Energetics of complementary side-chain packing in a protein hydrophobic core

The energetics of complementary packing of nonpolar side chains in the hydrophobic core of a protein were analyzed by protein engineering experiments. We have made the mutations Ile----Val, Ile----Ala, and Leu----Ala in a region of the small bacterial ribonuclease barnase where the major alpha-helix packs onto the central beta-sheet. The destabilization resulting from the creation of cavities was determined by measuring the decrease in free energy of folding from reversible denaturation induced by urea, guanidinium chloride, or heat. The different methods give consistent and reproducible results. The loss in free energy of folding for the mutant proteins is 1.0-1.6 kcal/mol per methylene group removed. This exceeds by severalfold the values obtained from model experiments of the partitioning of relevant side chains between aqueous and nonpolar solvents. Much of this discrepancy arises because two surfaces are buried when a protein folds--both the amino acid side chain in question and the portions of the protein into which it packs. These experiments directly demonstrate that the interior packing of a protein is crucial in stabilizing its three-dimensional structure: the conversion of leucine or isoleucine to alanine in the hydrophobic core loses half the net free energy of folding of barnase with a concomitant decrease in yield of the expressed recombinant protein.     

Amino-steroids as inhibitors and probes of the active site of cytochrome P-450scc. Effects on the enzyme from different sources

A series of analogues of cholesterol, each having a primary amine attached to a shortened side chain, were tested for their effects on cytochrome P-450scc from several different sources. Reconstituted enzyme systems using disrupted mitochondria from bovine adrenal and placenta, adult human adrenal and placenta, neonatal human adrenal, and rat adrenal and testis were used to assay for inhibitory effects on the side chain cleavage of cholesterol to pregnenolone. Two of the derivatives tested, 22-amino-23,24-bisnor-5-cholen-3 beta-ol and 23-amino-24-nor-5-cholen-3 beta-ol, were found to be potent inhibitors of this reaction; the derivatives in which the amine was attached closer to or further from the steroid ring, (20 R and S)-20-amino-5-pregnen-3 beta-ol and 24-amino-5-cholen-3 beta-ol, were much weaker inhibitors. In addition, spectral studies with rat adrenal mitochondria and a soluble preparation of human placental cytochrome P-450scc showed that binding of the 22-amine derivative to the enzyme produces difference spectra characteristic of nitrogen bonding to the heme; this indicates that the heme is positioned close to C-22 in the steroid-enzyme complex. These findings on the relative effectiveness of the amino-steroid inhibitors and the type of complex formed are similar to results obtained with purified bovine adrenocortical cytochrome P-450scc. This establishes that the proximity of the substrate binding site and the heme-iron catalytic site is a feature common to the enzyme from several sources and is therefore likely to be a necessary property of the active site structure.     

Inhibition of adrenocortical cytochrome P-450scc by (20R)-20-phenyl-5-pregnene-3 beta,20-diol

The effects of the cholesterol analogue, (20R)-20-phenyl-5-pregnene-3 beta,20-diol (20-PPD), on the catalytic and spectral properties of purified bovine adrenocortical cytochrome P-450scc were investigated. In contrast to results with cholesterol and (20R)-20-hydroxycholesterol, no conversion of 20-PPD to pregnenolone could be detected; instead, 20-PPD was found to be a potent inhibitor of cytochrome P-450scc. Kinetic analyses showed that the inhibition is reversible and competitive with respect to cholesterol with an apparent Ki = 30nM. Spectral binding studies with ferricytochrome P-450scc showed that 20-PPD formed a 1:1 complex with the enzyme, having an absorption spectrum similar to that produced by (20R)-20-hydroxycholesterol. These results indicate that 20-PPD binds with very high affinity to the substrate site on cytochrome P-450scc. The finding that the phenyl side chain is readily accommodated suggests the presence in this site of an open pocket which may be normally occupied by C-22 to C-27 of the cholesterol side chain.     

The effects of normalization method on antagonistic activity patterns during eccentric and concentric isokinetic knee extension and flexion

The purpose of this study was to compare different normalization methods of electromyographic (EMG) activity of antagonists during isokinetic eccentric and concentric knee movements. Twelve women performed three maximum knee extensions and flexions isometrically and at isokinetic concentric and eccentric angular velocities of 30 °·s⁻¹, 90 °·s⁻¹, 120 °·s⁻¹ and 150 °·s⁻¹. The EMG activity of the vastus lateralis, rectus femoris, vastus medialis and hamstrings was recorded. The antagonist integrated IEMG values were normalized relative to the EMG of the same muscle during an isometric maximal action (static method). The values were also expressed as a percentage of the EMG activity of the same muscle, at the same angle, angular velocity and muscle action (dynamic method) when the muscle was acting as an agonist. Three-way analysis of variance (ANOVA) designs indicated significantly greater IEMG normalized with the dynamic method compared to the EMG derived using the static method (P < 0.05). These differences were more evident at concentric angular velocities and at the first and last 20 ° of the movement. The present findings demonstrate that the method of normalization significantly influences the conclusions on antagonistic activity during isokinetic maximum voluntary efforts. The dynamic method of normalization is more appropriate because it considers the effects of muscle action, muscle length and angular velocity on antagonist IEMG.     

1H, 13C and 15N resonance assignment of the soluble form of the Lipid-modified Azurin from Neisseria gonorrhoeae

Lipid-modified azurin (Laz) from Neisseria gonorrhoeae is a type 1 copper protein proposed to be the electron donor to several enzymes involved in the resistance mechanism to reactive oxygen and nitrogen species. Here we report the backbone and side-chain resonance assignment of Laz in the reduced form, which has been complete at 97 %. The predicted secondary structure indicates that this protein belongs to the azurin subfamily of type 1 copper proteins.     

Large-scale evaluation of candidate genes identifies associations between VEGF polymorphisms and bladder cancer risk

Common genetic variation could alter the risk for developing bladder cancer. We conducted a large-scale evaluation of single nucleotide polymorphisms (SNPs) in candidate genes for cancer to identify common variants that influence bladder cancer risk. An Illumina GoldenGate assay was used to genotype 1,433 SNPs within or near 386 genes in 1,086 cases and 1,033 controls in Spain. The most significant finding was in the 5′ UTR of VEGF (rs25648, p for likelihood ratio test, 2 degrees of freedom = 1 × 10⁻⁵). To further investigate the region, we analyzed 29 additional SNPs in VEGF, selected to saturate the promoter and 5′ UTR and to tag common genetic variation in this gene. Three additional SNPs in the promoter region (rs833052, rs1109324, and rs1547651) were associated with increased risk for bladder cancer: odds ratio (95% confidence interval): 2.52 (1.06–5.97), 2.74 (1.26–5.98), and 3.02 (1.36–6.63), respectively; and a polymorphism in intron 2 (rs3024994) was associated with reduced risk: 0.65 (0.46–0.91). Two of the promoter SNPs and the intron 2 SNP showed linkage disequilibrium with rs25648. Haplotype analyses revealed three blocks of linkage disequilibrium with significant associations for two blocks including the promoter and 5′ UTR (global p = 0.02 and 0.009, respectively). These findings are biologically plausible since VEGF is critical in angiogenesis, which is important for tumor growth, its elevated expression in bladder tumors correlates with tumor progression, and specific 5′ UTR haplotypes have been shown to influence promoter activity. Associations between bladder cancer risk and other genes in this report were not robust based on false discovery rate calculations. In conclusion, this large-scale evaluation of candidate cancer genes has identified common genetic variants in the regulatory regions of VEGF that could be associated with bladder cancer risk.     

Does experimental evolution produce better biological control agents? A critical review of the evidence

Biological control of crop pests is considered a good alternative or complement to the use of pesticides. However, legislation restricts the importation of natural enemies of pests. A potential way to circumvent this limitation is by using experimental evolution and/or artificial selection to improve native biological control agents. Here, we review studies that have used these methodologies and evaluate their success. Experimental evolution or artificial selection has been used on a wide range of traits, with most focusing on improving the performance of natural enemies in ecologically relevant environments, such as in the presence of pesticides or at different temperatures. Although most studies were poorly replicated, the selected traits generally improved following the selection process. However, correlated responses (often in the form of trade‐offs) with other traits of interest were common. We suggest that the selection procedure can be improved by increasing replication and performing experimental evolution under more semi‐natural environments, to ensure that the most useful traits are being selected.