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The C-terminal region of G72 increases D-amino acid oxidase activity. Int J Mol Sci 2013; 15:29-43. [PMID: 24362575 PMCID: PMC3907796 DOI: 10.3390/ijms15010029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 11/28/2013] [Accepted: 12/06/2013] [Indexed: 12/11/2022] Open
Abstract
The schizophrenia-related protein G72 plays a unique role in the regulation of d-amino acid oxidase (DAO) in great apes. Several psychiatric diseases, including schizophrenia and bipolar disorder, are linked to overexpression of DAO and G72. Whether G72 plays a positive or negative regulatory role in DAO activity, however, has been controversial. Exploring the molecular basis of the relationship between G72 and DAO is thus important to understand how G72 regulates DAO activity. We performed yeast two-hybrid experiments and determined enzymatic activity to identify potential sites in G72 involved in binding DAO. Our results demonstrate that residues 123–153 and 138–153 in the long isoform of G72 bind to DAO and enhance its activity by 22% and 32%, respectively. A docking exercise indicated that these G72 peptides can interact with loops in DAO that abut the entrance of the tunnel that substrate and cofactor must traverse to reach the active site. We propose that a unique gating mechanism underlies the ability of G72 to increase the activity of DAO. Because upregulation of DAO activity decreases d-serine levels, which may lead to psychiatric abnormalities, our results suggest a molecular mechanism involving interaction between DAO and the C-terminal region of G72 that can regulate N-methyl-d-aspartate receptor-mediated neurotransmission.
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Hung TJ, Tomiya N, Chang TH, Cheng WC, Kuo PH, Ng SK, Lien PC, Lee YC, Chang MDT. Functional characterization of ECP-heparin interaction: a novel molecular model. PLoS One 2013; 8:e82585. [PMID: 24349317 PMCID: PMC3859622 DOI: 10.1371/journal.pone.0082585] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 10/15/2013] [Indexed: 12/29/2022] Open
Abstract
Human eosinophil cationic protein (ECP) and eosinophil derived neurotoxin (EDN) are two ribonuclease A (RNaseA) family members secreted by activated eosinophils. They share conserved catalytic triad and similar three dimensional structures. ECP and EDN are heparin binding proteins with diverse biological functions. We predicted a novel molecular model for ECP binding of heparin hexasaccharide (Hep6), [GlcNS(6S)-IdoA(2S)]3, and residues Gln(40), His(64) and Arg(105) were indicated as major contributions for the interaction. Interestingly, Gln(40) and His(64) on ECP formed a clamp-like structure to stabilize Hep6 in our model, which was not observed in the corresponding residues on EDN. To validate our prediction, mutant ECPs including ECP Q40A, H64A, R105A, and double mutant ECP Q40A/H64A were generated, and their binding affinity for heparins were measured by isothermal titration calorimetry (ITC). Weaker binding of ECP Q40A/H64A of all heparin variants suggested that Gln(40)-His(64) clamp contributed to ECP-heparin interaction significantly. Our in silico and in vitro data together demonstrate that ECP uses not only major heparin binding region but also use other surrounding residues to interact with heparin. Such correlation in sequence, structure, and function is a unique feature of only higher primate ECP, but not EDN.
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Affiliation(s)
- Ta-Jen Hung
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Noboru Tomiya
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tse-Hao Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Wen-Chi Cheng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Ping-Hsueh Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Sim-Kun Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Pei-Chun Lien
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
| | - Yuan-Chuan Lee
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Margaret Dah-Tsyr Chang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- Department of Medical Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
- * E-mail:
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Nyland SB, Krissinger DJ, Clemente MJ, Irby RB, Baab KT, Jarbadan NR, Sokol L, Schaefer E, Liao J, Cuthbertson D, Epling-Burnette P, Paquette R, List AF, Maciejewski JP, Loughran TP. Seroreactivity to LGL leukemia-specific epitopes in aplastic anemia, myelodysplastic syndrome and paroxysmal nocturnal hemoglobinuria: results of a bone marrow failure consortium study. Leuk Res 2012; 36:581-7. [PMID: 22386729 DOI: 10.1016/j.leukres.2012.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 12/02/2011] [Accepted: 02/03/2012] [Indexed: 12/21/2022]
Abstract
Large granular lymphocyte (LGL) leukemia is characterized by clonal expansion of antigen-activated cytotoxic T cells (CTL). Patients frequently exhibit seroreactivity against a human T-cell leukemia virus (HTLV) epitope, BA21. Aplastic anemia, paroxysmal nocturnal hemoglobinuria and myelodysplastic syndrome are bone marrow failure diseases that can also be associated with similar aberrant CTL activation (LGL-BMF). We identified a BA21 peptide that was specifically reactive with LGL leukemia sera and found significantly elevated antibody reactivity against the same peptide in LGL-BMF sera. This finding of shared seroreactivity in LGL-BMF conditions and LGL leukemia suggests that these diseases might share a common pathogenesis.
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Affiliation(s)
- Susan Bell Nyland
- Penn State Hershey Cancer Institute, Penn State Hershey College of Medicine, Hershey, PA, USA.
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Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification. J Biomed Biotechnol 2011; 2011:432830. [PMID: 21876642 PMCID: PMC3163029 DOI: 10.1155/2011/432830] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Accepted: 06/28/2011] [Indexed: 12/29/2022] Open
Abstract
Epitopes are antigenic determinants that are useful because they induce B-cell antibody production and stimulate T-cell activation. Bioinformatics can enable rapid, efficient prediction of potential epitopes. Here, we designed a novel B-cell linear epitope prediction system called LEPS, Linear Epitope Prediction by Propensities and Support Vector Machine, that combined physico-chemical propensity identification and support vector machine (SVM) classification. We tested the LEPS on four datasets: AntiJen, HIV, a newly generated PC, and AHP, a combination of these three datasets. Peptides with globally or locally high physicochemical propensities were first identified as primitive linear epitope (LE) candidates. Then, candidates were classified with the SVM based on the unique features of amino acid segments. This reduced the number of predicted epitopes and enhanced the positive prediction value (PPV). Compared to four other well-known LE prediction systems, the LEPS achieved the highest accuracy (72.52%), specificity (84.22%), PPV (32.07%), and Matthews' correlation coefficient (10.36%).
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Yang X, Yu X. An introduction to epitope prediction methods and software. Rev Med Virol 2009; 19:77-96. [PMID: 19101924 DOI: 10.1002/rmv.602] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this paper, current prediction methods and algorithms for both T- and B cell epitopes are reviewed, and a comprehensive summary of epitope prediction software and databases currently available online is also provided. This review can offer researchers in this field a sense of direction and insights for future work. However, our main purpose is to introduce clinical and basic biomedical researchers who are not familiar with these biological analysis tools and databases to these online resources and to provide guidance on how to use them effectively.
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Affiliation(s)
- Xingdong Yang
- Department of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan, P. R. China
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Felicori L, Fernandes PB, Giusta MS, Duarte CG, Kalapothakis E, Nguyen C, Molina F, Granier C, Chávez-Olórtegui C. An in vivo protective response against toxic effects of the dermonecrotic protein from Loxosceles intermedia spider venom elicited by synthetic epitopes. Vaccine 2009; 27:4201-8. [PMID: 19389441 DOI: 10.1016/j.vaccine.2009.04.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Revised: 04/08/2009] [Accepted: 04/13/2009] [Indexed: 11/19/2022]
Abstract
Loxoscelism is a necrotic-hemolytic syndrome caused by bites of brown spiders belonging to the genus Loxosceles. Many approaches for the treatment of Loxosceles poisoning have already been proposed, among which administration of specific antivenom is thought to be the more specific. We have evaluated the use of peptides as immunogen to raise in rabbits an antibody response that could protect animals from a challenge by the Loxtox isoform LiD1, one of the main toxic component of Loxosceles intermedia venom. Six antigenic regions of LiD1 were mapped by using the SPOT method. The corresponding peptides were further chemically synthesized, mixed, and used as immunogens in rabbits. Control animal received recombinant LiD1 alone or together with peptides. We found that the rabbit antibody response to peptides was cross-reactive with LiD1, although only one peptide from the mix of six was immunogenic. The dermonecrotic, hemorrhagic and oedema forming activities induced by LiD1 in naïve rabbits were inhibited by 82%, 35% and 35% respectively, by preincubation of LiD1 with anti-peptide antibodies prepared from immunized rabbits. Animals that were immunized with peptides or LiD1r, were found to be protected from the dermonecrotic, hemorrhagic and oedema forming activities induced by a challenge with LiD1. The protection conferred by peptides was, however, lower than that provided by the peptide protein combination or by the full-length protein. These results encourage us in the utilization of synthetic peptides for therapeutic serum development or vaccination approaches.
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Affiliation(s)
- Liza Felicori
- Departamento de Bioquímica-Imunologia, ICB, Universidade Federal de Minas Gerais, Brazil.
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Lee WL, Li J, Uttamchandani M, Sun H, Yao SQ. Inhibitor fingerprinting of metalloproteases using microplate and microarray platforms: an enabling technology in Catalomics. Nat Protoc 2007; 2:2126-38. [PMID: 17853868 DOI: 10.1038/nprot.2007.305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
One of the most fundamental properties of an enzyme is its selectivity, a property that has proved highly challenging to understand. Recent developments offer methodologies to rapidly establish activity-dependent profiles of enzymes. In this protocol, we describe methods to elucidate inhibitor fingerprints of enzymes. By taking advantage of well-defined small-molecule inhibitor libraries and the screening throughput offered from microplate and microarray platforms, we provide step-by-step application of the methodology toward the global characterization of metalloproteases, an important class of enzymes involved in numerous diseases and cellular processes. The same strategy is nonetheless applicable to virtually any given enzyme class, provided suitable experimental design and chemical inhibitor libraries are carefully implemented. We are able to routinely fingerprint as many as 2,000 independent enzyme interactions on the microplate platform within a span of approximately 7 h; however, the same throughput is attained within 5 h on the microarray platform.
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Affiliation(s)
- Wei L Lee
- Department of Biological Science, National University of Singapore, Singapore, Republic of Singapore
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Pai TW, Chang MDT, Tzou WS, Su BH, Wu PC, Chang HT, Chou WI. REMUS: a tool for identification of unique peptide segments as epitopes. Nucleic Acids Res 2006; 34:W198-201. [PMID: 16844991 PMCID: PMC1538771 DOI: 10.1093/nar/gkl188] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We provide a ‘REMUS’ (reinforced merging techniques for unique peptide segments) web server for identification of the locations and compositions of unique peptide segments from a set of protein family sequences. Different levels of uniqueness are determined according to substitutional relationship in the amino acids, frequency of appearance and biological properties such as priority for serving as candidates for epitopes where antibodies recognize. REMUS also provides interactive visualization of 3D structures for allocation and comparison of the identified unique peptide segments. Accuracy of the algorithm was found to be 70% in terms of mapping a unique peptide segment as an epitope. The REMUS web server is available at and the PC version software can be freely downloaded either at or . User guide and working examples for PC version are available at , and details of the proposed algorithm can be referred to the documents as described previously [H. T. Chang, T. W. Pai, T. C. Fan, B. H. Su, P. C. Wu, C. Y. Tang, C. T. Chang, S. H. Liu and M. D. T. Chang (2006) BMC Bioinformatics, 7, 38 and T. W. Pai, B. H. Su, P. C. Wu, M. D. T. Chang, H. T. Chang, T. C. Fan and S. H. Liu (2006) J. Bioinform. Comput. Biol., 4, 75–92].
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Affiliation(s)
- Tun-Wen Pai
- To whom correspondence should be addressed. Tel: +886 2 24622192, ext. 6618; Fax: +886 2 24623249;
| | - Margaret Dah-Tsyr Chang
- Department of Life Science, Institute of Molecular and Cellular Biology, National Tsing Hua UniversityHsinchu, Taiwan, Republic of China
- Correspondence may also be addressed to Margaret Dah-Tsyr Chang. Tel: +886 3 5742767; Fax: +886 3 5715934;
| | - Wen-Shyong Tzou
- Institute of Bioscience and BioTechnology, National Taiwan Ocean UniversityKeelung, Taiwan, Republic of China
| | | | | | - Hao-Teng Chang
- Department of Life Science, Institute of Molecular and Cellular Biology, National Tsing Hua UniversityHsinchu, Taiwan, Republic of China
| | - Wei-I Chou
- Department of Life Science, Institute of Molecular and Cellular Biology, National Tsing Hua UniversityHsinchu, Taiwan, Republic of China
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