Protein Binding Regions Research Articles

In Vitro Maturation of a Humanized Shark VNAR Domain to Improve Its Biophysical Properties.

VNAR domains are the binding regions of new antigen receptor proteins (IgNAR) which are unique to sharks, skates, and rays (Elasmobranchii). Individual VNAR domains can bind antigens independently and are the smallest reported adaptive immune recognition entities in the vertebrate kingdom. Sharing limited sequence homology with human immunoglobulin domains, their development and use as biotherapeutic agents require that they be humanized to minimize their potential immunogenicity. Efforts to humanize a human serum albumin (HSA)-specific VNAR, E06, resulted in protein molecules that initially had undesirable biophysical properties or reduced affinity for cognate antigen. Two lead humanized anti-HSA clones, v1.10 and v2.4, were subjected to a process of random mutagenesis using error-prone PCR. The mutated sequences for each humanized VNAR variant were screened for improvements in affinity for HSA and biophysical properties, achieved without a predicted increase in overall immunogenicity.

Continuous Developmental and Early Life Trichloroethylene Exposure Promoted DNA Methylation Alterations in Polycomb Protein Binding Sites in Effector/Memory CD4+ T Cells.

Trichloroethylene (TCE) is an industrial solvent and drinking water pollutant associated with CD4+ T cell-mediated autoimmunity. In our mouse model, discontinuation of TCE exposure during adulthood after developmental exposure did not prevent immunotoxicity. To determine whether persistent effects were linked to epigenetic changes we conducted whole genome reduced representation bisulfite sequencing (RRBS) to evaluate methylation of CpG sites in autosomal chromosomes in activated effector/memory CD4+ T cells. Female MRL+/+ mice were exposed to vehicle control or TCE in the drinking water from gestation until ~37 weeks of age [postnatal day (PND) 259]. In a subset of mice, TCE exposure was discontinued at ~22 weeks of age (PND 154). At PND 259, RRBS assessment revealed more global methylation changes in the continuous exposure group vs. the discontinuous exposure group. A majority of the differentially methylated CpG regions (DMRs) across promoters, islands, and regulatory elements were hypermethylated (~90%). However, continuous developmental TCE exposure altered the methylation of 274 CpG sites in promoters and CpG islands. In contrast, only 4 CpG island regions were differentially methylated (hypermethylated) in the discontinuous group. Interestingly, 2 of these 4 sites were also hypermethylated in the continuous exposure group, and both of these island regions are associated with lysine 27 on histone H3 (H3K27) involved in polycomb complex-dependent transcriptional repression via H3K27 tri-methylation. CpG sites were overlapped with the Open Regulatory Annotation database. Unlike the discontinuous group, continuous TCE treatment resulted in 129 DMRs including 12 unique transcription factors and regulatory elements; 80% of which were enriched for one or more polycomb group (PcG) protein binding regions (i.e., SUZ12, EZH2, JARID2, and MTF2). Pathway analysis of the DMRs indicated that TCE primarily altered the methylation of genes associated with regulation of cellular metabolism and cell signaling. The results demonstrated that continuous developmental exposure to TCE differentially methylated binding sites of PcG proteins in effector/memory CD4+ cells. There were minimal yet potentially biologically significant effects that occurred when exposure was discontinued. These results point toward a novel mechanism by which chronic developmental TCE exposure may alter terminally differentiated CD4+ T cell function in adulthood.

Rare De Novo Missense Variants in RNA Helicase DDX6 Cause Intellectual Disability and Dysmorphic Features and Lead to P-Body Defects and RNA Dysregulation

The human RNA helicase DDX6 is an essential component of membrane-less organelles called processing bodies (PBs). PBs are involved in mRNA metabolic processes including translational repression via coordinated storage of mRNAs. Previous studies in human cell lines have implicated altered DDX6 in molecular and cellular dysfunction, but clinical consequences and pathogenesis in humans have yet to be described. Here, we report the identification of five rare de novo missense variants in DDX6 in probands presenting with intellectual disability, developmental delay, and similar dysmorphic features including telecanthus, epicanthus, arched eyebrows, and low-set ears. All five missense variants (p.His372Arg, p.Arg373Gln, p.Cys390Arg, p.Thr391Ile, and p.Thr391Pro) are located in two conserved motifs of the RecA-2 domain of DDX6 involved in RNA binding, helicase activity, and protein-partner binding. We use functional studies to demonstrate that the first variants identified (p.Arg373Gln and p.Cys390Arg) cause significant defects in PB assembly in primary fibroblast and model human cell lines. These variants' interactions with several protein partners were also disrupted in immunoprecipitation assays. Further investigation via complementation assays included the additional variants p.Thr391Ile and p.Thr391Pro, both of which, similarly to p.Arg373Gln and p.Cys390Arg, demonstrated significant defects in P-body assembly. Complementing these molecular findings, modeling of the variants on solved protein structures showed distinct spatial clustering near known protein binding regions. Collectively, our clinical and molecular data describe a neurodevelopmental syndrome associated with pathogenic missense variants in DDX6. Additionally, we suggest DDX6 join the DExD/H-box genes DDX3X and DHX30 in an emerging class of neurodevelopmental disorders involving RNA helicases.

S-Layer Protein Coated Carbon Nanotubes

Carbon nanotubes (CNTs) have already been considered for medical applications due to their small diameter and ability to penetrate cells and tissues. However, since CNTs are chemically inert and non-dispersible in water, they have to be chemically functionalized or coated with biomolecules to carry payloads or interact with the environment. Proteins, although often only randomly bound to the CNT surface, are preferred because they provide a better biocompatibility and present functional groups for binding additional molecules. A new approach to functionalize CNTs with a closed and precisely ordered protein layer is offered by bacterial surface layer (S-layer) proteins, which have already attracted much attention in the functionalization of surfaces. We could demonstrate that bacterial S-layer proteins (SbpA of Lysinibacillus sphaericus CCM 2177 and the recombinant fusion protein rSbpA31-1068GG comprising the S-layer protein and two copies of the IgG binding region of Protein G) can be used to disperse and functionalize oxidized multi walled CNTs. Following a simple protocol, a complete surface coverage with a long-range crystalline S-layer lattice can be obtained. When rSbpA31-1068GG was used for coating, the introduced functionality could be confirmed by binding gold labeled antibodies via the IgG binding domain of the fusion protein. Since a great variety of functional S-layer fusion proteins has already been described, our new technology has the potential for a broad spectrum of functionalized CNTs.

Structural Basis for Allosteric Ligand Recognition in the Human CC Chemokine Receptor 7.

SummaryThe CC chemokine receptor 7 (CCR7) balances immunity and tolerance by homeostatic trafficking of immune cells. In cancer, CCR7-mediated trafficking leads to lymph node metastasis, suggesting the receptor as a promising therapeutic target. Here, we present the crystal structure of human CCR7 fused to the protein Sialidase NanA by using data up to 2.1 Å resolution. The structure shows the ligand Cmp2105 bound to an intracellular allosteric binding pocket. A sulfonamide group, characteristic for various chemokine receptor ligands, binds to a patch of conserved residues in the Gi protein binding region between transmembrane helix 7 and helix 8. We demonstrate how structural data can be used in combination with a compound repository and automated thermal stability screening to identify and modulate allosteric chemokine receptor antagonists. We detect both novel (CS-1 and CS-2) and clinically relevant (CXCR1-CXCR2 phase-II antagonist Navarixin) CCR7 modulators with implications for multi-target strategies against cancer.

Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain

MeCP2 is an abundant protein, involved in transcriptional repression by binding to CG and non-CG methylated DNA. However, MeCP2 might also function as a transcription activator as MeCP2 is found bound to sparsely methylated promoters of actively expressed genes. Furthermore, Attachment Region Binding Protein (ARBP), the chicken ortholog of MeCP2, has been reported to bind to Matrix/scaffold attachment regions (MARs/SARs) DNA with an unmethylated 5′-CAC/GTG-3′ consensus sequence. In our previous study, although we have systemically measured the binding abilities of MBDs to unmethylated CAC/GTG DNA and the complex structures reveal that the MBD2-MBD (MBD of MBD2) binds to the unmethylated CAC/GTG DNA by recognizing the complementary GTG trinucleotide, how the MeCP2-MBD (MBD of MeCP2) recognizes the unmethylated CAC/GTG DNA, especially the MARs DNA, is still unclear. In this study, we investigated the binding characteristics of MeCP2 in recognizing unmethylated 5′-CAC/GTG-3′ motif containing DNA by binding and structural studies. We found that MeCP2-MBD binds to MARs DNA with a comparable binding affinity to mCG DNA, and the MeCP2-CAC/GTG complex structure revealed that MeCP2 residues R111 and R133 form base-specific interactions with the GTG motif. For comparison, we also determined crystal structures of the MeCP2-MBD bound to mCG and mCAC/GTG DNA, respectively. Together, these crystal structures illustrate the adaptability of the MeCP2-MBD toward the GTG motif as well as the mCG DNA, and also provide structural basis of a biological role of MeCP2 as a transcription activator and its disease implications in Rett syndrome.

Satb2 regulates proliferation and nuclear integrity of pre-osteoblasts.

Special AT-rich sequence binding protein 2 (Satb2) is a matrix attachment region (MAR) binding protein. Satb2 impacts skeletal development by regulating gene transcription required for osteogenic differentiation. Although its role as a high-order transcription factor is well supported, other roles for Satb2 in skeletal development remain unclear. In particular, the impact of dosage sensitivity (heterozygous mutations) and variance on phenotypic severity is still not well understood. To further investigate molecular and cellular mechanisms of Satb2-mediated skeletal defects, we used the CRISPR/Cas9 system to generate Satb2 mutations in MC3T3-E1 cells. Our data suggest that, in addition to its role in differentiation, Satb2 regulates progenitor proliferation. We also find that mutations in Satb2 cause chromatin defects including nuclear blebbing and donut-shaped nuclei. These defects may contribute to a slight increase in apoptosis in mutant cells, but apoptosis is insufficient to explain the proliferation defects. Satb2 expression exhibits population-level variation and is most highly expressed from late G1 to late G2. Based on these data, we hypothesize that Satb2 may regulate proliferation through two separate mechanisms. First, Satb2 may regulate the expression of genes necessary for cell cycle progression in pre-osteoblasts. Second, similar to other MAR-binding proteins, Satb2 may participate in DNA replication. We also hypothesize that variation in the severity or penetrance of Satb2-mediated proliferation defects is due to stochastic variation in Satb2 binding to DNA, which may be buffered in some genetic backgrounds. Further elucidation of the role of Satb2 in proliferation has potential impacts on our understanding of both skeletal defects and cancer.

Developmental exposure to environmental toxicant trichloroethylene alters DNA methylation in polycomb protein binding regions in effector/memory CD4 + T cells from autoimmune-prone mice

Abstract Trichloroethylene (TCE) is an industrial solvent and drinking water pollutant associated with autoimmunity in human populations. Previous studies in autoimmune-prone MRL+/+ mice revealed autoimmune pathology and CD4 + T cell autoreactivity were more robust when exposure occurred during development rather than adulthood. To determine whether these effects were linked to epigenetic changes, mice were exposed to vehicle control or TCE in the drinking water beginning at gestation until 37 weeks of age. In some mice, TCE was removed from drinking water at 22 weeks of age. Whole genome reduced representation bisulfite sequencing (RRBS) was used to compare methylation of CpG sites in autosomal chromosomes in effector/memory CD4+ T cells. Few significant changes occurred in mice when TCE was removed from drinking water. In contrast, continuous developmental TCE exposure revealed differential methylation of 252 CpG sites relative to controls. When CpG sites were overlapped with the Open Regulatory Annotation database (ORegAnno), continuous TCE treatment resulted in 130 differentially methylated regions (DMRs) that included 12 unique transcription factors. Interestingly, 80% of DMRs occurred in areas known to bind Polycomb group (PcG) proteins that form the polycomb-repressive complex 2 (PRC2) in mammalian cells, namely, SUZ12, EZH2, JARID2, and MTF2. Pathway analysis of the DMRs indicated that TCE primarily altered the methylation of genes asociated with regulation of cellular metabolism and cell signaling pathways. In summary, TCE differentially methylated binding sites of PcG proteins in effector/memory CD4+ cells, and point toward a novel mechanism by which TCE could modulate CD4 + T cell function and promote autoimmunity.

Escherichia coli CrfC Protein, a Nucleoid Partition Factor, Localizes to Nucleoid Poles via the Activities of Specific Nucleoid-Associated Proteins.

The Escherichia coli CrfC protein is an important regulator of nucleoid positioning and equipartition. Previously we revealed that CrfC homo-oligomers bind the clamp, a DNA-binding subunit of the DNA polymerase III holoenzyme, promoting colocalization of the sister replication forks, which ensures the nucleoid equipartition. In addition, CrfC localizes at the cell pole-proximal loci via an unknown mechanism. Here, we demonstrate that CrfC localizes to the distinct subnucleoid structures termed nucleoid poles (the cell pole-proximal nucleoid-edges) even in elongated cells as well as in wild-type cells. Systematic analysis of the nucleoid-associated proteins (NAPs) and related proteins revealed that HU, the most abundant NAP, and SlmA, the nucleoid occlusion factor regulating the localization of cell division apparatus, promote the specific localization of CrfC foci. When the replication initiator DnaA was inactivated, SlmA and HU were required for formation of CrfC foci. In contrast, when the replication initiation was inhibited with a specific mutant of the helicase-loader DnaC, CrfC foci were sustained independently of SlmA and HU. H-NS, which forms clusters on AT-rich DNA regions, promotes formation of CrfC foci as well as transcriptional regulation of crfC. In addition, MukB, the chromosomal structure mainetanice protein, and SeqA, a hemimethylated nascent DNA region-binding protein, moderately stimulated formation of CrfC foci. However, IHF, a structural homolog of HU, MatP, the replication terminus-binding protein, Dps, a stress-response factor, and FtsZ, an SlmA-interacting factor in cell division apparatus, little or only slightly affected CrfC foci formation and localization. Taken together, these findings suggest a novel and unique mechanism that CrfC localizes to the nucleoid poles in two steps, assembly and recruitment, dependent upon HU, MukB, SeqA, and SlmA, which is stimulated directly or indirectly by H-NS and DnaA. These factors might concordantly affect specific nucleoid substructures. Also, these nucleoid dynamics might be significant in the role for CrfC in chromosome partition.

Dissection of the regulatory role for the N-terminal domain in Candida albicans protein phosphatase Z1.

The novel type, fungus specific protein phosphatase Z1 of the opportunistic pathogen, Candida albicans (CaPpz1) has several important physiological roles. It consists of a conserved C-terminal catalytic domain and a variable, intrinsically disordered, N-terminal regulatory domain. To test the function of these domains we modified the structure of CaPpz1 by in vitro mutagenesis. The two main domains were separated, four potential protein binding regions were deleted, and the myristoylation site as well as the active site of the enzyme was crippled by point mutations G2A and R262L, respectively. The in vitro phosphatase activity assay of the bacterially expressed recombinant proteins indicated that the N-terminal domain was inactive, while the C-terminal domain became highly active against myosin light chain substrate. The deletion of the N-terminal 1–16 amino acids and the G2A mutation significantly decreased the specific activity of the enzyme. Complementation of the ppz1 Saccharomyces cerevisiae deletion mutant strain with the different CaPpz1 forms demonstrated that the scission of the main domains, the two point mutations and the N-terminal 1–16 deletion rendered the phosphatase incompetent in the in vivo assays of LiCl tolerance and caffeine sensitivity. Thus our results confirmed the functional role of the N-terminal domain and highlighted the significance of the very N-terminal part of the protein in the regulation of CaPpz1.

DNA Cracks at the Region of Protein Binding Under the Action of Stretch

The binding of DNA to protein in the cellular nucleus is a common phenomenon. DNA molecules will soften at the binding region when they adhere to proteins. Softening will affect the mechanical properties significantly. Howeve... | Find, read and cite all the research you need on Tech Science Press

Characterization and Genomic Analysis of SFPH2, a Novel T7virus Infecting Shigella.

Shigellosis, caused by Shigella, is a major global health concern, with nearly 164.7 million cases and over a million deaths occurring annually worldwide. Shigella flexneri is one of the most common subgroups of Shigella with a high incidence of multidrug-resistance. The phage therapy approach is an effective method for controlling multidrug-resistant bacteria. However, only a few Shigella phages have been described to date. In this study, a novel lytic bacteriophage SFPH2 was isolated from a sewage sample obtained from a hospital in Beijing, China, using a multidrug-resistant S. flexneri 2a strain (SF2) isolated from the fecal sample of a dysentery patient. SFPH2 is a member of the Podoviridae virus family with an icosahedral capsid and a short, non-contractile tail. It was found to be stable over a wide range of temperatures (4–50°C) and pH values (pH 3–11). Moreover, SFPH2 could infect two other S. flexneri serotypes (serotypes 2 variant and Y). High-throughput sequencing revealed that SFPH2 has a linear double-stranded DNA genome of 40,387 bp with 50 open reading frames. No tRNA genes were identified in the genome. Comparative analysis of the genome revealed that the SFPH2 belongs to the subfamily Autographivirinae and genus T7virus. The genome shows high similarity with other enterobacterial T7virus bacteriophages such as Citrobacter phage SH4 (95% identity and 89% coverage) and Cronobacter phage Dev2 (94% identity and 92% coverage). A comparison of the fiber proteins showed that minor differences in the amino acid residues might specify different protein binding regions and determine host species. In conclusion, this is the first report of a T7virus that can infect Shigella; SFPH2 has a functional stability under a wide range of temperatures and pH values, showing the potential to be widely applied to control Shigella–associated clinical infections and reduce the transmission rates of S. flexneri serotype 2a and its variants in the environment.

Antioxidant, anticancer and molecular docking activity of tulsi plant

An investigation was carried out to study the antioxidant, anticancer and docking activities of medicinal plant, Tulsi – Ocimum sanctum. The results of antioxidant activity of Tulsi leaves extract showed that tulsi leaves has good free radical scavenging ability and IC50 value was found to be 54.23% at 500 µg/ml. The results of anticancer activity of Ocimum santum on normal VERO cell and MCF-7 cell line has showed good anticancer activity having the IC50 concentration at 51.1 ì|g/ml against MCF-7 cell lines – Human Breast cancer cell line thereby indicating that the percentage of cell viability increases with the increased concentration of Ocimum santum (Tulsi) whereas 24.4% cell viability was recorded in the normal VERO cell line. DNA laddering assay was performed on agarose gel electrophoresis. A clear fragmented DNA ladders were observed in tulsi treated MCF-7– Human Breast cancer cell lines. But the untreated normal VERO cell lines did not show any DNA fragmentation. Thereby confirms that Ocimum sanctum induced cell death on breast cancer cell line MCF-7 cancerous cell through apoptosis. Molecular docking was carried out (AutoDock tools), Docking simulations was performed using Lamarckian genetic algorithm of Solis and Wests local search method. Interaction between HDAC6 and Cirsilileon possessing binding energy showed +15.91kcal for interaction studies. It was found that most of the hydrogen bonding is with the residues TYR 76, TRP 35, SER 67, TYR 81, GLU 33, TYR 48, ILE 69 and MET 53 present in the binding pocket. The ligand was docked with the target protein, and the best docking poses were identified and the binding poses of the cirsilieon was shown. This act as the best docking poses shows how the ligand molecule fits into the binding region of the target protein.

Progesterone up-regulates p27 through an increased binding of the progesterone receptor-A-p53 protein complex onto the non-canonical p53 binding motif in HUVEC

We previously demonstrated that progesterone (P4) up-regulated p53 expression, which in turn increased p21 and p27 expression, and finally resulted in proliferation inhibition in human umbilical vein endothelial cells (HUVEC). While a direct transcriptional activation of p21 by p53 protein has been clearly elucidated, the mechanism by which p53 induces p27 expression has not been documented. In this study, we identified three putative p53 protein binding domains at the p27 promoter. Luciferase assay showed that the activity of ectopically introduced p27 promoter constructs containing the potential p53 protein binding region was significantly increased by P4. Immunoblotting analysis indicated that P4 increased the level of p53 protein. Treatment with pifithrin-α-HBr (PFTα), a specific blocker of p53-responsive gene transactivation, reduced the P4-increased p27 promoter activity and p27 protein expression. Transfection with dominant-negative mutants of p53 (C135Y, R175H and R248 W) abolished the P4-increased p27 promoter activity. Moreover, deletion or TCCT nucleotide sequence fill-in at the core site of any of p53 protein binding domains led to the irresponsiveness of the p27 promoter to P4 treatment. Interestingly, immunoprecipitation and chromatin-immunoprecipitation analyses demonstrated that P4 increased the complex of p53-P4 receptor (PR) protein in the nucleus and the assembly of PR protein to the p53 protein binding region of the p27 promoter. Ectopic co-overexpression of p53 and PR-A constructs further augmented the P4-increased p27 promoter activity. Taken together, the results from the present study suggest that P4-increased p53 expression might directly up-regulate p27 transactivation, and PR-A protein might promote this effect by forming complex with p53 protein.

PO-282 SMAR1 transcriptionally repress hTERT and alters the stem cell population in colorectal cancer cells

IntroductionOne of the distinguishing features that set the cancer cell apart is its ability for indefinite proliferation. Cancer progression is accompanied by perturbations in the chromatin structure that results in inappropriate gene expression and genomic instability. Aberrant activation of signalling pathways in cancer cells lead to a cascade of events resulting in ‘replicative immortality’. One of the mechanisms by which cancer cells keep dividing is by the reactivation of enzyme telomerase (hTERT). hTERT reactivation confers tumour cell with various advantages like protection against DNA damaging agents, maintenance of stem cell pool, increased angiogenesis, etc. This cancer stem cell (CSC) population then remains quiescent owing to its radio and chemo-resistant nature and leads to cancer relapse.Material and methodsWestern Blotting, Real time PCR, Co-Immunoprecipitation, Chromatin Immunoprecipitation, Telomerase Repeat Amplification Protocol (TRAP) Assay, Polyps generation in Balb/c mice.Results and discussionsOur study elucidates the role of a Martix Attachment Region Binding Protein (MARBP), SMAR1 as a transcriptional repressor of hTERT. SMAR1 directly interacts with HDAC1/mSin3a co-repressor complex and bind to the hTERT promoter. This binding of SMAR1 brings about Wnt/β-Catenin mediated repression of hTERT. Interestingly we find that occupancy of HDAC1 on hTERT promoter is SMAR1-dependent. The recruitment of repressor complex on the hTERT promoter results in the deacetylation of histones and an increase in the H3K9me2 mark.This helps maintain a repressive environment on the hTERT promoter and alters the occupancy of PolII on the promoter. We also find that knock-down of SMAR1 promotes CD133+ CSC’s and SMAR1 over-expression inhibits CD133+ CSC’s. Moreover, CD133high and CD133low populations exhibit differential SMAR1 and hTERT expression. We generated polyps in Balb/c mice using azoxymethane (AOM)/dextran sodium sulphate (DSS). When the levels of SMAR1 and hTERT were assessed; polyps expressed lower levels of SMAR1 and elevated hTERT as compared to the adjacent non-cancerous tissue.ConclusionWe show that SMAR1 transcriptionally repress hTERT. Given that hTERT reactivation is central for tumour development, progression and cancer stem cell maintenance, this regulation by SMAR1 represents an important mechanism of tumour suppression and inhibition of cancer stem cell trait.

Structural insights and characterization of human Npas4 protein.

Npas4 is an activity dependent transcription factor which is responsible for gearing the expression of target genes involved in neuro-transmission. Despite the importance of Npas4 in many neuronal diseases, the tertiary structure of Npas4 protein along with its physico-chemical properties is limited. In the current study, first we perfomed the phylogenetic analysis of Npas4 and determined the content of hydrophobic, flexible and order-disorder promoting amino acids. The protein binding regions, post-translational modifications and crystallization propensity of Npas4 were predicted through different in-silico methods. The three dimensional model of Npas4 was predicted through LOMET, SPARSKS-X, I-Tasser, RaptorX, MUSTER and Pyhre and the best model was selected on the basis of Ramachandran plot, PROSA, and Qmean scores. The best model was then subjected to further refinement though MODREFINER. Finally the interacting partners of Npas4 were identified through STRING database. The phylogenetic analysis showed the human Npas4 gene to be closely related to other primates such as chimpanzees, monkey, gibbon. The physiochemical properties of Npas4 showed that it is an intrinsically disordered protein with N-terminal ordered region. The post-translational modification analyses indicated absence of acetylation and mannosylation sites. Three potential phosphorylation sites (S108, T130 and T136) were found in PAS A domain whilst a single phosphorylation site (S273) was present in PAS B domain. The predicted tertiary structure of Npas4 showed that bHLH domain and PAS domain possess tertiary structures while the rest of the protein exhibited disorder property. Protein-protein interaction analysis revealed NPas4 interaction with various proteins which are mainly involved in nuclear trafficking of proteins to cytoplasm, activity regulated gene transcription and neurodevelopmental disorders. Moreover the analysis also highlighted the direct relation to proteins involved in promoting neuronal survival, plasticity and cAMP responsive element binding protein proteins. The current study helps in understanding the physicochemical properties and reveals the neuro-modulatory role of Npas4 in crucial pathways involved in neuronal survival and neural signalling hemostasis.

Identification and visualization of protein binding regions with the ArDock server.

ArDock (ardock.ibcp.fr) is a structural bioinformatics web server for the prediction and the visualization of potential interaction regions at protein surfaces. ArDock ranks the surface residues of a protein according to their tendency to form interfaces in a set of predefined docking experiments between the query protein and a set of arbitrary protein probes. The ArDock methodology is derived from large scale cross-docking studies where it was observed that randomly chosen proteins tend to dock in a non-random way at protein surfaces. The method predicts interaction site of the protein, or alternate interfaces in the case of proteins with multiple interaction modes. The server takes a protein structure as input and computes a score for each surface residue. Its output focuses on the interactive visualization of results and on interoperability with other services.

Polymorphism in merozoite surface protein-7E of Plasmodium vivax in Thailand: Natural selection related to protein secondary structure.

Merozoite surface protein 7 (MSP-7) is a multigene family expressed during malaria blood-stage infection. MSP-7 forms complex with MSP-1 prior to merozoite egress from erythrocytes, and could affect merozoite invasion of erythrocytes. To characterize sequence variation in the orthologue in P. vivax (PvMSP-7), a gene member encoding PvMSP-7E was analyzed among 92 Thai isolates collected from 3 major endemic areas of Thailand (Northwest: Tak, Northeast: Ubon Ratchathani, and South: Yala and Narathiwat provinces). In total, 52 distinct haplotypes were found to circulate in these areas. Although population structure based on this locus was observed between each endemic area, no genetic differentiation occurred between populations collected from different periods in the same endemic area, suggesting spatial but not temporal genetic variation. Sequence microheterogeneity in both N- and C- terminal regions was predicted to display 4 and 6 α-helical domains, respectively. Signals of purifying selection were observed in α-helices II-X, suggesting structural or functional constraint in these domains. By contrast, α-helix-I spanning the putative signal peptide was under positive selection, in which amino acid substitutions could alter predicted CD4+ T helper cell epitopes. The central region of PvMSP-7E comprised the 5’-trimorphic and the 3’-dimorphic subregions. Positive selection was identified in the 3’ dimorphic subregion of the central domain. A consensus of intrinsically unstructured or disordered protein was predicted to encompass the entire central domain that contained a number of putative B cell epitopes and putative protein binding regions. Evidences of intragenic recombination were more common in the central region than the remainders of the gene. These results suggest that the extent of sequence variation, recombination events and selective pressures in the PvMSP-7E locus seem to be differentially affected by protein secondary structure.

SMAR1 inhibits Wnt/β-catenin signaling and prevents colorectal cancer progression.

Reduced expression of Scaffold/Matrix Attachment Region Binding Protein 1 (SMAR1) is associated with various cancers resulting in poor prognosis of the diseases. However, the precise underlying mechanism elucidating the loss of SMAR1 requires ongoing study. Here, we show that SMAR1 is highly downregulated during aberrant Wnt3a signaling due to proteasomal degradation and predicted poor prognosis of colorectal cancer. However, substitution mutation (Arginine and Lysine to Alanine) in the D-box elements of SMAR1 viz. “RCHL” and “RQRL” completely abrogated its proteasomal degradation despite Wnt3a activity. SMAR1 inhibited Wnt/β-catenin signaling by recruiting Histone deacetylase-5 to β-catenin promoter resulting in reduced cell migration and invasion. Consequently, reduced tumor sizes in in-vivo NOD-SCID mice were observed that strongly associated with suppression of β-catenin. However, loss of SMAR1 led to enriched H3K9 Acetylation in the β-catenin promoter that further increased Wnt/β-catenin signaling activities and enhanced colorectal cancer progression drastically. Using docking and isothermal titration calorimetric studies we show that small microbial peptides viz. AT-01C and AT-01D derived from Mycobacterium tuberculosis mask the D-box elements of SMAR1. These peptides stabilized SMAR1 expression that further inhibited metastatic SW480 colorectal cancer cell migration and invasion. Drastically reduced subcutaneous tumors were observed in in-vivo NOD-SCID mice upon administration of these peptides (25 mg/kg body weight) intraperitoneally. Taken together our structural studies, in-vitro and in-vivo results strongly suggest that the D-box elements of SMAR1 represent novel druggable targets, where the microbial peptides hold promise as novel colorectal cancer therapeutics.

AnnoPeak: a web application to annotate and visualize peaks from ChIP-seq/ChIP-exo-seq.

Summary We developed annoPeak, a web application to annotate, visualize and compare predicted protein-binding regions derived from ChIP-seq/ChIP-exo-seq experiments using human and mouse cells. Users can upload peak regions from multiple experiments onto the annoPeak server to annotate them with biological context, identify associated target genes and categorize binding sites with respect to gene structure. Users can also compare multiple binding profiles intuitively with the help of visualization tools and tables provided by annoPeak. In general, annoPeak will help users identify patterns of genome wide transcription factor binding profiles, assess binding profiles in different biological contexts and generate new hypotheses. Availability and implementation The web service is freely accessible through URL: http://ccc-annopeak.osumc.edu/annoPeak . Source code is available at https://github.com/XingTang2014/annoPeak . Contact gustavo.leone@osumc.edu or kun.huang@osumc.edu. Supplementary information Supplementary data are available at Bioinformatics online.