Mapping of thyroglobulin epitopes: Presentation of a 9mer pathogenic peptide by different mouse MHC class II isotypes

We have previously reported that the 17mer thyroglobulin (Tg) peptide TgP1 (a.a. 2495–2511) induces experimental autoimmune thyroiditis (EAT) inH-2 ^k mice, a process requiring expression ofE ^k genes, and inH-2 ^S mice that lack functional E molecules. To test whether this apparent discrepancy was due to recognition of distinct TgP1 determinants in each strain, we mapped in this study minimal T -cell epitopes within TgP1 and examined their pathogenicity in C3H (H-2 ^k) or SJL (H-2 ^S) mice. Truncation analysis using TgP1-specific, CD4+ hybridomas from C3H mice identified two overlapping determinants, (2496-2504) and (2499–2507), that were restricted by the E^k and A^k molecules, respectively. Subsequent challenge of C3H and SJL mice with these 9mer peptides revealed that the Ekrestricted (2496–2504) determinant elicited EAT and specific proliferative LNC responses in both strains, suggesting recognition in the context of A^s, since this is the only class II molecule expressed in SJL mice. This was further confirmed by blocking of the proliferative LNC response by an As-specific monoclonal antibody. In contrast, the A^k-restricted (2499–2507) determinant induced weak EAT and no proliferative LNC responses in either strain. These data 1) delineate the 9mer (2496–2504) peptide as a minimal Tg T-cell epitope with direct pathogenic potential in mice and 2) highlight the use of nonisotypic MHC class II molecules for the presentation of this peptide in mice of differentH-2 haplotypes.     

lambda-conotoxins, a new family of conotoxins with unique disulfide pattern and protein folding. Isolation and characterization from the venom of Conus marmoreus

Conotoxins are multiple disulfide-bonded peptides isolated from marine cone snail venom. These toxins have been classified into several families based on their disulfide pattern and biological properties. Here, we report a new family of Conus peptides, which have a novel cysteine motif. Three peptides of this family (CMrVIA, CMrVIB, and CMrX) have been purified from Conus marmoreus venom, and their structures have been determined. Their amino acid sequences are VCCGYK-LCHOC (CMrVIA), NGVCCGYKLCHOC (CMrVIB), and GICCGVSFCYOC (CMrX), where O represents 4-trans-hydroxyproline. Two of these peptides (CMrVIA and CMrX) have been chemically synthesized. Using a selective protection and deprotection strategy during disulfide bond formation, peptides with both feasible cysteine-pairing combinations were generated. The disulfide pattern (C(1)-C(4), C(2)-C(3)) in native toxins was identified by their co-elution with the synthetic disulfide-isomeric peptides on reverse-phase high pressure liquid chromatography. Although cysteine residues were found in comparable positions with those of alpha-conotoxins, these toxins exhibited a distinctly different disulfide bonding pattern; we have named this new family "lambda -conotoxins." CMrVIA and CMrX induced different biological effects when injected intra-cerebroventricularly in mice; CMrVIA induces seizures, whereas CMrX induces flaccid paralysis. The synthetic peptide with lambda-conotoxin folding is about 1150-fold more potent in inducing seizures than the mispaired isomer with alpha-conotoxin folding. Thus it appears that the unique disulfide pattern, and hence the "ribbon" conformation, in lambda-conotoxins is important for their biological activity.     

Quantitative measurement of serotonin synthesis and sequestration in individual live neuronal cells

Synthesis and subsequent sequestration into vesicles are essential steps that precede neurotransmitter exocytosis, but neither the total neurotransmitter content nor the fraction sequestered into vesicles have been measured in individual live neurons. We use multiphoton microscopy to directly observe intracellular and intravesicular serotonin in the serotonergic neuronal cell line RN46A. We focus on how the relationship between synthesis and sequestration changes as synthesis is up-regulated by differentiation or down-regulated by chemical inhibition. Temperature-induced differentiation causes an increase of about 60% in the total serotonin content of individual cells, which goes up to about 10 fmol. However, the number of vesicles per cell increases by a factor of four and the proportion of serotonin sequestered inside the vesicles increases by a factor of five. When serotonin synthesis is inhibited in differentiated cells and the serotonin content goes down to the level present in undifferentiated cells, the sequestered proportion still remains at this high level. The total neurotransmitter content of a cell is, thus, an unreliable indicator of the sequestered amount.     

Integrating cell-level kinetic modeling into the design of engineered protein therapeutics

Functional genomics and proteomics are identifying many potential drug targets for novel therapeutic proteins, and both rational and combinatorial protein engineering methods are available for creating drug candidates. A central challenge is the definition of the most appropriate design criteria, which will benefit critically from computational kinetic models that incorporate integration from the molecular level to the whole systems level. Interpretation of these processes will require mathematical models that are refined in combination with relevant data derived from quantitative assays, to correctly set biophysical objectives for protein design.     

Use of a database of structural alignments and phylogenetic trees in investigating the relationship between sequence and structural variability among homologous proteins

The database PALI (Phylogeny and ALIgnment of homologous protein structures) consists of families of protein domains of known three-dimensional (3D) structure. In a PALI family, every member has been structurally aligned with every other member (pairwise) and also simultaneous superposition (multiple) of all the members has been performed. The database also contains 3D structure-based and structure-dependent sequence similarity-based phylogenetic dendrograms for all the families. The PALI release used in the present analysis comprises 225 families derived largely from the HOMSTRAD and SCOP databases. The quality of the multiple rigid-body structural alignments in PALI was compared with that obtained from COMPARER, which encodes a procedure based on properties and relationships. The alignments from the two procedures agreed very well and variations are seen only in the low sequence similarity cases often in the loop regions. A validation of Direct Pairwise Alignment (DPA) between two proteins is provided by comparing it with Pairwise alignment extracted from Multiple Alignment of all the members in the family (PMA). In general, DPA and PMA are found to vary rarely. The ready availability of pairwise alignments allows the analysis of variations in structural distances as a function of sequence similarities and number of topologically equivalent Calpha atoms. The structural distance metric used in the analysis combines root mean square deviation (r.m.s.d.) and number of equivalences, and is shown to vary similarly to r.m.s.d. The correlation between sequence similarity and structural similarity is poor in pairs with low sequence similarities. A comparison of sequence and 3D structure-based phylogenies for all the families suggests that only a few families have a radical difference in the two kinds of dendrograms. The difference could occur when the sequence similarity among the homologues is low or when the structures are subjected to evolutionary pressure for the retention of function. The PALI database is expected to be useful in furthering our understanding of the relationship between sequences and structures of homologous proteins and their evolution.     

PALI-a database of Phylogeny and ALIgnment of homologous protein structures

PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set comprises 604 families of homologous proteins involving 2739 protein domain structures with each family made up of at least two members. Each member in a family has been structurally aligned with every other member in the same family (pairwise alignment) and all the members in the family are also aligned using simultaneous super-position (multiple alignment). The structural alignments are performed largely automatically, with manual interventions especially in the cases of distantly related proteins, using the program STAMP (version 4.2). Every family is also associated with two dendrograms, calculated using PHYLIP (version 3.5), one based on a structural dissimilarity metric defined for every pairwise alignment and the other based on similarity of topologically equivalent residues. These dendrograms enable easy comparison of sequence and structure-based relationships among the members in a family. Structure-based alignments with the details of structural and sequence similarities, superposed coordinate sets and dendrograms can be accessed conveniently using a web interface. The database can be queried for protein pairs with sequence or structural similarities falling within a specified range. Thus PALI forms a useful resource to help in analysing the relationship between sequence and structure variation at a given level of sequence similarity. PALI also contains over 653 'orphans' (single member families). Using the web interface involving PSI_BLAST and PHYLIP it is possible to associate the sequence of a new protein with one of the families in PALI and generate a phylogenetic tree combining the query sequence and proteins of known 3-D structure. The database with the web interfaced search and dendrogram generation tools can be accessed at http://pauling.mbu.iisc.ernet. in/ approximately pali.     

Sonic hedgehog-Dependent Induction of MicroRNA 31 and MicroRNA 150 Regulates Mycobacterium bovis BCG-Driven Toll-Like Receptor 2 Signaling

Hedgehog (HH) signaling is a significant regulator of cell fate decisions during embryogenesis, development, and perpetuation of various disease conditions. Testing whether pathogen-specific HH signaling promotes unique innate recognition of intracellular bacteria, we demonstrate that among diverse Gram-positive or Gram-negative microbes, Mycobacterium bovis BCG, a vaccine strain, elicits a robust activation of Sonic HH (SHH) signaling in macrophages. Interestingly, sustained tumor necrosis factor alpha (TNF-α) secretion by macrophages was essential for robust SHH activation, as TNF-α^−/− macrophages exhibited compromised ability to activate SHH signaling. Neutralization of TNF-α or blockade of TNF-α receptor signaling significantly reduced the infection-induced SHH signaling activation both in vitro and in vivo. Intriguingly, activated SHH signaling downregulated M. bovis BCG-mediated Toll-like receptor 2 (TLR2) signaling events to regulate a battery of genes associated with divergent functions of M1/M2 macrophages. Genome-wide expression profiling as well as conventional gain-of-function or loss-of-function analysis showed that SHH signaling-responsive microRNA 31 (miR-31) and miR-150 target MyD88, an adaptor protein of TLR2 signaling, thus leading to suppression of TLR2 responses. SHH signaling signatures could be detected in vivo in tuberculosis patients and M. bovis BCG-challenged mice. Collectively, these investigations identify SHH signaling to be what we believe is one of the significant regulators of host-pathogen interactions.     

Males and Females Gain Differentially from Sociality in a Promiscuous Fruit Bat Cynopterus sphinx

Sociality emerges when the benefits of group living outweigh its costs. While both males and females are capable of strong social ties, the evolutionary drivers for sociality and the benefits accrued maybe different for each sex. In this study, we investigate the differential reproductive success benefits of group membership that males and females might obtain in the promiscuous fruit bat Cynopterus sphinx. Individuals of this species live in flexible social groups called colonies. These colonies are labile and there is high turnover of individuals. However, colony males sire more offspring within the colony suggesting that being part of a colony may result in reproductive benefits for males. This also raises the possibility that long-term loyalty towards the colony may confer additional advantage in terms of higher reproductive success. We used ten seasons of genetic parentage data to estimate reproductive success and relatedness of individuals in the colony. We used recapture data to identify long and short-term residents in the colony as well as to obtain rates of recapture for males and females. Our results reveal that males have a significantly higher chance of becoming long-term residents (than females), and these long-term resident males gain twice the reproductive success compared to short-term resident males. We also observed that long-term resident females are related to each other and also achieve higher reproductive success than short-term resident females. In contrast, long-term resident males do not differ from short-term resident males in their levels of relatedness. Our results re-iterate the benefits of sociality even in species that are promiscuous and socially labile and possible benefits of maintaining a colony.