STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Background  

The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.     

Genome-scale metabolic reconstruction and <Emphasis Type="Italic">in silico</Emphasis> analysis of methylotrophic yeast <Emphasis Type="Italic">Pichia pastoris</Emphasis> for strain improvement

Background  

Pichia pastoris has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive in silico model of P. pastoris can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism.     

A novel in silico approach to identify potential therapeutic targets in human bacterial pathogens

In recent years, genome-sequencing projects of pathogens and humans have revolutionized microbial drug target identification. Of the several known genomic strategies, subtractive genomics has been successfully utilized for identifying microbial drug targets. The present work demonstrates a novel genomics approach in which codon adaptation index (CAI), a measure used to predict the translational efficiency of a gene based on synonymous codon usage, is coupled with subtractive genomics approach for mining potential drug targets. The strategy adopted is demonstrated using respiratory pathogens, namely, Streptococcus pneumoniae and Haemophilus influenzae as examples. Our approach identified 8 potent target genes (Streptococcus pneumoniae?C2, H. influenzae?C6), which are functionally significant and also play key role in host-pathogen interactions. This approach facilitates swift identification of potential drug targets, thereby enabling the search for new inhibitors. These results underscore the utility of CAI for enhanced in silico drug target identification.     

Polymer optoelectronic structures for retinal prosthesis

This commentary highlights the effectiveness of optoelectronic properties of polymer semiconductors based on recent results emerging from our laboratory, where these materials are explored as artificial receptors for interfacing with the visual systems. Organic semiconductors based polymer layers in contact with physiological media exhibit interesting photophysical features, which mimic certain natural photoreceptors, including those in the retina. The availability of such optoelectronic materials opens up a gateway to utilize these structures as neuronal interfaces for stimulating retinal ganglion cells. In a recently reported work entitled “A polymer optoelectronic interface provides visual cues to a blind retina,” we utilized a specific configuration of a polymer semiconductor device structure to elicit neuronal activity in a blind retina upon photoexcitation. The elicited neuronal signals were found to have several features that followed the optoelectronic response of the polymer film. More importantly, the polymer-induced retinal response resembled the natural response of the retina to photoexcitation. These observations open up a promising material alternative for artificial retina applications.     

Apoptosis,cytokine and chemokine induction by non-structural 1 (NS1) proteins encoded by different influenza subtypes

Background

Influenza pandemic remains a serious threat to human health. Viruses of avian origin, H5N1, H7N7 and H9N2, have repeatedly crossed the species barrier to infect humans. Recently, a novel strain originated from swine has evolved to a pandemic. This study aims at improving our understanding on the pathogenic mechanism of influenza viruses, in particular the role of non-structural (NS1) protein in inducing pro-inflammatory and apoptotic responses.

Methods

Human lung epithelial cells (NCI-H292) was used as an in-vitro model to study cytokine/chemokine production and apoptosis induced by transfection of NS1 mRNA encoded by seven infleunza subtypes (seasonal and pandemic H1, H2, H3, H5, H7, and H9), respectively.

Results

The results showed that CXCL-10/IP10 was most prominently induced (> 1000 folds) and IL-6 was slightly induced (< 10 folds) by all subtypes. A subtype-dependent pattern was observed for CCL-2/MCP-1, CCL3/MIP-1α, CCL-5/RANTES and CXCL-9/MIG; where induction by H5N1 was much higher than all other subtypes examined. All subtypes induced a similar temporal profile of apoptosis following transfection. The level of apoptosis induced by H5N1 was remarkably higher than all others. The cytokine/chemokine and apoptosis inducing ability of the 2009 pandemic H1N1 was similar to previous seasonal strains.

Conclusions

In conclusion, the NS1 protein encoded by H5N1 carries a remarkably different property as compared to other avian and human subtypes, and is one of the keys to its high pathogenicity. NCI-H292 cells system proves to be a good in-vitro model to delineate the property of NS1 proteins.

     

Alzheimer Disease A�� Production in the Absence of S-Palmitoylation-dependent Targeting of BACE1 to Lipid Rafts

Alzheimer disease β-amyloid (Aβ) peptides are generated via sequential proteolysis of amyloid precursor protein (APP) by BACE1 and γ-secretase. A subset of BACE1 localizes to cholesterol-rich membrane microdomains, termed lipid rafts. BACE1 processing in raft microdomains of cultured cells and neurons was characterized in previous studies by disrupting the integrity of lipid rafts by cholesterol depletion. These studies found either inhibition or elevation of Aβ production depending on the extent of cholesterol depletion, generating controversy. The intricate interplay between cholesterol levels, APP trafficking, and BACE1 processing is not clearly understood because cholesterol depletion has pleiotropic effects on Golgi morphology, vesicular trafficking, and membrane bulk fluidity. In this study, we used an alternate strategy to explore the function of BACE1 in membrane microdomains without altering the cellular cholesterol level. We demonstrate that BACE1 undergoes S-palmitoylation at four Cys residues at the junction of transmembrane and cytosolic domains, and Ala substitution at these four residues is sufficient to displace BACE1 from lipid rafts. Analysis of wild type and mutant BACE1 expressed in BACE1 null fibroblasts and neuroblastoma cells revealed that S-palmitoylation neither contributes to protein stability nor subcellular localization of BACE1. Surprisingly, non-raft localization of palmitoylation-deficient BACE1 did not have discernible influence on BACE1 processing of APP or secretion of Aβ. These results indicate that post-translational S-palmitoylation of BACE1 is not required for APP processing, and that BACE1 can efficiently cleave APP in both raft and non-raft microdomains.Alzheimer disease-associated β-amyloid (Aβ)³ peptides are derived from the sequential proteolysis of β-amyloid precursor protein (APP) by β- and γ-secretases. The major β-secretase is an aspartyl protease, termed BACE1 (β-site APP-cleaving enzyme 1) (1–4). BACE1 cleaves APP within the extracellular domain of APP, generating the N terminus of Aβ. In addition, BACE1 also cleaves to a lesser extent within the Aβ domain between Tyr¹⁰ and Glu¹¹ (β′-cleavage site). Processing of APP at these sites results in the shedding/secretion of the large ectodomain (sAPPβ) and generating membrane-tethered C-terminal fragments +1 and +11 (β-CTF) (5). The multimeric γ-secretase cleaves at multiple sites within the transmembrane domain of β-CTF, generating C-terminal heterogeneous Aβ peptides (ranging in length between 38 and 43 residues) that are secreted, as well as cytosolic APP intracellular domains (6). In addition to BACE1, APP can be cleaved by α-secretase within the Aβ domain between Lys¹⁶ and Leu¹⁷, releasing sAPPα and generating α-CTF. γ-Secretase cleavage of α-CTF generates N-terminal truncated Aβ, termed p3.Genetic ablation of BACE1 completely abolishes Aβ production, establishing BACE1 as the major neuronal enzyme responsible for initiating amyloidogenic processing of APP (4, 7). Interestingly, both the expression and activity of BACE1 is specifically elevated in neurons adjacent to senile plaques in brains of individuals with Alzheimer disease (8). In the past few years additional substrates of BACE1 have been identified that include APP homologues APLP1 and APLP2 (9), P-selectin glycoprotein ligand-1 (10), β-galactoside α2,6-sialyltransferase (11), low-density lipoprotein receptor-related protein (12), β-subunits of voltage-gated sodium channels (13), and neuregulin-1 (14, 15), thus extending the physiological function of BACE1 beyond Alzheimer disease pathogenesis.BACE1 is a type I transmembrane protein with a long extracellular domain harboring a catalytic domain and a short cytoplasmic tail. BACE1 is synthesized as a proenzyme, which undergoes post-translational modifications that include removal of a pro-domain by a furin-like protease, N-glycosylation, phosphorylation, S-palmitoylation, and acetylation, during the transit in the secretory pathway (16–20). In non-neuronal cells the majority of BACE1 localizes to late Golgi/TGN and endosomes at steady-state and a fraction of BACE1 also cycles between the cell surface and endosomes (21). The steady-state localization of BACE1 is consistent with the acidic pH optimum of BACE1 in vitro, and BACE1 cleavage of APP is observed in the Golgi apparatus, TGN, and endosomes (22–25). BACE1 endocytosis and recycling are mediated by the GGA family of adaptors binding to a dileucine motif (⁴⁹⁶DISLL) in its cytoplasmic tail (21, 26–31). Phosphorylation at Ser⁴⁹⁸ within this motif modulates GGA-dependent retrograde transport of BACE1 from endosomes to TGN (21, 26–31).Over the years, a functional relationship between cellular cholesterol level and Aβ production has been uncovered, raising the intriguing possibility that cholesterol levels may determine the balance between amyloidogenic and non-amyloidogenic processing of APP (32–34). Furthermore, several lines of evidence from in vitro and in vivo studies indicate that cholesterol- and sphingolipid-rich membrane microdomains, termed lipid rafts, might be the critical link between cholesterol levels and amyloidogenic processing of APP. Lipid rafts function in the trafficking of proteins in the secretory and endocytic pathways in epithelial cells and neurons, and participate in a number of important biological functions (35). BACE1 undergoes S-palmitoylation (19), a reversible post-translational modification responsible for targeting a variety of peripheral and integral membrane proteins to lipid rafts (36). Indeed, a significant fraction of BACE1 is localized in lipid raft microdomains in a cholesterol-dependent manner, and addition of glycosylphosphatidylinositol (GPI) anchor to target BACE1 exclusively to lipid rafts increases APP processing at the β-cleavage site (37, 38). Antibody-mediated co-patching of cell surface APP and BACE1 has provided further evidence for BACE1 processing of APP in raft microdomains (33, 39). Components of the γ-secretase complex also associate with detergent-resistant membrane (DRM) fractions enriched in raft markers such as caveolin, flotillin, PrP, and ganglioside GM1 (40). The above findings suggest a model whereby APP is sequentially processed by BACE1 and γ-secretase in lipid rafts.Despite the accumulating evidence, cleavage of APP by BACE1 in non-raft membrane regions cannot be unambiguously ruled out because of the paucity of full-length APP (APP FL) and BACE1 in DRM isolated from adult brain and cultured cells (41). Moreover, it was recently reported that moderate reduction of cholesterol (<25%) displaces BACE1 from raft domains, and increases BACE1 processing by promoting the membrane proximity of BACE1 and APP in non-raft domains (34). Nevertheless, this study also found that BACE1 processing of APP is inhibited with further loss of cholesterol (>35%), consistent with earlier studies (32, 33). Nevertheless, given the pleiotropic effects of cholesterol depletion on membrane properties and vesicular trafficking of secretory and endocytic proteins (42–47), unequivocal conclusions regarding BACE1 processing of APP in lipid rafts cannot be reached based on cholesterol depletion studies.In this study, we explored the function of BACE1 in lipid raft microdomains without manipulating cellular cholesterol levels. In addition to the previously reported S-palmitoylation sites (Cys⁴⁷⁸/Cys⁴⁸²/Cys⁴⁸⁵) within the cytosolic tail of BACE1 (19), we have identified a fourth site (Cys⁴⁷⁴) within the transmembrane domain of BACE1 that undergoes S-palmitoylation. A BACE1 mutant with Ala substitution of all four Cys residues (BACE1-4C/A) fails to associate with DRM in cultured cells, but is not otherwise different from wtBACE1 in terms of protein stability, maturation, or subcellular localization. Surprisingly, APP processing and Aβ generation were unaffected in cells stably expressing the BACE1-4C/A mutant. Finally, we observed an increase in the levels of APP CTFs in detergent-soluble fractions of BACE1-4C/A as compared with wtBACE1 cells. Thus, our data collectively indicate a non-obligatory role of S-palmitoylation and lipid raft localization of BACE1 in amyloidogenic processing of APP.     

Modeling of phosphomethyl pyrimidine kinase from Leptospira interrogans serovar lai strain 56601

Many microorganisms, as well as plants and fungi, synthesize thiamin, but vertebrates do not produce it. Phosphomethyl pyrimidine kinase is an enzyme involved in an intermediary step of thiamin biosynthesis from purine molecules. This enzyme is absent in humans. Thus, it is a potential chemotherapeutic target for antileptospiral treatment. Structure of this enzyme from Leptospira interrogans serovar lai strain 56601 has not yet been elucidated. We used the structural template of phosphomethyl pyrimidine kinase from Thermus thermophilus HB8 for modeling the phosphomethyl pyrimidine kinase structure from Leptospira interrogans serovar lai strain 56601 . The model is deposited in Protein Data Bank (PDB ID: 2G53) at RCSB. Thus, we analyse and propose the usefulness of the modeled phosphomethyl pyrimidine kinase for the design of suitable inhibitors towards the treatment of leptospirosis.