Determiantion of creatine phosphate levels in brain tissue by isocratic reverse-phase,ion-paired high-performance liquid chromatography

The utilization of isocratic, reverse-phase, ion-paired high-performance liquid chromatography for analysis of creatine phosphate allows for rapid quantification of multiple samples. Cryogenic sample handling and the addition of ethylene glycol bis(β-aminoethyl ether) N,N′-tetraacetic acid as a Ca²⁺ sequestering agent during perchloric acid extraction enhance maximal recovery of creatine phosphate from brain samples. Peak identification is supported by a complete enzymatic shift with a phosphocreatine kinase, hexokinase, and glucose-6-phosphate dehydrogenase system.     

Genetic variation in the major histocompatibility complex of the European brown hare (Lepus europaeus) across distinct phylogeographic areas

The major histocompatibility complex is one of the best studied systems in vertebrates providing evidence for the long-term action of selection. Here, we examined the intra- and inter-population genetic diversity of the MHC class II DRB locus in European brown hare (Lepus europaeus) and correlated the results with genetic variability already estimated from the MHC DQA locus and from maternally (mitochondrial DNA (mtDNA)) and biparentally (allozymes, microsatellites) inherited loci. L. europaeus showed remarkable genetic polymorphism in both DQA and DRB1 loci. The Anatolian populations exhibited the highest genetic polymorphism for both loci. Balancing selection has established increased variability in the European populations despite the founder effects after the last glaciation. Different evolutionary rates were traced for DRB1 and DQA loci, as evidenced by the higher number of common DRB1 than DQA alleles and the greater differences between DRB1 alleles with common origin in comparison with DQA alleles. The high number of rare alleles with low frequencies detected implies that frequency-dependent selection drives MHC evolution in the brown hare through the advantage of rare alleles. Both loci were under the influence of positive selection within the peptide-binding region. The functional polymorphism, recorded as amino acid substitutions within the binding pockets, fell also within distinct geographic patterns, yet it was much narrower than the genetic polymorphism. We hypothesize that certain structural and functional characteristics of the binding pockets set limitations to the actual shape of genetic polymorphism in MHC.     

Localisation and interactions of the Vipp1 protein in cyanobacteria

The Vipp1 protein is essential in cyanobacteria and chloroplasts for the maintenance of photosynthetic function and thylakoid membrane architecture. To investigate its mode of action we generated strains of the cyanobacteria Synechocystis sp. PCC6803 and Synechococcus sp. PCC7942 in which Vipp1 was tagged with green fluorescent protein at the C‐terminus and expressed from the native chromosomal locus. There was little perturbation of function. Live‐cell fluorescence imaging shows dramatic relocalisation of Vipp1 under high light. Under low light, Vipp1 is predominantly dispersed in the cytoplasm with occasional concentrations at the outer periphery of the thylakoid membranes. High light induces Vipp1 coalescence into localised puncta within minutes, with net relocation of Vipp1 to the vicinity of the cytoplasmic membrane and the thylakoid membranes. Pull‐downs and mass spectrometry identify an extensive collection of proteins that are directly or indirectly associated with Vipp1 only after high‐light exposure. These include not only photosynthetic and stress‐related proteins but also RNA‐processing, translation and protein assembly factors. This suggests that the Vipp1 puncta could be involved in protein assembly. One possibility is that Vipp1 is involved in the formation of stress‐induced localised protein assembly centres, enabling enhanced protein synthesis and delivery to membranes under stress conditions.     

Nonyloxytryptamine mimics polysialic acid and modulates neuronal and glial functions in cell culture

Polysialic acid (PSA) is a major regulator of cell–cell interactions in the developing nervous system and in neural plasticity in the adult. As a polyanionic molecule with high water‐binding capacity, PSA increases the intercellular space generating permissive conditions for cell motility. PSA enhances stem cell migration and axon path finding and promotes repair in the lesioned peripheral and central nervous systems, thus contributing to regeneration. As a next step in developing an improved PSA‐based approach to treat nervous system injuries, we searched for small organic compounds that mimic PSA and identified as a PSA mimetic 5‐nonyloxytryptamine oxalate, described as a selective 5‐hydroxytryptamine receptor 1B (5‐HT_1B) agonist. Similar to PSA, 5‐nonyloxytryptamine binds to the PSA‐specific monoclonal antibody 735, enhances neurite outgrowth of cultured primary neurons and process formation of Schwann cells, protects neurons from oxidative stress, reduces migration of astrocytes and enhances myelination in vitro. Furthermore, nonyloxytryptamine treatment enhances expression of the neural cell adhesion molecule (NCAM) and its polysialylated form PSA‐NCAM and reduces expression of the microtubule‐associated protein MAP2 in cultured neuroblastoma cells. These results demonstrate that 5‐nonyloxytryptamine mimics PSA and triggers PSA‐mediated functions, thus contributing to the repertoire of molecules with the potential to improve recovery in acute and chronic injuries of the mammalian peripheral and central nervous systems.

     

Native structure-based modeling and simulation of biomolecular systems per mouse click

Background

Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Gō-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. Still, their setup and evaluation is quite complex even though sophisticated software packages support their realization.

Results

Here, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and UNICORE middleware. This infrastructure organizes the setup of such simulations resulting in increased comparability of simulation results. At the same time, complete workflows for advanced simulation protocols can be established and managed on remote resources by a graphical interface which increases reusability of protocols and additionally lowers the entry barrier into such simulations for, e.g., experimental scientists who want to compare their results against simulations. We demonstrate the power of this approach by illustrating it for protein folding simulations for a range of proteins.

Conclusions

We present software enhancing the entire workflow for native structure-based simulations including exception-handling and evaluations. Extending the capability and improving the accessibility of existing simulation packages the software goes beyond the state of the art in the domain of biomolecular simulations. Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-292) contains supplementary material, which is available to authorized users.     

Analysis of Modified Human Papillomavirus Type 16 L1 Capsomeres: the Ability To Assemble into Larger Particles Correlates with Higher Immunogenicity

L1 capsomeres purified from Escherichia coli represent an economic alternative to the recently launched virus-like particle (VLP)-based prophylactic vaccines against infection with human papillomavirus types 16 and 18 (HPV-16 and HPV-18), which are causative agents of cervical cancer. It was recently reported that capsomeres are much less immunogenic than VLPs. Numerous modifications of the L1 protein leading to the formation of capsomeres but preventing capsid assembly have been described, such as the replacement of the cysteine residues that form capsid-stabilizing disulfide bonds or the deletion of helix 4. So far, the influence of these modifications on immunogenicity has not been thoroughly investigated. Here, we describe the purification of eight different HPV-16 L1 proteins as capsomeres from Escherichia coli. We compared them for yield, structure, and immunogenicity in mice. All L1 proteins formed almost identical pentameric structures yet differed strongly in their immunogenicity, especially regarding the humoral immune responses. Immunization of TLR4^−/− mice and DNA immunization by the same constructs confirmed that immunogenicity was independent of different degrees of contamination with copurifying immune-stimulatory molecules from E. coli. We hypothesize that immunogenicity correlates with the intrinsic ability of the capsomeres to assemble into larger particles, as only assembly-competent L1 proteins induced high antibody responses. One of the proteins (L1ΔN10) proved to be the most immunogenic, inducing antibody titers equivalent to those generated in response to VLPs. However, preassembly prior to injection did not increase immunogenicity. Our data suggest that certain L1 constructs can be used to produce highly immunogenic capsomeres in bacteria as economic alternatives to VLP-based formulations.Certain types of human papillomavirus (HPV) are the cause of cervical cancer, most frequently HPV types 16 and 18 (HPV-16 and HPV-18), which are responsible for about 50% and 20% of cases, respectively (8, 15, 16). Recently, two vaccines that prevent infection with HPV-16 and HPV-18 have been introduced to the market. These vaccines are based on the viral major structural protein L1, which can spontaneously self-assemble in vitro into empty virus-like particles (VLPs) that resemble the native virions in size and shape. VLPs have been shown to be highly immunogenic, as they can induce high titers of neutralizing antibodies (29, 30). HPV virions and VLPs consist of 72 L1 pentamers, also called capsomeres, which are arranged in an icosahedral T=7 particle lattice with a diameter of 55 nm. Cryo-electron microscopic analysis has revealed the presence of 60 hexavalent and 12 pentavalent capsomeres (4).Capsid assembly has been reported to be optimal at low pH (pH 5.4) and high ionic strength, whereas both high pH (pH 8.2) and the presence of reducing agents favor disassembly into capsomeres, the latter because the viral particles are stabilized by intercapsomeric disulfide bonds between two conserved cysteine residues at positions 175 and 428 (11, 35, 44). VLP formation is not affected by deletions of up to 9 amino acids (aa) from the N terminus and up to 34 aa from the C terminus of the L1 protein (11, 36). An N-terminally truncated L1 protein lacking 10 aa has been shown to assemble into particles consisting of 12 L1-pentamers with a T=1 lattice referred to as small VLPs (11, 12). Crystallographic analysis of the T=1 particles revealed that interpentameric contacts are established by hydrophobic interactions between the α-helices 2 and 3 of one capsomere and α-helix 4 of a neighboring capsomere (12). Consequently, a mutant L1 with helix 4 deleted formed homogenous capsomeres but failed in T=1 and T=7 particle assembly (7). Deletion of helices 2 and 3 impeded even pentamer formation, as a large fraction of the L1 protein was found to be insoluble, which suggests an essential role for these regions in L1 folding (7, 11).VLP-based prophylactic vaccines have been shown to induce high titers of neutralizing antibodies, which protect against virus challenge and associated diseases in humans (24, 31). However, due to the relatively high production and distribution costs of the vaccines—they are expressed in and purified from eukaryotic cells and require a cold chain for storage—they will probably be largely unavailable to developing countries, where more than 80% of all cervical cancer cases occur (1, 38, 46).L1 capsomeres represent a potentially lower cost alternative to VLPs, as they can be produced in large amounts from Escherichia coli and are considered more stable at room temperature (11, 34, 35). Capsomeres have been shown to induce high titers of neutralizing antibodies and T-cell responses upon oral, intranasal, and subcutaneous immunization and have also protected against viral challenge in the canine oral papillomavirus model (18, 19, 37, 42, 48, 53). Most of the immunization data for HPV capsomeres have been obtained from administration of full-length or N-terminally deleted (10 aa) wild-type L1 proteins (18, 37, 53). A recent report in which the L1 pentamers were derived from an L1 protein in which the conserved cysteines (aa 175 and 428) were replaced by alanines revealed that HPV-16 VLPs induce about 20- to 40-fold-higher humoral immune responses than capsomeres (47). The influence on immunogenicity of the other mutations and deletions of the L1 protein that prevent capsid assembly has so far not been studied in depth.In a comparative analysis of eight differently modified HPV-16 L1 proteins purified as capsomeres from E. coli, we now report that their potential to induce humoral immune responses in mice correlates with their ability to assemble into particles larger than capsomeres. One of the constructs, L1ΔN10, encoded for capsomeres that exhibited immunogenicity similar to that of VLPs.