Neuropeptide Y(NPY) has a pivotal role in the regulation of many physiological processes. In this study, the gene encoding a NPY receptor-like from the common Chinese cuttlefish Sepiella japonica( SjNPYR-like) was ide...Neuropeptide Y(NPY) has a pivotal role in the regulation of many physiological processes. In this study, the gene encoding a NPY receptor-like from the common Chinese cuttlefish Sepiella japonica( SjNPYR-like) was identified and characterized. The full-length SjNPYR-like cDNA was cloned containing a 492-bp of 5′ untranslated region(UTR), 1 182 bp open reading frame(ORF) encoding a protein of 393 amino acid residues, and 228 bp of 3′ UTR. The putative protein was predicted to have a molecular weight of 45.54 kDa and an isoelectric point(pI) of 8.13. By informatic analyses, SjNPYR-like was identified as belonging to the class A G protein coupled receptor(GPCR) family(the rhodopsin-type). The amino acid sequence contained 12 potential phosphorylation sites and five predicted N-linked glycosylation sites. Multiple sequence alignment and 3D structure modeling were conducted to clarify SjNPYR bioinformatics characteristics. Phylogenetic analysis identifies it as an NPYR with identity of 33% to Lymnaea stagnalis NPFR. Transmembrane properties of SjNPYR-like were demonstrated in vitro using HEK293 cells and the p EGFP-N1 plasmid. Relative quantifi cation of SjNPYR-like mRNA level confi rmed a high level expression and broad distribution of SjNPYR-like in various tissues of female S. japonica. In addition, the transcriptional profile of SjNPYR-like in the brain, liver, and ovary during gonadal development was analyzed. The results provide basic understanding on the molecular characteristics of SjNPYR-like and its potentially physical functions.展开更多
lntemet services on bioinformatics still remain a popular tool for the researchers. Here the authors present a recently developed web-site http：//bri-shur.com where several tools and pipelines for protein structure p...lntemet services on bioinformatics still remain a popular tool for the researchers. Here the authors present a recently developed web-site http：//bri-shur.com where several tools and pipelines for protein structure prediction are implemented. The prediction of a structure for a particular protein often requires a sensitive and iterative approach, and the web-site provides an environment for this kind of work. Software that is used in the services includes both free programs available in the Internet and newly developed algorithms. The service on homology screening in PDB for a structure template is implemented using an approach that is alternative to well-known BLAST algorithm and it has some advantages over BLAST. The service on homology modeling uses well-known Nest program. The service on protein energy estimate allows selecting a best template in the set of homologs and adds a functionality of fold recognition to the environment. The design of the site simplifies several of the most useful bioinformatics routines, thus making them available to a large community of researchers. Services are provided free of charge without registration, and the user＇s privacy is taken care of.展开更多
G-protein coupled receptor (GPCR) is one of the most important protein families for drug target. GPCR agonists and antagonists occupy approximately one third of the world small molecule drug market. Much effort has be...G-protein coupled receptor (GPCR) is one of the most important protein families for drug target. GPCR agonists and antagonists occupy approximately one third of the world small molecule drug market. Much effort has been invested in GPCR study by both academic institutions and pharmaceutical industries. With seven-transmembrane do-mains, GPCR plays significant roles in intercellular signal transduction and is involved in a variety of biological path-ways. With the availability of sequence data of human and other mammalian genomes, as well as their expressed se-quence tag (EST) data, the bioinformatics and genomics approaches can be applied to identifying novel GPCR in the post genomic era. Deorphanizing GPCR or matching ligands with GPCR greatly facilitates target validation process and automatically provides a possible compound screening assay. Similarly, bioinformatics data mining approach could also be applied to the identification of GPCR peptide or protein ligands. Here we give a general review of recent advances in the study of GPCR structure, function, as well as GPCR and ligand identification with the emphasis on the bioinformatics database mining of GPCR and their peptide or protein ligands.展开更多
基金Supported by the Public Welfare Technical Applied Research Project of Zhejiang Province(No.2017C32074)the International Science&Technology Cooperation Program of China(No.2014DFT30120)the Open Foundation from Marine Sciences in the Most Important Subjects of Zhejiang(No.20130202)
文摘Neuropeptide Y(NPY) has a pivotal role in the regulation of many physiological processes. In this study, the gene encoding a NPY receptor-like from the common Chinese cuttlefish Sepiella japonica( SjNPYR-like) was identified and characterized. The full-length SjNPYR-like cDNA was cloned containing a 492-bp of 5′ untranslated region(UTR), 1 182 bp open reading frame(ORF) encoding a protein of 393 amino acid residues, and 228 bp of 3′ UTR. The putative protein was predicted to have a molecular weight of 45.54 kDa and an isoelectric point(pI) of 8.13. By informatic analyses, SjNPYR-like was identified as belonging to the class A G protein coupled receptor(GPCR) family(the rhodopsin-type). The amino acid sequence contained 12 potential phosphorylation sites and five predicted N-linked glycosylation sites. Multiple sequence alignment and 3D structure modeling were conducted to clarify SjNPYR bioinformatics characteristics. Phylogenetic analysis identifies it as an NPYR with identity of 33% to Lymnaea stagnalis NPFR. Transmembrane properties of SjNPYR-like were demonstrated in vitro using HEK293 cells and the p EGFP-N1 plasmid. Relative quantifi cation of SjNPYR-like mRNA level confi rmed a high level expression and broad distribution of SjNPYR-like in various tissues of female S. japonica. In addition, the transcriptional profile of SjNPYR-like in the brain, liver, and ovary during gonadal development was analyzed. The results provide basic understanding on the molecular characteristics of SjNPYR-like and its potentially physical functions.
文摘lntemet services on bioinformatics still remain a popular tool for the researchers. Here the authors present a recently developed web-site http：//bri-shur.com where several tools and pipelines for protein structure prediction are implemented. The prediction of a structure for a particular protein often requires a sensitive and iterative approach, and the web-site provides an environment for this kind of work. Software that is used in the services includes both free programs available in the Internet and newly developed algorithms. The service on homology screening in PDB for a structure template is implemented using an approach that is alternative to well-known BLAST algorithm and it has some advantages over BLAST. The service on homology modeling uses well-known Nest program. The service on protein energy estimate allows selecting a best template in the set of homologs and adds a functionality of fold recognition to the environment. The design of the site simplifies several of the most useful bioinformatics routines, thus making them available to a large community of researchers. Services are provided free of charge without registration, and the user＇s privacy is taken care of.
基金supposed by the State“863”High-tech Program of China(Grant No.2001AA231011).
文摘G-protein coupled receptor (GPCR) is one of the most important protein families for drug target. GPCR agonists and antagonists occupy approximately one third of the world small molecule drug market. Much effort has been invested in GPCR study by both academic institutions and pharmaceutical industries. With seven-transmembrane do-mains, GPCR plays significant roles in intercellular signal transduction and is involved in a variety of biological path-ways. With the availability of sequence data of human and other mammalian genomes, as well as their expressed se-quence tag (EST) data, the bioinformatics and genomics approaches can be applied to identifying novel GPCR in the post genomic era. Deorphanizing GPCR or matching ligands with GPCR greatly facilitates target validation process and automatically provides a possible compound screening assay. Similarly, bioinformatics data mining approach could also be applied to the identification of GPCR peptide or protein ligands. Here we give a general review of recent advances in the study of GPCR structure, function, as well as GPCR and ligand identification with the emphasis on the bioinformatics database mining of GPCR and their peptide or protein ligands.
