Structure-function Analysis of Inflammatory Bowel Disease Associated Proteins and Moonlighting Proteins

Proteins are fundamental functional and structural components of life. The central dogma describes how DNA sequences encode protein sequences, and a protein’s sequence generally corresponds to a specific three-dimensional structure and function. In this set of projects, we studied examples where a protein’s sequence enables it to have more than one function and examples where genetic changes in the DNA sequence lead to changes in the protein sequence and structure that are associated with disease. Moonlighting proteins have two or more physiologically relevant distinct functions performed by a single polypeptide chain. MoonProt is a comprehensive open access database storing expert curated annotations for moonlighting proteins. In the latest release, we expanded the number of annotated proteins to 370 and modified several dozen protein annotations with additional or updated information, including more links to protein structures in the Protein Data Bank, compared with the previous release. The most common types of moonlighting proteins include enzymes, chaperones, DNA binding proteins, and transcription factors. The new entries in version 2.0 include more examples from humans and several model organisms, more proteins involved in disease, and proteins with different combinations of functions. Inflammatory bowel disease (IBD) is a group of autoimmune diseases affecting the gastrointestinal tract, including Crohn’s disease (CD) and ulcerative colitis (UC). With a growing number of protein structures available, computer-based analysis of the effects of the amino acid substitutions on the three-dimensional structure can be used to provide more insight as to how these changes lead to disease predisposition. A list of single amino acid substitutions associated with CD and/or UC was collected from GWAS (Genome Wide Association Study) and NGS (Next Generation Sequencing) clinical platforms, and used to develop insights about protein structural changes leading to pathogenesis of inflammatory bowel diseases. In this study, more than 200 single amino acid polymorphisms within 109 proteins were identified. Changes in a variety of biochemical and biophysical properties of the amino acids including polarity, volume, and hydrophobicity and characteristics about the location of the substitution within the sequence and structure, including local secondary structure, hydrogen bonding of the sidechain, crystallographic B (thermal) factor, and conservation, were studied. The sites of the inflammatory bowel disease-associated mutations are not highly conserved, and almost all the mutations are located on the surface of the protein, which are results that differ from previous studies of disease-associated mutations in general. This study can be helpful for selecting proteins for further biochemical and biophysical analysis and for aiding in the development of improved clinical diagnostic methods and therapeutics for Crohn’s disease and ulcerative colitis

Mapping of the APE1 domains responsible for GSNO-induced nuclear export

<p><b>Copyright information:</b></p><p>Taken from "Nitric oxide controls nuclear export of APE1/Ref-1 through S-nitrosation of Cysteines 93 and 310"</p><p></p><p>Nucleic Acids Research 2007;35(8):2522-2532.</p><p>Published online 1 Apr 2007</p><p>PMCID:PMC1885639.</p><p>© 2007 The Author(s)</p> () Immunofluorescence images depicting the subcellular localization of APE1 truncated mutants in transfected HEK293 cells. () Schematic representation of the N-terminal and C-terminal truncated mutants of APE1. The NLS and the predicted NES and MTS within the full-length protein are indicated. C, cytoplasmic staining; N, nuclear staining; M, mitochondrial staining. () The subcellular distribution of HA-APE1(Δ64-80) and HA-APE1(1-305) determined by immunofluorescence in the presence of GSNO treatment. () Three-dimensional localization of the B1 (amino acids 61–69) and B2 (amino acids 311–317) beta-strands and the S-nitrosation sites C93 and C310 in the closed conformation of APE1. B1 and B2 form an antiparallel beta-fold. C93 and C310 are close to B1 and B2, respectively

Nitric-oxide-repressed classical importin-mediated nuclear import pathway

<p><b>Copyright information:</b></p><p>Taken from "Nitric oxide controls nuclear export of APE1/Ref-1 through S-nitrosation of Cysteines 93 and 310"</p><p></p><p>Nucleic Acids Research 2007;35(8):2522-2532.</p><p>Published online 1 Apr 2007</p><p>PMCID:PMC1885639.</p><p>© 2007 The Author(s)</p> () Left: Schematic presentation of the NLS-containing APE1(1-64) mutant. Right: Immunofluorescence images depicting the localization of APE1(1-64)-Myc in HEK293 cells challenged with or without 1 mM GSNO for 4 h. () Confocal images depicting the localization of (GFP)2-NLS and (GFP)2-M9 in HEK293 cells treated with GSNO for 4 h. () Left: Schematic presentation of the NLS-truncated mutant APE1(43-318)-Myc Right: Immunofluorescence images depicting the localization of APE1(43-318)-Myc in HEK293 cells challenged with or without 1 mM GSNO for 4 h

A model for nuclear-cytosolic translocation of APE1 in response to NO stimulation

<p><b>Copyright information:</b></p><p>Taken from "Nitric oxide controls nuclear export of APE1/Ref-1 through S-nitrosation of Cysteines 93 and 310"</p><p></p><p>Nucleic Acids Research 2007;35(8):2522-2532.</p><p>Published online 1 Apr 2007</p><p>PMCID:PMC1885639.</p><p>© 2007 The Author(s)</p> APE1 carries an importin-dependent NLS at the N-terminal end (not shown). Two antiparellel beta-strands (B1 and B2) in close proximity to C93 and C310 are masked in the internal structure. In rested cells, APE1 resides in the nucleus due to the existence of NLS. Upon nitrosative stress, S-nitrosation of C93 and C310 contributes to unmasking of the B1 and/or B2 by changing conformation, which may facilitate the nuclear export of APE1 in a CRM1-independet manner (perhaps mediated by an unknown transport protein). At the same time, importin-dependent nuclear import pathway is repressed by NO insult, which may prevent the already exported cytosolic APE1 from re-import into the nucleus. However, once the intracellular environment becomes reductive (e.g. the increased reducing molecules such as DTT), both NO-elicited S-nitrosation of APE1 and NO-caused repression of importin can be abrogated; thus, the inducible nuclear export of APE1 by NO could be prevented or reversed

The effects of CHX and LMB on GSNO-induced cytosolic translocation of APE1

<p><b>Copyright information:</b></p><p>Taken from "Nitric oxide controls nuclear export of APE1/Ref-1 through S-nitrosation of Cysteines 93 and 310"</p><p></p><p>Nucleic Acids Research 2007;35(8):2522-2532.</p><p>Published online 1 Apr 2007</p><p>PMCID:PMC1885639.</p><p>© 2007 The Author(s)</p> () Effect of CHX. 30 h after transfection, cells were treated with 1 mM GSNO for 4 h in the presence or absence of CHX, and then fixed and immunostained by HA antibody and a Texas-red labeled secondary antibody, counterstained with Hoechst 33342, and analyzed by fluorescence microscopy. () Effect of LMB. HEK293 cells transfected with HA-APE1 were treated with 5 ng/ml LMB for 4 h, followed by 1 mM GSNO for another 4 h, and then the subcellular distribution of HA-APE1 was determined. () Positive control of the effect of LMB on the localization of GFP-IκB expressed in HEK293 cells

MoonProt 2.0: An expansion and update of the moonlighting proteins database

MoonProt 2.0 (http://moonlightingproteins.org) is an updated, comprehensive and open-access database storing expert-curated annotations for moonlighting proteins. Moonlighting proteins contain two or more physiologically relevant distinct functions performed by a single polypeptide chain. Here, we describe developments in the MoonProt website and database since our previous report in the Database Issue of Nucleic Acids Research. For this V 2.0 release, we expanded the number of proteins annotated to 370 and modified several dozen protein annotations with additional or updated information, including more links to protein structures in the Protein Data Bank, compared with the previous release. The new entries include more examples from humans and several model organisms, more proteins involved in disease, and proteins with different combinations of functions. The updated web interface includes a search function using BLAST to enable users to search the database for proteins that share amino acid sequence similarity with a protein of interest. The updated website also includes additional background information about moonlighting proteins and an expanded list of links to published articles about moonlighting protein

Total leukocyte counts in men and women in different age groups.

<p>Data shown are mean ± standard error of mean in men and women, respectively, in each age group; *indicates p<0.05 comparing men and women in the respective age group.</p

Deep Neural Network with Walsh-Hadamard Transform Layer For Ember Detection during a Wildfire

No description supplie

Facile Synthesis of One Dimensional AgBr@Ag Nanostructures and Their Visible Light Photocatalytic Properties

In this work, we successfully prepared one dimensional (1D) AgBr@Ag nanostructures in high yield by a facile wet chemical method, and the plausible growth mechanism was discussed. The synthesis of as-prepared AgBr@Ag nanostructure is a dissolution and recrystallization process, and the PVP and DMSO have a synergistic and competitive effect on the preparation of 1D AgBr@Ag products. Moreover, the AgBr@Ag nanorods exhibit excellent photocatalytic activities under visible light illumination, which may be attributed to their large surface area as well as superior charge separation and transfer efficiency compared to AgBr@Ag particles

Counts and percentages of neutrophil and lymphocyte, and neutrophil-to-lymphocyte ratio, in men and women in different age groups.

<p>Data shown are mean ± standard error of mean in men and women, respectively, in each age group; *indicates p<0.05 comparing men and women in the respective age group.</p