Journal of Amino Acids最新文献

{"title":"Metal preferences of zinc-binding motif on metalloproteases.","authors":"Kayoko M Fukasawa,&nbsp;Toshiyuki Hata,&nbsp;Yukio Ono,&nbsp;Junzo Hirose","doi":"10.4061/2011/574816","DOIUrl":"https://doi.org/10.4061/2011/574816","url":null,"abstract":"<p><p>Almost all naturally occurring metalloproteases are monozinc enzymes. The zinc in any number of zinc metalloproteases has been substituted by some other divalent cation. Almost all Co(II)- or Mn(II)-substituted enzymes maintain the catalytic activity of their zinc counterparts. However, in the case of Cu(II) substitution of zinc proteases, a great number of enzymes are not active, for example, thermolysin, carboxypeptidase A, endopeptidase from Lactococcus lactis, or aminopeptidase B, while some do have catalytic activity, for example, astacin (37%) and DPP III (100%). Based on structural studies of various metal-substituted enzymes, for example, thermolysin, astacin, aminopeptidase B, dipeptidyl peptidase (DPP) III, and del-DPP III, the metal coordination geometries of both active and inactive Cu(II)-substituted enzymes are shown to be the same as those of the wild-type Zn(II) enzymes. Therefore, the enzyme activity of a copper-ion-substituted zinc metalloprotease may depend on the flexibility of catalytic domain.</p>","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":" ","pages":"574816"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4061/2011/574816","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39968042","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mackerel trypsin purified from defatted viscera by supercritical carbon dioxide.","authors":"Byung-Soo Chun, Hideki Kishimura, Sitthipong Nalinanon, Sappasith Klomklao, Soottawat Benjakul","doi":"10.4061/2011/728082","DOIUrl":"10.4061/2011/728082","url":null,"abstract":"<p><p>Viscera of mackerel (Scomber sp.) were defatted by supercritical carbon dioxide (SCO(2)) treatment. Trypsin (SC-T) was then extracted from the defatted powder and purified by a series of chromatographies including Sephacryl S-200 and Sephadex G-50. The purified SC-T was nearly homogeneous on SDS-PAGE, and its molecular weight was estimated as approximately 24,000 Da. N-terminal twenty amino acids sequence of SC-T was IVGGYECTAHSQPHQVSLNS. The specific trypsin inhibitors, soybean trypsin inhibitor and TLCK, strongly inhibited the activities of SC-T. The pH and temperature optimums of SC-T were at around pH 8.0 and 60°C, respectively, using N(α)-p-tosyl-L-arginine methyl ester as a substrate. The SC-T was unstable below pH 5.0 and above 40°C, and it was stabilized by calcium ion. These enzymatic characteristics of SC-T were the same as those of other fish trypsins, especially spotted mackerel (S. borealis) trypsin, purified from viscera defatted by acetone. Therefore, we concluded that the SCO(2) defatting process is useful as a substitute for organic solvent defatting process.</p>","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":" ","pages":"728082"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268041/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39968121","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diversified carbohydrate-binding lectins from marine resources.","authors":"Tomohisa Ogawa,&nbsp;Mizuki Watanabe,&nbsp;Takako Naganuma,&nbsp;Koji Muramoto","doi":"10.4061/2011/838914","DOIUrl":"https://doi.org/10.4061/2011/838914","url":null,"abstract":"<p><p>Marine bioresources produce a great variety of specific and potent bioactive molecules including natural organic compounds such as fatty acids, polysaccharides, polyether, peptides, proteins, and enzymes. Lectins are also one of the promising candidates for useful therapeutic agents because they can recognize the specific carbohydrate structures such as proteoglycans, glycoproteins, and glycolipids, resulting in the regulation of various cells via glycoconjugates and their physiological and pathological phenomenon through the host-pathogen interactions and cell-cell communications. Here, we review the multiple lectins from marine resources including fishes and sea invertebrate in terms of their structure-activity relationships and molecular evolution. Especially, we focus on the unique structural properties and molecular evolution of C-type lectins, galectin, F-type lectin, and rhamnose-binding lectin families.</p>","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":" ","pages":"838914"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4061/2011/838914","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39968501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Catalytic site cysteines of thiol enzyme: sulfurtransferases.","authors":"Noriyuki Nagahara","doi":"10.4061/2011/709404","DOIUrl":"10.4061/2011/709404","url":null,"abstract":"<p><p>Thiol enzymes have single- or double-catalytic site cysteine residues and are redox active. Oxidoreductases and isomerases contain double-catalytic site cysteine residues, which are oxidized to a disulfide via a sulfenyl intermediate and reduced to a thiol or a thiolate. The redox changes of these enzymes are involved in their catalytic processes. On the other hand, transferases, and also some phosphatases and hydrolases, have a single-catalytic site cysteine residue. The cysteines are redox active, but their sulfenyl forms, which are inactive, are not well explained biologically. In particular, oxidized forms of sulfurtransferases, such as mercaptopyruvate sulfurtransferase and thiosulfate sulfurtransferase, are not reduced by reduced glutathione but by reduced thioredoxin. This paper focuses on why the catalytic site cysteine of sulfurtransferase is redox active.</p>","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":"2011 ","pages":"709404"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30458579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simple preparation of pacific cod trypsin for enzymatic Peptide synthesis.","authors":"Tomoyoshi Fuchise, Haruo Sekizaki, Hideki Kishimura, Sappasith Klomklao, Sitthipong Nalinanon, Soottawat Benjakul, Byung-Soo Chun","doi":"10.4061/2011/912382","DOIUrl":"10.4061/2011/912382","url":null,"abstract":"<p><p>Trypsin from the pyloric caeca of Pacific cod (Gadus macrocephalus) was easily prepared by affinity chromatography on Benzamidine Sepharose 6B and gel filtration on Superdex 75. Pacific cod trypsin was composed of three isozymes, and their molecular masses were estimated 23,756.34 Da, 23,939.62 Da, and 24,114.81 Da by desorption/ionization time-of-flight mass spectroscopy (MALDI/TOF-MS) and their isoelectric points (pIs) were approximately 5.1, 6.0, and 6.2, respectively. The isolated Pacific cod trypsin showed high similarity to other frigid-zone fish trypsins. The kinetic behavior of tryptic hydrolysis toward N-p-tosyl-L-arginine methyl ester hydrochloride (TAME), N-benzoyl-L-arginine p-nitroanilide hydrochloride (BAPA), and p-amidinophenyl ester were also analyzed. In addition, the cod trypsin-catalyzed dipeptide synthesis was investigated using twelve series of \"inverse subdtrates\" that is p- and m-isomer of amidinophenyl, guanidinophenyl, (amidinomethyl)phenyl, (guanidinomethyl)phenyl, and four position isomers of guanidinonaphtyl esters derived from N-(tert-butoxycarbonyl)amino acid as acyl donor components. They were found to couple with an acyl acceptor such as L-alanine p-nitroanilide to produce dipeptide in the presence of the trypsin. All inverse substrates tested in this study undergo less enantioselective coupling reaction. The p-guanidinophenyl ester was most practical substrate in twelve series tested. The enzymatic hydrolysis of the resulting products was negligible.</p>","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":" ","pages":"912382"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268023/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39967658","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Decreased Phosphorylation and Increased Methionine Oxidation of α-Synuclein in the Methionine Sulfoxide Reductase A Knockout Mouse.","authors":"Derek B Oien,&nbsp;Gonzalo A Carrasco,&nbsp;Jackob Moskovitz","doi":"10.4061/2011/721094","DOIUrl":"https://doi.org/10.4061/2011/721094","url":null,"abstract":"<p><p>Previously, we have showed that overexpression of methionine-oxidized α-synuclein in methionine sulfoxide reductase A (MsrA) null mutant yeast cells inhibits α-synuclein phosphorylation and increases protein fibrillation. The current studies show that ablation of mouse MsrA gene caused enhanced methionine oxidation of α-synuclein while reducing its own phophorylation levels, especially in the hydrophobic cell-extracted fraction. These data provide supportive evidence that a compromised MsrA function in mammalian brain may cause enhanced pathologies associated with altered α-synuclein oxidation and phosphorylation levels.</p>","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":"2011 ","pages":"721094"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4061/2011/721094","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30458581","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional residues in proteins.","authors":"Shandar Ahmad,&nbsp;Jung-Ying Wang,&nbsp;Zulfiqar Ahmad,&nbsp;Faizan Ahmad","doi":"10.4061/2011/606354","DOIUrl":"https://doi.org/10.4061/2011/606354","url":null,"abstract":"We are delighted to present a special issue on the subject of functional residues of proteins. Finding focused articles within the time frame of a special issue is always challenging, which is further compounded by authors' reluctance in making their contributions to new journals. We have been fortunate enough that some leading researchers in the field agreed to support this special issue and contributed their work at our request. We present here nine articles on various aspects of the subject. We received some more submissions, which could not be accommodated because of a strict quality control, we tried to maintain. Finally compiled special issue starts with a very interesting commentary on posttranslated modifications leading to normal and disease-associated biological functions, contributed by T. M. Karve and A. K. Cheema. This is followed by the analysis of a specific biological system of ATP synthetase, contributed by Z. Ahmad et al., exploring its catalytic sites and focusing on charged residues. R. Prasad et al. then describe a related system of ABC transporters and review the state of the knowledge on its functional residues. Functional residues in a protein do not always follow a universal pattern, and this is demonstrated by R. Kumar et al. in describing the dynamic structure of estrogen receptors. This paper is then followed by a special group of functional residues, that is, cysteins in sulfurtransferases by N. Nagahara. Viola et al. present an excellent study of catalytic machinery in the biosynthesis of amino acids. Subsequntly, K. M. Fukasawa et al. then present their analysis of functionally relevant zinc-binding sites in metalloproteases. Subsequently, M. S. Khan et al. provide an elaborate discussion on the mechanism of serpin inhibition, specially focusing on the role of polymerization. Finally, M. A. Kabir et al. present an investigation of a eukaryotic chaperon, involved in protein-folding. \u0000 \u0000Thus, the special issue covers a wide range of systems and describes an overview of some of the most significant studies on the subject of finding functional residues in proteins. We would like to express our most sincere gratitude to the authors who agreed to contribute and referees who provided useful feedback, allowing the papers to meet the high standards of publication. \u0000 \u0000We hope that the readers of Journal of Amino Acids will find these articles of great interest and look forward to any comments to improve our future efforts. \u0000 \u0000 \u0000Shandar Ahmad \u0000 \u0000Jung-Ying Wang \u0000 \u0000Zulfiqar Ahmad \u0000 \u0000Faizan Ahmad","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":" ","pages":"606354"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4061/2011/606354","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39968065","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functionally Relevant Residues of Cdr1p: A Multidrug ABC Transporter of Human Pathogenic Candida albicans.","authors":"Rajendra Prasad,&nbsp;Monika Sharma,&nbsp;Manpreet Kaur Rawal","doi":"10.4061/2011/531412","DOIUrl":"https://doi.org/10.4061/2011/531412","url":null,"abstract":"<p><p>Reduced intracellular accumulation of drugs (due to rapid efflux) mediated by the efflux pump proteins belonging to ABC (ATP Binding Cassette) and MFS (Major Facilitators) superfamily is one of the most common strategies adopted by multidrug resistance (MDR) pathogenic yeasts. To combat MDR, it is essential to understand the structure and function of these transporters so that inhibitors/modulators to these can be developed. The sequence alignments of the ABC transporters reveal selective divergence within much conserved domains of Nucleotide-Binding Domains (NBDs) which is unique to all fungal transporters. Recently, the role of conserved but divergent residues of Candida Drug Resistance 1 (CDR1), an ABC drug transporter of human pathogenic Candida albicans, has been examined with regard to ATP binding and hydrolysis. In this paper, we focus on some of the recent advances on the relevance of divergent and conserved amino acids of CaCdr1p and also discuss as to how drug interacts with Trans Membrane Domains (TMDs) residues for its extrusion from MDR cells.</p>","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":" ","pages":"531412"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4061/2011/531412","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39968544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Peptides regulate cortical thymocytes differentiation, proliferation, and apoptosis.","authors":"V Kh Khavinson,&nbsp;V O Polyakova,&nbsp;N S Linkova,&nbsp;A V Dudkov,&nbsp;I M Kvetnoy","doi":"10.4061/2011/517137","DOIUrl":"https://doi.org/10.4061/2011/517137","url":null,"abstract":"The processes of differentiation, proliferation, and apoptosis were studied in a cell culture of human cortical thymocytes under the influence of short peptides T-32 (Glu-Asp-Ala) and T-38 (Lys-Glu-Asp). Peptides T-32 and T-38 amplified cortical thymocytes differentiation towards regulatory T cells, increased their proliferative activity, and decreased the level of apoptosis. Moreover, peptides under study stimulated proliferative and antiapoptotic activity of the mature regulatory T cells.","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":" ","pages":"517137"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4061/2011/517137","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39968546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The catalytic machinery of a key enzyme in amino Acid biosynthesis.","authors":"Ronald E Viola,&nbsp;Christopher R Faehnle,&nbsp;Julio Blanco,&nbsp;Roger A Moore,&nbsp;Xuying Liu,&nbsp;Buenafe T Arachea,&nbsp;Alexander G Pavlovsky","doi":"10.4061/2011/352538","DOIUrl":"https://doi.org/10.4061/2011/352538","url":null,"abstract":"<p><p>The aspartate pathway of amino acid biosynthesis is essential for all microbial life but is absent in mammals. Characterizing the enzyme-catalyzed reactions in this pathway can identify new protein targets for the development of antibiotics with unique modes of action. The enzyme aspartate β-semialdehyde dehydrogenase (ASADH) catalyzes an early branch point reaction in the aspartate pathway. Kinetic, mutagenic, and structural studies of ASADH from various microbial species have been used to elucidate mechanistic details and to identify essential amino acids involved in substrate binding, catalysis, and enzyme regulation. Important structural and functional differences have been found between ASADHs isolated from these bacterial and fungal organisms, opening the possibility for developing species-specific antimicrobial agents that target this family of enzymes.</p>","PeriodicalId":14901,"journal":{"name":"Journal of Amino Acids","volume":"2011 ","pages":"352538"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4061/2011/352538","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30458577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}