreatment method is one of the challenging steps in the production of biofuel through the biorefinery process that unlocks the recalcitrant nature of lignocellulosic biomass. Ionic liquid pretreatment gained attention for being highly effective to improve the enzymatic saccharification of the biomass, however its high cost hinders its industrial application. In this study, the combined effect of ionic liquid 1- ethyl-3-methylimidazolium acetate (EMIM-Ac) with inorganic salts (NaCl and KCl) was used for the pretreatment of rice straw. Optimization of pretreatment was conducted based on Response Surface Methodology and sugar yields obtained by EMIM-Ac+NaCl (160 °C, 88.7 min, 7.6%wt) and EMIMAc+ KCl (160 °C, 68.2 min, 12.5%wt) were 670.7 and 392.9 mg/g-biomass, respectively. The effect of combined pretreatment on ethanol production was analyzed after 48h fermentation. The results showed that the ethanol yield from pretreated samples with EMIM-Ac+NaCl (0.72%) and EMIM+KCl (0.76%) was increased by 2.18 and 2.25 fold times, respectively, compared to untreated sample (0.33%). This combined effect of inorganic salts and ionic liquid significantly removed the lignin during pretreatment, while maintaining efficient enzymatic saccharification of rice straw. Thus, this cost-effective combined chemical method may be an alternative strategy for increasing cellulosic ethanol production.

Unlimited Sampling From Theory to Practice: Fourier-Prony Recovery and Prototype ADC

Following the Unlimited Sampling strategy to alleviate the omnipresent dynamic range barrier, we study the problem of recovering a bandlimited signal from point-wise modulo samples, aiming to connect theoretical guarantees with hardware implementation considerations. Our starting point is a class of non-idealities that we observe in prototyping an unlimited sampling based analog-to-digital converter. To address these non-idealities, we provide a new Fourier domain recovery algorithm. Our approach is validated both in theory and via extensive experiments on our prototype analog-to-digital converter, providing the first demonstration of unlimited sampling for data arising from real hardware, both for the current and previous approaches. Advantages of our algorithm include that it is agnostic to the modulo threshold and it can handle arbitrary folding times. We expect that the end-to-end realization studied in this paper will pave the path for exploring the unlimited sampling methodology in a number of real world applications.

Four-Dimensional Printing Technology at the Frontier of Advanced Modeling and Applications in Brain Tissue Engineering

The complex process behind the brain topology, which has been extensively studied for the last ten years, is still unclear. Therefore, neural tissue engineering studies are needed to better understand cortical folds. With the development of 4-dimensional (4D) bioprinters using cell-loaded smart materials, a promising path has been opened in the mimicry of the neural tissue. In our study, we review the usage areas of 4D printers, which have been developing in recent years, in modelling brain tissue. As a result of development of smart materials printed with 3-dimensional (3D) printers caused emerging of 4D printers, rapidly. Smart materials can change their properties based on physical, chemical and biological stimuli, and this change can be a reversible process. Cell-loaded printed smart materials should have little effect on cell viability of both the incoming stimulus and the physical change. It is also important that the material used is non-toxic and the solvent is suitable for cell viability. On the other hand, hydrogels are frequently studied to mimic the complex neural network of neural tissue. Agents that affect the crosslinking or degree of crosslinking of hydrogels can be easily controlled and changed. In addition, studies with neural stem cells have shown that hydrogels have a supportive effect on the proliferation and maturation of neural stem cells. Since the folding time, strength and location of smart materials cannot be known precisely, it can be an advantage of 4D bioprinters as it can be controlled and studied whether the results of the stress on the cells in this region will affect other cells. It is an ideal methodology to study the effect of cortical folding on neural stem cells, especially thanks to the ease of experimental manipulations provided by 4D bioprinters. It is expected that 4D bioprinters will be adopted and rapid developments will occur in the multidisciplinary field of tissue engineering of brain tissue in the near coming years.

Characterization of biologically active compounds from different herbs: Influence of drying and extraction methods

The hot air (HA) method is the most widely implemented drying method for plants (herbs, vegetables, and fruits). This method has a few drawbacks that include long drying time, limited heat transfer, and limited thermal conductivity. This study investigated the effects of HA and infra-red (IR) heating method on biologically active compounds from different herbs (Khaffir lime, Lemongrass, Prai, Tamarind, and Turmeric). The efficiency of the drying methods was evaluated by considering (a) moisture ratio (MR), (b) specific energy consumption (SEC, MJ/kg.H2O), (c) moisture diffusivity (Deff), and (d) activation energy (Ea, kJ/mol). The active compounds were extracted from HA and IR dried herbs using different solvents (hexane, water, and ethanol) through Solid-Liquid Extraction (SLE) and Soxhlet Solvent Extraction (SSE) methods. The moisture removal in the IR drying process increased 10–11% for the herb samples. Specific energy consumption (SEC) increase during the IR drying process is attributed to the rapid evaporation of water at shorter time intervals than HA. Activation energy (Ea) values decreased by 1.66, 1.48, 2.24, 3.13, and 2.07 fold times for IR dried prai, turmeric, lemongrass, tamarind, and kaffir lime, respectively. The higher yields of herbal extracts and the abundance of bioactive terpene derivatives in hexane extracts were obtained from HA herbs compared to IR samples. Therefore, it is concluded that the IR method and SSE process using hexane was suitable to dry and retain the bioactive active compounds within herbs. Further, the IR method over the HA method was considered based on energy consumption, processing time, yield, and active compounds.

Slowest-first protein translation scheme: Structural asymmetry and co-translational folding

Proteins are translated from the N to the C terminus, raising the basic question of how this innate directionality affects their evolution. To explore this question, we analyze 16,200 structures from the Protein Data Bank (PDB). We find remarkable enrichment of α helices at the C terminus and β strands at the N terminus. Furthermore, this α−β asymmetry correlates with sequence length and contact order, both determinants of folding rate, hinting at possible links to co-translational folding (CTF). Hence, we propose the “slowest-first” scheme, whereby protein sequences evolved structural asymmetry to accelerate CTF: the slowest of the cooperatively folding segments are positioned near the N terminus so they have more time to fold during translation. A phenomenological model predicts that CTF can be accelerated by asymmetry in folding rate, up to double the rate, when folding time is commensurate with translation time; analysis of the PDB predicts that structural asymmetry is indeed maximal in this regime. This correspondence is greater in prokaryotes, which generally require faster protein production. Altogether, this indicates that accelerating CTF is a substantial evolutionary force whose interplay with stability and functionality is encoded in secondary structure asymmetry.

Abstract 14420: STIM and Orai Spatial Distribution in the Infarcted Mouse Heart Reveals Their Role in Fibroblast Activation

Introduction: Heart failure (HF) remains a major source of late morbidity and mortality after myocardial infarction (MI). Calcium handling and the signaling pathways that govern the functional remodeling associated with HF are unclear. Store-operated calcium entry (SOCE) is a key factor in modulating Ca2+ signals. SOCE is mediated by the STIM protein and Orai channels. Monitoring STIM and Orai distribution is of great interest for studying cardiac remodeling after MI. This study investigated the spatial distribution of STIM and Orai in the heart after MI injury. Methods: The myocardial injury was induced in adult mice via ligation of the left anterior descending artery. MI- and sham-operated animals were euthanized, and hearts were harvested for ex-vivo analyses at 3, 7, 14, and 28 days after MI. We used western blot coupled with immunostaining to detect temporal and spatial profiling of specific STIM and Orai isoforms in different physiological zones and timepoints of MI to generate an integrative high-resolution map of STIM-Orai expression during cardiac remodeling. Results: We found that STIM1 and Orai1 proteins were upregulated from 3-day post-MI throughout day 28 post-MI, (3-4 fold times higher than controls, p&lt;0.001). STIM1 and Orai1 were the most abundant isoforms present in the injured heart. In contrast, Orai3 expression was found to transiently increase at 3- and 7-day post-MI (1.5 fold, p&gt;0.01), STIM2 and Orai2 expression did not change. Spatial pattern analysis revealed a marked gradient of STIM1 and Orai1 expression (decreasing from the border zone, the infarcted area, and the distal area). Co-labeling with cell-specific markers revealed that cardiac fibroblasts exhibited a high level of STIM1 and Orai1 expression. In vitro activation of cardiac fibroblasts showed a marked increase of STIM1 and Orai1 protein expression. Conclusions: Taken together, these data demonstrate that STIM1 and Orai1 expression is associated with fibroblast activation during fibrotic remodeling in the MI. Ca2+ signaling pathways that drive the expansion of fibrosis may rely on sustained STIM1 and Orai1 expression in scar formation and fibroblast activation, of which could provide future targets to exploit for treatment to prevent HF.

Molecular dynamics simulation of the fold of alkyl groups with different lengths when N-hexane molecules forming ordered structure on their functionalized graphene

The organic functionalized modification of graphene surface is of great significance for the fabrication of graphene based composites. And the study of fold of alkyl groups under the constraint of alkanes is helpful for understanding the fold behavior of polymers. Molecular dynamics simulation was used to study the fold behavior of a single alkyl group on the graphene surface under the constraint of alkane chains. The fold details of alkyl groups were described. With the increasing of alkyl group length, the maximum fold time increases. The alkyl groups lengths determine their fold way. The C6 molecules and graphene surface both influence the orientation of alkyl group. The fold of alkyl groups has undergone two basic processes: adsorption and orientation. The time of alkyl group fold is also related to the length of alkyl group.

Folding stress analysis of a sandwich plate based on transversely isotropic and rate-dependent constitutive relationship of adhesive

ABSTRACT Flexible and foldable electronic products often contain adhesive layers, and failure generally initiates at the adhesive interfaces. To analyze the interfacial stress accurately, correct constitutive relationship of adhesive layers is necessary. However, soft adhesives used in foldable sandwich plates can show rate-dependent and anisotropic mechanical behaviors, which can hardly be implemented by traditional linear elastic and hyperelastic constitutive models in the folding process simulation. Through experiments in material’s principal axes and the strain energy equivalence principle, a transversely isotropic and rate-dependent constitutive relationship of adhesive has been developed in a three-dimensional form. By commercial finite element (FE) software ABAQUS and its user subroutine UMAT, the folding stress of a sandwich plate has been analyzed. The results of FE simulation show that folding time would affect stress distributions significantly due to the anisotropic and rate-dependent properties of adhesive.

Non-Markovian modeling of protein folding

We extract the folding free energy landscape and the time-dependent friction function, the two ingredients of the generalized Langevin equation (GLE), from explicit-water molecular dynamics (MD) simulations of the α-helix forming polypeptide [Formula: see text] for a one-dimensional reaction coordinate based on the sum of the native H-bond distances. Folding and unfolding times from numerical integration of the GLE agree accurately with MD results, which demonstrate the robustness of our GLE-based non-Markovian model. In contrast, Markovian models do not accurately describe the peptide kinetics and in particular, cannot reproduce the folding and unfolding kinetics simultaneously, even if a spatially dependent friction profile is used. Analysis of the GLE demonstrates that memory effects in the friction significantly speed up peptide folding and unfolding kinetics, as predicted by the Grote-Hynes theory, and are the cause of anomalous diffusion in configuration space. Our methods are applicable to any reaction coordinate and in principle, also to experimental trajectories from single-molecule experiments. Our results demonstrate that a consistent description of protein-folding dynamics must account for memory friction effects.