Methods of biochemical analysis最新文献

{"title":"Biochemical thermodynamics: applications of Mathematica.","authors":"Robert A Alberty","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The most efficient way to store thermodynamic data on enzyme-catalyzed reactions is to use matrices of species properties. Since equilibrium in enzyme-catalyzed reactions is reached at specified pH values, the thermodynamics of the reactions is discussed in terms of transformed thermodynamic properties. These transformed thermodynamic properties are complicated functions of temperature, pH, and ionic strength that can be calculated from the matrices of species values. The most important of these transformed thermodynamic properties is the standard transformed Gibbs energy of formation of a reactant (sum of species). It is the most important because when this function of temperature, pH, and ionic strength is known, all the other standard transformed properties can be calculated by taking partial derivatives. The species database in this package contains data matrices for 199 reactants. For 94 of these reactants, standard enthalpies of formation of species are known, and so standard transformed Gibbs energies, standard transformed enthalpies, standard transformed entropies, and average numbers of hydrogen atoms can be calculated as functions of temperature, pH, and ionic strength. For reactions between these 94 reactants, the changes in these properties can be calculated over a range of temperatures, pHs, and ionic strengths, and so can apparent equilibrium constants. For the other 105 reactants, only standard transformed Gibbs energies of formation and average numbers of hydrogen atoms at 298.15 K can be calculated. The loading of this package provides functions of pH and ionic strength at 298.15 K for standard transformed Gibbs energies of formation and average numbers of hydrogen atoms for 199 reactants. It also provides functions of temperature, pH, and ionic strength for the standard transformed Gibbs energies of formation, standard transformed enthalpies of formation, standard transformed entropies of formation, and average numbers of hydrogen atoms for 94 reactants. Thus loading this package makes available 774 mathematical functions for these properties. These functions can be added and subtracted to obtain changes in these properties in biochemical reactions and apparent equilibrium constants.</p>","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"48 ","pages":"1-458"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26174629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidation of mechanisms of acid stress in Listeria monocytogenes by proteomic analysis.","authors":"Luu Phan-Thanh,&nbsp;Lothar Jänsch","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"49 ","pages":"75-88"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26275544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tale of two metal reducers: comparative proteome analysis of Geobacter sulferreducens PCA and Shewanella oneidensis MR-1.","authors":"Carol S Giometti","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Geobacter sulfurreducens and S. oneidensis are the subjects of intense research efforts due to their potential applications to bioremediation. The characterization of their proteomes, being done in parallel with the analysis of their genome sequences, transcriptomes, and metabolomes, is providing valuable insights to both their similarities and their differences. A primary target of interest in the proteomes of both of these metal-reducing microbes is the characterization of their c-type cytochromes. The discovery of their full compliment of c-type cytochromes and the description of what growth conditions trigger their expression is central to harnessing their bioremediation potential. Proteome analyses thus far show that both G. sulfurreducens and S. oneidensis share the common location of a majority of their c-type cytochromes in their outer membranes. The c-type cytochromes of G. sulfurreducens, however, appear to be less soluble and therefore more difficult to isolate from the membranes than those expressed by S. oneidensis. The majority of the G. sulfurreducens c-type cytochromes also differ from those of S. oneidensis in that they have higher isoelectric points, most higher than pH 8.0. These characteristics of solubility and isoelectric point could be related and could indicate an underlying functional difference in the strategy for metal reduction between these two microbes. The global proteome results available for G. sulfurreducens and S. oneidensis at the time of this writing are primarily the result of 2DE analysis coupled to protein identification by LC-MS/MS of tryptic peptides from in-gel digests and represent the most abundant proteins detected by Coomassie blue or silver nitrate staining. Currently, several complimentary efforts utilising the 2D-LC-MS/MS approaches are in progress, promising a more complete protein inventory for these microbes in the near future. As these data are added to those already available, the intricate network of metabolic processes, regulation of protein synthesis and protein function, transport of nutrients, and signal transduction will be elucidated. The existing tools of proteomics will be complimented with newer methods such as protein chips and phage display to further characterize these microbial systems. The end result, in the not too distant future, will be predictive models of G. sulfurreducens and S. oneidensis behavior in their natural habitats under a variety of environmental conditions.</p>","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"49 ","pages":"97-111"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26275546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Green fluorescent protein applications in Drosophila.","authors":"Tulle Hazelrigg,&nbsp;Jennifer H Mansfield","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"47 ","pages":"227-57"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25727945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analyzing bacterial pathogenesis at level of proteome.","authors":"P. Cash","doi":"10.1002/0471973165.CH13","DOIUrl":"https://doi.org/10.1002/0471973165.CH13","url":null,"abstract":"","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"26 1","pages":"211-35"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83251700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tale of two metal reducers: comparative proteome analysis of Geobacter sulferreducens PCA and Shewanella oneidensis MR-1.","authors":"C. Giometti","doi":"10.1002/0471973165.CH8","DOIUrl":"https://doi.org/10.1002/0471973165.CH8","url":null,"abstract":"Geobacter sulfurreducens and S. oneidensis are the subjects of intense research efforts due to their potential applications to bioremediation. The characterization of their proteomes, being done in parallel with the analysis of their genome sequences, transcriptomes, and metabolomes, is providing valuable insights to both their similarities and their differences. A primary target of interest in the proteomes of both of these metal-reducing microbes is the characterization of their c-type cytochromes. The discovery of their full compliment of c-type cytochromes and the description of what growth conditions trigger their expression is central to harnessing their bioremediation potential. Proteome analyses thus far show that both G. sulfurreducens and S. oneidensis share the common location of a majority of their c-type cytochromes in their outer membranes. The c-type cytochromes of G. sulfurreducens, however, appear to be less soluble and therefore more difficult to isolate from the membranes than those expressed by S. oneidensis. The majority of the G. sulfurreducens c-type cytochromes also differ from those of S. oneidensis in that they have higher isoelectric points, most higher than pH 8.0. These characteristics of solubility and isoelectric point could be related and could indicate an underlying functional difference in the strategy for metal reduction between these two microbes. The global proteome results available for G. sulfurreducens and S. oneidensis at the time of this writing are primarily the result of 2DE analysis coupled to protein identification by LC-MS/MS of tryptic peptides from in-gel digests and represent the most abundant proteins detected by Coomassie blue or silver nitrate staining. Currently, several complimentary efforts utilising the 2D-LC-MS/MS approaches are in progress, promising a more complete protein inventory for these microbes in the near future. As these data are added to those already available, the intricate network of metabolic processes, regulation of protein synthesis and protein function, transport of nutrients, and signal transduction will be elucidated. The existing tools of proteomics will be complimented with newer methods such as protein chips and phage display to further characterize these microbial systems. The end result, in the not too distant future, will be predictive models of G. sulfurreducens and S. oneidensis behavior in their natural habitats under a variety of environmental conditions.","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"2 1","pages":"97-111"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83465699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery and properties of GFP-like proteins from nonbioluminescent anthozoa.","authors":"K. Lukyanov, D. Chudakov, A. Fradkov, Y. Labas, M. Matz, S. Lukyanov","doi":"10.1002/0471739499.CH6","DOIUrl":"https://doi.org/10.1002/0471739499.CH6","url":null,"abstract":"","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"29 1","pages":"121-38"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73738099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic survey through secretome of Bacillus subtilis.","authors":"Haike Antelmann,&nbsp;Jan Maarten Van Dijl,&nbsp;Sierd Bron,&nbsp;Michael Hecker","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"49 ","pages":"179-208"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26275423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomics of Archaea.","authors":"Ricardo Cavicchioli,&nbsp;Amber Goodchild,&nbsp;Mark Raftery","doi":"10.1002/0471973165.ch5","DOIUrl":"https://doi.org/10.1002/0471973165.ch5","url":null,"abstract":"","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"49 ","pages":"57-72"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/0471973165.ch5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"26275543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolution of function and color in GFP-like proteins.","authors":"Mikhail V Matz,&nbsp;Yulii A Labas,&nbsp;Juan Ugalde","doi":"10.1002/0471739499.ch7","DOIUrl":"https://doi.org/10.1002/0471739499.ch7","url":null,"abstract":"","PeriodicalId":18579,"journal":{"name":"Methods of biochemical analysis","volume":"47 ","pages":"139-61"},"PeriodicalIF":0.0,"publicationDate":"2006-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/0471739499.ch7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25742848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}