Structural insight into protein–protein interactions between intestinal microbiome and host

Protein–protein interactions between the microbiome and host organism play an important role in shaping host health. These host-modulating proteins have therapeutic potential in treating microbiome-linked disorders such as inflammatory bowel disease and obesity. Structural analysis of interacting proteins provides highly mechanistic insight into the domains driving these interactions and the resulting influence on host cell processes. Here, we briefly review recent publication of microbiome protein structures involved in host binding interactions, the effects of these interactions on host physiology, and the need for further study to increase the ability to detect proteins with therapeutic potential.     

Structural insights into E2–E3 interaction for LC3 lipidation

The members of the LC3/Atg8 family of proteins are covalently attached to phagophore and autophagosomal membranes. At the last step of the LC3 lipidation cascade, LC3 is transferred from the E2 enzyme ATG3 to phosphatidylethanolamine (PE). This transfer is stimulated by the ATG12–ATG5-ATG16L1 E3 complex, but the mechanism is not fully understood. We recently found that ATG12 of the E3 binds to a short sequence in the flexible region (FR) of ATG3 with high affinity, and that this interaction is critical for E2–E3 complex formation. These findings, together with detailed structural analyses of this interaction, define the properties of ATG12 and provide new insights of how LC3 transfer begins with ATG3 recruitment by ATG12.     

Structural insights into E2–E3 interaction for LC3 lipidation

The members of the LC3/Atg8 family of proteins are covalently attached to phagophore and autophagosomal membranes. At the last step of the LC3 lipidation cascade, LC3 is transferred from the E2 enzyme ATG3 to phosphatidylethanolamine (PE). This transfer is stimulated by the ATG12–ATG5-ATG16L1 E3 complex, but the mechanism is not fully understood. We recently found that ATG12 of the E3 binds to a short sequence in the flexible region (FR) of ATG3 with high affinity, and that this interaction is critical for E2–E3 complex formation. These findings, together with detailed structural analyses of this interaction, define the properties of ATG12 and provide new insights of how LC3 transfer begins with ATG3 recruitment by ATG12.     

A new structural insight into XPA–DNA interactions

XPA (xeroderma pigmentosum group A) protein is an essential factor for NER (nucleotide excision repair) which is believed to be involved in DNA damage recognition/verification, NER factor recruiting and stabilization of repair intermediates. Past studies on the structure of XPA have focused primarily on XPA interaction with damaged DNA. However, how XPA interacts with other DNA structures remains unknown though recent evidence suggest that these structures could be important for its roles in both NER and non-NER activities. Previously, we reported that XPA recognizes undamaged DNA ds/ssDNA (double-strand/single-strandDNA) junctions with a binding affinity much higher than its ability to bind bulky DNA damage. To understand how this interaction occurs biochemically we implemented a structural determination of the interaction using a MS-based protein footprinting method and limited proteolysis. By monitoring surface accessibility of XPA lysines to NHS-biotin modification in the free protein and the DNA junction-bound complex we show that XPA physically interacts with the DNA junctions via two lysines, K168 and K179, located in the previously known XPA(98–219) DBD (DNA-binding domain). Importantly, we also uncovered new lysine residues, outside of the known DBD, involved in the binding. We found that residues K221, K222, K224 and K236 in the C-terminal domain are involved in DNA binding. Limited proteolysis analysis of XPA–DNA interactions further confirmed this observation. Structural modelling with these data suggests a clamp-like DBD for the XPA binding to ds/ssDNA junctions. Our results provide a novel structure-function view of XPA–DNA junction interactions.     

Structural features of the tmRNA–ribosome interaction

Trans-translation is a process which switches the synthesis of a polypeptide chain encoded by a nonstop messenger RNA to the mRNA-like domain of a transfer-messenger RNA (tmRNA). It is used in bacterial cells for rescuing the ribosomes arrested during translation of damaged mRNA and directing this mRNA and the product polypeptide for degradation. The molecular basis of this process is not well understood. Earlier, we developed an approach that allowed isolation of tmRNA–ribosomal complexes arrested at a desired step of tmRNA passage through the ribosome. We have here exploited it to examine the tmRNA structure using chemical probing and cryo-electron microscopy tomography. Computer modeling has been used to develop a model for spatial organization of the tmRNA inside the ribosome at different stages of trans-translation.     

Structural insight into the binding complex: β-arrestin/CCR5 complex

The chemokine receptor 5 (CCR5) belongs to the superfamily of serpentine G protein-coupled receptors (GPCRs). The DRY motif (Asp, Arg, Tyr) of the intracellular loop 2 (ICL2), which is highly conserved in the GPCRs has been shown to be essential for the stability of folding of CCR5 and the interaction with β-arrestin. But the molecular mechanism by which it recognizes and interacts with β-arrestin has not been elucidated. In the present study, we described the active state of the β-arrestin structure using normal mode analysis and characterized the binding cleft of CCR5-ICL2 with β-arrestin using SABRE© docking tool and molecular dynamics simulation. Based on our computational results, we proposed a mode of binding between the ICL2 loop of CCR5 and β-arrestin structure, and modeled the energetically stable β-arrestin/CCR5 complex. In view of CCR5’s importance as a therapeutic target for the treatment of HIV, this observation provides novel insight into the β-arrestin/CCR5 pathway. As a result, the current computational study of the detailed β-arrestin/CCR5 binding complex could provide the rationale for the development of next generation of HIV peptide inhibitors as therapeutic agents.     

Isotopic insight into host–endosymbiont relationships in Liolaemid lizards

Nitrogen isotopes have been widely used to investigate trophic levels in ecological systems. Isotopic enrichment of 2–5‰ occurs with trophic level increases in food webs. Host–parasite relationships deviate from traditional food webs in that parasites are minimally enriched relative to their hosts. Although this host–parasite enrichment pattern has been shown in multiple systems, few studies have used isotopic relationships to examine other potential symbioses. We examined the relationship between two gut-nematodes and their lizard hosts. One species, Physaloptera retusa, is a documented parasite in the stomach, whereas the relationship of the other species, Parapharyngodon riojensis (pinworms), to the host is putatively commensalistic or mutualistic. Based on the established trophic enrichments, we predicted that, relative to host tissue, parasitic nematodes would be minimally enriched (0–1‰), whereas pinworms, either as commensals or mutualists, would be significantly enriched by 2–5‰. We measured the ¹⁵N values of food, digesta, gut tissue, and nematodes of eight lizard species in the family Liolaemidae. Parasitic worms were enriched 1±0.2‰ relative to host tissue, while the average enrichment value for pinworms relative to gut tissue was 6.7±0.2‰. The results support previous findings that isotopic fractionation in a host–parasite system is lower than traditional food webs. Additionally, the larger enrichment of pinworms relative to known parasites suggests that they are not parasitic and may be several trophic levels beyond the host.     

Putting the insect into the birch–insect interaction

Leaf maturation in mountain birch (Betula pubescens ssp. czerepanovii) is characterized by rapid shifts in the types of dominant phenolics: from carbon-economic flavonoids aglycons in flushing leaves, via hydrolysable tannins and flavonoid glycosides, to carbon-rich proanthocyanidins (condensed tannins) in mature foliage. This shift accords with the suggested trade-offs between carbon allocation to plant defense and growth, but may also relate to the simultaneous decline in nutritive leaf traits, such as water, proteins and sugars, which potentially limit insect growth. To elucidate how birch leaf quality translates into insect growth, I introduce a simple model that takes into account defensive compounds but also acknowledges insect demand for nutritive compounds. The effects of defensive compounds on insect growth depend strongly on background variation in nutritive leaf traits: compensatory feeding on low nutritive diets increases the intake of defensive compounds, and the availability of growth-limiting nutritive compounds may modify the effects of defenses. The ratio of consumption to larval growth (both in dry mass) increases very rapidly with leaf maturation: from 2.9 to 9.8 over 2 weeks in June-July, and to 15 by August. High concentrations in mature birch leaves of "quantitative" defenses, such as proanthocyanidins (15-20% of dry mass), presumably prevent further consumption. If the same compounds had also protected half-grown leaves (which supported the same larval growth with only one third of the dry matter consumption of older leaves), the same intake of proanthocyanidins would have demanded improbably high concentrations (close to 50%) in young leaves. The model thus suggests an adaptive explanation for the high levels of "quantitative" defenses, such as proanthocyanidins, in low-nutritive but not in high-nutritive leaves because of the behavioral responses of insect feeding to leaf nutritive levels.     

Structural insight into human CK2α in complex with the potent inhibitor ellagic acid

We determined the 2.35-Å crystal structure of a human CK2 catalytic subunit (referred to as CK2α complexed with the ATP-competitive, potent CK2 inhibitor ellagic acid. The inhibitor binds to CK2α with a novel binding mode, including water-mediated hydrogen bonds. This structural information may support discovery of potent CK2 inhibitors.     

An insight into major signaling pathways and protein–protein interaction networks involved in the pathogenesis of gestational diabetes mellitus

Gestational diabetes mellitus (GDM) is associated with the increase of glucose in the blood rather than being absorbed by the cells. A better understanding of the signaling pathways is necessary to understand the pathophysiology of GDM. This study provides details about a series of signaling pathways and protein–protein interactions involved in the pathogenesis of GDM and their evaluations in GDM development. Protein–protein interactions were found between proteins of several signaling pathways that suggest interlink between these signaling pathways. Protein–protein interactions were generated with high confidence interaction scores based on textmining, cooccurrence, coexpression, neighborhood, gene fusion, experiments, and databases. The dysregulation of signaling pathways may also contribute to the increased risk of complications associated with GDM in the mother and child. Further, studies on signaling pathways involved in the pathogenesis of GDM would help in the development of an effective intervention to prevent GDM along with the identification of key targets for effective therapies in the future.     

Structural basis of protein–protein interaction studied by NMR

This paper describes efforts of the structural genomics project in the nuclear magnetic resonance (NMR) laboratory at the University of Science and Technology of China. This structural genomics project is biological-functional driven. Targets are mainly selected from two systems: proteins related with regulation of gene expression in humans and other eukaryotes, and proteins existing in the cell junction in humans. The majority of proteins selected from these two systems are related with human health and diseases, and some are potential drug targets. Twenty-five protein structures from Homo sapiens and other eukaryotes have been determined during last 5 years in this laboratory. Nuclear magnetic resonance (NMR) spectroscopy is highly suited to investigate molecular interactions at a close physiological condition and is particularly suited for the study of low-affinity, transient complexes. It can provide information on protein surface interaction, their complex structure, and their dynamic properties during protein recognition. Several examples are given in this paper.     

Molecular insight into activated sludge producing polyhydroxyalkanoates under aerobic–anaerobic conditions

One of the options enabling more economic production of polyhydroxyalkanoates compared to pure cultures is the application of mixed cultures. The use of a microbial community in a sequencing batch reactor has a few advantages: a simple process control, no necessity for sterile processing, and possibilities of using cheap substrates as a source of carbon. Nevertheless, while cultivation methods to achieve high PHAs biomass concentration and high productivity in wild and recombinant strains are defined, knowledge about the cultivation strategy for PHAs production by mixed culture and species composition of bacterial communities is still very limited. The main object of this study was to characterize on the molecular level the composition and activity of PHAs producing microorganism in activated sludge cultivated under oxygen limitation conditions. PHAs producers were detected using a PCR technique and the created PHA synthase gene library was analyzed by DNA sequencing. The obtained results indicate that PHAs-producers belonged to Pseudomonas sp., and possessed genes coding for mcl-PHA synthase. The kinetics of mcl-PHA synthase expression was relatively estimated using real-time PCR technology at several timepoints. Performed quantitative and qualitative analysis of total bacterial activity showed that there were differences in total activity during the process but differential expression of various groups of microorganisms examined by using DGGE was not observed.     

Insight into the HIV-1 Vif SOCS-box–ElonginBC interaction

The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif''s proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.     

Structural and functional insights into IκB-α/HIV-1 Tat interaction

Protein-protein interactions play fundamental roles in physiological and pathological biological processes. The characterization of the structural determinants of protein-protein recognition represents an important step for the development of molecular entities able to modulate these interactions. We have recently found that IκB-α (nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha) blocks the HIV-1 expression and replication in a NF-κB-independent manner by directly binding to the virus-encoded Tat transactivator. Here, we report the evaluation of the entity of binding of IκB-α to Tat through in vitro Surface Plasmon Resonance assay. Moreover, by designing and characterizing a set of peptides of the C-terminus region of IκB-α, we show that the peptide corresponding to the IκB-α sequence 262-287 was able to bind to Tat with high affinity (300 nM). The characterization of a number of IκB-α-based peptides also provided insights into their intrinsic folding properties. These findings have been corroborated by mutagenesis studies on the full-length IκB-α, which unveil that different IκB-α residues are involved in NF-κB or Tat recognition.     

Conformational insight into multi-protein signaling assemblies by hydrogen–deuterium exchange mass spectrometry

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Structural insights into the extra cellular segment of integrinβ5 and molecular interaction studies

Abstract

Primary tumor cells often spread to other organs by metastasis. Despite of it, primary tumor cells break their surrounding extra cellular matrix (ECM) proteins and reach the destination organ by the process of intravasation and extravasation. Metastasized tumor cells induce the process of angiogenesis, this highly regulated process involves several ECM proteins. However, integrins are primarily involved in the blood vessel growth and repair. Therefore, integrins are promising angiogenesis targets. Integrins are receptors on cell surface, involved in signal transduction and attachments in extra cellular matrix (ECM). IntegrinαVβ3 and αVβ5 are implicated in tumor angiogenesis, metastasis, inflammation and bone resorption. The crystal structure of integrinαvβ5 is not available in protein structural databases, therefore; molecular model of integrinβ5 structure was prepared and stereo chemical model quality was checked. Integrin β5 active sites were identified based on insilico analysis tools. Further, molecular level interactions between integrinβ5 and ECM proteins were predicted. In the present study ECM proteins such as focal adhesion kinase 1 (FAK1), annexin A5 and P21 activated kinase 4 (PAK4) were considered for protein-protein docking, to understand inter molecular interactions. The predicted model is conceived to be stereo chemically good and can be used for molecular interaction studies of angiogenic inhibitors.     

Atomistic insight into micro-phase separation and gas diffusion in PEO–PBT multiblock copolymers

Atomistic simulation is reported for micro-phase separation and H₂ diffusion in poly(ethylene oxide) (PEO)–poly(butylene terephthalate) (PBT) multiblock copolymers with varying PEO segment length. The simulated densities of copolymers agree well with available experimental data with only 1–2% deviations. A strong interaction exists between PEO segments as evidenced by the sharp peaks in radial distribution functions. With increasing PEO segment length, the fractional free volume marginally increases, PEO and PBT segments tend to be more immiscible and segregated domain size increases. This is consistent with experimental and theoretical studies in the literature. The mobility of PBT segments is almost one order of magnitude smaller than that of PEO segments. With increasing PEO segment length, the mobility of PEO–PBT copolymers is enhanced. For H₂ diffusion in PEO–PBT copolymers, the diffusivity increases with increasing PEO segment length, as experimentally observed. This simulation study provides atomistic insight into the micro-structure and gas transport properties in PEO–PBT copolymers.     

Structural insight into the mechanism of activation of the Toll receptor by the dimeric ligand Spätzle

The Drosophila Toll receptor, which functions in both embryonic patterning and innate immunity to fungi and Gram-positive bacteria, is activated by a dimeric cytokine ligand, Sp?tzle (Spz). Previous studies have suggested that one Spz cross-links two Toll receptor molecules to form an activated complex. Here we report electron microscopy structures of the Toll ectodomain in the absence and presence of Spz. Contrary to expectations, Spz does not directly cross-link two Toll ectodomains. Instead, Spz binding at the N-terminal end of Toll predominantly induces the formation of a 2:2 complex, with two sites of interaction between the ectodomain chains, one located near to the N terminus of the solenoid and the other between the C-terminal juxtamembrane sequences. Moreover, Toll undergoes a ligand-induced conformational change, becoming more tightly curved than in the apo form. The unexpected 2:2 complex was confirmed by mass spectrometry under native conditions. These results suggest that activation of Toll is an allosteric mechanism induced by an end-on binding mode of its ligand Spz.