N-terminal ectodomain of BTNL2 inhibits T cell activation via a non-canonical interaction with its putative receptor that results in a delayed progression of DSS-induced ulcerative colitis

Butyrophilin-like 2 (BTNL2) is a T cell inhibitory molecule that interacts with unknown binding partners to modulate the immune response in a number of inflammatory and autoimmune diseases. In this study, we found that the inhibitory effects of BTNL2 on T cell activation and effector functions can be executed by its N-terminal IgV domain (BTNL2 IgV1) alone. Structure-guided mutation of key residues on BTNL2 IgV1 based on known receptor-ligand interfaces involving immunoglobulin superfamily members revealed that BTNL2 uses a non-canonical binding interface with its putative receptor. A high avidity BTNL2 IgV1 probe revealed that in an inducible model of ulcerative colitis, severe colitis was accompanied by a selective enrichment of BTNL2-receptor expressing effector-memory CD4+ and CD8+ T cells in the Peyer's patches. Intraperitoneal administration of BTNL2 IgV1 resulted in a significant delay in the progression of DSS-induced colitis and also showed reduced activation of the BTNL2-receptor-expressing T cells in the Peyer's patches. Thus, this study demonstrates that the BTNL2-receptor-expressing T cells in the Peyer's patches participate in the disease pathogenesis and can serve as a novel therapeutic target in ulcerative colitis, which can be modulated by BTNL2 IgV1.

Structural basis of molecular recognition among classical cadherins mediating cell adhesion

Cadherins are type-I membrane glycoproteins that primarily participate in calcium-dependent cell adhesion and homotypic cell sorting in various stages of embryonic development. Besides their crucial role in cellular and physiological processes, increasing studies highlight their involvement in pathophysiological functions ranging from cancer progression and metastasis to being entry receptors for pathogens. Cadherins mediate these cellular processes through homophilic, as well as heterophilic interactions (within and outside the superfamily) by their membrane distal ectodomains. This review provides an in-depth structural perspective of molecular recognition among type-I and type-II classical cadherins. Furthermore, this review offers structural insights into different dimeric assemblies like the 'strand-swap dimer' and 'X-dimer' as well as mechanisms relating these dimer forms like 'two-step adhesion' and 'encounter complex'. Alongside providing structural details, this review connects structural studies to bond mechanics merging crystallographic and single-molecule force spectroscopic findings. Finally, the review discusses the recent discoveries on dimeric intermediates that uncover prospects of further research beyond two-step adhesion.

A nanobody based ultrasensitive electrochemical biosensor for the detection of soluble CTLA-4 -A candidate biomarker for cancer development and progression

A soluble isoform of cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) has been found in the serum of healthy individuals and alterations in its expression level have been linked with the development and progression of various cancers. Conventionally, soluble CTLA-4 (sCTLA-4) has been quantified by techniques such as ELISA, western blot, and flow cytometry, which however are time-consuming, highly expensive and require large sample volumes. Therefore, rapid, cost-effective and real-time monitoring of soluble CTLA-4 levels is much needed to facilitate timely diagnosis of a worsening disease and help patient selection for immunotherapeutic interventions in cancer. Here, for the first time, we report an ultrasensitive, highly selective electrochemical nanobody (NAb) based biosensor for the quantitative detection of soluble CTLA-4 employing poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) and gold nanoparticles modified electrode with attomole sensitivity. Incorporating nanomaterials with conductive polymers enhances the sensitivity of the electrochemical biosensor, while the nanobody's stability, specificity and ease of production make it a suitable choice as a bioreceptor. The proposed NAb-based sensor can detect sCTLA-4 from pure recombinant protein in a wide concentration range of 100 ag mL-1- 500 μg mL-1, with a limit of detection of 1.19 ag mL-1 (+3σ of the blank signal). The sensor's relative standard deviation for reproducibility is less than 0.4% and has effective real sample analytics for cell culture supernatant with no significant difference with pure recombinant protein (p < 0.05). Our proposed nanobody based sensor exhibits stability for up to 2 weeks (<3% variation). Moreover, this nanobody-based sensor presents a future opportunity for quantitative, ultrasensitive, and economical biosensor development that can be adapted to monitor the immune landscape of cancer patients to provide a larger therapeutic window.

Activation and differentiation of cognate T cells by a dextran-based antigen-presenting system for cancer immunotherapy

Immunotherapeutic modulation of antigen-specific T-cell responses instead of the whole repertoire helps avoid immune-related adverse events. We have developed an artificial antigen-presenting system (aAPS) where multiple copies of a multimeric peptide-MHC class I complex presenting a murine class I MHC restricted ovalbumin-derived peptide (signal 1), along with a costimulatory ligand (signal 2) are chemically conjugated to a dextran backbone. Cognate naive CD8+ T cells, when treated with this aAPS underwent significant expansion and showed an activated phenotype. Furthermore, elevated expression of effector cytokines led to the differentiation of these cells to cytotoxic T lymphocytes which resulted in target cell lysis, indicative of the functional efficacy of the aAPS. CD8+ T cells with decreased proliferative potential due to repeated antigenic stimulation could also be re-expanded by the developed aAPS. Thus, the developed aAPS warrants further engineering for future application as a rapidly customizable personalized immunotherapeutic agent, incorporating patient-specific MHC-restricted tumor antigens and different costimulatory signals to modulate both naive and antigen-experienced but exhausted tumor-specific T cells in cancer.

Molecular and structural basis of TIGIT: Nectin-4 interaction, a recently discovered pathway crucial for cancer immunotherapy

TIGIT (T cell immunoglobulin and ITIM domain) is an inhibitory receptor expressed on T and NK cells that interact with cell surface glycoprotein belonging to the nectin and nectin-like family of cell adhesion molecules, particularly nectin-2 and nectin-like 5 (PVR). Nectin-4 has been recently identified as a novel ligand for TIGIT and the interaction among them inhibits NK cell cytotoxicity. In this study, biophysical experiments were conducted to decipher the mechanism of this novel interaction, followed by structure-guided mutagenesis studies to map the nectin-4 binding interface on TIGIT. Using surface plasmon resonance, we deduced that TIGIT recognizes the membrane distal ectodomain of nectin-4 and the interaction is weaker than the well-characterized TIGIT: nectin-2 interaction. Deciphering the molecular basis of this newly identified interaction between TIGIT and nectin-4 will provide us important insight into the manipulation of this inhibitory signaling pathway, especially targeting cancer cells overexpressing nectin-4 that evade the immune surveillance of the body.

Molecular mimicry of host short linear motif-mediated interactions utilised by viruses for entry

Viruses are obligate intracellular parasites that depend on host cellular machinery for performing even basic biological functions. One of the many ways they achieve this is through molecular mimicry, wherein the virus mimics a host sequence or structure, thereby being able to hijack the host's physiological interactions for its pathogenesis. Such adaptations are specific recognitions that often confer tissue and species-specific tropisms to the virus, and enable the virus to utilise previously existing host signalling networks, which ultimately aid in further steps of viral infection, such as entry, immune evasion and spread. A common form of sequence mimicry utilises short linear motifs (SLiMs). SLiMs are short-peptide sequences that mediate transient interactions and are major elements in host protein interaction networks. This work is aimed at providing a comprehensive review of current literature of some well-characterised SLiMs that play a role in the attachment and entry of viruses into host cells, which mimic physiological receptor-ligand interactions already present in the host. Considering recent trends in emerging diseases, further research on such motifs involved in viral entry can help in the discovery of previously unknown cellular receptors utilised by viruses, as well as help in the designing of targeted therapeutics such as vaccines or inhibitors directed towards these interactions.

Heterophilic recognition between E-cadherin and N-cadherin relies on same canonical binding interface as required for E-cadherin homodimerization

Cadherins are a family of cell surface glycoproteins that mediate Ca²⁺-dependent cell to cell adhesion. They organize to form large macromolecular assemblies at the junctions of cells in order to form and maintain the integrity of tissue structures, thereby playing an indispensable role in the multicellular organization. Notably, a large body of research on E- and N-cadherin, the two most widely studied members of the cadherin superfamily, suggest for homophilic associations among them to drive cell adhesion. Interestingly, latest studies also highlight for direct crosstalk among these two classical cadherins to form heterotypic connections in physiological as well as in disease environment. However, the molecular details for the heterophilic association of E-cadherin and N-cadherin has not been investigated yet, which we aimed to address in this work. Using surface plasmon resonance and flow cytometry based biophysical studies we observed heterophilic interaction between E- and N-cadherin mediated through the membrane distal ectodomains. Further, the heterodimeric interface of E-cadherin and N-cadherin was mapped using structure-guided mutational studies followed by complementary biophysical analyses to identify the important interface residues involved in the interaction. The results obtained imply significant resemblance in the interface residues of E-cadherin that are crucial for homophilic recognition of E-cadherin and heterophilic recognition of N-cadherin as well.

Cryptic association of B7-2 molecules and its implication for clustering

T-cell co-stimulation through CD28/CTLA4:B7-1/B7-2 axis is one of the extensively studied pathways that resulted in the discovery of several FDA-approved drugs for autoimmunity and cancer. However, many aspects of the signaling mechanism remain elusive, including oligomeric association and clustering of B7-2 on the cell surface. Here, we describe the structure of the IgV domain of B7-2 and its cryptic association into 1D arrays that appear to represent the pre-signaling state of B7-2 on the cell membrane. Super-resolution microscopy experiments on heterologous cells expressing B7-2 and B7-1 suggest, B7-2 form relatively elongated and larger clusters compared to B7-1. The sequence and structural comparison of other B7 family members, B7-1:CTLA4 and B7-2:CTLA-4 complex structures, support our view that the observed B7-2 1D zipper array is physiologically important. This observed 1D zipper-like array also provides an explanation for its clustering, and upright orientation on the cell surface, and avoidance of spurious signaling.

Immunoglobulin-fold containing bacterial adhesins: molecular and structural perspectives in host tissue colonization and infection

Immunoglobulin (Ig) domains are one of the most widespread protein domains encoded by the human genome and are present in a large array of proteins with diverse biological functions. These Ig domains possess a central structure, the immunoglobulin-fold, which is a sandwich of two β sheets, each made up of anti-parallel β strands, surrounding a central hydrophobic core. Apart from humans, proteins containing Ig-like domains are also distributed in a vast selection of organisms including vertebrates, invertebrates, plants, viruses and bacteria where they execute a wide array of discrete cellular functions. In this review, we have described the key structural deviations of bacterial Ig-folds when compared to the classical eukaryotic Ig-fold. Further, we have comprehensively grouped all the Ig-domain containing adhesins present in both Gram-negative and Gram-positive bacteria. Additionally, we describe the role of these particular adhesins in host tissue attachment, colonization and subsequent infection by both pathogenic and non-pathogenic Escherichia coli as well as other bacterial species. The structural properties of these Ig-domain containing adhesins, along with their interactions with specific Ig-like and non Ig-like binding partners present on the host cell surface have been discussed in detail.

Emerging roles of the nectin family of cell adhesion molecules in tumour-associated pathways

Tumour cells achieve maximum survival by modifying cellular machineries associated with processes such as cell division, migration, survival, and apoptosis, resulting in genetically complex and heterogeneous populations. While nectin and nectin-like cell adhesion molecules control development and maintenance of multicellular organisation in higher vertebrates by mediating cell-cell adhesion and related signalling processes, recent studies indicate that they also critically regulate growth and development of different types of cancers. In this review, we detail current knowledge about the role of nectin family members in various tumours. Furthermore, we also analyse the seemingly opposing roles of some members of nectin family in tumour-associated pathways, as they function as both tumour suppressors and oncogenes. Understanding this functional duality of nectin family in tumours will further our knowledge of molecular mechanisms regulating tumour development and progression, and contribute to the advancement of tumour diagnosis and therapy.

Cadherin-mediated host-pathogen interactions

Cell adhesion molecules mediate cell-to-cell and cell-to-matrix adhesions and play an immense role in a myriad of physiological processes during the growth and development of a multicellular organism. Cadherins belong to a major group of membrane-bound cell surface proteins that, in coordination with nectins, drive the formation and maintenance of adherens junctions for mediating cell to cell adhesion, cellular communication and signalling. Alongside adhesive function, the involvement of cadherins in mediating host-pathogen interactions has been extensively explored in recent years. In this review, we provide an in-depth understanding of microbial pathogens and their virulence factors that exploit cadherins for their strategical invasion into the host cell. Furthermore, macromolecular interactions involving cadherins and various microbial factors such as secretory toxins and adhesins lead to the disintegration of host cell junctions followed by the entry of the pathogen or triggering downstream signalling pathways responsible for successful invasion of the pathogenic microbes are discussed. Besides providing a comprehensive insight into some of the structural complexes involving cadherins and microbial factors to offer the mechanistic details of host-pathogen interactions, the current review also highlights novel constituents of various cell signalling events such as endocytosis machinery elicited upon microbial infections.

An evolutionarily conserved charged residue dictates the specificity of heterophilic interactions among nectins

Nectins are a family of four cell surface glycoproteins belonging to the immunoglobulin superfamily that mediate cell-cell adhesion and associated signalling pathways, thereby regulating several physiological processes including morphogenesis, growth and development of multicellular organisms. Nectins interact among themselves through their extracellular domains from the adjacent cells in both homophilic and heterophilic fashions to support cell-cell adhesion. Although nectins form homodimers as demonstrated in experimental set-ups, only the specific heterophilic interactions among nectins are physiologically relevant as shown by in vivo studies. It has been hypothesised that a conserved charged residue present at the binding interface acts as the molecular switch for heterophilic nectin-nectin recognitions. In this work, we have analysed the energetics of homophilic and heterophilic interactions of nectins, followed by surface plasmon resonance-based binding studies and complementary in silico analyses. Our findings confirm that the conserved charged residues at the binding interfaces dictate the specificity of the nectin-nectin heterophilic interactions. Furthermore, these residues also play a role in conferring higher affinity to the heterophilic interactions, thereby making them physiologically more prevalent compared to homophilic interactions. Thus, this work reveals the molecular basis of heterophilic recognitions among nectins that contribute to their physiological functions.

Structural Insights into N-terminal IgV Domain of BTNL2, a T Cell Inhibitory Molecule, Suggests a Non-canonical Binding Interface for Its Putative Receptors

T cell costimulation is mediated by the interaction of a number of receptors and ligands present on the surface of the T cell and antigen-presenting cell, respectively. Stimulatory or inhibitory signals from these receptor-ligand interactions work in tandem to preserve immune homeostasis. BTNL2 is a type-1 membrane protein that provides inhibitory signal to T cells and plays an important role in several inflammatory and autoimmune diseases. Therefore, manipulation of the molecular interaction of BTNL2 with its putative receptor could provide strategies to restore immune homeostasis in these diseases. Hence, it is imperative to study the structural characteristics of this molecule, which will provide important insights into its function as well. In this study, the membrane-distal ectodomain of murine BTNL2 was expressed in bacteria as inclusion bodies, refolded in vitro and purified for functional and structural characterization. The domain is monomeric in solution as demonstrated by size-exclusion chromatography and analytical ultracentrifugation, and also binds to its putative receptor on naïve B cells and activated T cell subsets. Importantly, for the first time, we report the structure of BTNL2 as determined by solution NMR spectroscopy and also the picosecond-nanosecond timescale backbone dynamics of this domain. The N-terminal ectodomain of BTNL2, which was able to inhibit T cell function as well, exhibits distinctive structural features. The N-terminal ectodomain of BTNL2 has a significantly reduced surface area in the front sheet due to the non-canonical conformation of the CC' loop, which provides important insights into the recognition of its presently unknown binding partner.

Tracing the evolution of nectin and nectin-like cell adhesion molecules

Nectin and nectin-like cell adhesion molecules (collectively referred as nectin family henceforth) are known to mediate cell-cell adhesion and related functions. While current literature suggests that nectins are prevalent in vertebrates, there are no in-depth analyses regarding the evolution of nectin family as a whole. In this work, we examine the evolutionary origin of the nectin family, using selected multicellular metazoans representing diverse clades whose whole genome sequencing data is available. Our results show that this family may have appeared earlier during metazoan evolution than previously believed. Systematic analyses indicate the order in which various members of nectin family seem to have evolved, with some nectin-like molecules appearing first, followed by the evolution of other members. Furthermore, we also found a few possible ancient homologues of nectins. While our study confirms the previous grouping of the nectin family into nectins and nectin-like molecules, it also shows poliovirus receptor (PVR/nectin-like-5) to possess characteristics that are intermediate between these two groups. Interestingly, except for PVR, the other nectins show surprising sequence conservations across species, suggesting evolutionary constraints due to critical roles played by these proteins.

A Possible Role of the Full-Length Nascent Protein in Post-Translational Ribosome Recycling

Each cycle of translation initiation in bacterial cell requires free 50S and 30S ribosomal subunits originating from the post-translational dissociation of 70S ribosome from the previous cycle. Literature shows stable dissociation of 70S from model post-termination complexes by the concerted action of Ribosome Recycling Factor (RRF) and Elongation Factor G (EF-G) that interact with the rRNA bridge B2a/B2b joining 50S to 30S. In such experimental models, the role of full-length nascent protein was never considered seriously. We observed relatively slow release of full-length nascent protein from 50Sof post translation ribosome, and in that process, its toe prints on the rRNA in vivo and in in vitro translation with E.coli S30 extract. We reported earlier that a number of chemically unfolded proteins like bovine carbonic anhydrase (BCA), lactate dehydrogenase (LDH), malate dehydrogenase (MDH), lysozyme, ovalbumin etc., when added to free 70Sin lieu of the full length nascent proteins, also interact with identical RNA regions of the 23S rRNA. Interestingly the rRNA nucleotides that slow down release of the C-terminus of full-length unfolded protein were found in close proximity to the B2a/B2b bridge. It indicated a potentially important chemical reaction conserved throughout the evolution. Here we set out to probe that conserved role of unfolded protein conformation in splitting the free or post-termination 70S. How both the RRF-EFG dependent and the plausible nascent protein–EFG dependent ribosome recycling pathways might be relevant in bacteria is discussed here.

Structural, mutational and biophysical studies reveal a canonical mode of molecular recognition between immune receptor TIGIT and nectin-2

In addition to antigen-specific stimulation of T cell receptor (TCR) by a peptide-MHC complex, the functional outcome of TCR engagement is regulated by antigen-independent costimulatory signals. Costimulatory signals are provided by an array of interactions involving activating and inhibitory receptors expressed on T cells and their cognate ligands on antigen presenting cells. T cell immunoglobulin and ITIM domain (TIGIT), a recently identified immune receptor expressed on T and NK cells, upon interaction with either of its two ligands, nectin-2 or poliovirus receptor (PVR), inhibits activation of T and NK cells. Here we report the crystal structure of the human TIGIT ectodomain, which exhibits the classic two-layer β-sandwich topology observed in other immunoglobulin super family (IgSF) members. Biophysical studies indicate that TIGIT is monomeric in solution but can form a dimer at high concentrations, consistent with the observation of a canonical immunoglobulin-like dimer interface in the crystalline state. Based on existing structural data, we present a model of the TIGIT:nectin-2 complex and utilized complementary biochemical studies to map the nectin-binding interface on TIGIT. Our data provide important structural and biochemical determinants responsible for the recognition of nectin-2 by TIGIT. Defining the TIGIT:nectin-2 binding interface provides the basis for rational manipulation of this molecular interaction for the development of immunotherapeutic reagents in autoimmunity and cancer.

Compensatory mechanisms allow undersized anchor-deficient class I MHC ligands to mediate pathogenic autoreactive T cell responses

Self-reactive T cells must escape thymic negative selection to mediate pathogenic autoimmunity. In the NOD mouse model of autoimmune diabetes, several β cell-cytotoxic CD8 T cell populations are known, with the most aggressive of these represented by AI4, a T cell clone with promiscuous Ag-recognition characteristics. We identified a long-elusive β cell-specific ligand for AI4 as an unusually short H-2D(b)-binding 7-mer peptide lacking a C-terminal anchor residue and derived from the insulin A chain (InsA14-20). Crystallography reveals that compensatory mechanisms permit peptides lacking a C-terminal anchor to bind sufficiently to the MHC to enable destructive T cell responses, yet allow cognate T cells to avoid negative selection. InsA14-20 shares two solvent-exposed residues with previously identified AI4 ligands, providing a structural explanation for AI4's promiscuity. Detection of AI4-like T cells, using mimotopes of InsA14-20 with improved H-2D(b)-binding characteristics, establishes the AI4-like T cell population as a consistent feature of the islet infiltrates of NOD mice. Our work establishes undersized peptides as previously unrecognized targets of autoreactive CD8 T cells and presents a strategy for their further exploration as Ags in autoimmune disease.

Scaling of near-wall flows in quasi-two-dimensional turbulent channels

The law of the wall and the log law rule the near-wall mean velocity profile of three-dimensional turbulent flows. These well-known laws, which are validated by legions of experiments and simulations, may be universal. Here, using a soap-film channel, we report the first experimental test of these laws in quasi-two-dimensional turbulent channel flows under two disparate turbulent spectra. We find that despite the differences with three-dimensional flows, the laws prevail, albeit with notable distinctions: the two parameters of the log law are markedly distinct from their three-dimensional counterpart; further, one parameter (the von Kármán constant) is independent of the spectrum whereas the other (the offset of the log law) depends on the spectrum. Our results suggest that the classical theory of scaling in wall-bounded turbulence is incomplete wherein a key missing element is the link with the turbulent spectrum.

Unusual antigen recognition provides clue to pathogenicity of diabetogenic CD8 T cell (APP2P.101)

The defined length restriction as well as preference for amino acids at particular positions for each MHC allele is imposed by the physical as well as chemical nature of the peptide binding groove of the MHC molecule. Accordingly, the preferred peptide for the mouse MHC class I allele H-2Db is a 9mer with anchor residues N at P5 and M/I or L at position 9. However, in this study, we found that AI4, one of the most pathogenic CD8 T cell clones that participates in type 1 diabetes pathogenesis, recognizes an unusual 7mer peptide from the β cell specific protein insulin (InsA14-20) in the context of H-2Db. Further investigation showed that a majority of NOD mice had islet infiltrating T cells that recognized InsA14-20 or mimotopes derived from it, making the AI4-like T cells a very prevalent population. Crystallographic analysis revealed that InsA14-20 shares two solvent-exposed residues with all previously identified AI4 ligands which could explain the promiscuous nature of the AI4 T cell receptor. In addition, accessory anchoring residues were observed to compensate for the lack of the C-terminal anchor residue. In sum, the study demonstrates that less than ideal peptide-MHC interaction can still trigger T cell reactivity and contribute to disease pathogenesis, aided further by lack of thymic negative selection due to weak binding affinity.

Biochemical and structural studies reveal a canonical mode of molecular recognition between TIGIT and nectin-2 (IRM10P.735)

Besides antigen-specific signal from the interaction between T-cell receptor and peptide-MHC complex expressed on antigen presenting cells (APCs), the process of optimal T-cell activation and differentiation requires antigen-independent costimulatory signals. Costimulatory signals are provided by interaction between a number of activating as well as inhibitory receptors expressed on T cells with specific ligands expressed on APCs. The balance between activating and inhibitory signals critically controls the mammalian immune responses. Therefore, understanding the mechanisms and designing corrective therapeutics involving T-cell costimulation are imperative in both infectious as well as autoimmune diseases. TIGIT (T cell immunoglobulin and ITIM domain), a recently identified immune receptor expressed on T and NK cells, upon interaction with either of its two ligands, nectin-2 or PVR, that are over-expressed on certain tumors, inhibits activation of T and NK cells. Several biophysical studies, including X-ray crystallography suggest that TIGIT may exist in its monomeric as well as dimeric forms. Based on the structural and biochemical studies, we mapped the nectin-binding interface on TIGIT. Interestingly, structure-guided mutations that disrupt the interaction between nectin-2 and TIGIT also limit the homodimerization of TIGIT in solution. Our data provide structural insights into how TIGIT recognizes a cell-adhesion molecule nectin-2 to execute immunoregulatory function.

The antiprion compound 6-aminophenanthridine inhibits the protein folding activity of the ribosome by direct competition

Domain V of the 23S/25S/28S rRNA of the large ribosomal subunit constitutes the active center for the protein folding activity of the ribosome (PFAR). Using in vitro transcribed domain V rRNAs from Escherichia coli and Saccharomyces cerevisiae as the folding modulators and human carbonic anhydrase as a model protein, we demonstrate that PFAR is conserved from prokaryotes to eukaryotes. It was shown previously that 6-aminophenanthridine (6AP), an antiprion compound, inhibits PFAR. Here, using UV cross-linking followed by primer extension, we show that the protein substrates and 6AP interact with a common set of nucleotides on domain V of 23S rRNA. Mutations at the interaction sites decreased PFAR and resulted in loss or change of the binding pattern for both the protein substrates and 6AP. Moreover, kinetic analysis of human carbonic anhydrase refolding showed that 6AP decreased the yield of the refolded protein but did not affect the rate of refolding. Thus, we conclude that 6AP competitively occludes the protein substrates from binding to rRNA and thereby inhibits PFAR. Finally, we propose a scheme clarifying the mechanism by which 6AP inhibits PFAR.

Structure of Nectin-2 reveals determinants of homophilic and heterophilic interactions that control cell-cell adhesion

Nectins are members of the Ig superfamily that mediate cell-cell adhesion through homophilic and heterophilic interactions. We have determined the crystal structure of the nectin-2 homodimer at 1.3 Å resolution. Structural analysis and complementary mutagenesis studies reveal the basis for recognition and selectivity among the nectin family members. Notably, the close proximity of charged residues at the dimer interface is a major determinant of the binding affinities associated with homophilic and heterophilic interactions within the nectin family. Our structural and biochemical data provide a mechanistic basis to explain stronger heterophilic versus weaker homophilic interactions among these family members and also offer insights into nectin-mediated transinteractions between engaging cells.

Identical RNA-protein interactions in vivo and in vitro and a scheme of folding the newly synthesized proteins by ribosomes

A distinct three-dimensional shape of rRNA inside the ribosome is required for the peptidyl transfer activity of its peptidyltransferase center (PTC). In contrast, even the in vitro transcribed PTC RNA interacts with unfolded protein(s) at about five sites to let them attain their native states. We found that the same set of conserved nucleotides in the PTC interact identically with nascent and chemically unfolded proteins in vivo and in vitro, respectively. The time course of this interaction, difficult to follow in vivo, was observed in vitro. It suggested nucleation of folding of cytosolic globular proteins vectorially from hydrophilic N to hydrophobic C termini, consistent with our discovery of a regular arrangement of cumulative hydrophobic indices of the peptide segments of cytosolic proteins from N to C termini. Based on this observation, we propose a model here for the nucleation of folding of the nascent protein chain by the PTC.

Structure of Nectin-2 reveals determinants of homophilic and heterophilic interactions that control cell-cell adhesion and immune regulation (176.10)

Nectin comprises a family of four immunoglobulin-like molecules. Homophilic and heterophilic interactions among nectins are implicated in cell-cell adhesion, while their interactions with members of other protein families have diverse biological functions like host-pathogen interaction and immune modulation. In particular, nectin-2, found to be up-regulated on cancer cells is capable of interacting with two receptors, CD226 and TIGIT, expressed on T and NK cells. These interactions lead to the delivery of two opposing signals to both T and NK cells. This situation is reminiscent of the well-studied pathways in T cells, in which the coinhibitory receptor CTLA-4 binds the same ligand (B7) as the coactivating receptor CD28. In order to define the molecular and structural determinants underlying the homophilic and heterophilic recognitions of nectin-2, we examined the biochemical, biophysical and structural properties of human nectin-2. The structure of nectin-2 at 1.3 Å resolution reveals that the architecture of the nectin-2 homophilic dimer resembles other members of the immunoglobulin superfamily and defines the details responsible for recognition and selectivity. Of particular note, the close proximity of charged residues at the interface is a major determinant of binding affinity. Using these biochemical and structural data, we also characterized the heterophilic binding of nectin-2 with TIGIT, which is implicated in T cell and NK cell-mediated immune modulation.

Involvement of mitochondrial ribosomal proteins in ribosomal RNA-mediated protein folding

The peptidyl transferase center of the domain V of large ribosomal RNA in the prokaryotic and eukaryotic cytosolic ribosomes acts as general protein folding modulator. We showed earlier that one part of the domain V (RNA1 containing the peptidyl transferase loop) binds unfolded protein and directs it to a folding competent state (FCS) that is released by the other part (RNA2) to attain the folded native state by itself. Here we show that the peptidyl transferase loop of the mitochondrial ribosome releases unfolded proteins in FCS extremely slowly despite its lack of the rRNA segment analogous to RNA2. The release of FCS can be hastened by the equivalent activity of RNA2 or the large subunit proteins of the mitochondrial ribosome. The RNA2 or large subunit proteins probably introduce some allosteric change in the peptidyl transferase loop to enable it to release proteins in FCS.

Structural and functional characterization of a single-chain peptide-MHC molecule that modulates both naive and activated CD8+ T cells

Peptide-MHC (pMHC) multimers, in addition to being tools for tracking and quantifying antigen-specific T cells, can mediate downstream signaling after T-cell receptor engagement. In the absence of costimulation, this can lead to anergy or apoptosis of cognate T cells, a property that could be exploited in the setting of autoimmune disease. Most studies with class I pMHC multimers used noncovalently linked peptides, which can allow unwanted CD8(+) T-cell activation as a result of peptide transfer to cellular MHC molecules. To circumvent this problem, and given the role of self-reactive CD8(+) T cells in the development of type 1 diabetes, we designed a single-chain pMHC complex (scK(d).IGRP) by using the class I MHC molecule H-2K(d) and a covalently linked peptide derived from islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP(206-214)), a well established autoantigen in NOD mice. X-ray diffraction studies revealed that the peptide is presented in the groove of the MHC molecule in canonical fashion, and it was also demonstrated that scK(d).IGRP tetramers bound specifically to cognate CD8(+) T cells. Tetramer binding induced death of naive T cells and in vitro- and in vivo-differentiated cytotoxic T lymphocytes, and tetramer-treated cytotoxic T lymphocytes showed a diminished IFN-γ response to antigen stimulation. Tetramer accessibility to disease-relevant T cells in vivo was also demonstrated. Our study suggests the potential of single-chain pMHC tetramers as possible therapeutic agents in autoimmune disease. Their ability to affect the fate of naive and activated CD8(+) T cells makes them a potential intervention strategy in early and late stages of disease.

Renal amyloidosis secondary to childhood tuberculosis: a report of two cases

Childhood renal amyloidosis is a rare entity and is mostly secondary in nature. We describe two cases of renal amyloidosis in association with childhood tuberculosis. The first case was a 10-year-old girl who presented with abdominal tuberculosis and nephrotic syndrome, while the second case was a 5-year-old boy who presented with disseminated tuberculosis and nephrotic syndrome. They were found to have amyloidosis on renal biopsy. The former was treated with anti-tubercular drugs, while the latter required anti-tubercular drugs and steroids. Both the cases showed clinical improvement with remission of nephrotic syndrome. Successful treatment of tuberculosis can result in remission of nephrotic syndrome due to secondary renal amyloidosis. It is important, especially in developing countries, to be aware that tuberculosis continues to be part of the differential diagnosis of amyloidosis in children.

Mechanism of ribosome assisted protein folding: a new insight into rRNA functions

The peptidyl transferase center (PTC), present in the domain V of 23S rRNA of bacteria can act as a general protein folding modulator. Any general function of a nucleic acid polymer (DNA or RNA) is always related to specific sequence/sequences. The ribosome mediated protein folding also involves a specific interaction between the nucleotides of peptidyl transferase center and the amino acids of an unfolded protein. In this article the mechanism of rRNA assisted protein folding and its significance in the light of high resolution crystal structure of ribosome are discussed.

Role of the ribosome in protein folding

In all organisms, the ribosome synthesizes and folds full length polypeptide chains into active three-dimensional conformations. The nascent protein goes through two major interactions, first with the ribosome which synthesizes the polypeptide chain and holds it for a considerable length of time, and then with the chaperones. Some of the chaperones are found in solution as well as associated to the ribosome. A number of in vitro and in vivo experiments revealed that the nascent protein folds through specific interactions of some amino acids with the nucleotides in the peptidyl transferase center (PTC) in the large ribosomal subunit. The mechanism of this folding differs from self-folding. In this article, we highlight the folding of nascent proteins on the ribosome and the influence of chaperones etc. on protein folding.