Kavita Singh

Epitope Recognition by Diverse Antibodies Suggests Conformational Convergence in an Antibody Response

Crystal structures of distinct mAbs that recognize a common epitope of a peptide Ag have been determined and analyzed in the unbound and bound forms. These Abs display dissimilar binding site structures in the absence of the Ag. The dissimilarity is primarily expressed in the conformations of complementarity-determining region H3, which is responsible for defining the epitope specificity. Interestingly, however, the three Abs exhibit similar complementarity-determining region conformations in the Ag binding site while recognizing the common epitope, indicating that different pathways of binding are used for Ag recognition. The epitope also exhibits conformational similarity when bound to each of these Abs, although the peptide Ag was otherwise flexible. The observed conformational convergence in the epitope and the Ag binding site was facilitated by the plasticity in the nature of interactions.

Crystal Structure of an Antibody Bound to an Immunodominant Peptide Epitope: Novel Features in Peptide-Antibody Recognition

The crystal structure of Fab of an Ab PC283 complexed with its corresponding peptide Ag, PS1 (HQLDPAFGANSTNPD), derived from the hepatitis B virus surface Ag was determined. The PS1 stretch Gln2P to Phe7P is present in the Ag binding site of the Ab, while the next three residues of the peptide are raised above the binding groove. The residues Ser11P, Thr12P, and Asn13P then loop back onto the Ag-binding site of the Ab. The last two residues, Pro14P and Asp15P, extend outside the binding site without forming any contacts with the Ab. The PC283-PS1 complex is among the few examples where the light chain complementarity-determining regions show more interactions than the heavy chain complementarity-determining regions, and a distal framework residue is involved in Ag binding. As seen from the crystal structure, most of the contacts between peptide and Ab are through the five residues, Leu3-Asp4-Pro5-Ala6-Phe7, of PS1. The paratope is predominantly hydrophobic with aromatic residues lining the binding pocket, although a salt bridge also contributes to stabilizing the Ag-Ab interaction. The molecular surface area buried upon PS1 binding is 756 Å2 for the peptide and 625 Å2 for the Fab, which is higher than what has been seen to date for Ab-peptide complexes. A comparison between PC283 structure and a homology model of its germline ancestor suggests that paratope optimization for PS1 occurs by improving both charge and shape complementarity.

The expression of CYP2D22, an ortholog of human CYP2D6, in mouse striatum and its modulation in 1-methyl 4-phenyl-1,2,3,6-tetrahydropyridine-induced Parkinson's disease phenotype and nicotine-mediated neuroprotection.

The main contributory factors of Parkinsons disease (PD) are aging, genetic factors, and environmental exposure to pesticides and heavy metals. CYP2D22, a mouse ortholog of human CYP2D6, is expected to participate in a chemically induced PD phenotype due to its structural resemblance with CYP2D6. Despite its expected participation in PD, its expression in the nigrostriatal tissues and modulation by the chemicals that induce PD or offer neuroprotection have not yet been investigated. The present study was undertaken to investigate CYP2D22 expression in mouse striatum and to assess its involvement in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced PD phenotype and nicotine-mediated neuroprotection. The animals were treated intraperitoneally daily with nicotine (1 mg/kg) for 8 weeks, followed by MPTP (20 mg/kg) + nicotine (1 mg/kg) for 2-4 weeks and vice versa, along with respective controls. In some sets of experiments, the animals were treated with ketoconazole (300 mg/kg), a CYP3AH/CYP2D22 inhibitor, along with nicotine and/or MPTP. Tyrosine hydroxylase (TH)-immunoreactivity in the substantia nigra, the expression of nicotinic acetylcholine receptors (nAChRs) alpha6 and alpha4, dopamine content, and 1-methyl-4-phenylpyridinium ion (MPP(+)) level in the striatum were measured to confirm the MPTP-induced PD phenotype and nicotine-mediated neuroprotection. CYP2D22 and nAChRs expressions were measured in the striatum by RT-PCR/western blotting and dopamine level; CYP2D22 catalytic activity and MPP(+) content were determined by high-performance liquid chromatography (HPLC). MPTP increased dopaminergic neuronal degeneration and the striatal MPP(+) level and reduced striatal dopamine content; it attenuated expression/activity of CYP2D22 and nAChRs that were significantly restored in nicotine-treated animals. Ketoconazole reduced the nicotine-mediated increase in CYP2D22 expression and activity, dopamine content, and TH-immunoreactivity. The results indicate the expression of CYP2D22 in mouse striatum and its possible role in the MPTP-induced PD phenotype and nicotine-mediated neuroprotection.

Mimicry of native peptide antigens by the corresponding retro-inverso analogs is dependent on their intrinsic structure and interaction propensities.

Retro-inverso (ri) analogs of model T cell and B cell epitopes were predictively designed as mimics and then assayed for activity to understand the basis of functional ri-antigenic peptide mimicry. ri versions of two MHC class I binding peptide epitopes, one from a vesicular stomatitis virus glycoprotein (VSVp) and another from OVA (OVAp), exhibit structural as well as functional mimicry of their native counterparts. The two ri peptides exhibit conformational plasticity and they bind to MHC class I (H-2Kb) similar to their native counterparts both in silico and in vivo. In fact, ri-OVAp is also presented to an OVAp-specific T cell line in a mode similar to native OVAp. In contrast, the ri version of an immunodominant B cell peptide epitope from a hepatitis B virus protein, PS1, exhibits no structural or functional correlation with its native counterpart. PS1 and its ri analog do not exhibit similar conformational propensities. PS1 is less flexible relative to its ri version. These observed structure-function relationships of the ri-peptide epitopes are consistent with the differences in recognition properties between peptide-MHC vs peptide-Ab binding where, while the recognition of the epitope by MHC is pattern based, the exquisitely specific recognition of Ag by Ab arises from the high complementarity between the Ag and the binding site of the Ab. It is evident that the correlation of conformational and interaction propensities of native l-peptides and their ri counterparts depends both on their inherent structural properties and on their mode of recognition.

Proteomics in Parkinson's disease: current trends, translational snags and future possibilities.

Proteomic technologies are widely used to understand the molecular mechanism of Parkinson’s disease (PD) and to develop biomarkers for its early diagnosis. The differential expression patterns of brain, cerebrospinal fluid and blood proteins of patients or chemically induced animal models are used to identify protein fingerprints for developing diagnostic and therapeutic strategies for PD. A number of differentially expressed proteins associated with energy metabolism, oxidative stress, signal transduction, electron transport and detoxification pathways are identified using proteomic strategies. Proteomics immensely contributed to the detection of qualitative and quantitative changes of expressed proteins and their post-translational modifications. An update on proteomics-driven research for developing early biomarkers and understanding the molecular aspects of PD, along with their translational snags, challenges and future possibilities, are discussed in this review.

Nicotine- and caffeine-mediated changes in gene expression patterns of MPTP-lesioned mouse striatum: Implications in neuroprotection mechanism

Exposure to 1-methyl 4-phenyl 1,2,3,6-tetrahydropyridine (MPTP) induces dopaminergic neurodegeneration in the nigrostriatal pathway and nicotine and caffeine ameliorate neurodegenerative changes in MPTP-lesioned mouse model of Parkinsons disease (PD). The present study was undertaken to investigate the effect of nicotine and caffeine on the expression patterns of genes in the striatum of control and MPTP-treated mice to identify the differentially expressed transcripts and to assess their possible implications in neuroprotection. Mice were treated intraperitoneally with caffeine (20mg/kg) or nicotine (1mg/kg), daily, for the first 8 weeks followed by MPTP (20mg/kg) co-treatment for further 4 weeks along with respective controls. RNA was isolated from the striatum of control and treated mice; reverse transcribed separately into labeled cDNA and a mixture of equal quantities of labeled cDNA was hybridized with mouse 15k array. The expression levels of toll-interleukin-1 receptor domain-containing adaptor protein, nuclear protein-1, cathepsin B, interleukin-4 receptor, caspase 9, complement component-1, heat shock protein-1 and cytochrome c-oxidase-VIIc were validated by quantitative real-time polymerase chain reaction (qRT-PCR). MPTP differentially regulated the expression of many genes involved in apoptotic cell death, oxidative stress, cell cycle regulation, protein modification and mitochondrial dysfunction. The expression patterns of many of these transcripts were significantly restored in caffeine- and nicotine-treated mice. The results demonstrate the involvement of multiple molecular events in MPTP-induced toxicity and nicotine or caffeine-mediated neuroprotection.

Effect of caffeine on the expression of cytochrome P450 1A2, adenosine A2A receptor and dopamine transporter in control and 1-methyl 4-phenyl 1, 2, 3, 6-tetrahydropyridine treated mouse striatum.

Parkinsons disease (PD) is a progressive neurodegenerative disorder, characterized by the selective loss of dopaminergic neurons of the nigrostriatal pathway. Epidemiological studies have shown an inverse relationship between coffee consumption and susceptibility to PD. Cytochrome P450 1A2 (CYP1A2) is involved in caffeine metabolism and its clearance. Caffeine, on the other hand, antagonizes adenosine A(2A) receptor and regulates dopamine signaling through dopamine transporter (DAT). The present study was undertaken to investigate the expression of CYP1A2, adenosine A(2A) receptor and DAT in mouse striatum and to assess their levels in 1-methyl 4-phenyl 1, 2, 3, 6-tetrahydropryridine (MPTP) treated mouse striatum with and without caffeine treatment. The animals were treated intraperitoneally daily with caffeine (20 mg/kg) for 8 weeks, followed by MPTP (20 mg/kg)+caffeine (20 mg/kg) for 4 weeks or vice versa, along with respective controls. Tyrosine hydroxylase immunoreactivity, levels of dopamine and 1-methyl 4-phenylpyridinium ion (MPP(+)), expressions of CYP1A2, adenosine A(2A) receptor and DAT and CYP1A2 catalytic activity were measured in control and treated mouse brain. Caffeine partially protected MPTP-induced neurodegenerative changes and modulated MPTP-mediated alterations in the expression and catalytic activity of CYP1A2, expression of adenosine A(2A) receptor and DAT. The results demonstrate that caffeine alters the striatal CYP1A2, adenosine A(2A) receptor and DAT expressions in mice exposed to MPTP.

The prophage-encoded hyaluronate lyase has broad substrate specificity and is regulated by the N-terminal domain.

Background: Phage hyaluronate lyases (HLs) of streptococci are intracellular and specifically cleave hyaluronan. Results: HLs completely degrade glycosaminoglycans, have catalytically independent TSβH domains, and are functional in physiological conditions. Conclusion: Phage HL has a broad glycosaminoglycan degrading activity that is regulated by its own N-terminal region. Significance: Degradation of ECM components by HLs may facilitate the diffusion of toxins etc. Streptococcus equi is the causative agent of the highly contagious disease “strangles” in equines and zoonotic meningitis in human. Spreading of infection in host tissues is thought to be facilitated by the bacterial gene encoded extracellular hyaluronate lyase (HL), which degrades hyaluronan (HA), chondroitin 6-sulfate, and dermatan sulfate of the extracellular matrix). The clinical strain S. equi 4047 however, lacks a functional extracellular HL. The prophages of S. equi and other streptococci encode intracellular HLs which are reported to partially degrade HA and do not cleave any other glycosaminoglycans. The phage HLs are thus thought to play a role limited to the penetration of streptococcal HA capsules, facilitating bacterial lysogenization and not in the bacterial pathogenesis. Here we systematically looked into the structure-function relationship of S. equi 4047 phage HL. Although HA is the preferred substrate, this HL has weak activity toward chondroitin 6-sulfate and dermatan sulfate and can completely degrade all of them. Even though the catalytic triple-stranded β-helix domain of phage HL is functionally independent, its catalytic efficiency and specificity is influenced by the N-terminal domain. The phage HL also interacts with human transmembrane glycoprotein CD44. The above results suggest that the streptococci can use phage HLs to degrade glycosaminoglycans of the extracellular matrix for spreading virulence factors and toxins while utilizing the disaccharides as a nutrient source for proliferation at the site of infection.

Leishmania donovani Exploits Tollip, a Multitasking Protein, To Impair TLR/IL-1R Signaling for Its Survival in the Host

IL-1R/TLR signaling plays a significant role in sensing harmful foreign pathogens and mounting effective innate and adaptive immune responses. However, the precise mechanism by which Leishmania donovani, an obligate intramacrophagic pathogen, breaches IL-1R/TLR signaling and host-protective immunity remains obscure. In this study, we report the novel biphasic role of Toll-interacting protein (Tollip), a negative regulator of the IL-1R/TLR pathway, in the disease progression of experimental visceral leishmaniasis. We observed that during early hours of infection, L. donovani induced phosphorylation of IRAK-1, resulting in the release of Tollip from the IL-1R–associated kinase (IRAK)-1 complex in J774 macrophages, which then acted as an endocytic adaptor on cell surface IL-1R1 and promoted its lysosomal degradation. In the later stage, Tollip shuttled back to IRAK-1, thereby inhibiting IRAK-1 phosphorylation in association with IRAK-M to neutralize downstream TLR signaling in infected macrophages. Moreover, during late infection, L. donovani enhanced nuclear translocation and recruitment of transcription factors early growth response protein 2, NF erythroid 2–related factor 2, and Ahr on Tollip promoter for its induction. Small interfering RNA–mediated silencing of Tollip in infected macrophages significantly enhanced NF-κB activation and induced host-defensive IL-12 and TNF-α synthesis, thereby reducing amastigote multiplication. Likewise, abrogation of Tollip in L. donovani–infected BALB/c mice resulted in STAT-1–, IRF-1–, and NF-κB–mediated upregulation of host-protective cytokines and reduced organ parasite burden, thereby implicating its role in disease aggravation. Taken together, we conclude that L. donovani exploited the multitasking function of Tollip for its own establishment through downregulating IL-1R1/TLR signaling in macrophages.