Contribution of surface salt bridges to protein stability: guidelines for protein engineering

The small globular protein, ubiquitin, contains a pair of oppositely charged residues, K11 and E34, that according to the three-dimensional structure are located on the surface of this protein with a spatial orientation characteristic of a salt bridge. We investigated the strength of this salt bridge and its contribution to the global stability of the ubiquitin molecule. Using the "double mutant cycle" analysis, the strength of the pairwise interactions between K11 and E34 was estimated to be favorable by 3.6kJ/mol. Further, the salt bridge of the reverse orientation, i.e. E11/K34, can be formed and is found to have a strength (3.8kJ/mol) similar to that of the K11/E34 pair. However, the global stability of the K11/E34 variant of ubiquitin is 2.2kJ/mol higher than that of the E11/K34 variant. The difference in the contribution of the opposing salt bridge orientations to the overall stability of the ubiquitin molecule is attributed to the difference in the charge-charge interactions between residues forming the salt bridge and the rest of the ionizable groups in this protein. On the basis of these results, we concluded that surface salt bridges are stabilizing, but their contribution to the overall protein stability is strongly context-dependent, with charge-charge interactions being the largest determinant. Analysis of 16 salt bridges from six different proteins, for which detailed experimental data on energetics have been reported, support the conclusions made from the analysis of the salt bridge in ubiquitin. Implications of these findings for engineering proteins with enhanced thermostability are discussed.     

Haemolytic activity,cytotoxicity and membrane cell permeabilization of semi-synthetic and natural lupane- and oleanane-type saponins

The haemolysis of red blood cells inducing toxicity in most animals including humans is a major drawback for the clinical development of saponins as antitumour agents. In this study, the haemolytic and cytotoxic activities as well as the membrane cell permeabilization property of a library of 31 semi-synthetic and natural lupane- and oleanane-type saponins were evaluated and the structure–activity relationships were established. It was shown that lupane-type saponins do not exhibit any haemolytic activity and membrane cell permeabilization property at the maximum concentration tested (100 μM) independently of the nature of the sugar moieties. While oleanane-type saponins such as β-hederin (25) and hederacolchiside A₁ (27) cause the death of cancer cell lines by permeabilizing the cellular membranes, lupane-type saponins seem to proceed via another mechanism, which could be related to the induction of apoptosis. Altogether, the results indicate that the cytotoxic lupane-type glycosides 10 and 22 bearing an α-l-rhamnopyranose moiety at the C-3 position represent promising antitumour agents for further studies on tumour-bearing mice since they are devoid of toxicity associated with the haemolysis of red blood cells.     

Energetics of charge-charge interactions between residues adjacent in sequence

Statistical analysis of the residue separation between a pair of ionizable side chains within 4 ? of each other was performed on a set of 1560 non-homologous PDB structures. We found that the frequency of pairs of like charges (i.e., pairs consisting of acidic residues Asp and Glu or pairs consisting of basic residues Arg and Lys) is two orders of magnitude lower than the pairs of oppositely charged residues (salt-bridges). We also found that for pairs of like charges the distribution is skewed dramatically towards short residue separation (<3). On the basis of these observations, we hypothesize that at short residue separation the repulsion between charges does not contribute much to the protein stability and the effects are largely dominated by the long range charge-charge interactions with other ionizable groups in the protein molecule. To test this hypothesis, we incorporated various pairs of charged residues at position 63 and 64 of ubiquitin and compared the stabilities of these variants. We also performed calculations of the expected changes in the charge-charge interactions. A very good correlation between experimental changes in the stability of ubiquitin variants, and changes in the energy of charge-charge interactions provides support for the hypothesis that a pair of ionizable residues next to each other in sequence modulates protein stability via long range charge-charge interactions with the rest of the protein.     

Heat capacity changes upon burial of polar and nonpolar groups in proteins

In this paper we address the question of whether the burial of polar and nonpolar groups in the protein locale is indeed accompanied by the heat capacity changes, DeltaC(p), that have an opposite sign, negative for nonpolar groups and positive for polar groups. To accomplish this, we introduced amino acid substitutions at four fully buried positions of the ubiquitin molecule (Val5, Val17, Leu67, and Gln41). We substituted Val at positions 5 and 17 and Leu at position 67 with a polar residue, Asn. As a control, Ala was introduced at the same three positions. We also replaced the buried polar Gln41 with Val and Leu, nonpolar residues that have similar size and shape as Gln. As a control, Asn was introduced at Gln41 as well. The effects of these amino acid substitutions on the stability, and in particular, on the heat capacity change upon unfolding were measured using differential scanning calorimetry. The effect of the amino acid substitutions on the structure was also evaluated by comparing the (1)H-(15)N HSQC spectra of the ubiquitin variants. It was found that the Ala substitutions did not have a considerable effect on the heat capacity change upon unfolding. However, the substitutions of aliphatic side chains (Val or Leu) with a polar residue (Asn) lead to a significant (> 30%) decrease in the heat capacity change upon unfolding. The decrease in heat capacity changes does not appear to be the result of significant structural perturbations as seen from the HSQC spectra of the variants. The substitution of a buried polar residue (Gln41) to a nonpolar residue (Leu or Val) leads to a significant (> 25%) increase in heat capacity change upon unfolding. These results indicate that indeed the heat capacity change of burial of polar and nonpolar groups has an opposite sign. However, the observed changes in DeltaC(p) are several times larger than those predicted, based on the changes in water accessible surface area upon substitution.     

Cytotoxic activity of withanolides isolated from Tunisian Datura metel L

Withanolide-type steroids, withametelin Q (1) and 12α-hydroxydaturametelin B (2) along with three known withanolides, were isolated from leaves of Datura metel L. (Solanaceae). The respective structures, characterized mainly by NMR spectroscopy, were identified as (20R,22R,24R)-21,24-epoxy-1α,3β-dihydroxywitha-5,25(27)-dienolide-3-O-β-d-glucopyranoside (1) and (20R,22R,24R)-12α,21,27-trihydroxy-1-oxowitha-2,5,24-trienolide-27-O-β-d-glucopyranoside (2). The cytotoxicity of isolated compounds was evaluated against human lung carcinoma cells (A549) and human colorectal adenocarcinoma cells (DLD-1), respectively. Compound 2 exhibited cytotoxicity against A549 and DLD-1 cell lines, with IC₅₀ values of 7 and 2.0 μM, respectively. However, for compounds 6 and 7, cytotoxicities were higher against DLD-1 cells with IC₅₀ values of 0.6 and 0.7 μM. Both compounds blocked the cell cycle in the S-phase and induced apoptosis.     

<Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis> morphological changes and cytokinesis arrest elicited by hypoxia during scale-up for production of therapeutic recombinant proteins

Background

Scaling up of bioprocesses represents a crucial step in the industrial production of biologicals. However, our knowledge about the impact of scale-up on the organism’s physiology and function is still incomplete. Our previous studies have suggested the existence of morphological changes during the scale-up of a yeast (Saccharomyces cerevisiae) fermentation process as inferred from the volume fraction occupied by yeast cells and exometabolomics analyses. In the current study, we noticed cell morphology changes during scale-up of a yeast fermentation process from bench (10 L) to industrial scale (10,000 L). We hypothesized that hypoxia observed during scale-up partially impaired the availability of N-acetyl-glucosamine, a precursor of chitin synthesis, a key polysaccharide component of yeast mother-daughter neck formation.

Results

Using a combination of flow cytometry with two high throughput cell imaging technologies, Vi-CELL and Flow Imaging, we found changes in the distribution of cell size and morphology as a function of process duration at the industrial scale of the production process. At the end of run, concomitantly with lowest levels of dissolved oxygen (DO), we detected an increase in cell subpopulations exhibiting low aspect ratio corresponding to morphologies exhibited by large-single-budded and multi-budded cells, reflecting incomplete cytokinesis at the M phase of the yeast mitotic cycle. Metabolomics from the intracellular milieu pointed to an impaired supply of precursors for chitin biosynthesis likely affecting the septum formation between mother and daughter and cytokinesis. Inducing hypoxia at the 10 L bench scale by varying DO levels, confirmed the existence and impact of hypoxic conditions on yeast cell size and morphology observed at the industrial scale.

Conclusions

We conclude that the observed increments in wet cell weight at the industrial scale correspond to morphological changes characterized by the large diameter and low aspect ratio exhibited by cell subpopulations comprising large single-budded and multi-budded cells. These changes are consistent with impairment of cytokinesis triggered by hypoxia as indicated by experiments mimicking this condition at DO 5% and 10 L scale. Mechanistically, hypoxia impairs N-acetyl-glucosamine availability, a key precursor of chitin synthesis.

     

Effects of Leontice smirnowii tuber monodesmosides and crude extract in carrageenan- and histamine-induced acute inflammation model of rats

Leontice smirnowii is a member of the Berberidaceae family. We have recently reported the 1,1-diphenyl-2-picryl-hydrazyl radical scavenging, superoxide anion radical scavenging, hydrogen peroxide scavenging, reducing power and metal chelating activities of L. smirnowii products. In the current study we investigated the possible effects of the crude extracts of L. smirnowii (CELS) and the monodesmoside's purified extract (MPE) of L. smirnowii in the carrageenan- and histamine-induced acute inflammation models in rats. The experiment revealed that CELS and MPE have anti-inflammatory effects, dose dependently in carrageenan-induced acute inflammation. On the other hand, their proinflammatory effects were surprisingly observed, especially in low doses, in the histamine-induced acute inflammation model. Summarizing these data, we may state that CELS and MPE exert their anti-inflammatory effects via non-histaminergic pathways.     

Strain Improvement of Streptomyces xanthochromogenes RIA 1098 for Enhanced Pravastatin Production at High Compactin Concentrations

Pravastatin is one of the most popular cholesterol-lowering drugs. Its industrial production represents a two-stage process including the microbial production of compactin and its further biocatalytic conversion to pravastatin. To increase a conversion rate, a higher compactin content in fermentation medium should be used; however, high compactin concentrations inhibit microbial growth. Therefore, the improvement of the compactin resistance of a producer still remains a relevant problem. A multi-step random UV mutagenesis of a Streptomyces xanthochromogenes strain RIA 1098 and the further selection of high-yield compactin-resistant mutants have resulted in a highly productive compactin-resistant strain S 33-1. After the fermentation medium improvement, the maximum bioconversion rate of this strain has reached 91 % at the daily compactin dose equal to 1 g/L and still remained high (83 %) even at the doubled dose (2 g/L). A 1-year study of the mutant strain stability has proved a stable inheritance of its characteristics that provides this strain to be very promising for the pravastatin-producing industry.

Electronic supplementary material

The online version of this article (doi:10.1007/s12088-015-0537-5) contains supplementary material, which is available to authorized users.     

Acute anti-inflammatory activity of four saponins isolated from ivy: alpha-hederin, hederasaponin-C, hederacolchiside-E and hederacolchiside-F in carrageenan-induced rat paw edema.

The anti-inflammatory potential of alpha-hederin (monodesmoside) and hederasaponin-C from Hedera helix, and hederacolchisides-E and -F (bidesmosides) from H. colchica was investigated in carrageenan-induced acute paw edema in rats. Saponins and indomethacin were given orally in concentrations of 0.02 and 20mg/kg body wt. For the first phase of acute inflammation, indomethacin was found as the most potent drug. Alpha-hederin and hederasaponin-C were found ineffective, while hederacolchisides-E and -F showed slight anti-inflammatory effects on the first phase. For the second phase of acute inflammation, indomethacin and hederacolchiside-F were determined as very potent compounds. alpha-hederin was found ineffective for the second phase, either. Despite hederasaponin-C and -E were found effective in the second phase of inflammation, they were not found as effective as indomethacin and hederacolchiside-F. As a conclusion, hederasaponin-C, -E and -F, may exert their anti-inflammatory effects by blocking bradykinin or other inflammation mediators. The latter affect may occur via affecting prostaglandin pathways. Regarding the structure activity relationship, it is likely that sugars at C3 position and Rha7-Glcl-6Glc moiety at C28 position are essential for the acute anti-inflammatory effect.     

Acute and chronic antiinflammatory profile of the ivy plant, Hedera helix, in rats.

Hedera helix is a plant well-known as ivy or English ivy, and a member of the Araliaceae family. In the present study, we tested the possible antiinflammatory effects of a crude saponin extract (CSE) and a saponin's purified extracts (SPE) of Hedera helix in carrageenan- and cotton-pellet-induced acute and chronic inflammation models in rats. Both the CSE and SPE of Hedera helix were found to have antiinflammatory effects. The most potent drug screened was indomethacin (89.2% acute antiinflammatory effect), while the most potent extract screened was the CSE of Hedera helix at 100 and 200 mg/kg body wt. doses with 77% acute antiinflammatory effects. For testing chronic antiinflammatory (antiproliferative) effects, the cotton-pellet-granuloma test was conducted. Indomethacin was found to be the most potent drug in the chronic phase of inflammation, with 66% effect. The SPE of Hedera helix was more potent than the CSE in its chronic antiinflammatory effect (60% and 49%, respectively).