Unfolding action of alcohols on a highly negatively charged state of cytochrome C

The food and pharmaceutical additive benzoic acid induces amyloid fibrillation of an intrinsically disordered protein

Benzoic acid (BA) is a microbe-inhibiting flavoring agent used extensively as an additive in foods, pharmaceuticals, and hygiene and cosmetic products. The level of BA in foodstuffs prescribed by world bodies and governmental agencies is assumed to be safe so as to prevent adverse health effects. The safety level of BA is however controversial, and whether different conditions of its use would be generally regarded as safe (GRAS) has been rarely determined. In the quest of how food additives affect the structure and conformation of proteins, this study evaluates the interaction of BA with an intrinsically disordered protein (IDP) at pH 4.2 that matches the pH conditions applicable for the commercial use of benzoate preservatives, and examines its structural transformation by NMR, fluorescence, and high-resolution microscopy. The interaction with BA transforms the protein to a denatured aggregated mesophase that undergoes reconfiguration to yield rigid amyloid fibrils. Significantly, fibrils are observed even with 0.1 mM BA while the recommended level of its use as a preservative is in the 0.4-8 mM range. The discussion refrains from safety comments with no projection of the BA level that could be GRAS.

A Critical Review on the Economically Feasible and Sustainable Poly(3-Hydroxybutyrate-co-3-hydroxyvalerate) Production from Alkyl Alcohols

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (P(3HB-co-3HV)) is the most studied short-chain-length polyhydroxyalkanoates (PHA) with high application importance in various fields. The domination of high-cost propionate and valerate over other 3-hydroxyvalerate (3HV) precursors owing to their wide preference among PHA-producing bacteria has hindered the development of diverse production processes. As alkyl alcohols are mainly produced from inexpensive starting materials through oxo synthesis, they contribute a cost-effective advantage over propionate and valerate. Moreover, alkyl alcohols can be biosynthesized from natural substrates and organic wastes. Despite their great potential, their toxicity to most PHA-producing bacteria has been the major drawback for their wide implementation as 3HV precursors for decades. Although the standard PHA-producing bacteria Cupriavidus necator showed promising alcohol tolerance, the 3HV yield was discouraging. Continuous discovery of alkyl alcohols-utilizing PHA-producing bacteria has enabled broader choices in 3HV precursor selection for diverse P(3HB-co-3HV) production processes with higher economic feasibility. Besides continuous effort in searching for promising wild-type strains, genetic engineering to construct promising recombinant strains based on the understanding of the mechanisms involved in alkyl alcohols toxicity and tolerance is an alternative approach. However, more studies are required for techno-economic assessment to analyze the economic performance of alkyl alcohol-based production compared to that of organic acids.

Spectroscopic Insight on Ethanol-Induced Aggregation of Papain

In this contribution, the structural and dynamic changes occurring to papain in ethanol-water binary solvent mixtures have been investigated and compared with its denatured state. Steady-state fluorescence, solvation dynamics, time-resolved rotational anisotropy, circular dichroism (CD), and single molecular-level fluorescence correlation spectroscopic (FCS) studies were performed for this purpose. In ethanol-water mixtures with X_EtOH = 0.6, N-(7-dimethylamino-4-methylcoumarin-3-yl)iodoacetamide (DACIA)-tagged papain was found to undergo a blue shift of 12 nm, while in the presence of 5 M GnHCl, a red shift of 5 nm was observed. Solvation dynamics of the system was also found to be different in the presence of these external agents. In ethanol-water mixtures, the average solvation time was found to increase almost 2-fold as compared to that in water, while in the presence of GnHCl, only a marginal increase could be observed. These changes of DACIA-tagged papain in ethanol-water mixtures are attributed to the aggregation of the protein in the presence of ethanol. The residual anisotropy was found to increase 14-fold, and the rotational time component corresponding to the rotation of the probe molecule was found to increase by 4-fold in the ethanol-water mixture which also gives a notion of the papain aggregation. Atomic force microscopy (AFM) confirms this aggregate formation, which is also quantified by the FCS study. The hydrodynamic radius of the protein aggregates in ethanol-water mixtures was calculated to be ∼155 Å as compared to the corresponding value of 18.4 Å in the case of native monomer papain. Also, it confirmed that the aggregate formation takes place even in the nanomolar concentration of papain. Analysis of circular dichroism spectra of papain showed that an increase in the β-sheet content of papain at the expense of α-helix and the random coil with an increase of the ethanol mole fraction may be responsible for this aggregation process.

Conformational disorder and solvation properties of the key-residues of a protein in water-ethanol mixed solutions

A small number of key-residues in a protein sequence play vital roles in the function, stability, and folding of the protein. The nonuniform conformational disorder of a small protein Chymotrypsin Inhibitor 2 (CI2) and its secondary segments has been quantified in the ethanol governed temperature induced unfolding process by estimating its change in configurational entropy in several water-ethanol mixed solutions. Such calculations further assist us in identifying the key-residues, from where the unfolding of the protein was initiated. Our findings match well with the reported experimental results. We then make an attempt to explore the properties of the solvent water and ethanol around the key-residues of the protein in its folded and unfolded forms at ambient temperature to identify the individual role of ethanol and water in the protein unfolding. We find that the key-residues of the unfolded protein are in good contact with both water and ethanol as compared to those of the folded protein. In the presence of ethanol, water molecules are noticed to form a rigid structurally bound solvation layer around the key-residues of the protein, irrespective of its conformational state. The restricted translational motion and prominent caging effect of the water and ethanol molecules present around the key-residues of the unfolded protein are a signature of the existence of a rigid mixed water-ethanol layer as compared to that around the folded protein. Furthermore, comparable restricted structural relaxation of the key-residue-water and key-residue-ethanol hydrogen bonds in the unfolded protein as compared to that in the folded one implies that the formation of a strong long-lived hydrogen bonding environment nourishes the unfolding process. We believe that our findings will shed light to several co-solvent governed unfolding processes of a protein in general.

Effects of Desolvating Agent Types, Ratios, and Temperature on Size and Nanostructure of Nanoparticles from α-Lactalbumin and Ovalbumin

In this study, we compare the preparation of ovalbumin (OVA) and α-lactalbumin (α-LA) nanoparticles using different desolvating agents (ethanol, acetone, and methanol) and water: desolvating agent volume ratios (1:3, 1:4, 1:5, 1:10, and 1:20). Also the effects of protein solution temperature (25, 50, and 80 ℃) on the size of nanoparticles and the stability of crosslinked nanoparticles for 30 d were studied. OVA and α-LA were shown to be good candidates for nanoparticulation and nanoparticles in the range of 60 to 230 nm were obtained. The comparison between the 2 proteins offers guidance to optimize OVA and α-LA nanoparticle fabrication and to efficiently obtain nanoparticles with desired characteristics. The particle sizes of OVA nanoparticles were found to be in the range of 60 to 160 nm, and the particle sizes of α-LA were between 150 and 230 nm. The sizes varied with different desolvating agents: for OVA, ethanol, and methanol both produced nanoparticles smaller than 100 nm; for α-LA, methanol produced the smallest nanoparticles. Water: desolvating agent ratios, in the studied range, did not show a significant effect on the particle sizes for both OVA and α-LA nanoparticles. The size and morphology of the nanoparticles were found to change when the protein solutions were heated up to 50 and 80 ℃ and cooled down before nanoparticulation and most nanoparticles had a smaller diameter.

Pentanol and Benzyl Alcohol Attack Bacterial Surface Structures Differently

The genus Methylobacterium tolerates hygiene agents like benzalkonium chloride (BAC), and infection with this organism is an important public health issue. Here, we found that the combination of BAC with particular alcohols at nonlethal concentrations in terms of their solitary uses significantly reduced bacterial viability after only 5 min of exposure. Among the alcohols, Raman spectroscopic analyses showed that pentanol (pentyl alcohol [PeA]) and benzyl alcohol (BzA) accelerated the cellular accumulation of BAC. Fluorescence spectroscopic assays and morphological assays with giant vesicles indicated that PeA rarely attacked membrane structures, while BzA increased the membrane fluidity and destabilized the structures. Other fluorescent spectroscopic assays indicated that PeA and BzA inactivate bacterial membrane proteins, including an efflux pump for BAC transportation. These findings suggested that the inactivation of membrane proteins by PeA and BzA led to the cellular accumulation but that only BzA also enhanced BAC penetration by membrane fluidization at nonlethal concentrations.

Preferential water exclusion in protein unfolding

Association of water with protein plays a central role in the latter's folding, structure acquisition, ligand binding, catalytic reactivity, oligomerization, and crystallization. Because these phenomena are also influenced by the net charge content on the protein, the present study examines the association of water with cytochrome c held at different pH values so as to allow its side chains to ionize to variable extents. Equilibrium unfolding of differently charged cytochrome c molecules in water-methanol binary mixtures, where the alcohol acts as the cosolvent denaturant, was used to quantify the preferential exclusion of water during the unfolding transition. The extent of exclusion was found to be related to the net-charge-dependent molecular expansion of the protein in an alcohol-free aqueous medium. The degree of water exclusion was also found to be linearly related to the observed rate of protein unfolding, where the net charge contents of the initial and final states are the same. The results suggest that side-chain ionization, molecular expansion due to charge repulsion, and hence the loss of tertiary contacts lead to additional water-protein association. Protein unfolding rates appear to be linearly correlated with the effective number of water molecules excluded across the end states of unfolding equilibria.

Structural transformation of bovine serum albumin induced by dimethyl sulfoxide and probed by fluorescence correlation spectroscopy and additional methods

Determining the structure of a protein and its transformation under different conditions is key to understanding its activity. The structural stability and activity of proteins in aqueous-organic solvent mixtures, which is an intriguing topic of research in biochemistry, is dependent on the nature of the protein and the properties of the medium. Herein, the effect of a commonly used cosolvent, dimethyl sulfoxide (DMSO), on the structure and conformational dynamics of bovine serum albumin (BSA) protein is studied by fluorescence correlation spectroscopy (FCS) measurements on fluorescein isothiocyanate (FITC)-labeled BSA. The FCS study reveals a change of the hydrodynamic radius of BSA from 3.7 nm in the native state to 7.0 nm in the presence of 40% DMSO, which suggests complete unfolding of the protein under these conditions. Fluorescence self-quenching of FITC has been exploited to understand the conformational dynamics of BSA. The time constant of the conformational dynamics of BSA is found to change from 35 μs in its native state to 50 μs as the protein unfolds with increasing DMSO concentration. The FCS results are corroborated by the near-UV circular dichroism spectra of the protein, which suggest a loss of its tertiary structure with increasing concentration of DMSO. The intrinsic fluorescence of BSA and the fluorescence response of 1-anilinonaphthalene-8-sulfonic acid, used as a probe molecule, provide information that is consistent with the FCS measurements, except that aggregation of BSA is observed in the presence of 40% DMSO in the ensemble measurements.

Dieselzymes: development of a stable and methanol tolerant lipase for biodiesel production by directed evolution

BACKGROUND

Biodiesels are methyl esters of fatty acids that are usually produced by base catalyzed transesterification of triacylglyerol with methanol. Some lipase enzymes are effective catalysts for biodiesel synthesis and have many potential advantages over traditional base or acid catalyzed transesterification. Natural lipases are often rapidly inactivated by the high methanol concentrations used for biodiesel synthesis, however, limiting their practical use. The lipase from Proteus mirabilis is a particularly promising catalyst for biodiesel synthesis as it produces high yields of methyl esters even in the presence of large amounts of water and expresses very well in Escherichia coli. However, since the Proteus mirabilis lipase is only moderately stable and methanol tolerant, these properties need to be improved before the enzyme can be used industrially.

RESULTS

We employed directed evolution, resulting in a Proteus mirabilis lipase variant with 13 mutations, which we call Dieselzyme 4. Dieselzyme 4 has greatly improved thermal stability, with a 30-fold increase in the half-inactivation time at 50°C relative to the wild-type enzyme. The evolved enzyme also has dramatically increased methanol tolerance, showing a 50-fold longer half-inactivation time in 50% aqueous methanol. The immobilized Dieselzyme 4 enzyme retains the ability to synthesize biodiesel and has improved longevity over wild-type or the industrially used Brukholderia cepacia lipase during many cycles of biodiesel synthesis. A crystal structure of Dieselzyme 4 reveals additional hydrogen bonds and salt bridges in Dieselzyme 4 compared to the wild-type enzyme, suggesting that polar interactions may become particularly stabilizing in the reduced dielectric environment of the oil and methanol mixture used for biodiesel synthesis.

CONCLUSIONS

Directed evolution was used to produce a stable lipase, Dieselzyme 4, which could be immobilized and re-used for biodiesel synthesis. Dieselzyme 4 outperforms the industrially used lipase from Burkholderia cepacia and provides a platform for still further evolution of desirable biodiesel production properties.