Proline inhibits aggregation during protein refolding

Modulation of insulin aggregation by betaine and proline directly observed via real-time super-resolution microscopy

Protein aggregation is associated with a spectrum of neurodegenerative diseases. Although many small ligands have been found to modulate or inhibit protein aggregation, their molecular mechanisms remain unclear. One reason for this is the inherent heterogeneity of protein aggregation pathways with different kinetics that result in the coexistence of multiple structures, for example, protein spherulites and fibrils, challenging the analysis of protein-ligand interactions. To address this issue, we evaluated the roles of betaine and proline in insulin aggregation. We employed our recently developed super-resolution microscopy real-time kinetics via binding and photobleaching localization microscopy (REPLOM) to directly observe the formation and morphological evolution of individual insulin aggregates in real time, with or without betaine/proline. Utilizing our machine learning approach, we monitor the effect of betaine and proline on the aggregation pathways and extract the growth kinetics of each individual aggregate type. Our results show that a high concentration of betaine or proline modulates the heterogeneity of the final aggregates, leading to the formation of smaller aggregates in a mixture with spherulites. The fraction of small aggregates increases with betaine/proline concentration, highlighting the heterogeneity of protein aggregation, and our toolbox can unravel the effects of small molecule ligands on individual protein aggregation pathways and the resulting aggregate types and abundances.

Helix Folding in One Dimension: Effects of Proline Co-Solvent on Free Energy Landscape of Hydrogen Bond Dynamics in Alanine Peptides

The effects of proline co-solvent on helix folding are explored through the single discrete coordinate of the number of helical hydrogen bonds. The analysis is based on multi-microsecond length molecular dynamics simulations of alanine-based helix-forming peptides, (ALA)n, of length n = 4, 8, 15 and 21 residues, in an aqueous solution with 2 M concentration of proline. The effects of addition of proline on the free energy landscape for helix folding were analyzed using the graph-based Dijkstra algorithm, Optimal Dimensionality Reduction kinetic coarse graining, committor functions, as well as through the diffusion of the helix boundary. Viewed at a sufficiently long time-scale, helix folding in the coarse-grained hydrogen bond space follows a consecutive mechanism, with well-defined initiation and propagation phases, and an interesting set of intermediates. Proline addition slows down the folding relaxation of all four peptides, increases helix content and induces subtle mechanistic changes compared to pure water solvation. A general trend is for transition state shift towards earlier stages of folding in proline relative to water. For ALA5 and ALA8 direct folding is dominant. In ALA8 and ALA15 multiple pathways appear possible. For ALA21 a simple mechanism emerges, with a single path from helix to coil through a set of intermediates. Overall, this work provides new insights into effects of proline co-solvent on helix folding, complementary to more standard approaches based on three-dimensional molecular structures.

Microscopic effects of proline co-solvent on alanine homopeptide structure, solvation and helix folding dynamics

We present a computational investigation to explore the influence of the protective osmolyte proline as a co-solvent on peptide structure and dynamics for a series of alanine-based peptides, (ALA)n of length n = 5, 8, 15, and 21 residues. Applying multi-microsecond molecular dynamics simulations in a 2 M proline solution, we evaluate peptide structure, solvation and helix folding dynamics and compare to behavior in pure water. Proline addition enhances helix content and significantly slows folding and unfolding times, correlating with a 1.9-fold increase in solvent viscosity. Notably, ALA15 helix content increases from 25% to 49% and relaxation time rises from 110 ns to 540 ns in proline relative to water. Microscopic solvation effects of proline include peptide compaction and dehydration, exclusion of proline from the backbone, formation of weak interactions with the ALA methyl sidechains, and strong interactions with water. The differences of these effects on the helix and coil states drive helix stabilization by proline. Low-dimensional kinetic modeling with Optimal Dimensionality Reduction predicts distinct folding mechanisms: shorter peptides (ALA5-ALA15) exhibit direct helix-coil transitions, and only the longest ALA21 follows a more complex folding pathway involving intermediates. Statistically, enhanced stability of hydrogen bonds in the peptide centers and strong correlation between transitions on neighboring residues are shared between water and proline solutions. However, there is a preference for helix initiation at the N-terminus under proline influence. Our analysis describes the molecular mechanisms of how proline modulates peptide behavior, offering atomistic insights into helix stabilization and folding mechanisms mediated by osmolytes.

Effect of Low-Density Lipoprotein (LDL) and High-Density Lipoprotein (HDL) on Frozen Gelation of Egg Yolk

This study aimed to investigate the roles of low-density lipoprotein (LDL) and high-density lipoprotein (HDL) in the gelatinization behavior of egg yolk, as well as the underlying mechanisms of action. This research examined the rheological properties, moisture distribution, and structural characteristics of a system containing reconstituted egg yolk components during the freezing process. The results indicated that increasing the concentration of LDL and HDL in the egg yolk system enhanced the apparent viscosity of egg yolk following a freeze-thaw treatment. Specifically, as the LDL and HDL content increased, G' and G" values increased significantly, whereas tanδ values decreased significantly and l* values declined. These findings suggest that both LDL and HDL are critical contributors to the gelatinization process of egg yolk. Furthermore, as the concentrations of LDL and HDL in the system increased, the amount of fixed water also rose, while the bound and free water content decreased. This observation implies that LDL and HDL facilitate water migration during the freezing of egg yolk. The increase in fluorescence intensity observed in the fluorescence spectra indicates a greater exposure of tyrosine residues on the protein surface, an enhancement of surface hydrophobicity, and a modification of protein conformation. Fluorescence inverted microscopy revealed that elevated levels of LDL and HDL in the system led to increased structural damage to the protein due to freezing, which subsequently promoted the aggregation of yolk proteins. This suggests that both LDL and HDL undergo aggregation during gelation. In egg yolk, LDL and HDL are essential for gel formation during the freezing of liquid egg yolk and play critical roles in both protein structure and water migration. Of the two lipoproteins, HDL has a more pronounced effect on gel formation during liquid egg yolk freezing. This study investigates the key substances involved in the gelatinization of egg yolk, providing a reference for further improvements in egg yolk gelatinization during freezing.

Electrosynthesis of Mussel-inspired Adhesive Polymers as a Novel Class of Transient Enzyme Stabilizers

Multifunctional ortho-quinones are required for the formation of thiol-catechol-connectivities (TCC) but can be delicate to handle. We present the electrochemical oxidation of the dipeptide DiDOPA, achieving up to 92 % conversion efficiency of the catechols to ortho-quinones. Graphite and stainless steel could be employed as cost-efficient electrodes. The electrochemical activation yields quinone-solutions, which are free of undesired reactive compounds and eliminates the challenging step of isolating the reactive quinones. The DiDOPA quinones were employed in polyaddition reactions with multi-thiols, forming oligomers that functioned as transient enzyme stabilizers (TES). These TCC-TES-additives improved the thermal stability and the activity of tyrosinase in heat stress assays.

Modulation of conformational integrity and aggregation propensity of α-synuclein by osmolytes: Implications in therapeutic intervention of Parkinson's disease

Understanding the factors capable of modulation of conformational stability and aggregation propensity of α-synuclein (α-Syn), a hallmark of Parkinson's disease (PD), is crucial for developing future therapeutic interventions for this disease. This chapter aims at exploring the roles of osmolytes in affecting the structural dynamics of α-Syn as well as focuses on how these osmolytes impact folding, stability, and aggregation behavior of this important intrinsically disordered protein. A number of potent osmolytes, including trimethylamine N-oxide (TMAO), trehalose, myo-inositol, taurine, glycine, glutamate, and glycerol were discussed along with their overall effect on α-Syn. These osmolytes can stabilize native conformations or promote alternative folding pathways, thereby influencing α-Syn aggregation. The chapter highlights the dual role of osmolytes in either preventing or exacerbating aggregation, depending on their concentration and interaction mechanism with α-Syn. Moreover, by integrating current research results, the chapter provides insights into how osmolytes might be utilized for therapeutic interventions with potential avenues for managing PD. Overall, the chapter underscores the significance of osmolyte-induced modulation of α-Syn aggregation in the context of PD and highlights future research areas in this direction.

"Anchoring Capture" Effect Mimicking Proline in Hardy Deep-Sea Fish to Stabilize the Zinc Anode with Lower Operating Temperature

The low plating/stripping efficiency of zinc anodes, dendrite growth, and high freezing points of aqueous solutions hinder the practical application of aqueous zinc-ion batteries. This paper proposes a zwitterionic permeable network solid-state electrolyte based on the "anchor-capture" effect to address these problems by incorporating proline (Pro, a biological antifreeze agent) into the electrolyte. Extensive validation tests, Quantum Chemistry (QC) calculations, Molecular Dynamics (MD) Simulations, and ab initio molecular dynamics simulations consistently indicate that the amino groups in proline adsorb onto the Zn metal surface, stabilizing the zinc anode-electrolyte interface, suppressing side reactions from water decomposition, and homogenizing zinc-ion flux. This electrolyte demonstrates excellent reversibility in Zn-Mn2O3 cells and Zn-Zn half-cells, achieving a high coulombic efficiency of over 99.4% across 2000 cycles in Zn-Mn2O3 full cells, and delivering a discharge-specific capacity of 175.2 mAh g-1 at -35 °C and 1 A g-1. Additionally, an appropriate concentration of proline lowers the electrolyte's freezing point to -45 °C through the network's solid-state effect, ensuring the stable operation of the solid-state battery at -35 °C. This innovative concept of network solid-state electrolytes injects new vitality into the development of multifunctional solid-state electrolytes.

Proline and ROS: A Unified Mechanism in Plant Development and Stress Response?

The proteinogenic amino acid proline plays crucial roles in both plant development and stress responses, far exceeding its role in protein synthesis. However, the molecular mechanisms and the relative importance of these additional functions of proline remain under study. It is well documented that both stress responses and developmental processes are associated with proline accumulation. Under stress conditions, proline is believed to confer stress tolerance, while under physiological conditions, it assists in developmental processes, particularly during the reproductive phase. Due to proline's properties as a compatible osmolyte and potential reactive oxygen species (ROS) scavenger, most of its beneficial effects have historically been attributed to the physicochemical consequences of its accumulation in plants. However, emerging evidence points to proline metabolism as the primary driver of these beneficial effects. Recent reports have shown that proline metabolism, in addition to supporting reproductive development, can modulate root meristem size by controlling ROS accumulation and distribution in the root meristem. The dynamic interplay between proline and ROS highlights a sophisticated regulatory network essential for plant resilience and survival. This fine-tuning mechanism, enabled by the pro-oxidant and antioxidant properties of compartmentalized proline metabolism, can modulate redox balance and ROS homeostasis, potentially explaining many of the multiple roles attributed to proline. This review uniquely integrates recent findings on the dual role of proline in both ROS scavenging and signaling, provides an updated overview of the most recent research published to date, and proposes a unified mechanism that could account for many of the multiple roles assigned to proline in plant development and stress defense. By focusing on the interplay between proline and ROS, we aim to provide a comprehensive understanding of this proposed mechanism and highlight the potential applications in improving crop resilience to environmental stress. Additionally, we address current gaps in understanding and suggest future research directions to further elucidate the complex roles of proline in plant biology.

Insulin Stabilization Designs for Enhanced Therapeutic Efficacy and Accessibility

Insulin has remained indispensable in the treatment of diabetes since it was first discovered in 1921. Unlike small molecular drugs, insulin and other protein drugs are prone to degradation when exposed to elevated temperatures, mechanical agitation during transportation, and prolonged storage periods. Therefore, strict cold-chain management is crucial for the insulin supply, requiring significant resources, which can limit the access to insulin, particularly in low-income areas. Moreover, although insulin formulations have advanced tremendously in the last century, insulin treatment still imposes a challenging regimen and provides suboptimal outcomes for the majority of patients. There is an increasing focus on pursuing improved pharmacology, specifically on safer, more user-friendly insulin therapies that minimize the self-management burden. These challenges underscore the need for developing novel insulin formulations with improved stability that are compatible with advanced insulin therapy. Insulin stabilization can be achieved through either chemical modification of insulin or formulation component design. Inspired by insulin-like peptides from invertebrates, we have developed novel stable insulin analogs based on a fundamental understanding of the insulin receptor engagement for insulin bioactivity. We created a novel four-disulfide insulin analog with high aggregation stability and potency by introducing a fourth disulfide bond between a C-terminal extended insulin A-chain and residues near the C-terminus of the B-chain. In an effort to stabilize insulin in its monomeric state to develop ultrafast-acting insulin with rapid absorption upon injection, we have developed a series of structurally miniaturized yet fully active insulin analogs that do not form dimers due to the lack of the canonical B-chain C-terminal octapeptide. Additionally, our study provided strategies for expanding the scope of cucurbit[7]uril (CB[7])-assisted insulin stabilization by engineering safe and biodegradable CB[7]-zwitterionic polypeptide excipients. We also explored insulin N-terminal substitution methods to achieve pH-dependent insulin stabilization without prolonging the duration of action. This Account describes our exploration of engineering stable insulin analogs and formulation design strategies for stabilizing insulin in aqueous solutions. Beyond conventional stabilization strategies for insulin injections, the unmet challenges and recent innovations in insulin stabilization are discussed, addressing the growing demand for alternative, less invasive routes of insulin administration. Additionally, we aim to provide a thorough overview of insulin stabilization from the perspective of commercially available insulin drugs and common pharmaceutical engineering practices in the industry. We also highlight unresolved insulin stabilization challenges and ongoing research strategies. We anticipate that further emphasis on collective efforts of protein engineering, pharmaceutical formulation design, and drug delivery will inform the development of stable and advanced insulin therapy.

Role of protein aggregates in bacteria

Protein misfolding and aggregation in bacteria, induced by a variety of intrinsic and environmental stresses, have often been associated with proteostasis disruption and toxic effects. However, a growing body of evidence suggests that these aggregates may also serve as functional membrane-less organelles (MLOs), playing a protective role in bacterial cells. The main mechanism responsible for the formation of MLOs is liquid-liquid phase separation (LLPS), a process that transforms a homogenous solution of macromolecules into dense condensates (liquid droplets) and a diluted phase. Over time, these liquid droplets can be transformed into solid aggregates. Bacterial MLOs, containing one dominant component or hundreds of cytoplasmic proteins, have been shown to be involved in various processes, including replication, transcription, cell division, and stress tolerance. The protective function of bacterial MLOs involves sequestration and protection of proteins and RNA from irreversible inactivation or degradation, upregulation of molecular chaperones, and induction of a dormant state. This protective role is particularly significant in the case of pathogenic bacteria exposed to antibiotic therapy. In a dormant state triggered by protein aggregation, pathogens can survive antibiotic therapy as persisters and, after resuming growth, can cause recurrent infections. Recent research has explored the potential use of bacterial MLOs as nanoreactors that catalyze biochemical reactions or serve as protein reservoirs and biosensors, highlighting their potential in biotechnology.

A comprehensive review on freeze-induced deterioration of frozen egg yolks: Freezing behaviors, gelation mechanisms, and control techniques

Over the years, the production of eggs has increased tremendously, with an estimated global egg production of 9.7 billion by 2050. Further processing of shell eggs to egg products has gained growing popularity. Liquid egg yolks, an innovative form of egg replacement, still suffer from short shelf-life issues, and freezing has been applied to maintain freshness. An undesirable phenomenon called "gelation" was found during the production of frozen egg yolks, which has attracted numerous scholars to study its mechanism and quality control methods. Therefore, we comprehensively reviewed the history of the studies on frozen egg yolks, including the production procedure, the fundamentals of freezing, the gelation mechanism, the factors affecting gelation behaviors, and the techniques to control the gelation behaviors of frozen egg yolks. Reporting the production procedure and freezing fundamentals of frozen egg yolks will give readers a better understanding of the science and technological aspects of frozen egg yolks. Furthermore, a comprehensive summary of the mechanism of egg yolk gel formation induced by freeze-thawing and relevant control techniques will provide insights to researchers and manufacturers in the field of frozen egg processing.

In situ analysis of osmolyte mechanisms of proteome thermal stabilization

Organisms use organic molecules called osmolytes to adapt to environmental conditions. In vitro studies indicate that osmolytes thermally stabilize proteins, but mechanisms are controversial, and systematic studies within the cellular milieu are lacking. We analyzed Escherichia coli and human protein thermal stabilization by osmolytes in situ and across the proteome. Using structural proteomics, we probed osmolyte effects on protein thermal stability, structure and aggregation, revealing common mechanisms but also osmolyte- and protein-specific effects. All tested osmolytes (trimethylamine N-oxide, betaine, glycerol, proline, trehalose and glucose) stabilized many proteins, predominantly via a preferential exclusion mechanism, and caused an upward shift in temperatures at which most proteins aggregated. Thermal profiling of the human proteome provided evidence for intrinsic disorder in situ but also identified potential structure in predicted disordered regions. Our analysis provides mechanistic insight into osmolyte function within a complex biological matrix and sheds light on the in situ prevalence of intrinsically disordered regions.

Spatiotemporal Control of Protein Refolding through Flash-Change Reaction Conditions

Recombinant protein production is an essential aspect of biopharmaceutical manufacturing, with Escherichia coli serving as a primary host organism. Protein refolding is vital for protein production; however, conventional refolding methods face challenges such as scale-up limitations and difficulties in controlling protein conformational changes on a millisecond scale. In this study, we demonstrate the novel application of flow microreactors (FMR) in controlling protein conformational changes on a millisecond scale, enabling efficient refolding processes and opening up new avenues in the science of FMR technology. FMR technology has been primarily employed for small-molecule synthesis, but our novel approach successfully expands its application to protein refolding, offering precise control of the buffer pH and solvent content. Using interleukin-6 as a model, the system yielded an impressive 96% pure refolded protein and allowed for gram-scale production. This FMR system allows flash changes in the reaction conditions, effectively circumventing protein aggregation during refolding. To the best of our knowledge, this is the first study to use FMR for protein refolding, which offers a more efficient and scalable method for protein production. The study results highlight the utility of the FMR as a high-throughput screening tool for streamlined scale-up and emphasize the importance of understanding and controlling intermediates in the refolding process. The FMR technique offers a promising approach for enhancing protein refolding efficiency and has demonstrated its potential in streamlining the process from laboratory-scale research to industrial-scale production, making it a game-changing technology in the field.

Amyloid β-Peptide Segment Conjugated Side-Chain Proline-Based Polymers as Potent Inhibitors in Lysozyme Amyloidosis

Developing effective amyloidosis inhibitors poses a significant challenge due to the dynamic nature of the protein structures, the complex interplay of interfaces in protein-protein interactions, and the irreversible nature of amyloid assembly. The interactions of amyloidogenic polypeptides with other peptides play a pivotal role in modulating amyloidosis and fibril formation. This study presents a novel approach for designing and synthesizing amyloid interaction surfaces using segments derived from the amyloid-promoting sequence of amyloid β-peptide [VF(Aβ(18-19)/FF(Aβ(19-20)/LVF(Aβ(17-19)/LVFF(Aβ(17-20)], where VF, FF, LVF and LVFF stands for valine phenylalanine dipeptide, phenylalanine phenylalanine dipeptide, leucine valine phenylalanine tripeptide and leucine valine phenylalanine phenylalanine tetrapeptide, respectively. These segments are conjugated with side-chain proline-based methacrylate polymers serving as potent lysozyme amyloidosis inhibitors and demonstrating reduced cytotoxicity of amyloid aggregations. Di-, tri-, and tetra-peptide conjugated chain transfer agents (CTAs) were synthesized and used for the reversible addition-fragmentation chain transfer polymerization of tert-butoxycarbonyl (Boc)-proline methacryloyloxyethyl ester (Boc-Pro-HEMA). Deprotection of Boc-groups from the side-chain proline pendants resulted in water-soluble polymers with defined peptide chain ends as peptide-polymer bioconjugates. Among them, the LVFF-conjugated polymer acted as a potent inhibitor with significantly suppressed lysozyme amyloidosis, a finding supported by comprehensive spectroscopic, microscopic, and computational analyses. These results unveil the synergistic effect between the segment-derived amyloid β-peptide and side-chain proline-based polymers, offering new prospects for targeting lysozyme amyloidosis.

Amino acids and glycine derivatives differently affect refolding of mesophilic and thermophilic like α-amylases: implications in protein refolding and aggregation

α-amylases are industrially important enzymes which are used in different starch-based industries. They are adapted to different environmental conditions like extremes of temperature, pH and salinity. Herein, α-amylases from Bacillus amyloliquifaciens (BAA) and Bacillus licheniformis (BLA), representing mesophilic and thermophilic-like proteins, respectively, have been used to investigate the effect of naturally occurring osmolytes like arginine, proline, glycine and its methyl derivatives, sarcosine and betaine on their refolding. In this study, we have shown that among amino acids and glycine derivatives, betaine is the most promising osmolyte, while arginine and glycine exhibit moderately positive effect at their lower concentrations on the refolding of BAA only. Except betaine, all other osmolytes above 0.25 M showed inhibitory effect on the native enzyme activity of BLA and BAA. However, aggregation kinetics monitored by static light scattering indicates suppression of aggregation by all of these osmolytes. Further investigation by tryptophan and ANS fluorescence spectroscopy indicates the formation of compact hydrophobic core in the presence of the osmolytes. The morphology of protein aggregates having different sizes was visualized by atomic force microscopy ,and it was observed that amorphous aggregates of variable heights were formed. Our study highlights the importance of differential effects of arginine, proline, glycine, sarcosine and betaine on the native state as well as on refolding of BLA and BAA which may be helpful in devising strategies for developing effective protein formulation and prevention of aggregation of industrially and therapeutically important proteins.

Stress response and adaptation mechanisms in Kluyveromyces marxianus

Kluyveromyces marxianus is a non-Saccharomyces yeast that has gained importance due to its great potential to be used in the food and biotechnology industries. In general, K. marxianus is a known yeast for its ability to assimilate hexoses and pentoses; even this yeast can grow in disaccharides such as sucrose and lactose and polysaccharides such as agave fructans. Otherwise, K. marxianus is an excellent microorganism to produce metabolites of biotechnological interest, such as enzymes, ethanol, aroma compounds, organic acids, and single-cell proteins. However, several studies highlighted the metabolic trait variations among the K. marxianus strains, suggesting genetic diversity within the species that determines its metabolic functions; this diversity can be attributed to its high adaptation capacity against stressful environments. The outstanding metabolic characteristics of K. marxianus have motivated this yeast to be a study model to evaluate its easy adaptability to several environments. This chapter will discuss overview characteristics and applications of K. marxianus and recent insights into the stress response and adaptation mechanisms used by this non-Saccharomyces yeast.

Targeting Amyloids with Coated Nanoparticles: A Review on Potential Combinations of Nanoparticles and Bio-Compatible Coatings

Amyloidosis is the major cause of many neurodegenerative diseases, such as, Alzheimer's and Parkinson's where the misfolding and deposition of a previously functional protein make it inept for carrying out its function. The genesis of amyloid fibril formation and the strategies to inhibit it have been studied extensively, although some parts of this puzzle still remain unfathomable to date. Many classes of molecules have been explored as potential drugs in vitro, but their inability to work in vivo by crossing the blood-brain-barrier has made them an inadequate treatment option. In this regard, nanoparticles (NPs) have turned out to be an exciting alternative because they could overcome many drawbacks of previously studied molecules and provide advantages, such as, greater bioavailability of molecules and target-specific delivery of drugs. In this paper, we present an overview on several coated NPs which have shown promising efficiency in inhibiting fibril formation. A hundred and thirty papers published in the past two decades have been comprehensively reviewed, which majorly encompass NPs comprising different materials like gold, silver, iron-oxide, poly(lactic-co-glycolic acid), polymeric NP, etc., which are coated with various molecules of predominantly natural origin, such as different types of amino acids, peptides, curcumin, drugs, catechin, etc. We hope that this review will shed light on the advancement of symbiotic amalgamation of NPs with molecules from natural sources and will inspire further research on the tremendous therapeutic potential of these combinations for many amyloid-related diseases.

Nano-Osmolyte Conjugation: Tailoring the Osmolyte-Protein Interactions at the Nanoscale

Osmolytes are small organic compounds accumulated at higher concentrations in the cell under various stress conditions like high temperature, high salt, high pressure, etc. Osmolytes mainly include four major classes of compounds including sugars, polyols, methylamines, and amino acids and their derivatives. In addition to their ability to maintain protein stability and folding, these osmolytes, also termed as chemical chaperones, can prevent protein misfolding and aggregation. Although being efficient protein folders and stabilizers, these osmolytes exhibit certain unavoidable limitations such as nearly molar concentrations of osmolytes being required for their effect, which is quite difficult to achieve inside a cell or in the extracellular matrix due to nonspecificity and limited permeability of the blood-brain barrier system and reduced bioavailability. These limitations can be overcome to a certain extent by using smart delivery platforms for the targeted delivery of osmolytes to the site of action. In this context, osmolyte-functionalized nanoparticles, termed nano-osmolytes, enhance the protein stabilization and chaperone efficiency of osmolytes up to 105 times in certain cases. For example, sugars, polyols, and amino acid functionalized based nano-osmolytes have shown tremendous potential in preventing protein aggregation. The enhanced potential of nano-osmolytes can be attributed to their high specificity at low concentrations, high tunability, amphiphilicity, multivalent complex formation, and efficient drug delivery system. Keeping in view the promising potential of nano-osmolytes conjugation in tailoring the osmolyte-protein interactions, as compared to their molecular forms, the present review summarizes the recent advancements of the nano-osmolytes that enhance the protein stability/folding efficiency and ability to act as artificial chaperones with increased potential to prevent protein misfolding disorders. Some of the potential nano-osmolyte aggregation inhibitors have been highlighted for large-scale screening with future applications in aggregation disorders. The synthesis of nano-osmolytes by numerous approaches and future perspectives are also highlighted.

Regulation of proline metabolism, AsA-GSH cycle, cadmium uptake and subcellular distribution in Brassica napus L. under the effect of nano-silicon

Cadmium (Cd) is known to have detrimental effects on plant growth and human health. Recent studies showed that silicon nanoparticles (SNPs) can decrease Cd toxicity in plants. Therefore, a study was conducted using 50 μM Cd and 1.50 mM SNPs to investigate Cd uptake, subcellular distribution, proline (Pro) metabolism, and the antioxidant defense system in rapeseed seedlings. In this study, results indicated that Cd stress negatively affected rapeseed growth, and high Cd contents accumulated in both shoots and roots. However, SNPs significantly decreased Cd contents in shoots and roots. Moreover, substantial increases were found in root fresh weight by 40.6% and dry weight by 46.6%, as well as shoot fresh weight by 60.1% and dry weight by 113.7% with the addition of SNPs. Furthermore, the addition of SNPs alleviated oxidative injury by maintaining the ascorbate-glutathione (AsA-GSH) cycle and increased Pro biosynthesis which could be due to high activities of Δ1-pyrroline-5-carboxylate synthase (P5CS) and reductase (P5CR) and decreased proline dehydrogenase (ProDH) activity. Furthermore, the addition of SNPs accumulated Cd in the soluble fraction (42%) and cell wall (45%). Results indicate that SNPs effectively reduce Cd toxicity in rapeseed seedlings which may be effective in promoting both rapeseed productivity and human health preservation.

Proline pre-conditioning of Jurkat cells improves recovery after cryopreservation

Cell therapies such as allogenic CAR T-cell therapy, natural killer cell therapy and stem cell transplants must be cryopreserved for transport and storage. This is typically achieved by addition of dimethyl sulfoxide (DMSO) but the cryoprotectant does not result in 100% cell recovery. New additives or technologies to improve their cryopreservation could have major impact for these emerging therapies. l-Proline is an amino acid osmolyte produced as a cryoprotectant by several organisms such as the codling moth Cydia pomonella and the larvae of the fly Chymomyza costata, and has been found to modulate post-thaw outcomes for several cell lines but has not been studied with Jurkat cells, a T lymphocyte cell line. Here we investigate the effectiveness of l-proline compared to d-proline and l-alanine for the cryopreservation of Jurkat cells. It is shown that 24-hour pre-freezing incubation of Jurkat cells with 200 mM l-proline resulted in a modest increase in cell recovery post-thaw at high cell density, but a larger increase in recovery was observed at the lower cell densities. l-Alanine was as effective as l-proline at lower cell densities, and addition of l-proline to the cryopreservation media (without incubation) had no benefit. The pre-freeze incubation with l-proline led to significant reductions in cell proliferation supporting an intracellular, biochemical, mechanism of action which was shown to be cell-density dependent. Controls with d-proline were found to reduce post-thaw recovery attributed to osmotic stress as d-proline cannot enter the cells. Preliminary analysis of apoptosis/necrosis profiles by flow cytometry indicated that inhibition of apoptosis is not the primary mode of action. Overall, this supports the use of l-proline pre-conditioning to improve T-cell post-thaw recovery without needing any changes to cryopreservation solutions nor methods and hence is simple to implement.

Novel Design of an α-Amylase with an N-Terminal CBM20 in Aspergillus niger Improves Binding and Processing of a Broad Range of Starches

In the starch processing industry including the food and pharmaceutical industries, α-amylase is an important enzyme that hydrolyses the α-1,4 glycosidic bonds in starch, producing shorter maltooligosaccharides. In plants, starch molecules are organised in granules that are very compact and rigid. The level of starch granule rigidity affects resistance towards enzymatic hydrolysis, resulting in inefficient starch degradation by industrially available α-amylases. In an approach to enhance starch hydrolysis, the domain architecture of a Glycoside Hydrolase (GH) family 13 α-amylase from Aspergillus niger was engineered. In all fungal GH13 α-amylases that carry a carbohydrate binding domain (CBM), these modules are of the CBM20 family and are located at the C-terminus of the α-amylase domain. To explore the role of the domain order, a new GH13 gene encoding an N-terminal CBM20 domain was designed and found to be fully functional. The starch binding capacity and enzymatic activity of N-terminal CBM20 α-amylase was found to be superior to that of native GH13 without CBM20. Based on the kinetic parameters, the engineered N-terminal CBM20 variant displayed surpassing activity rates compared to the C-terminal CBM20 version for the degradation on a wide range of starches, including the more resistant raw potato starch for which it exhibits a two-fold higher Vmax underscoring the potential of domain engineering for these carbohydrate active enzymes.

Stability of the Aβ42 Peptide in Mixed Solutions of Denaturants and Proline

Amyloid β-peptide (Aβ) is responsible for the neuronal damage and death of a patient with Alzheimer's disease (AD). Aβ42 oligomeric forms are dominant neurotoxins and are related to neurodegeneration. Their different forms are related to various pathological conditions in the brain. We investigated Aβ42 peptides in different environments of proline, urea, and GdmCl solutions (in pure and mixed binary forms) through atomistic molecular dynamics simulations. Preferential exclusion from the protein surface and facile formation of a large number of weak molecular interactions are the driving forces for the osmolyte's action. We have focused on these interactions between peptide monomers and pure/mixed osmolytes and denaturants. Urea, as usual, denatures the peptide strongly compared to the GdmCl by accumulation around the peptide. GdmCl shows lesser build-up around protein in contrast to urea but is involved in destabilizing the salt bridge formation of Asp23 and Lys28. Proline as an osmolyte protects the peptide from aggregation when mixed with urea and GdmCl solutions. In mixed solutions of two denaturants and osmolyte plus denaturant, the peptide shows enhanced stability as compared to pure denaturant urea solution. The enhanced stability of peptides in proline may be attributed to its exclusion from the peptide surface and favoring salt bridge formation.

Improving the productivity of malic acid by alleviating oxidative stress during Aspergillus niger fermentation

BACKGROUND

As an attractive platform chemical, malic acid has been commonly used in the food, feed and pharmaceutical field. Microbial fermentation of biobased sources to produce malic acid has attracted great attention because it is sustainable and environment-friendly. However, most studies mainly focus on improving yield and ignore shortening fermentation time. A long fermentation period means high cost, and hinders the industrial applications of microbial fermentation. Stresses, especially oxidative stress generated during fermentation, inhibit microbial growth and production, and prolong fermentation period. Previous studies have shown that polypeptides could effectively relieve stresses, but the underlying mechanisms were poorly understood.

RESULTS

In this study, polypeptides (especially elastin peptide) addition improves the productivity of malic acid in A. niger, resulting in shortening of fermentation time from 120 to 108 h. Transcriptome and biochemical analyses demonstrated that both antioxidant enzyme-mediated oxidative stress defense system, such as superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX), and nonenzymatic antioxidant system, such as glutathione, were enhanced in the presence of elastin peptide, suggesting elastin peptide relieving oxidative stresses is involved in many pathways. In order to further investigate the relationship between oxidative stress defense and malic acid productivity, we overexpressed three enzymes (Sod1, CAT, Tps1) related to oxidation resistance in A. niger, respectively, and these resulting strains display varying degree of improvement in malic acid productivity. Especially, the strain overexpressing the Sod1 gene achieved a malate titer of 91.85 ± 2.58 g/L in 96 h, corresponding to a productivity of 0.96 g/L/h, which performs better than elastin peptide addition.

CONCLUSIONS

Our investigation provides an excellent reference for alleviating the stress of the fungal fermentation process and improving fermentation efficiency.

Polyols, increasing global stability of cytochrome c, destabilize the thermal unfolding intermediate

Studies on the intermediate states of proteins provide essential information on folding pathway and energy landscape of proteins. Osmolytes, known to alter the stability of proteins, might also affect the structure and energy states of folding intermediates. This was examined using cytochrome c (Cyt) as a model protein which forms a spectroscopically detectable intermediate during thermal denaturation transition. Most of the secondary structure and the native heme-ligation were intact in the intermediate state of the protein. Denaturants, urea and guanidinium hydrochloride, and ionic salt destabilizes the intermediate and drive the protein to follow two-state transition. The effect of polyol class of osmolytes, glycol, glycerol, erythritol, xylitol and sorbitol (with OH-groups two to six), on the intermediate was studied using Soret absorbance and far-UV circular dichroism. With the increasing concentration of any of the polyols, the transition-midpoint temperature (T_m) and the enthalpy change (ΔH) for native to intermediate transition were decreased. This indicated that the intermediate was destabilized by the polyols. However, the polyols increased the overall stability of the protein by increasing T_m and ΔH for intermediate to unfolded transition, except for glycol which destabilized the protein. These results show that the polyols could alter the energy state of the intermediate, and the effect of lower and higher polyols might be different on the stability and folding pathway of the protein.Communicated by Ramaswamy H. Sarma.

Refolding in the modern biopharmaceutical industry

Inclusion bodies (IBs) often emerge upon overexpression of recombinant proteins in E. coli. From IBs, refolding is necessary to generate the native protein that can be further purified to obtain pure and active biologicals. This work focusses on refolding as a significant process step during biopharmaceutical manufacturing with an industrial perspective. A theoretical and historical background on protein refolding gives the reader a starting point for further insights into industrial process development. Quality requirements on IBs as starting material for refolding are discussed and further economic and ecological aspects are considered with regards to buffer systems and refolding conditions. A process development roadmap shows the development of a refolding process starting from first exploratory screening rounds to scale-up and implementation in manufacturing plant. Different aspects, with a direct influence on yield, such as the selection of chemicals including pH, ionic strength, additives, etc., and other often neglected aspects, important during scale-up, such as mixing, and gas-fluid interaction, are highlighted with the use of a quality by design (QbD) approach. The benefits of simulation sciences (process simulation and computer fluid dynamics) and process analytical technology (PAT) for seamless process development are emphasized. The work concludes with an outlook on future applications of refolding and highlights open research inquiries.

Impact of Cadmium Stress on Growth and Physio-Biochemical Attributes of Eruca sativa Mill

Plants may experience adverse effects from Cadmium (Cd). As a result of its toxicity and mobility within the soil-plant continuum, it is attracting the attention of soil scientists and plant nutritionists. In this study, we subjected young Eruca sativa Mill. seedlings to different levels of Cd applications (0, 1.5, 6 and 30 µmol/L) via pot experiment to explore its morpho-physio-biochemical adaptations. Our results revealed a significant Cd accumulation in leaves at high Cd stress. It was also demonstrated that Cd stress inhibited photosynthetic rate and pigment levels, ascorbate peroxidase (APX), guaiacol peroxidase (GPX), catalase (CAT), and superoxide dismutase (SOD) enzyme activities, and increased malondialdehyde (MDA) levels. Conversely, the concentration of total ascorbate (TAS) increased at all levels of Cd application, whereas that of ascorbic acid (ASA), and dehydroascorbate (DHA) increased at 1.5 (non-significant), 6, 30 and 6 µmol/L (significant), though their concentrations decreased non-significantly at 30 µmol/L application. In conclusion, Cd-subjected E. sativa seedlings diverted much energy from growth towards the synthesis of anti-oxidant metabolites and osmolytes. However, they did not seem to have protected the E. sativa seedlings from Cd-induced oxidative stress, causing a decrease in osmotic adjustment, and an increase in oxidative damage, which resulted in a reduction in photosynthesis and growth. Accordingly, we recommend that the cultivation of E. sativa should be avoided on soil with Cd contamination.

The Effect of Trehalose Coating for Magnetite Nanoparticles on Stability of Egg White Lysozyme

In this study, the protein stability of hen egg-white lysozymes (HEWL) by Fe₃O₄ and Fe₃O₄-coated trehalose (Fe₃O₄@Tre) magnetic nanoparticles (NPs) is investigated. For this purpose, the co-precipitation method was used to synthesize magnetic NPs. The synthesized NPs were characterized by XRD, FT-IR spectroscopy, FE-SEM, and VSM analysis. In addition, the stability of HEWLs exposed to different NP concentrations in the range of 0.001–0.1 mg mL⁻¹ was investigated by circular dichroism (CD) spectroscopy, fluorescence, and UV-Vis analysis. Based on the results, in the NP concentration range of 0.001–0.04 mg mL⁻¹ the protein structure is more stable, and this range was identified as the range of kosmotropic concentration. The helicity was measured at two concentration points of 0.02 and 0.1 mg mL⁻¹. According to the results, the α-helix at 0.02 mg mL⁻¹ of Fe₃O₄ and Fe₃O₄@Tre was increased from 35.5% for native protein to 37.7% and 38.7%, respectively. The helicity decreased to 36.1% and 37.4%, respectively, with increasing the concentration of Fe₃O₄ and Fe₃O₄@Tre to 0.1 mg mL⁻¹. The formation of hydrated water shells around protein molecules occurred by using Fe₃O₄@Tre NPs. Hence, it can be concluded that the trehalose as a functional group along with magnetic NPs can improve the stability of proteins in biological environments.

Scan-Find-Scan-Model: Discrete Site-Targeted Suppressor Design Strategy for Amyloid-β

Alzheimer's disease is undoubtedly the most well-studied neurodegenerative disease. Consequently, the amyloid-β (Aβ) protein ranks at the top in terms of getting attention from the scientific community for structural property-based characterization. Even after decades of extensive research, there is existing volatility in terms of understanding and hence the effective tackling procedures against the disease that arises due to the lack of knowledge of both specific target- and site-specific drugs. Here, we develop a multidimensional approach based on the characterization of the common static-dynamic-thermodynamic trait of the monomeric protein, which efficiently identifies a small target sequence that contains an inherent tendency to misfold and consequently aggregate. The robustness of the identification of the target sequence comes with an abundance of a priori knowledge about the length and sequence of the target and hence guides toward effective designing of the target-specific drug with a very low probability of bottleneck and failure. Based on the target sequence information, we further identified a specific mutant that showed the maximum potential to act as a destabilizer of the monomeric protein as well as enormous success as an aggregation suppressor. We eventually tested the drug efficacy by estimating the extent of modulation of binding affinity existing within the fibrillar form of the Aβ protein due to a single-point mutation and hence provided a proof of concept of the entire protocol.

Effects of Chilling Stress on Morphological, Physiological, and Biochemical Attributes of Silage Corn Genotypes during Seedling Establishment

Chilling stress is one of the major abiotic stresses which hinder seedling emergence and growth. Herein, we investigated the effects of chilling/low temperature stress on the morphological, physiological, and biochemical attributes of two silage corn genotypes during the seedling establishment phase. The experiment was conducted in a growth chamber, and silage corn seedlings of Yukon-R and A4177G-RIB were grown at optimum temperature up to V3 stage and then subjected to five temperature regimes (25 °C as control, 20 °C, 15 °C, 10 °C, and 5 °C) for 5 days. After the temperature treatment, the morphological, physiological, and biochemical parameters were recorded. Results indicated that temperatures of 15 °C and lower significantly affected seedling growth, photosynthesis system, reactive oxygen species (ROS) accumulation, and antioxidant enzyme activities. Changes in seedlings’ growth parameters were in the order of 25 °C > 20 °C > 15 °C > 10 °C > 5 °C, irrespective of genotypes. The chlorophyll content, photosynthetic rate, and maximal photochemical efficiency of PS-II (Fv/Fm) were drastically decreased under chilling conditions. Moreover, chilling stress induced accumulation of hydrogen peroxide (H2O2)and malonaldehyde (MDA) contents. Increased proline content and enzymatic antioxidants, including superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxide (APX), were found to alleviate oxidative damage under chilling stress. However, the genotype of Yukon-R exhibited better adaption to chilling stress than A4177G3-RIB. Yukon-R showed significantly higher proline content and enzymatic antioxidant activities than A4177G3-RIB under severe chilling conditions (temperature ≤ 10 °C). Similarly, Yukon-R expressed low temperature-induced ROS accumulation. Furthermore, the interaction effects were found between temperature treatment and genotype on the ROS accumulation, proline content and antioxidant enzyme activities. In summary, the present study indicated that Yukon-R has shown better adaptation and resilience against chilling temperature stress, and therefore could be considered a potential candidate genotype to be grown in the boreal climate.

Proline-based solution maintains cell viability and stemness of canine adipose-derived mesenchymal stem cells after hypothermic storage

Transportation of mesenchymal stem cells (MSCs) under hypothermic conditions in 0.9% normal saline solution (NSS) might increase cell death and alter the stemness of MSCs. The present study aimed to evaluate the effect of proline-based solution (PL-BS) on cell viability and the stemness of newly established canine adipose-derived mesenchymal stem cells (cAD-MSCs) under hypothermic conditions. Characterized cAD-MSCs were stored in 1, 10, and 100 mM PL-BS or NSS at 4°C for 6, 9, and 12 hours prior to an evaluation. The results demonstrated that storage in 1 mM PL-BS for 6 hours decreased cell apoptosis and proliferation ability, but improved cell viability and mitochondrial membrane potential. cAD-MSCs maintained their high expression of CD44 and CD90, but had a low expression of CD34 and MHC class II. Trilineage differentiation ability of cAD-MSCs was not affected by storage in 1 mM PL-BS. Gene expression analysis demonstrated that immunomodulatory genes, including IDO, HGF, PGE-2, and IL-6, were upregulated in cAD-MSCs stored in 1 mM PL-BS. In conclusion, PL-BS can be effectively applied for storing cAD-MSCs under hypothermic conditions. These findings provide a new solution for effective handling of cAD-MSCs which might be promising for clinical applications.

The mechanism of thermal aggregation of glutamate dehydrogenase. The effect of chemical chaperones

Chemical chaperones are low-molecular compounds counteracting protein aggregation. Understanding of the mechanism of their effects is key to their potential use in biotechnology. The aggregation of bovine liver glutamate dehydrogenase (GDH) was studied at 40 °C and 50 °C using dynamic light scattering, analytical ultracentrifugation, size-exclusion chromatography and differential scanning calorimetry. At 40 °C the GDH aggregation proceeds through the slow stages of hexamer dissociation and formation of small oligomeric aggregates. At 50 °C these stages are transient. The rate-limiting stage of the overall aggregation process is unfolding of the protein molecule; the order of aggregation with respect to protein, n = 1. The test system based on GDH aggregation at 50 °C was used to quantify the anti-aggregation activity of chemical chaperones by comparing their half-saturation concentrations [L]_0.5. Arginine ethyl ester had the highest anti-aggregation activity, with [L]_0.5 = 4 ± 1 mM. For other additives, [L]_0.5 was 22 ± 1 mM (arginine), 18 ± 1 mM (argininamide) and 95 ± 12 mM (proline). Arginine at concentrations up to 300 mM, argininamide at concentrations higher than 300 mM and arginine ethyl ester at concentrations higher than 500 mM enhance aggregate-aggregate sticking. These results explain the mechanism of heat-induced GDH aggregation and its peculiarities at different temperatures or in the presence of chemical chaperones.

Effects of amino acid additives on protein solubility - insights from desorption and direct electrospray ionization mass spectrometry

Naturally occurring amino acids have been broadly used as additives to improve protein solubility and inhibit aggregation. In this study, improvements in protein signal intensity obtained with the addition of L-serine, and structural analogs, to the desorption electrospray ionization mass spectrometry (DESI-MS) spray solvent were measured. The results were interpreted at the hand of proposed mechanisms of solution additive effects on protein solubility and dissolution. DESI-MS allows for these processes to be studied efficiently using dilute concentrations of additives and small amounts of proteins, advantages that represent real benefits compared to classical methods of studying protein stability and aggregation. We show that serine significantly increases the protein signal in DESI-MS when native proteins are undergoing unfolding during the dissolution process with an acidic solvent system (p-value = 0.0001), or with ammonium bicarbonate under denaturing conditions for proteins with high isoelectric points (p-value = 0.001). We establish that a similar increase in the protein signal cannot be observed with direct ESI-MS, and the observed increase is therefore not related to ionization processes or changes in the physical properties of the bulk solution. The importance of the presence of serine during protein conformational changes while undergoing dissolution is demonstrated through comparisons between the analyses of proteins deposited in native or unfolded states and by using native state-preserving and denaturing desorption solvents. We hypothesize that direct, non-covalent interactions involving all three functional groups of serine are involved in the beneficial effect on protein solubility and dissolution. Supporting evidence for a direct interaction include a reduction in efficacy with D-serine or the racemic mixture, indicating a non-bulk-solution physical property effect; insensitivity to the sample surface type or relative placement of serine addition; and a reduction in efficacy with any modifications to the serine structure, most notably the carboxyl functional group. An alternative hypothesis, also supported by some of our observations, could involve the role of serine clusters in the mechanism of solubility enhancement. Our study demonstrates the capability of DESI-MS together with complementary ESI-MS experiments as a novel tool for understanding protein solubility and dissolution and investigating the mechanism of action for solubility-enhancing additives.

Kinetics theories to understand the mechanism of aggregation of a protein and to design strategies for its inhibition

Protein aggregation phenomenon is closely related to the formation of amyloids which results in many neurodegenerative diseases like Alzheimer's, Parkinson's, Huntington's, and Amyotrophic Lateral Sclerosis. In order to prevent and treat these diseases, a clear understanding of the mechanism of misfolding and self-assembly of peptides and proteins is very crucial. The aggregation of a protein may involve various microscopic events. Multiple simulations utilizing the solutions of the master equation have given a better understanding of the kinetic profiles involved in the presence and absence of a particular microscopic event. This review focuses on understanding the contribution of these molecular events to protein aggregation based on the analysis of kinetic profiles of aggregation. We also discuss the effect of inhibitors, which target various species of aggregation pathways, on the kinetic profile of protein aggregation. At the end of this review, some strategies for the inhibition of aggregation that can be utilized by combining the chemical kinetics approach with thermodynamics are proposed.

The Multifaceted Roles of Proline in Cell Behavior

Herein, we review the multifaceted roles of proline in cell biology. This peculiar cyclic imino acid is: (i) A main precursor of extracellular collagens (the most abundant human proteins), antimicrobial peptides (involved in innate immunity), salivary proteins (astringency, teeth health) and cornifins (skin permeability); (ii) an energy source for pathogenic bacteria, protozoan parasites, and metastatic cancer cells, which engage in extracellular-protein degradation to invade their host; (iii) an antistress molecule (an osmolyte and chemical chaperone) helpful against various potential harms (UV radiation, drought/salinity, heavy metals, reactive oxygen species); (iv) a neural metabotoxin associated with schizophrenia; (v) a modulator of cell signaling pathways such as the amino acid stress response and extracellular signal-related kinase pathway; (vi) an epigenetic modifier able to promote DNA and histone hypermethylation; (vii) an inducer of proliferation of stem and tumor cells; and (viii) a modulator of cell morphology and migration/invasiveness. We highlight how proline metabolism impacts beneficial tissue regeneration, but also contributes to the progression of devastating pathologies such as fibrosis and metastatic cancer.

Clostridium cellulovorans Proteomic Responses to Butanol Stress

Combination of butanol-hyperproducing and hypertolerant phenotypes is essential for developing microbial strains suitable for industrial production of bio-butanol, one of the most promising liquid biofuels. Clostridium cellulovorans is among the microbial strains with the highest potential for direct production of n-butanol from lignocellulosic wastes, a process that would significantly reduce the cost of bio-butanol. However, butanol exhibits higher toxicity compared to ethanol and C. cellulovorans tolerance to this solvent is low. In the present investigation, comparative gel-free proteomics was used to study the response of C. cellulovorans to butanol challenge and understand the tolerance mechanisms activated in this condition. Sequential Window Acquisition of all Theoretical fragment ion spectra Mass Spectrometry (SWATH-MS) analysis allowed identification and quantification of differentially expressed soluble proteins. The study data are available via ProteomeXchange with the identifier PXD024183. The most important response concerned modulation of protein biosynthesis, folding and degradation. Coherent with previous studies on other bacteria, several heat shock proteins (HSPs), involved in protein quality control, were up-regulated such as the chaperones GroES (Cpn10), Hsp90, and DnaJ. Globally, our data indicate that protein biosynthesis is reduced, likely not to overload HSPs. Several additional metabolic adaptations were triggered by butanol exposure such as the up-regulation of V- and F-type ATPases (involved in ATP synthesis/generation of proton motive force), enzymes involved in amino acid (e.g., arginine, lysine, methionine, and branched chain amino acids) biosynthesis and proteins involved in cell envelope re-arrangement (e.g., the products of Clocel_4136, Clocel_4137, Clocel_4144, Clocel_4162 and Clocel_4352, involved in the biosynthesis of saturated fatty acids) and a redistribution of carbon flux through fermentative pathways (acetate and formate yields were increased and decreased, respectively). Based on these experimental findings, several potential gene targets for metabolic engineering strategies aimed at improving butanol tolerance in C. cellulovorans are suggested. This includes overexpression of HSPs (e.g., GroES, Hsp90, DnaJ, ClpC), RNA chaperone Hfq, V- and F-type ATPases and a number of genes whose function in C. cellulovorans is currently unknown.

Effects of cadmium stress on growth and physiological characteristics of sassafras seedlings

The effects of cadmium stress on the growth and physiological characteristics of Sassafras tzumu Hemsl. were studied in pot experiments. Five Cd levels were tested [CT(Control Treatment) : 0 mg/kg, Cd5: 5 mg/kg, Cd20: 20 mg/kg, Cd50: 50 mg/kg, and Cd100: 100 mg/kg]. The growth and physiological characteristics of the sassafras seedlings in each level were measured. The results showed that soil Cd had negative influences on sassafras growth and reduced the net growth of plant height and the biomass of leaf, branch and root. Significant reductions were recorded in root biomass by 18.18%(Cd5), 27.35%(Cd20), 27.57%(Cd50) and 28.95%(Cd100). The contents of hydrogen peroxide decreased first then increased while malondialdehyde showed the opposite trend with increasing cadmium concentration. Decreases were found in hydrogen peroxide contents by 10.96%(Cd5), 11.82%(Cd20) and 7.02%(Cd50); increases were found in malondialdehyde contents by 15.47%(Cd5), 16.07%(Cd20) and 7.85%(Cd50), indicating that cadmium stress had a certain effect on the peroxidation of the inner cell membranes in the seedlings that resulted in damage to the cell membrane structure. Superoxide dismutase activity decreased among treatments by 17.05%(Cd5), 10,68%(Cd20), 20.85%(Cd50) and 8.91%(Cd100), while peroxidase activity increased steadily with increasing cadmium concentration; these results suggest that peroxidase is likely the main protective enzyme involved in the reactive oxygen removal system in sassafras seedlings. Upward trends were observed in proline content by 90.76%(Cd5), 74.36%(Cd20), 99.73%(Cd50) and 126.01%(Cd100). The increase in proline content with increasing cadmium concentration indicated that cadmium stress induced proline synthesis to resist osmotic stress in the seedlings. Compared to that in CT, the soluble sugar content declined under the different treatments by 32.84%(Cd5), 5.85%(Cd20), 25.55%(Cd50) and 38.69%(Cd100). Increases were observed in the soluble protein content by 2.34%(Cd5), 21.36%(Cd20), 53.15%(Cd50) and 24.22%(Cd100). At different levels of cadmium stress, the chlorophyll content in the seedlings first increased and then decreased, and it was higher in the Cd5 and Cd20 treatments than that in the CT treatment. These results reflected that cadmium had photosynthesis-promoting effects at low concentrations and photosynthesis-suppressing effects at high concentrations. The photosynthetic gas exchange parameters and photosynthetic light-response parameters showed downward trends with increasing cadmium concentration compared with those in CT; these results reflected the negative effects of cadmium stress on photosynthesis in sassafras seedlings.

History and Domestication of Saccharomyces cerevisiae in Bread Baking

The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.

Drought-induced AtbZIP62 transcription factor regulates drought stress response in Arabidopsis

We investigated the role of AtbZIP62, an uncharacterized Arabidopsis bZIP TF, in oxidative, nitro-oxidative and drought stress conditions using reverse genetics approach. We further monitored the expression of AtPYD1 gene (orthologous to rice OsDHODH1 involved in the pyrimidine biosynthesis) in atbzip62 knock-out (KO) plants in order to investigate the transcriptional interplay of AtbZIP62 and AtPYD1. The atbzip62 KO plants showed significant increase in shoot length under oxidative stress, while no significant difference was recorded for root length compared to WT. However, under nitro-oxidative stress conditions, atbzip62 showed differential response to both NO-donors. Further characterization of AtbZIP62 under drought conditions showed that both atbzip62 and atpyd1-2 showed a sensitive phenotype to drought stress, and could not recover after re-watering. Transcript accumulation of AtbZIP62 and AtPYD1 showed that both were highly up-regulated by drought stress in wild type (WT) plants. Interestingly, AtPYD1 transcriptional level significantly decreased in atbzip62 exposed to drought stress. However, AtbZIP62 expression was highly induced in atpyd1-2 under the same conditions. Both AtbZIP62 and AtPYD1 were up-regulated in atnced3 and atcat2 while showing a contrasting expression pattern in atgsnor1-3. The recorded increase in CAT, POD, and PPO-like activities, the accumulation of chlorophylls and total carotenoids, and the enhanced proline and malondialdehyde levels would explain the sensitivity level of atbzip62 towards drought stress. All results collectively suggest that AtbZIP62 could be involved in AtPYD1 transcriptional regulation while modulating cellular redox state and photosynthetic processes. In addition, AtbZIP62 is suggested to positively regulate drought stress response in Arabidopsis.

Lactobacillus plantarum PMO 08 as a Probiotic Starter Culture for Plant-Based Fermented Beverages

Lactobacillus plantarum PMO 08 was evaluated as a starter culture for plant-based probiotic beverages. Its viability under various culture conditions and acidification ability in standardized tomato medium, fermentation parameters, and beverage properties were assessed. Lactobacillus plantarum PMO 08 could grow under various culture conditions; there was a high correlation between the incubation time to reach the optimal conditions and the inoculation concentration of lactic acid bacteria (LAB) (r² = 0.997). Acidity (0.958 ± 0.002%) and LAB count (9.78 ± 0.14 Log₁₀ CFU/mL) were significantly higher when fermented with L. plantarum than with the yogurt starter culture. A survival rate of 96% and 95% in artificial gastric juice and artificial intestinal juice, respectively, indicated that the probiotic requirements were met. The total polyphenol and glutamine content, and antioxidant activity increased after fermentation. The proline content significantly increased in L. plantarum PMO 08- fermented beverage. Thus, L. plantarum PMO 08 is an effective starter culture for non-dairy probiotic beverages whose functional quality may be improved by fermentation.

Effect of Disease-Associated P123H and V70M Mutations on β-Synuclein Fibrillation

Synucleinopathies are a class of neurodegenerative diseases, including Parkinson's disease (PD), Dementia with Lewy bodies (DLB), and Multiple System Atrophy (MSA). The common pathological hallmark of synucleinopathies is the filamentous α-synuclein (α-Syn) aggregates along with membrane components in cytoplasmic inclusions in the brain. β-Synuclein (β-Syn), an isoform of α-Syn, inhibits α-Syn aggregation and prevents its neurotoxicity, suggesting the neuroprotective nature of β-Syn. However, this notion changed with the discovery of disease-associated β-Syn mutations, V70M and P123H, in patients with DLB. It is still unclear how these missense mutations alter the structural and amyloidogenic properties of β-Syn, leading to neurodegeneration. Here, we characterized the biophysical properties and investigated the effect of mutations on β-Syn fibrillation under different conditions. V70M and P123H show high membrane binding affinity compared to wild-type β-Syn, suggesting their potential role in membrane interactions. β-Syn and its mutants do not aggregate under normal physiological conditions; however, the proteins undergo self-polymerization in a slightly acidic microenvironment and/or in the presence of an inducer, forming long unbranched amyloid fibrils similar to α-Syn. Strikingly, V70M and P123H mutants exhibit accelerated fibrillation compared to native β-Syn under these conditions. NMR study further revealed that these point mutations induce local perturbations at the site of mutation in β-Syn. Overall, our data provide insight into the biophysical properties of disease-associated β-Syn mutations and demonstrate that these mutants make the native protein more susceptible to aggregation in an altered microenvironment.

Quantitative Interpretation of Solvent Paramagnetic Relaxation for Probing Protein-Cosolute Interactions

Protein-small cosolute molecule interactions are ubiquitous and known to modulate the solubility, stability, and function of many proteins. Characterization of such transient weak interactions at atomic resolution remains challenging. In this work, we develop a simple and practical NMR method for extracting both energetic and dynamic information on protein-cosolute interactions from solvent paramagnetic relaxation enhancement (sPRE) measurements. Our procedure is based on an approximate (non-Lorentzian) spectral density that behaves exactly at both high and low frequencies. This spectral density contains two parameters, one global related to the translational diffusion coefficient of the paramagnetic cosolute, and the other residue specific. These parameters can be readily determined from sPRE data, and then used to calculate analytically a concentration normalized equilibrium average of the interspin distance, ⟨r^-6⟩_norm, and an effective correlation time, τ_C, that provide measures of the energetics and dynamics of the interaction at atomic resolution. We compare our approach with existing ones, and demonstrate the utility of our method using experimental ¹H longitudinal and transverse sPRE data recorded on the protein ubiquitin in the presence of two different nitroxide radical cosolutes, at multiple static magnetic fields. The approach for analyzing sPRE data outlined here provides a powerful tool for deepening our understanding of extremely weak protein-cosolute interactions.

Effect of exogenous proline on the ethanolic tolerance and malolactic performance of Oenococcus oeni

The use of malolactic starter cultures, often offer no guarantee of microbiological success due to the chemical and physical factors (pH, ethanol, SO₂, nutrient availability) that occur during the winemaking process. This study was born with the aim of improving the performance of the lactic acid bacteria used as a starter culture in the de-acidification of wines. Two commercial strains of Oenococcus oeni, were used. Was evaluated the effect of exogenous l-proline added during the bacterial growth, on the improvement of their survival in the presence of different ethanol concentrations and their ability to degrade l-malic acid in synthetic wine with the presence of 12% (v/v) and 13% (v/v) of ethanol. The results showed that l-proline improve ethanol tolerance and so the malolactic performances of O. oeni. This work represents an important strategy to ensure good vitality and improve the performance of the malolactic starter.

Entrapment of enzyme in the presence of proline: effective approach to enhance activity and stability of horseradish peroxidase

In this report, activity and stability of horseradish peroxidase (HRP) entrapped in polyacrylamide gel in the presence of proline (HEP) are compared with that of enzyme entrapped in absence of proline (HE). Within polyacrylamide (8%) beads, 80% entrapment yield for peroxidase was observed in the presence as well as absence of proline. The HEP (1.5 M proline) showed 170% higher activity compared to HE. HEP also showed significant increase in K _M, V _max and K _cat. At 8th cycle of use, HEP retained 40% of its activity, whereas HE retained only 10% of activity. In addition, in comparison with HE, HEP showed increased storage stability and thermo-stability. HEP showed higher activity compared to HE over an extensive range of pH (4-8), temperature (30-80 °C) and inhibitors such as NaN₃, Cd²⁺ and Pb²⁺. Our results suggest that peroxidase entrapment in polyacrylamide gel in the presence of proline can be a useful approach for increasing activity and stability of horseradish peroxidase.