Structural search and retrieval using a tableau representation of protein folding patterns

Comparison and classification of folding patterns from a database of protein structures is crucial to understand the principles of protein architecture, evolution and function. Current search methods for proteins with similar folding patterns are slow and computationally intensive. The sharp growth in the number of known protein structures poses severe challenges for methods of structural comparison. There is a need for methods that can search the database of structures accurately and rapidly. We provide several methods to search for similar folding patterns using a concise tableau representation of proteins that encodes the relative geometry of secondary structural elements. Our first approach allows the extraction of identical and very closely-related protein folding patterns in constant-time (per hit). Next, we address the hard computational problem of extraction of maximally-similar subtableaux, when comparing two tableaux. We solve the problem using Quadratic and Linear integer programming formulations and demonstrate their power to identify subtle structural similarities, especially when protein structures significantly diverge. Finally, we describe a rapid and accurate method for comparing a query structure against a database of protein domains, TableauSearch. TableauSearch is rapid enough to search the entire structural database in seconds on a standard desktop computer. Our analysis of TableauSearch on many queries shows that the method is very accurate in identifying similarities of folding patterns, even between distantly related proteins. AVAILABILITY: A web server implementing the TableauSearch is available from http://hollywood.bx.psu.edu/TabSearch.     

Mechanosensitive Channels: Insights from Continuum-Based Simulations

Mechanotransduction plays an important role in regulating cell functions and it is an active topic of research in biophysics. Despite recent advances in experimental and numerical techniques, the intrinsic multiscale nature imposes tremendous challenges for revealing the working mechanisms of mechanosensitive channels. Recently, a continuum-mechanics-based hierarchical modeling and simulation framework has been established and applied to study the mechanical responses and gating behaviors of a prototypical mechanosensitive channel, the mechanosensitive channel of large conductance (MscL) in bacteria Escherichia coli (E. coli), from which several putative gating mechanisms have been tested and new insights are deduced. This article reviews these latest findings using the continuum mechanics framework and suggests possible improvements for future simulation studies. This computationally efficient and versatile continuum-mechanics-based protocol is poised to make contributions to the study of a variety of mechanobiology problems.     

Extraproteasomal Rpn10 restricts access of the polyubiquitin-binding protein Dsk2 to proteasome

Polyubiquitin is a diverse signal both in terms of chain length and linkage type. Lysine 48-linked ubiquitin is essential for marking targets for proteasomal degradation, but the significance and relative abundance of different linkages remain ambiguous. Here we dissect the relationship of two proteasome-associated polyubiquitin-binding proteins, Rpn10 and Dsk2, and demonstrate how Rpn10 filters Dsk2 interactions, maintaining proper function of the ubiquitin-proteasome system. Using quantitative mass spectrometry of ubiquitin, we found that in S. cerevisiae under normal growth conditions the majority of conjugated ubiquitin was linked via lysine 48 and lysine 63. In contrast, upon DSK2 induction, conjugates accumulated primarily in the form of lysine 48 linkages correlating with impaired proteolysis and cytotoxicity. By restricting Dsk2 access to the proteasome, extraproteasomal Rpn10 was essential for alleviating the cellular stress associated with Dsk2. This work highlights the importance of polyubiquitin shuttles such as Rpn10 and Dsk2 in controlling the ubiquitin landscape.     

In vitro evaluation of Datura innoxia (thorn-apple) for potential antibacterial activity

Various parts of Datura innoxia were examined for potential antibacterial activity by preparing their crude aqueous and organic extracts against Gram-negative bacteria (Escherichia coli and Salmonella typhi) and Gram-positive bacteria (Bacillus cereus, Bacillus subtilis and Staphylococcus aureus). The results of agar well diffusion assay indicated that the pattern of inhibition depends largely upon the plant part, solvent used for extraction and the organism tested. Extracts prepared from leaves were shown to have better efficacy than stem and root extracts. Organic extracts provided potent antibacterial activity as compared to aqueous extracts. Among all the extracts, methanolic extract was found most active against almost all the bacterial species tested. Gram-positive bacteria were found most sensitive as compared to Gram-negative bacteria. Staphylococcus aureus was signifi cantly inhibited by almost all the extracts even at very low MIC followed by other Gram-positives. For Escherichia coli (a Gram-negative bacterium), the end point was not reached for ethyl acetate extract while it was very high for other extracts. The study promises an interesting future for designing a potentially active antibacterial agent from Datura innoxia.     

Hematology of sloth bears (Melursus ursinus ursinus) from two locations in India

Standard hematology parameters were determined for 122 sloth bears (Melursus ursinus ursinus) at the Sur Sarovar Bird Sanctuary, Uttar Pradesh, India (27 degrees 0'N; 77 degrees 45'E), and the Bannerghatta Biological Park, Karnataka, India (12 degrees 48'N; 77 degrees 34'E) from March 2003 to July 2006. These two native sloth bear habitats have different climatic conditions and provided an opportunity to examine the effect of climate on the physiologic hematology values of these bears. We primarily analyzed the influence of age, sex, season, and body weight on the different hematology parameters. Several values were significantly different in sloth bear cubs (1 yr). The cubs had a lower erythrocyte count, hemoglobin concentration, packed cell volume (PCV), and mean cell hemoglobin (MCV) values when compared to adult and subadult bears. The cubs also had higher leukocyte counts, due to higher circulating neutrophils, as compared to adult and subadult bears. Within subadult and adult bears, we also identified a sexual dimorphic difference in leukocyte count in adult and subadult bears, wherein female bears had higher counts than males. This difference was the result of a significantly higher number of circulating neutrophils in female bears. Platelet counts were also higher in females as compared to males. On comparing different seasons, leukocyte counts were higher in winter as compared to the summer and monsoon seasons. When compared based on location, erythrocyte counts were higher in subadult and adult bears at Bannerghatta, which was at a higher altitude than Sur Sarovar. Within subadult and adult bears, we did not find any significant influence of age or body weight on the different hematologic parameters. In this study we have obtained mean hematologic values for sloth bears in their native habitat to serve as a reference for this species. This report will be useful to develop and evaluate health profiles of sloth bears under various ecological conditions.     

Enhancement of growth and chitosan production by Rhizopus oryzae in whey medium by plant growth hormones

The effect of some plant growth hormones, viz., gibberellic acid, indole-3-acetic acid, indole-3-butyric acid, and kinetin on chitosan production by Rhizopus oryzae in deproteinized whey was studied. Hormones, at different concentrations, increase the mycelial growth by 19-32%. However, increase in chitosan content of the mycelia was relatively small (1.7-14.3%) over the control. Maximum enhancement was observed with gibberellic acid. Fifty percent more chitosan could be obtained from 1L of whey containing 0.1mg/L gibberellic acid. Hormones, at higher dose, instead of stimulation inhibited both growth and mycelial chitosan content. This study showed that hormones have no influence on degree of deacetylation of chitosan but increase the quality of the chitosan by increasing weight average molecular weight and decreasing polydispersity. All the hormones had been found to enhance chitin deacetylase activity of R. oryzae by 1.067-1.267-fold and may be one of the reasons for increased chitosan production.     

On the origin of distribution patterns of motifs in biological networks

Background

Data from high-throughput experiments of protein-protein interactions are commonly used to probe the nature of biological organization and extract functional relationships between sets of proteins. What has not been appreciated is that the underlying mechanisms involved in assembling these networks may exhibit considerable probabilistic behaviour.

Results

We find that the probability of an interaction between two proteins is generally proportional to the numerical product of their individual interacting partners, or degrees. The degree-weighted behaviour is manifested throughout the protein-protein interaction networks studied here, except for the high-degree, or hub, interaction areas. However, we find that the probabilities of interaction between the hubs are still high. Further evidence is provided by path length analyses, which show that these hubs are separated by very few links.

Conclusion

The results suggest that protein-protein interaction networks incorporate probabilistic elements that lead to scale-rich hierarchical architectures. These observations seem to be at odds with a biologically-guided organization. One interpretation of the findings is that we are witnessing the ability of proteins to indiscriminately bind rather than the protein-protein interactions that are actually utilized by the cell in biological processes. Therefore, the topological study of a degree-weighted network requires a more refined methodology to extract biological information about pathways, modules, or other inferred relationships among proteins.     

Adult-like anti-mycobacterial T cell and in vivo dendritic cell responses following neonatal immunization with Ag85B-ESAT-6 in the IC31 adjuvant

Background

With the exception of some live vaccines, e.g. BCG, subunit vaccines formulated with “classical” adjuvants do not induce similar responses in neonates as in adults. The usual neonatal profile is characterized by lower levels of TH1-associated biomarkers. This has hampered the development of new neonatal vaccines for diseases that require early protection. Tuberculosis is one of the major targets for neonatal immunization. In this study, we assessed the immunogenicity of a novel candidate vaccine comprising a mycobacterial fusion protein, Ag85B-ESAT-6, in a neonatal murine immunization model.

Methods/Findings

The Ag85B-ESAT-6 fusion protein was formulated either with a classical alum based adjuvant or with the novel IC31® adjuvant. Following neonatal or adult immunization, 3 parameters were studied in vivo: (1) CD4⁺ T cell responses, (2) vaccine targeting/activation of dendritic cells (DC) and (3) protection in a surrogate mycobacterial challenge model. Conversely to Alum, IC31® induced in both age groups strong Th1 and Th17 responses, characterized by multifunctional T cells expressing IL-2 and TNF-α with or without IFN-γ. In the draining lymph nodes, a similarly small number of DC contained the adjuvant and/or the antigen following neonatal or adult immunization. Expression of CD40, CD80, CD86 and IL-12p40 production was focused on the minute adjuvant-bearing DC population. Again, DC targeting/activation was similar in adults and neonates. These DC/T cell responses resulted in an equivalent reduction of bacterial growth following infection with M. bovis BCG, whereas no protection was observed when Alum was used as adjuvant.

Conclusion

Neonatal immunization with the IC31®- adjuvanted Ag85B-ESAT-6 subunit vaccine elicited adult-like multifunctional protective anti-mycobacterial T cell responses through the induction of an adult pattern of in vivo DC activation.     

The irony of highly-effective bacterial therapy of a patient-derived orthotopic xenograft (PDOX) model of Ewing's sarcoma,which was blocked by Ewing himself 80 years ago

William B. Coley developed bacterial therapy of cancer more than 100 years ago and had clinical success. James Ewing, a very famous cancer pathologist for whom the Ewing sarcoma is named, was Coley's boss at Memorial Hospital in New York and terminated Coley's bacterial therapy of cancer. A tumor from a patient with soft-tissue Ewing's sarcoma, who failed doxorubicin (DOX) therapy, was previously implanted in nude mice to establish a patient-derived orthotopic xenograft (PDOX) model. In the present study, the Ewing's sarcoma PDOX was treated with tumor-targeting S. typhimurium A1-R expressing green fluorescent (GFP), alone and in combination with DOX. S. typhimurium A1-R-GFP was detected in the tumors after intratumor (i.t.) or intravenous (i.v.) injection. The combination of S. typhimurium A1-R and DOX significantly reduced tumor weight (37.8 ± 15.6 mg) compared to the untreated control (73.8 ± 10.1 mg, P < 0.01). S. typhimurium A1-R monotherapy-treated tumors tended to be smaller (50.9 ± 17.8 mg, P = 0.051). DOX monotherapy did not show efficacy (66.3 ± 26.4 mg, P = 0.82), as was the case with the patient. The PDOX model faithfully replicated the DOX resistance the Ewing's sarcoma had in the patient. S. typhimurium A1-R converted the Ewing's sarcoma from DOX resistant to sensitive. One can only wonder how bacterial therapy and immunotherapy of cancer would have developed over the past 80 years if Ewing did not stop Coley.