Computational study of the conformational preferences of the (R)-8-amino-pentacyclo[5.4.0.0(2,6).0(3,10).0(5,9)]undecane-8-carboxylic acid monopeptide.

alpha-Amino acids are important building blocks for the synthesis of a large number of bioactive compounds and pharmaceutical drugs. However, a literature survey revealed that no theoretical conformational study of alpha-amino acids with cage carbon frameworks has been performed to date. This paper reports the results of a conformational study on the (R)-8-amino-pentacyclo[5.4.0.0(2,6).0(3,10).0(5,9)]undecane-8-carboxylic acid monopeptide (cage monopeptide), using molecular mechanics and ab initio methods. The in vacuo Ramachandran maps computed using the different parameterizations of the AMBER force field show the C7eq structure as the most favourable conformation, in contrast to the C7ax structure, that is the lowest energy conformation at the ab initio level. Analysis of these maps reveals the helical preference for the monopeptide and provides the potential for the cage residue to be incorporated into constrained peptide analogues.     

Cooperativity network of Trp‐cage miniproteins: probing salt‐bridges

Trp‐cage miniprotein was used to investigate the role of a salt‐bridge (Asp⁹–Arg¹⁶) in protein formation, by mutating residues at both sides, we mapped its contribution to overall stability and its role in folding mechanism. We found that both of the above side‐chains are also part of a dense interaction network composed of electrostatic, H‐bonding, hydrophobic, etc. components. To elucidate the fold stabilizing effects, we compared and contrasted electronic circular dichroism and NMR data of miniproteins equipped with a salt‐bridge with those of the salt‐bridge deleted mutants. Data were acquired both in neutral and in acidic aqueous solutions to decipher the pH dependency of both fully and partially charged partners. Our results indicate that the folding of Trp‐cage miniproteins is more complex than a simple two‐state process as we detected an intermediate state that differs significantly from the native fold. The intermediate formation is related to the salt‐bridge stabilization; in the miniprotein variants equipped with salt‐bridge the population of the intermediate state at acidic pH is significantly higher than it is for the salt‐bridge deleted mutants. In this molecular framework Arg¹⁶ stabilizes more than Asp⁹ does, because of its higher degree of 3D‐fold cooperation. In conclusion, the Xxx$^{9} \leftrightarrow$ Yyy¹⁶ salt‐bridge is not an isolated entity of this fold; rather it is an integrated part of a complex interaction network. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

An improved counterselection cassette for use in Haemophilus influenzae

Counterselectable cassettes are extremely useful in molecular biology and allow for the creation of unmarked deletion mutants or the introduction of point mutations. I have constructed an inducible sacB cassette, using the tetracycline repressor. When used in tandem with a kanamycin-resistance marker, the cassette was successful in creating unmarked mutants in Haemophilus influenzae. The inducible nature of the cassette avoids some of the common problems associated with the utilization of sacB in counterselection.     

Effects of Metabolic Cage Housing on Rat Behavior and Performance in the Social Interaction Test

Although the metabolic cage is commonly used for housing nonhuman animals in the laboratory, it has been recognized as constituting a unique stressor. Such an environment would be expected to affect behavioral change in animals housed therein. However, few studies have specifically addressed the nature or magnitude of this change. The current study sought to characterize the behavioral time budget of rats in metabolic cage housing in comparison to that of individually housed animals in standard open-top cages. Rats in metabolic cages spent less time moving, manipulating enrichment, and carrying out rearing behaviors, and there was a corresponding shift toward inactivity. In an applied Social Interaction Test, behavioral scoring implied that metabolic cage housing had an anxiogenic effect. In conclusion, metabolic cage housing produces measurable effects on spontaneous and evoked behavior in rats in the laboratory. These behavioral changes may lead to a negative emotional state in these animals, which could have negative welfare consequences. Further research is needed to quantify the existence and magnitude of such an effect on rat well being.     

Vertical distribution of Atlantic salmon (Salmo salar) as a function of illumination

The vertical distribution of cultured Atlantic salmon larger than 1 kg was monitored by hydroacoustics in both a shallow (6 m) and a deep (20 m) cage. Surface light levels and fish distribution were registered for three periods throughout the year. The two fish groups were fed calculated rations twice a day. During the winter and spring (including vernal equinox), the fish were distributed at around 5 m depth in both cages when not feeding. Around summer solstice, the fish preferred deeper waters when not feeding. The light dependency of the vertical migration was pronounced, and indicates clearly that even a 20 m deep cage is not deep enough to meet the depth requirements of large Atlantic salmon during summer.     

Solvent interactions with the Trp-cage peptide in 35% ethanol-water

Intermolecular NOE experiments have been used to explore interactions of water and ethanol molecules in 35% ethanol/65% water (v/v) with the peptide Trp-cage at temperatures from 5 to 25 degrees C. Magnetic dipole-dipole cross-relaxation terms sigma(HH) (NOE) and sigma(HH) (ROE) for interaction of solvent components with spins of the peptide suggest that ethanol molecules associate with backbone atoms for times of the order of nanoseconds at 5 degrees C. Formation of peptide-ethanol complexes can also account for the larger-than-expected values of cross-relaxation terms at higher temperatures. Hydrocarbon side chains of the peptide do not appear to experience such interactions with ethanol. Cross relaxation resulting from water-peptide interactions are consistent with long-lived water interactions with the backbone atoms. Water cross relaxation with nonpolar side chains of the peptide (Leu2, Ile4, Leu7, and proline residues) are only those expected for bulk solvent. However, long-lived association of both water and ethanol with the polar side chains of Tyr3 and Trp6 is indicated by the data. (c) 2008 Wiley Periodicals, Inc. Biopolymers 89: 862-872, 2008.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com.     

Thermostability and molecular encapsulation within an engineered caged protein scaffold

Self-assembling biological complexes such as viral capsids have been manipulated to function in innovative nanotechnology applications. The E2 component of pyruvate dehydrogenase from Bacillus stearothermophilus forms a dodecahedral complex and potentially provides another platform for these purposes. In this investigation, we show that this protein assembly exhibits unusual stability and can be modified to encapsulate model drug molecules. To distill the E2 protein down to its structural scaffold core, we synthesized a truncated gene optimized for expression in Escherichia coli. The correct assembly and dodecahedral structure of the resulting scaffold was confirmed with dynamic light scattering and transmission electron microscopy. Using circular dichroism and differential scanning calorimetry, we found the thermostability of the complex to be unusually high, with an onset temperature of unfolding at 81.1 +/- 0.9 degrees C and an apparent midpoint unfolding temperature of 91.4 +/- 1.4 degrees C. To evaluate the potential of this scaffold for encapsulation of guest molecules, we made variants at residues 381 and 239 which altered the physicochemical properties of the hollow internal cavity. These mutants, yielding 60 and 120 mutations within this cavity, assembled into the correct architecture and exhibited high thermostability that was comparable to the wild-type scaffold. To show the applicability of this scaffold, two different fluorescent dye molecules were covalently coupled to the cysteine mutant at site 381. We demonstrate that these mutations can introduce non-native functionality and enable molecular encapsulation within the cavity while still retaining the dodecahedral structure. The unusually robust nature of this scaffold and its amenability to internal changes reveal its potential for nanoscale applications.     

Biomaterial-loaded allograft threaded cage for the treatment of femoral head osteonecrosis in a goat model

The purpose of this study was to evaluate the efficacy of core decompression with a biomaterial-loaded allograft threaded cage (ATC) for the treatment of femoral head osteonecrosis in an established goat model. First, bilateral early-stage osteonecrosis was induced. After core decompression, the remaining goats were randomly divided into three groups: Group A, the goats were left without any treatment; Group B, the goats were treated with implanting a composite of autologous bone and decalcified bone matrix (DBM); Group C, the goats were treated using insertion of ATC loaded with DBM and autogenous bone graft. Then radiographic, histological and biomechanical analysis were taken in each group at 5, 10, and 20 weeks postoperation. In Group A, the classical signs of osteonecrosis of the femoral head were identified 10 weeks after the induction. Twenty weeks later, the density, surface and biomechanical stability of the femoral head were normal in Group C, while an irregular surface and an inhomogeneous microstructure or variation of density/hardness were identified in Group B. The specimens revealed a continuous trabaecular bone structure throughout the cage and extensive bone ingrowth and remodeling in Group C, while fibrous tissue was evident in Group B. Core decompression with a biomaterial loaded ATC almost uniformly delays or arrests the progression of the disease before articular collapse, and it could help to get the balance between bone resorption and new bone formation, strengthen structural mechanics of the femoral head, provide structure support of articular cartilage.     

三种免疫制剂对真鲷弧菌病的免疫保护性

菌体疫苗按不同的方式对真鲷进行免疫2周后,对实验鱼均具有免疫保护性,免疫保护性最好的免疫组,免疫保护率在初次免疫后高达60%,强化免疫后免疫保护率可提高到80%;粗制LPS经去毒处理后初次免疫真鲷,不同浓度的LPS对实验鱼具有不同程度的免疫保护性,强化免疫后,免疫保护率均有明显的提高,浓度越高,免疫保护性越强,对真鲷的免疫保护率最高可达90%,最小弧菌产生的外毒素经福尔马林灭活后制成毒素苗,这种毒素苗能产生较好的免疫保护性,其免疫保护率可达80%,这表明外毒素不仅是最小弧菌产生的毒力因子,同时也是菌体产生的有效保护性抗原。