The osmophobic effect: natural selection of a thermodynamic force in protein folding

Biophysical insights into osmolytes-driven enhancements in urate oxidase activity and stability

The thermal instability of pharmaceutical enzymes such as uricase or urate oxidase (UOX) in liquid solutions is a major problem. Notably, compatible osmolytes are a specific class of osmolytes that can preferentially stabilize the folded state of proteins. However, the detailed molecular interactions that enable them to affect protein stability are still not completely elucidated. This study aimed to investigate how the enzyme environment could be altered using osmolytes to improve its catalytic activity and stability. Initially, experimental conditions were optimized using response surface methodology (RSM). Then, kinetic and thermodynamic properties, as well as structural changes of urate oxidase, were assessed using spectroscopic and computational techniques in the presence and absence of mixed osmolytes. Kinetic parameters indicated an improvement in the catalytic function of urate oxidase and the results of thermodynamic analysis indicated that the van der Waals forces and hydrogen bonding network played a crucial role in the UOX-osmolytes interactions. Fluorescence measurements suggested that osmolyte-UOX interactions alter the enzyme's structure. The data revealed a complex quenching mechanism between the enzyme and osmolyte. Molecular dynamics (MD) simulations showed an increase in stability and structural compactness of the enzyme in the presence of mixed osmolytes. Furthermore, it depicted an increase in the abundance of secondary structure contents of the enzyme, which in turn maintained the integrity of its active site. Also, the molecular docking analysis further supported the experimental results. These findings revealed mechanisms by which binary-compatible osmolytes could have relevant effects on the catalytic function and stability of urate oxidase.

Chemical control of colloidal self-assembly driven by the electrosolvation force

Self-assembly of matter in solution generally relies on attractive interactions that overcome entropy and drive the formation of higher-order molecular and particulate structures. Such interactions are central to a variety of molecular processes, e.g., crystallisation, biomolecular folding and condensation, pathological protein aggregation and biofouling. The electrosolvation force introduces a distinct conceptual paradigm to the existing palette of interactions that govern the spontaneous accretion and organisation of matter. However, an understanding of the underlying physical chemistry, and therefore the ability to exert control over and tune the interaction, remains incomplete. Here we provide further evidence that this force arises from the structure of the interfacial electrolyte. Neutral molecules such as a different solvent, osmolytes or surfactants, may - even at very low concentrations in the medium - disrupt or reinforce pre-existing interfacial solvent structure, thereby delivering unanticipated chemical tuning of the ability of matter to self-assemble. The observations present unexpected mechanistic elements that may explain the impact of co-solvents and osmolytes on protein structure, stability and biomolecular condensation. Our findings thus furnish insight into the microscopic mechanisms that drive the emergence of order and structure from molecular to macroscopic scales in the solution phase.

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.

Enhancing osmotic stress tolerance of cell mimetics by modulating lipid bilayer

Seeking effective ways to maintain cellular homeostasis is crucial to the survival of organisms when they encounter osmotic stress. Glycine betaine (GB) is a widely generated natural osmolyte, but its endogenous production and action are limited. Herein, a kind of nonionic surfactant dodecyl-β-d-glucopyranoside (DG) and a common polymer polyethylene glycol (PEG) are proven to have the ability to enhance the osmotic stress (induced by sugar concentration changes) tolerance of cell and organism models, those are giant unilamellar vesicles (GUVs) and gram-negative Escherichia coli. DG or PEG only induces small size decrease and certain shape change of GUVs. Importantly, DG or PEG at the concentration 100 times lower than that of GB effectively increases the survival rate of bacteria under both hypoosmotic and hyperosmotic conditions. This intriguing result is attributed to the insertion of DG or adsorption of PEG in the lipid bilayer membrane, leading to enhanced membrane permeability. These exogenous substances can replace GB to facilely and highly efficiently augment adaptation of organisms to osmotic stress.

Characterizing Interactions Between Small Peptides and Dimethyl Sulfoxide Using Infrared Spectroscopy and Computational Methods

This study provides a comprehensive analysis of the interactions between dimethyl sulfoxide (DMSO) and two small peptides, diglycine and N-acetyl-glycine-methylamide (NAGMA), in aqueous solutions using FTIR spectroscopy and density functional theory (DFT) calculations. ATR-FTIR spectroscopy and DFT results revealed that DMSO does not form direct bonds with the peptides, suggesting that DMSO indirectly influences both peptides by modifying the surrounding water molecules. The analysis of HDO spectra allowed for the isolation of the contribution of water molecules that were simultaneously altered by the peptide and DMSO, and it also explained the changes in the hydration shells of the peptides in the presence of DMSO. In the DMSO-diglycine system, DMSO contributes to the additional strengthening of water hydrogen bonds in the reinforced hydration sphere of diglycine. In contrast, DMSO has a more moderate effect on the water molecules surrounding NAGMA due to the similarity of their hydration shells, leading to a slight weakening of the hydrogen bonds in the NAGMA hydration sphere. DFT/ONIOM calculations confirmed these observations. These findings demonstrated that DMSO influences peptide stability differentially based on their structural characteristics.

Osmolytes as structure-function regulators of intrinsically disordered casein proteins

Intrinsically disordered proteins (IDPs), despite lacking a stable structure, play crucial role in majority of the cellular processes. Casein, a key milk protein, represents this category of proteins, due to its dynamic and flexible structure which contributes towards the nutritional and functional properties of milk. The present chapter summarizes the role of osmolytes (small molecular weight organic molecules generally accumulated by cells to protect against denaturing stresses) in regulating the structure-function integrity of intrinsically disordered casein proteins. Osmolyte - casein interplay is of particular interest as these osmolytes have been found to affect the conformational flexibility and functional properties of casein proteins and thus can affect their overall behavior in the cellular environment. The present chapter delves into this by discussing the unique structural and functional properties of casein IDPs and the influence of osmolytes on their structure, stability, and chaperone activity. Elucidation of the osmolyte effects on the structural-functional integrity of caseins should advance our understanding of the dynamics of protein structure and function in complex biological environments and also offer practical perceptions for their future applications.

Regulation of the structural dynamics, aggregation, and pathogenicity of polyQ-expanded Huntingtin by osmolytes

Huntington Disease is an autosomal dominant neurodegenerative disease caused by expansion of the polymorphic trinucleotide CAG repeat of the HTT gene to code for an expanded glutamine track of the mutant Huntingtin protein (mHTT). Like other neurodegenerative diseases, symptomatic presentation of Huntington Disease is age-dependent or age-related. This age-dependent manifestation of an autosomal dominant disease trait underscores important and possibly priming role of age-related changes in cellular physiology that are conducive to disease presentation. Herein, we present studies on the effects of osmolytes on mHTT structuring and aggregation, vis-a-vis pathogenicity. We show that stabilizing polyol osmolytes, by their generic activity in promoting protein structuring and compaction, drive aggregation of the disordered mHTT protein and simultaneously inhibit their binding to and sequestration of key transcription factors for improved homeostasis and cell survival under stress. These and related observations in the literature give strong support to the notion that lower molecular weight and structurally dynamic forms of mHTT contribute importantly to disease pathogenesis. Aging is associated with important changes in the cell environment-disease protein accumulation, reduced hydration, and macromolecular crowding as examples. These changes have significant consequences on the structuring and pathogenicity of the disordered mHTT protein. A crowded and less hydrated aging cell environment is conducive to mHTT binding to and inhibition of cell regulatory protein function on the one hand, and in promoting mHTT aggregation on the other hand, to culminate in Huntington disease presentation.

The contrasting roles of co-solvents in protein formulations and food products

Protein aggregation is a major hurdle in developing biopharmaceuticals, in particular protein formulation area, but plays a pivotal role in food products. Co-solvents are used to suppress protein aggregation in pharmaceutical proteins. On the contrary, aggregation is encouraged in the process of food product making. Thus, it is expected that co-solvents play a contrasting role in biopharmaceutical formulation and food products. Here, we show several examples that utilize co-solvents, e.g., salting-out salts, sugars, polyols and divalent cations in promoting protein-protein interactions. The mechanisms of co-solvent effects on protein aggregation and solubility have been studied on aqueous protein solution and applied to develop pharmaceutical formulation based on the acquired scientific knowledge. On the contrary, co-solvents have been used in food industries based on empirical basis. Here, we will review the mechanisms of co-solvent effects on protein-protein interactions that can be applied to both pharmaceutical and food industries and hope to convey knowledge acquired through research on co-solvent interactions in aqueous protein solution and formulation to those involved in food science and provide those involved in protein solution research with the observations on aggregation behavior of food proteins.

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.

Trimethylamine N-oxide (TMAO) doubly locks the hydrophobic core and surfaces of protein against desiccation stress

Interactions between proteins and osmolytes are ubiquitous within cells, assisting in response to environmental stresses. However, our understanding of protein-osmolyte interactions underlying desiccation tolerance is limited. Here, we employ solid-state NMR (ssNMR) to derive information about protein conformation and site-specific interactions between the model protein, SH3, and the osmolyte trimethylamine N-oxide (TMAO). The data show that SH3-TMAO interactions maintain key structured regions during desiccation and facilitate reversion to the protein's native state once desiccation stress is even slightly relieved. We identify 10 types of residues at 28 sites involved in the SH3-TMAO interactions. These sites comprise hydrophobic, positively charged, and aromatic amino acids located in SH3's hydrophobic core and surface clusters. TMAO locks both the hydrophobic core and surface clusters through its zwitterionic and trimethyl ends. This double locking is responsible for desiccation tolerance and differs from ideas based on exclusion, vitrification, and water replacement. ssNMR is a powerful tool for deepening our understanding of extremely weak protein-osmolyte interactions and providing insight into the evolutionary mechanism of environmental tolerance.

Bacterial cell volume regulation and the importance of cyclic di-AMP

SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.

Protecting Proteins from Desiccation Stress Using Molecular Glasses and Gels

Faced with desiccation stress, many organisms deploy strategies to maintain the integrity of their cellular components. Amorphous glassy media composed of small molecular solutes or protein gels present general strategies for protecting against drying. We review these strategies and the proposed molecular mechanisms to explain protein protection in a vitreous matrix under conditions of low hydration. We also describe efforts to exploit similar strategies in technological applications for protecting proteins in dry or highly desiccated states. Finally, we outline open questions and possibilities for future explorations.

Trimethylamine-N-oxide depletes urea in a peptide solvation shell

Trimethylamine-N-oxide (TMAO) and urea are metabolites that are used by some marine animals to maintain their cell volume in a saline environment. Urea is a well-known denaturant, and TMAO is a protective osmolyte that counteracts urea-induced protein denaturation. TMAO also has a general protein-protective effect, for example, it counters pressure-induced protein denaturation in deep-sea fish. These opposing effects on protein stability have been linked to the spatial relationship of TMAO, urea, and protein molecules. It is generally accepted that urea-induced denaturation proceeds through the accumulation of urea at the protein surface and their subsequent interaction. In contrast, it has been suggested that TMAO's protein-stabilizing effects stem from its exclusion from the protein surface, and its ability to deplete urea from protein surfaces; however, these spatial relationships are uncertain. We used neutron diffraction, coupled with structural refinement modeling, to study the spatial associations of TMAO and urea with the tripeptide derivative glycine-proline-glycinamide in aqueous urea, aqueous TMAO, and aqueous urea-TMAO (in the mole ratio 1:2 TMAO:urea). We found that TMAO depleted urea from the peptide's surface and that while TMAO was not excluded from the tripeptide's surface, strong atomic interactions between the peptide and TMAO were limited to hydrogen bond donating peptide groups. We found that the repartition of urea, by TMAO, was associated with preferential TMAO-urea bonding and enhanced urea-water hydrogen bonding, thereby anchoring urea in the bulk solution and depleting urea from the peptide surface.

Micropolarized to the core

Macromolecules can undergo liquid–liquid phase separation to form condensates that have critical roles in biological functions and dysfunctions. A new study demonstrates that differences in micropolarity between components is a prime determinant of the multiphasic architecture of biomolecular condensates.

Do Ionic Liquids Exhibit the Required Characteristics to Dissolve, Extract, Stabilize, and Purify Proteins? Past-Present-Future Assessment

Proteins are highly labile molecules, thus requiring the presence of appropriate solvents and excipients in their liquid milieu to keep their stability and biological activity. In this field, ionic liquids (ILs) have gained momentum in the past years, with a relevant number of works reporting their successful use to dissolve, stabilize, extract, and purify proteins. Different approaches in protein-IL systems have been reported, namely, proteins dissolved in (i) neat ILs, (ii) ILs as co-solvents, (iii) ILs as adjuvants, (iv) ILs as surfactants, (v) ILs as phase-forming components of aqueous biphasic systems, and (vi) IL-polymer-protein/peptide conjugates. Herein, we critically analyze the works published to date and provide a comprehensive understanding of the IL-protein interactions affecting the stability, conformational alteration, unfolding, misfolding, and refolding of proteins while providing directions for future studies in view of imminent applications. Overall, it has been found that the stability or purification of proteins by ILs is bispecific and depends on the structure of both the IL and the protein. The most promising IL-protein systems are identified, which is valuable when foreseeing market applications of ILs, e.g., in "protein packaging" and "detergent applications". Future directions and other possibilities of IL-protein systems in light-harvesting and biotechnology/biomedical applications are discussed.

Desiccation induces varied responses within a soil bacterial genus

Desiccation impacts a suite of physiological processes in microbes by elevating levels of damaging reactive oxygen species and inducing DNA strand breaks. In response to desiccation-induced stress, microbes have evolved specialized mechanisms to help them survive. Here, we performed a 128-day lab desiccation experiment on nine strains from three clades of an abundant soil bacterium, Curtobacterium. We sequenced RNA from each strain at three time points to investigate their response. Curtobacterium was highly resistant to desiccation, outlasting both Escherichia coli and a famously DNA damage-resistant bacterium, Deinococcus radiodurans. However, within the genus, there were also 10-fold differences in survival rates among strains. Transcriptomic profiling revealed responses shared within the genus including up-regulation of genes involved in DNA damage repair, osmolyte production, and efflux pumps, but also up-regulation of pathways and genes unique to the three clades. For example, trehalose synthesis gene otsB, the chaperone groEL, and the oxygen scavenger katA were all found in either one or two clades but not the third. Here, we provide evidence of considerable variation in closely related strains, and further elucidation of the phylogenetic conservation of desiccation tolerance remains an important goal for microbial ecologists.

Ectoine Globally Hypomethylates DNA in Skin Cells and Suppresses Cancer Proliferation

Epigenetic modifications, mainly aberrant DNA methylation, have been shown to silence the expression of genes involved in epigenetic diseases, including cancer suppression genes. Almost all conventional cancer therapeutic agents, such as the DNA hypomethylation drug 5-aza-2-deoxycytidine, have insurmountable side effects. To investigate the role of the well-known DNA protectant (ectoine) in skin cell DNA methylation and cancer cell proliferation, comprehensive methylome sequence analysis, 5-methyl cytosine (5mC) analysis, proliferation and tumorigenicity assays, and DNA epigenetic modifications-related gene analysis were performed. The results showed that extended ectoine treatment globally hypomethylated DNA in skin cells, especially in the CpG island (CGIs) element, and 5mC percentage was significantly reduced. Moreover, ectoine mildly inhibited skin cell proliferation and did not induce tumorigenicity in HaCaT cells injected into athymic nude mice. HaCaT cells treated with ectoine for 24 weeks modulated the mRNA expression levels of Dnmt1, Dnmt3a, Dnmt3b, Dnmt3l, Hdac1, Hdac2, Kdm3a, Mettl3, Mettl14, Snrpn, and Mest. Overall, ectoine mildly demethylates DNA in skin cells, modulates the expression of epigenetic modification-related genes, and reduces cell proliferation. This evidence suggests that ectoine is a potential anti-aging agent that prevents DNA hypermethylation and subsequently activates cancer-suppressing genes.

The variable domain from dynamin-related protein 1 promotes liquid-liquid phase separation that enhances its interaction with cardiolipin-containing membranes

Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" important for regulation. For the mitochondrial fission dynamin, dynamin-related protein 1, a regulatory role for the variable domain (VD) is demonstrated by gain- and loss-of-function mutations, yet the basis for this is unclear. Here, the isolated VD is shown to be intrinsically disordered and undergo a cooperative transition in the stabilizing osmolyte trimethylamine N-oxide. However, the osmolyte-induced state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, which appears to promote phase separation. Since dynamin-related protein 1 is found assembled into discrete punctate structures on the mitochondrial surface, the inference from the present work is that these structures might arise from a condensed state involving the VD that may enable rapid tuning of mechanoenzyme assembly necessary for fission.

Not Always Sticky: Specificity of Protein Stabilization by Sugars Is Conferred by Protein-Water Hydrogen Bonds

Solutes added to buffered solutions directly impact protein folding. Protein stabilization by cosolutes or crowders has been shown to be largely driven by protein-cosolute volume exclusion complemented by chemical and soft interactions. By contrast to previous studies that indicate the invariably destabilizing role of soft protein-sugar attractions, we show here that soft interactions with sugar cosolutes are protein-specific and can be stabilizing or destabilizing. We experimentally follow the folding of two model miniproteins that are only marginally stable but in the presence of sugars and polyols fold into representative and distinct secondary structures: β-hairpin or α-helix. Our mean-field model reveals that while protein-sugar excluded volume interactions have a similar stabilizing effect on both proteins, the soft interactions add a destabilizing contribution to one miniprotein but further stabilize the other. Using molecular dynamics simulations, we link the soft protein-cosolute interactions to the weakening of direct protein-water hydrogen bonding due to the presence of sugars. Although these weakened hydrogen bonds destabilize both the native and denatured states of the two proteins, the resulting contribution to the folding free energy can be positive or negative depending on the amino acid sequence. This study indicates that the significant variation between proteins in their soft interactions with sugar determines the specific response of different proteins, even to the same sugar.

The variable domain from the mitochondrial fission mechanoenzyme Drp1 promotes liquid-liquid phase separation

Dynamins are an essential superfamily of mechanoenzymes that remodel membranes and often contain a "variable domain" (VD) important for regulation. For the mitochondrial fission dynamin, Drp1, a regulatory role for the VD is demonstrated by mutations that can elongate, or fragment, mitochondria. How the VD encodes inhibitory and stimulatory activity is unclear. Here, isolated VD is shown to be intrinsically disordered (ID) yet undergoes a cooperative transition in the stabilizing osmolyte TMAO. However, the TMAO stabilized state is not folded and surprisingly appears as a condensed state. Other co-solutes including known molecular crowder Ficoll PM 70, also induce a condensed state. Fluorescence recovery after photobleaching experiments reveal this state to be liquid-like indicating the VD undergoes a liquid-liquid phase separation under crowding conditions. These crowding conditions also enhance binding to cardiolipin, a mitochondrial lipid, raising the possibility that phase separation may enable rapid tuning of Drp1 assembly necessary for fission.

Phase separation propensity of the intrinsically disordered AB region of human RXRβ

RXRβ is one of three subtypes of human retinoid X receptor (RXR), a transcription factor that belongs to the nuclear receptor superfamily. Its expression can be detected in almost all tissues. In contrast to other subtypes - RXRα and RXRγ - RXRβ has the longest and unique N-terminal sequence called the AB region, which harbors a ligand-independent activation function. In contrast to the functional properties of this sequence, the molecular properties of the AB region of human RXRβ (AB_hRXRB) have not yet been characterized. Here, we present a systematic biochemical and biophysical analysis of recombinant AB_hRXRB, along with in silico examinations, which demonstrate that AB_hRXRB exhibits properties of a coil-like intrinsically disordered region. AB_hRXRB possesses a flexible structure that is able to adopt a more ordered conformation under the influence of different environmental factors. Interestingly, AB_hRXRB promotes the formation of liquid-liquid phase separation (LLPS), a phenomenon previously observed for the AB region of another human subtype of RXR - RXRγ (AB_hRXRG). Although both AB regions seem to be similar in terms of their ability to induce phase separation, they clearly differ in the sensitivity to factors driving and regulating LLPS. This distinct LLPS response to environmental factors driven by the unique amino acid compositions of AB_hRXRB and AB_hRXRG can be significant for the specific modulation of the transcriptional activation of target genes by different subtypes of RXR. Video Abstract.

Osmolytes: Wonder molecules to combat protein misfolding against stress conditions

The proper functioning of any protein depends on its three dimensional conformation which is achieved by the accurate folding mechanism. Keeping away from the exposed stress conditions leads to cooperative unfolding and sometimes partial folding, forming the structures like protofibrils, fibrils, aggregates, oligomers, etc. leading to several neurodegenerative diseases like Parkinson's disease, Alzheimer's, Cystic fibrosis, Huntington, Marfan syndrome, and also cancers in some cases, too. Hydration of proteins is necessary, which may be achieved by the presence of organic solutes called osmolytes within the cell. Osmolytes belong to different classes in different organisms and play their role by preferential exclusion of osmolytes and preferential hydration of water molecules and achieves the osmotic balance in the cell otherwise it may cause problems like cellular infection, cell shrinkage leading to apoptosis and cell swelling which is also the major injury to the cell. Osmolyte interacts with protein, nucleic acids, intrinsically disordered proteins by non-covalent forces. Stabilizing osmolytes increases the Gibbs free energy of the unfolded protein and decreases that of folded protein and vice versa with denaturants (urea and guanidinium hydrochloride). The efficacy of each osmolyte with the protein is determined by the calculation of m value which reflects its efficiency with protein. Hence osmolytes can be therapeutically considered and used in drugs.

Impact of an Ionic Liquid on Amino Acid Side Chains: A Perspective from Molecular Simulation Studies

Ionic liquids (ILs) are known to modify the structural stability of proteins. The modification of the protein conformation is associated with the accumulation of ILs around the amino acid (AA) side chains and the nature of interactions between them. To understand the microscopic picture of the structural arrangements of ILs around the AA side chains, room temperature molecular dynamics (MD) simulations have been carried out in this work with a series of hydrophobic, polar and charged AAs in aqueous solutions containing the IL 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF₄]) at 2 M concentration. The calculations revealed distinctly nonuniform distribution of the IL components around different AAs. In particular, it is demonstrated that the BMIM⁺ cations preferentially interact with the aromatic AAs through favorable stacking interactions between the cation imidazolium head groups and the aromatic AA side chains. This results in preferential parallel alignments and enhanced population of the cations around the aromatic AAs. The potential of mean force (PMF) calculations revealed that such favorable stacking interactions provide greater stability to the contact pairs (CPs) formed between the aromatic AAs and the IL cations as compared to the other AAs. It is further quantified that for most of the AAs (except the cationic ones), a favorable enthalpy contribution more than compensates for the entropy cost to form stable CPs with the IL cations. These findings are likely to provide valuable fundamental information toward understanding the effects of ILs on protein conformational stability.

Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns

Staphylococcus epidermidis and S. aureus are highly problematic bacteria in hospital settings. This stems, at least in part, from strong abilities to form biofilms on abiotic or biotic surfaces. Biofilms are well-organized multicellular aggregates of bacteria, which, when formed on indwelling medical devices, lead to infections that are difficult to treat. Cell wall-anchored (CWA) proteins are known to be important players in biofilm formation and infection. Many of these proteins have putative stalk-like regions or regions of low complexity near the cell wall-anchoring motif. Recent work demonstrated the strong propensity of the stalk region of the S. epidermidis accumulation-associated protein (Aap) to remain highly extended under solution conditions that typically induce compaction or other significant conformational changes. This behavior is consistent with the expected function of a stalk-like region that is covalently attached to the cell wall peptidoglycan and projects the adhesive domains of Aap away from the cell surface. In this study, we evaluate whether the ability to resist compaction is a common theme among stalk regions from various staphylococcal CWA proteins. Circular dichroism spectroscopy was used to examine secondary structure changes as a function of temperature and cosolvents along with sedimentation velocity analytical ultracentrifugation and SAXS to characterize structural characteristics in solution. All stalk regions tested are intrinsically disordered, lacking secondary structure beyond random coil and polyproline type II helix, and they all sample highly extended conformations. Remarkably, the Ser-Asp dipeptide repeat region of SdrC exhibited nearly identical behavior in solution when compared to the Aap Pro/Gly-rich region, despite highly divergent sequence patterns, indicating conservation of function by various distinct staphylococcal CWA protein stalk regions.

Faecal metabolite deficit, gut inflammation and diet in Parkinson's disease: Integrative analysis indicates inflammatory response syndrome

BACKGROUND

Gut-brain axis is widely implicated in the pathophysiology of Parkinson's disease (PD). We take an integrated approach to considering the gut as a target for disease-modifying intervention, using continuous measurements of disease facets irrespective of diagnostic divide.

METHODS

We characterised 77 participants with diagnosed-PD, 113 without, by dietary/exogenous substance intake, faecal metabolome, intestinal inflammation, serum cytokines/chemokines, clinical phenotype including colonic transit time. Complete-linkage hierarchical cluster analysis of metabolites discriminant for PD-status was performed.

RESULTS

Longer colonic transit was linked to deficits in faecal short-chain-fatty acids outside PD, to a 'tryptophan-containing metabolite cluster' overall. Phenotypic cluster analysis aggregated colonic transit with brady/hypokinesia, tremor, sleep disorder and dysosmia, each individually associated with tryptophan-cluster deficit. Overall, a faster pulse was associated with deficits in a metabolite cluster including benzoic acid and an imidazole-ring compound (anti-fungals) and vitamin B3 (anti-inflammatory) and with higher serum CCL20 (chemotactic for lymphocytes/dendritic cells towards mucosal epithelium). The faster pulse in PD was irrespective of postural hypotension. The benzoic acid-cluster deficit was linked to (well-recognised) lower caffeine and alcohol intakes, tryptophan-cluster deficit to higher maltose intake. Free-sugar intake was increased in PD, maltose intake being 63% higher (p = .001). Faecal calprotectin was 44% (95% CI 5%, 98%) greater in PD [p = .001, adjusted for proton-pump inhibitors (p = .001)], with 16% of PD-probands exceeding a cut-point for clinically significant inflammation compatible with inflammatory bowel disease. Higher maltose intake was associated with exceeding this calprotectin cut-point.

CONCLUSIONS

Emerging picture is of (i) clinical phenotype being described by deficits in microbial metabolites essential to gut health; (ii) intestinal inflammation; (iii) a systemic inflammatory response syndrome.

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.

TMAO to the rescue of pathogenic protein variants

Trimethylamine N-oxide (TMAO) is a chemical chaperone found in various organisms including humans. Various studies unveiled that it is an excellent protein-stabilizing agent, and induces folding of unstructured proteins. It is also well established that it can counteract the deleterious effects of urea, salt, and hydrostatic pressure on macromolecular integrity. There is also existence of large body of data regarding its ability to restore functional deficiency of various mutant proteins or pathogenic variants by correcting misfolding defects and inhibiting the formation of high-order toxic protein oligomers. Since an important class of human disease called "protein conformational disorders" is due to protein misfolding and/or formation of high-order oligomers, TMAO stands as a promising molecule for the therapeutic intervention of such diseases. The present review has been designed to gather a comprehensive knowledge of the TMAO's effect on the functional restoration of various mutants, identify its shortcomings and explore its potentiality as a lead molecule. Future prospects have also been suitably incorporated.

Protein Fibrillation under Crowded Conditions

Protein amyloid fibrils have widespread implications for human health. Over the last twenty years, fibrillation has been studied using a variety of crowding agents to mimic the packed interior of cells or to probe the mechanisms and pathways of the process. We tabulate and review these results by considering three classes of crowding agent: synthetic polymers, osmolytes and other small molecules, and globular proteins. While some patterns are observable for certain crowding agents, the results are highly variable and often depend on the specific pairing of crowder and fibrillating protein.

Biopolymers and Osmolytes - A Focus towards the Prospects of Stability and Adjuvanticity of Vaccines

‘New-Gen Vaccines’ are grabbing the attention of scientists as they are much suitable for an immune-compromised group of individuals as well as infants. The major drawbacks of these vaccines are lower immunogenicity and instability. The need for a convenient and safe adjuvant is still under exploration. On the other hand, thermal instability leads to the inactivation of the vaccine and becomes detrimental in many cases. Thus, there is a need to incorporate new kinds of excipients into vaccine formulation to enhance the potency/immunogenicity of vaccine antigens and also act as stabilizers. A limited or single excipient in providing the required dual-activity is vital to break the stereotypical usage of the well-entrenched adverse ingredients. In the proposed review, the efficiency of naturally occurring biocompatible carbohydrate polymers and osmolytes and their ‘dual-role’ is briefed. In addition, the information on the possible mechanisms of action of carbohydrate polymers in vaccines as adjuvants and stabilizers are also discussed.

L-Proline Synthesis Mutants of Bacillus subtilis Overcome Osmotic Sensitivity by Genetically Adapting L-Arginine Metabolism

The accumulation of the compatible solute L-proline by Bacillus subtilis via synthesis is a cornerstone in the cell’s defense against high salinity as the genetic disruption of this biosynthetic process causes osmotic sensitivity. To understand how B. subtilis could potentially cope with high osmolarity surroundings without the functioning of its natural osmostress adaptive L-proline biosynthetic route (ProJ-ProA-ProH), we isolated suppressor strains of proA mutants under high-salinity growth conditions. These osmostress-tolerant strains carried mutations affecting either the AhrC transcriptional regulator or its operator positioned in front of the argCJBD-carAB-argF L-ornithine/L-citrulline/L-arginine biosynthetic operon. Osmostress protection assays, molecular analysis and targeted metabolomics showed that these mutations, in conjunction with regulatory mutations affecting rocR-rocDEF expression, connect and re-purpose three different physiological processes: (i) the biosynthetic pathway for L-arginine, (ii) the RocD-dependent degradation route for L-ornithine, and (iii) the last step in L-proline biosynthesis. Hence, osmostress adaptation without a functional ProJ-ProA-ProH route is made possible through a naturally existing, but inefficient, metabolic shunt that allows to substitute the enzyme activity of ProA by feeding the RocD-formed metabolite γ-glutamate-semialdehyde/Δ¹-pyrroline-5-carboxylate into the biosynthetic route for the compatible solute L-proline. Notably, in one class of mutants, not only substantial L-proline pools but also large pools of L-citrulline were accumulated, a rather uncommon compatible solute in microorganisms. Collectively, our data provide an example of the considerable genetic plasticity and metabolic resourcefulness of B. subtilis to cope with everchanging environmental conditions.

Trimethylamine N-Oxide (TMAO) and Trimethylamine (TMA) Determinations of Two Hadal Amphipods

Hadal trenches are a unique habitat with high hydrostatic pressure, low temperature and scarce food supplies. Amphipods are the dominant scavenging metazoan species in this ecosystem. Trimethylamine (TMA) and trimethylamine oxide (TMAO) have been shown to play important roles in regulating osmotic pressure in mammals, hadal dwellers and even microbes. However, the distributions of TMAO and TMA concentrations of hadal animals among different tissues have not been reported so far. Here, the TMAO and TMA contents of eight tissues of two hadal amphipods, Hirondellea gigas and Alicella gigantea from the Mariana Trench and the New Britain Trench, were detected by using the ultrahigh performance liquid chromatography–mass spectrometry (UPLC-MS/MS) method. Compared with the shallow water Decapoda, Penaeus vannamei, the hadal amphipods possessed significantly higher TMAO concentrations and a similar level of TMA in all the detected tissues. A higher level of TMAO was detected in the external organs (such as the eye and exoskeleton) for both of the two hadal amphipods, which indicated that the TMAO concentration was not evenly distributed, although the same hydrostatic pressure existed in the outer and internal organs. Moreover, a strong positive correlation was found between the concentrations of TMAO and TMA in the two hadal amphipods. In addition, evolutionary analysis regarding FMO3, the enzyme to convert TMA into TMAO, was also conducted. Three positive selected sites in the conserved region and two specific mutation sites in two conserved motifs were found in the A. gigantea FMO3 gene. Combined together, this study supports the important role of TMAO for the environmental adaptability of hadal amphipods and speculates on the molecular evolution and protein structure of FMO3 in hadal species.

Improving coarse-grained models of protein folding through weighting of polar-polar/hydrophobic-hydrophobic interactions into crowded spaces

Herein were tested 7 hydrophobic-polar sequences in two types of 2D-square space lattices, homogeneous and correlated, the latter simulating molecular crowding included as a geometric boundary restriction. Optimization of 2D structures was carried out using a variant of Dill's model, inspired by convex function, taking into account both hydrophobic (Dill's model) and polar interactions, including more structural information to reach better folding solutions. While using correlated networks, degrees of freedom in the folding of sequences were limited; as a result in all cases, more successful structural trials were found in comparison to a homogeneous lattice. The majority of employed sequences were designed by our workgroup, two of them were folded with other approaches, and another is a modified version of a previous sequence, initial forms of the other two have been employed but without taking into account polar-polar contributions. Three of them are newly proposed, intended to test the conjoint hydrophobic-hydrophobic and polar-polar contributions in crowded spaces. One sequence turned out to be the most difficult of the seven folded, this perhaps due to intrinsic (i) degrees of freedom and (ii) motifs of the expected 2D HP structure. Meanwhile two-sequence, although optimal folding was not achieved for neither of the two approaches, folding with correlated network approach not only produced better results than homogeneous space, but for them the best values found with crowding were very close to the expected optimal fitness. In general, five sequences were better folded with medium lattice units for correlated media; instead, another two sequences were better folded with a bit larger degree of lattice unit, revealing that depending on the degrees of freedom and particular folding, motifs in each sequence would require tuned crowding to achieve better folding. Therefore, the main goal herein was to obtain a modified 2D HP lattice model to mimic folding of proteins or secondary structures, like β-sheets, taking into account both hydrophobic-hydrophobic and polar-polar interactions, and fold them in a crowded environment. This simple but enough construction would be conducted to determine the needed information to fold sequences in a sort of a minimal but complete heuristic model. Finally, we claim that all folded sequences into crowded spaces achieve better results than homogeneous ones.

The Role of Taurine in Skeletal Muscle Functioning and Its Potential as a Supportive Treatment for Duchenne Muscular Dystrophy

Taurine (2-aminoethanesulfonic acid) is required for ensuring proper muscle functioning. Knockout of the taurine transporter in mice results in low taurine concentrations in the muscle and associates with myofiber necrosis and diminished exercise capacity. Interestingly, regulation of taurine and its transporter is altered in the mdx mouse, a model for Duchenne Muscular Dystrophy (DMD). DMD is a genetic disorder characterized by progressive muscle degeneration and weakness due to the absence of dystrophin from the muscle membrane, causing destabilization and contraction-induced muscle cell damage. This review explores the physiological role of taurine in skeletal muscle and the consequences of a disturbed balance in DMD. Its potential as a supportive treatment for DMD is also discussed. In addition to genetic correction, that is currently under development as a curative treatment, taurine supplementation has the potential to reduce muscle inflammation and improve muscle strength in patients.

A pressure-jump study on the interaction of osmolytes and crowders with cubic monoolein structures

Many vital processes that take place in biological cells involve remodeling of lipid membranes. These processes take place in a milieu that is packed with various solutes, ranging from ions and small organic osmolytes to proteins and other macromolecules, occupying about 30% of the available volume. In this work, we investigated how molecular crowding, simulated with the polymer polyethylene glycol (PEG), and the osmolytes urea and trimethylamine-N-oxide (TMAO) affect the equilibration of cubic monoolein structures after a phase transition from a lamellar state induced by an abrupt pressure reduction. In absence of additives, swollen cubic crystallites form after the transition, releasing excess water over several hours. This process is reflected in a decreasing lattice constant and was monitored with small angle X-ray scattering. We found that the osmotic pressure exerted by PEG and TMAO, which are displaced from narrow inter-bilayer spaces, accelerates the equilibration. When the radius of gyration of the added PEG was smaller than the radius of the water channels of the cubic phase, the effect became more pronounced with increasing molecular weight of the polymers. As the release of hydration water from the cubic structures is accompanied by an increasing membrane curvature and a reduction of the interface between lipids and aqueous phase, urea, which has a slight affinity to reside near membrane surfaces, stabilized the swollen crystallites and slowed down the equilibration dynamics. Our results support the view that cellular solutes are important contributors to dynamic membrane processes, as they can accelerate dehydration of inter-bilayer spaces and promote or counteract membrane curvature.

Improving biocatalytic properties of an azoreductase via the N-terminal fusion of formate dehydrogenase

Azoreductases require NAD(P)H to reduce azo dyes but the costly price of NAD(P)H limits its application. Formate dehydrogenase (FDH) allows NAD(P)+ recycling and therefore, the fusion of these two biocatalysts seems promising. This study investigated the changes to the fusion protein involving azoreductase (AzoRo) of Rhodococcus opacus 1CP and FDH (FDHC23S and FDHC23SD195QY196H) of Candida boidinii in different positions with His-tag as the linker. The position affected enzyme activities as AzoRo activity decreased by 20-fold when it is in the N-terminus of the fusion protein. FDHC23S+AzoRo was the most active construct and was further characterized. Enzymatic activities of FDHC23S+AzoRo decreased compared to parental enzymes but showed improved substrate scope - accepting bulkier dyes. Moreover, pH has an influence on the stability and activity of the fusion protein because at pH 6 (pH that is suboptimal for FDH), the dye reduction decreased to more than 50% and this could be attributed to the impaired NADH supply for the AzoRo part.

Combined action of chemical chaperones on stability, aggregation and oligomeric state of muscle glycogen phosphorylase b

Chemical chaperones are a class of small molecules, which enhance protein stability, folding, inhibit protein aggregation, and are used for long-term storage of therapeutic proteins. The combined action of chemical chaperones trehalose, betaine and lysine on stability, aggregation and oligomeric state of muscle glycogen phosphorylase b (Phb) has been studied. Dynamic light scattering data indicate that the affinity of trehalose to Phb increased in the presence of betaine or lysine at both stages (stage of nucleation and aggregate growth) of enzyme aggregation at 48 °C, in contrast, the affinity of betaine to the enzyme in the presence of lysine remained practically unchanged. According to differential scanning calorimetry and analytical ultracentrifugation data, the mixture of trehalose and betaine stabilized Phb stronger than either of them in total. Moreover, the destabilizing effect of lysine on the enzyme was almost completely compensated by trehalose and only partially by betaine. The main protective effect of the mixtures of osmolytes and lysine is associated with their influence on the dissociation/denaturation stage, which is the rate-limiting one of Phb aggregation. Thus, a pair of chaperones affects the stability, oligomeric state, and aggregation of Phb differently than individual chaperones.

On the osmotic pressure of cells

The chemical potential of water ( $ {\mu}_{{\mathrm{H}}_2\mathrm{O}} $ ) provides an essential thermodynamic characterization of the environment of living organisms, and it is of equal significance as the temperature. For cells, $ {\mu}_{{\mathrm{H}}_2\mathrm{O}} $ is conventionally expressed in terms of the osmotic pressure (πosm). We have previously suggested that the main contribution to the intracellular πosm of the bacterium E. coli is from soluble negatively-charged proteins and their counter-ions. Here, we expand on this analysis by examining how evolutionary divergent cell types cope with the challenge of maintaining πosm within viable values. Complex organisms, like mammals, maintain constant internal πosm ≈ 0.285 osmol, matching that of 0.154 M NaCl. For bacteria it appears that optimal growth conditions are found for similar or slightly higher πosm (0.25-0.4 osmol), despite that they represent a much earlier stage in evolution. We argue that this value reflects a general adaptation for optimising metabolic function under crowded intracellular conditions. Environmental πosm that differ from this optimum require therefore special measures, as exemplified with gram-positive and gram-negative bacteria. To handle such situations, their membrane encapsulations allow for a compensating turgor pressure that can take both positive and negative values, where positive pressures allow increased frequency of metabolic events through increased intracellular protein concentrations. A remarkable exception to the rule of 0.25-0.4 osmol, is found for halophilic archaea with internal πosm ≈ 15 osmol. The internal organization of these archaea differs in that they utilize a repulsive electrostatic mechanism operating only in the ionic-liquid regime to avoid aggregation, and that they stand out from other organisms by having no turgor pressure.

The gut metabolite, trimethylamine N-oxide inhibits protein folding by affecting cis-trans isomerization and induces cell cycle arrest

Trimethylamine N-Oxide (TMAO) is an important metabolite, which is derived from choline, betaine, and carnitine in various organisms. In humans, it is synthesized through gut microbiota and is abundantly found in serum and cerebrospinal fluid (CSF). Although TMAO is a stress protectant especially in urea-rich organisms, it is an atherogenic agent in humans and is associated with various diseases. Studies have also unveiled its exceptional role in protein folding and restoration of mutant protein functions. However, most of these data were obtained from studies carried on fast-folding proteins. In the present study, we have investigated the effect of TMAO on the folding behavior of a well-characterized protein with slow folding kinetics, carbonic anhydrase (CA). We discovered that TMAO inhibits the folding of this protein via its effect on proline cis-trans isomerization. Furthermore, TMAO is capable of inducing cell cycle arrest. This study highlights the potential role of TMAO in developing proteopathies and associated diseases.

Interaction of Zwitterionic Osmolyte Trimethylamine N-oxide (TMAO) with Molecular Hydrophobes: An Interplay of Hydrophobic and Electrostatic Interactions

Interaction of trimethylamine N-oxide (TMAO) with charged/uncharged moieties of proteins and lipids is an important elementary step toward the multifaceted biofunctions of TMAO. Using minimum area Raman difference spectroscopy (MA-RDS) of aqueous TMAO (1.0 M) in the presence of deuterated molecular hydrophobes (e.g., deuterated tetramethylammonium cation (d-TMA⁺) and tert-butylalcohol (d-TBA)), we show that TMAO exhibits two distinct motifs of interaction with the cationic (d-TMA⁺) and uncharged (d-TBA) hydrophobes. Specifically, the trimethylammonium moiety of TMAO undergoes van der Waals attraction with the tert-butyl group of d-TBA, which is governed by their mutual hydrophobic interaction with water. This makes their methyl groups less exposed to water. In contrast, for the cationic hydrophobe (d-TMA⁺), TMAO interacts electrostatically via its negatively charged-oxygen, which in turn orients the TMAO-methyls away from the hydrophobe (d-TMA⁺), keeping them exposed to water.

Structural Changes in the Cap of Rv0183/mtbMGL Modulate the Shape of the Binding Pocket

Tuberculosis continues to be a major threat to the human population. Global efforts to eradicate the disease are ongoing but are hampered by the increasing occurrence of multidrug-resistant strains of Mycobacterium tuberculosis. Therefore, the development of new treatment, and the exploration of new druggable targets and treatment strategies, are of high importance. Rv0183/mtbMGL, is a monoacylglycerol lipase of M. tuberculosis and it is involved in providing fatty acids and glycerol as building blocks and as an energy source. Since the lipase is expressed during the dormant and active phase of an infection, Rv0183/mtbMGL is an interesting target for inhibition. In this work, we determined the crystal structures of a surface-entropy reduced variant K74A Rv0183/mtbMGL in its free form and in complex with a substrate mimicking inhibitor. The two structures reveal conformational changes in the cap region that forms a major part of the substrate/inhibitor binding region. We present a completely closed conformation in the free form and semi-closed conformation in the ligand-bound form. These conformations differ from the previously published, completely open conformation of Rv0183/mtbMGL. Thus, this work demonstrates the high conformational plasticity of the cap from open to closed conformations and provides useful insights into changes in the substrate-binding pocket, the target of potential small-molecule inhibitors.

Hydration of Simple Model Peptides in Aqueous Osmolyte Solutions

The biology and chemistry of proteins and peptides are inextricably linked with water as the solvent. The reason for the high stability of some proteins or uncontrolled aggregation of others may be hidden in the properties of their hydration water. In this study, we investigated the effect of stabilizing osmolyte–TMAO (trimethylamine N-oxide) and destabilizing osmolyte–urea on hydration shells of two short peptides, NAGMA (N-acetyl-glycine-methylamide) and diglycine, by means of FTIR spectroscopy and molecular dynamics simulations. We isolated the spectroscopic share of water molecules that are simultaneously under the influence of peptide and osmolyte and determined the structural and energetic properties of these water molecules. Our experimental and computational results revealed that the changes in the structure of water around peptides, caused by the presence of stabilizing or destabilizing osmolyte, are significantly different for both NAGMA and diglycine. The main factor determining the influence of osmolytes on peptides is the structural-energetic similarity of their hydration spheres. We showed that the chosen peptides can serve as models for various fragments of the protein surface: NAGMA for the protein backbone and diglycine for the protein surface with polar side chains.

The ups and downs of ectoine: structural enzymology of a major microbial stress protectant and versatile nutrient

Ectoine and its derivative 5-hydroxyectoine are compatible solutes and chemical chaperones widely synthesized by Bacteria and some Archaea as cytoprotectants during osmotic stress and high- or low-growth temperature extremes. The function-preserving attributes of ectoines led to numerous biotechnological and biomedical applications and fostered the development of an industrial scale production process. Synthesis of ectoines requires the expenditure of considerable energetic and biosynthetic resources. Hence, microorganisms have developed ways to exploit ectoines as nutrients when they are no longer needed as stress protectants. Here, we summarize our current knowledge on the phylogenomic distribution of ectoine producing and consuming microorganisms. We emphasize the structural enzymology of the pathways underlying ectoine biosynthesis and consumption, an understanding that has been achieved only recently. The synthesis and degradation pathways critically differ in the isomeric form of the key metabolite N-acetyldiaminobutyric acid (ADABA). γ-ADABA serves as preferred substrate for the ectoine synthase, while the α-ADABA isomer is produced by the ectoine hydrolase as an intermediate in catabolism. It can serve as internal inducer for the genetic control of ectoine catabolic genes via the GabR/MocR-type regulator EnuR. Our review highlights the importance of structural enzymology to inspire the mechanistic understanding of metabolic networks at the biological scale.

Conformational dynamics of 13 amino acids long NSP11 of SARS-CoV-2 under membrane mimetics and different solvent conditions

The intrinsically disordered proteins/regions (IDPs/IDPRs) are known to be responsible for multiple cellular processes and are associated with many chronic diseases. In viruses, the existence of a disordered proteome is also proven and is related to its conformational dynamics inside the host. The SARS-CoV-2 has a large proteome, in which, structure and functions of all proteins are not known yet, along with non-structural protein 11 (nsp11). In this study, we have performed extensive experimentation on nsp11. Our results based on the CD spectroscopy gives characteristic disordered spectrum for IDPs. Further, we investigated the conformational behavior of nsp11 in the presence of membrane mimetic environment, α-helix inducer, and natural osmolyte. In the presence of negatively charged and neutral liposomes, nsp11 remains disordered. However, with SDS micelle, it adopted an α-helical conformation, suggesting the helical propensity of nsp11. Finally, we again confirmed the IDP behavior of nsp11 using MD simulations. In future, this conformational dynamic study could help to clarify its functional importance in SARS-CoV-2 infection.

Trimethylamine N-oxide alters structure-function integrity of β-casein: Structural disorder co-regulates the aggregation propensity and chaperone activity

Intrinsically disordered proteins (IDPs), involved in the regulation and function of various cellular processes like transcription, translation, cell cycle etc., exist as ensembles of rapidly interconverting structures with functional plasticity. Among numerous cellular regulatory mechanisms involved in structural and functional regulation of IDPs, osmolytes are emerging as promising regulatory agents due to their ability to affect the structure-function integrity of IDPs. The present study investigated the effect of methylamine osmolytes on β-casein, an IDP essential for maintaining the overall stability of casein complex in milk. It was observed that trimethylamine N-oxide induces a compact structural state in β-casein with slightly decreased chaperone activity and insignificant aggregation propensity. However, the other two osmolytes from this group, i.e., sarcosine and betaine, had no significant effect on the overall structure and chaperone activity of the IDP. The present study hints towards the possible evolutionary selection of higher structural disorder in β-casein, compared to α-casein, for stability of the casein complex and prevention of amyloidosis in the mammary gland.

Enhanced Recombinant Protein Production Under Special Environmental Stress

Regardless of bacteria or eukaryotic microorganism hosts, improving their ability to express heterologous proteins is always a goal worthy of elaborate study. In addition to traditional methods including intracellular synthesis process regulation and extracellular environment optimization, some special or extreme conditions can also be employed to create an enhancing effect on heterologous protein production. In this review, we summarize some extreme environmental factors used for the improvement of heterologous protein expression, including low temperature, hypoxia, microgravity and high osmolality. The applications of these strategies are elaborated with examples of well-documented studies. We also demonstrated the confirmed or hypothetical mechanisms of environment stress affecting the host behaviors. In addition, multi-omics techniques driving the stress-responsive research for construction of efficient microbial cell factories are also prospected at the end.

Enhanced Glutamate Synthesis and Export by the Thermotolerant Emerging Industrial Workhorse Bacillus methanolicus in Response to High Osmolarity

The thermotolerant methylotroph Bacillus methanolicus MGA3 was originally isolated from freshwater marsh soil. Due to its ability to use methanol as sole carbon and energy source, B. methanolicus is increasingly explored as a cell factory for the production of amino acids, fine chemicals, and proteins of biotechnological interest. During high cell density fermentation in industrial settings with the membrane-permeable methanol as the feed, the excretion of low molecular weight products synthesized from it will increase the osmotic pressure of the medium. This in turn will impair cell growth and productivity of the overall biotechnological production process. With this in mind, we have analyzed the core of the physiological adjustment process of B. methanolicus MGA3 to sustained high osmolarity surroundings. Through growth assays, we found that B. methanolicus MGA3 possesses only a restricted ability to cope with sustained osmotic stress. This finding is consistent with the ecophysiological conditions in the habitat from which it was originally isolated. None of the externally provided compatible solutes and proline-containing peptides affording osmostress protection for Bacillus subtilis were able to stimulate growth of B. methanolicus MGA3 at high salinity. B. methanolicus MGA3 synthesized the moderately effective compatible solute L-glutamate in a pattern such that the cellular pool increased concomitantly with increases in the external osmolarity. Counterintuitively, a large portion of the newly synthesized L-glutamate was excreted. The expression of the genes (gltAB and gltA2) for two L-glutamate synthases were upregulated in response to high salinity along with that of the gltC regulatory gene. Such a regulatory pattern of the system(s) for L-glutamate synthesis in Bacilli is new. Our findings might thus be generally relevant to understand the production of the osmostress protectant L-glutamate by those Bacilli that exclusively rely on this compatible solute for their physiological adjustment to high osmolarity surroundings.