Pub Date : 2008-04-22DOI: 10.2174/1874383800802010001
R. D'Agata, G. Grasso, G. Spoto
Surface Plasmon Resonance Imaging (SPRI) is an optical technique emerged as a powerful tool for the simul- taneous monitoring of interactions of biomolecules arrayed onto gold substrates. To take fully advantage of the SPRI ap- proach a precise control of the fluidic of the analyte solution is imposed. The diffusion between the flowing buffer and the analyte solution which is established within the fluidic system creates a liquid volume where a gradient in the analyte con- centration is present. Such gradient is shown to affect the kinetics parameters obtained from the SPRI response. We pre- sent results obtained from a new delivery approach based on the use of air bubbles. The advantages offered by the new approach are demonstrated by using two different interacting biomolecular systems: the streptavidin-biotin system and the Ricinus Communis Agglutinin lectin-asialofetuin.
{"title":"Real-Time Binding Kinetics Monitored with Surface Plasmon Resonance Imaging in a Diffusion-Free Environment","authors":"R. D'Agata, G. Grasso, G. Spoto","doi":"10.2174/1874383800802010001","DOIUrl":"https://doi.org/10.2174/1874383800802010001","url":null,"abstract":"Surface Plasmon Resonance Imaging (SPRI) is an optical technique emerged as a powerful tool for the simul- taneous monitoring of interactions of biomolecules arrayed onto gold substrates. To take fully advantage of the SPRI ap- proach a precise control of the fluidic of the analyte solution is imposed. The diffusion between the flowing buffer and the analyte solution which is established within the fluidic system creates a liquid volume where a gradient in the analyte con- centration is present. Such gradient is shown to affect the kinetics parameters obtained from the SPRI response. We pre- sent results obtained from a new delivery approach based on the use of air bubbles. The advantages offered by the new approach are demonstrated by using two different interacting biomolecular systems: the streptavidin-biotin system and the Ricinus Communis Agglutinin lectin-asialofetuin.","PeriodicalId":88758,"journal":{"name":"The open spectroscopy journal","volume":"2 1","pages":"1-9"},"PeriodicalIF":0.0,"publicationDate":"2008-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68069597","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}
Pub Date : 2008-04-22DOI: 10.2174/1874383800802010010
Kai Schwedhelm, Martin Horstmann, J. Faber, Yana Reichert, M. Büchner, G. Bringmann, C. Faber
Complex formation between the antimalarial drug chloroquine and its presumed target ferriprotoporphyrin IX in three different solutions (pH 6.5, pH 9, and in a water methanol mixture) is characterized by nuclear magnetic resonance, UV spectroscopy, and mass spectrometry. NMR paramagnetic relaxation measurements are used to derive intermolecular distances between the molecules and model structures of the complexes are calculated by molecular dynamics simulations. Observation of an unusual spin state in NMR measurements leads to the postulation of a novel 4:2 stoichiometry of the complex, which is supported by mass spectrometry and UV spectroscopy.
{"title":"Spin State of Chloroquine-Heme Complexes: Formation of a Hemin Tetramer Adduct","authors":"Kai Schwedhelm, Martin Horstmann, J. Faber, Yana Reichert, M. Büchner, G. Bringmann, C. Faber","doi":"10.2174/1874383800802010010","DOIUrl":"https://doi.org/10.2174/1874383800802010010","url":null,"abstract":"Complex formation between the antimalarial drug chloroquine and its presumed target ferriprotoporphyrin IX in three different solutions (pH 6.5, pH 9, and in a water methanol mixture) is characterized by nuclear magnetic resonance, UV spectroscopy, and mass spectrometry. NMR paramagnetic relaxation measurements are used to derive intermolecular distances between the molecules and model structures of the complexes are calculated by molecular dynamics simulations. Observation of an unusual spin state in NMR measurements leads to the postulation of a novel 4:2 stoichiometry of the complex, which is supported by mass spectrometry and UV spectroscopy.","PeriodicalId":88758,"journal":{"name":"The open spectroscopy journal","volume":"2 1","pages":"10-18"},"PeriodicalIF":0.0,"publicationDate":"2008-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68069608","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}
Pub Date : 2007-11-09DOI: 10.2174/1874383800701010009
C. Pennington, Craig P. Dufresne, G. Fanciulli, T. D. Wood
Liquid chromatography-tandem mass spectrometry was employed to monitor for gluten exorphins (GEs) in blood from samples collected from Celiac Disease subjects after the consumption of a physiological meal. GE-B4 and B5 were detected in three of the four subjects, the first time GEs have been detected in human blood.
{"title":"Detection of Gluten Exorphin B4 and B5 in Human Blood by Liquid Chromatography-Mass Spectrometry/Mass Spectrometry","authors":"C. Pennington, Craig P. Dufresne, G. Fanciulli, T. D. Wood","doi":"10.2174/1874383800701010009","DOIUrl":"https://doi.org/10.2174/1874383800701010009","url":null,"abstract":"Liquid chromatography-tandem mass spectrometry was employed to monitor for gluten exorphins (GEs) in blood from samples collected from Celiac Disease subjects after the consumption of a physiological meal. GE-B4 and B5 were detected in three of the four subjects, the first time GEs have been detected in human blood.","PeriodicalId":88758,"journal":{"name":"The open spectroscopy journal","volume":"1 1","pages":"9-16"},"PeriodicalIF":0.0,"publicationDate":"2007-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68069580","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}
Pub Date : 2007-09-11DOI: 10.2174/1874383800701010001
Irina Fedulova, Zheng Ouyang, Charles R. Buck, Xiang Zhang
In recent years a number of de novo sequencing software products became available providing possible partial or complete amino acid sequence tags for MS/MS spectra of peptides. However, for a variety of reasons including spectral chemical noise and imperfect fragmentation these sequence tags almost always contain errors. Additional difficulties arise from actual protein sequence variation and post-translational modifications. We present a search engine named PepTiger which is capable of correctly matching de novo sequence tags with errors to protein sequences in a protein database. The algorithm is based on approximate string matching followed by a novel scoring procedure which takes into account mass differences and the string distance between de novo sequence and matched peptides and similarities between theoretical and experimental MS/MS spectra. Comparison of PepTiger with other protein identification software shows that PepTiger is better able to assign de novo sequence tags with errors to the correct peptide sequences.
{"title":"PepTiger: Search Engine for Error-Tolerant Protein Identification from de Novo Sequences","authors":"Irina Fedulova, Zheng Ouyang, Charles R. Buck, Xiang Zhang","doi":"10.2174/1874383800701010001","DOIUrl":"https://doi.org/10.2174/1874383800701010001","url":null,"abstract":"In recent years a number of de novo sequencing software products became available providing possible partial or complete amino acid sequence tags for MS/MS spectra of peptides. However, for a variety of reasons including spectral chemical noise and imperfect fragmentation these sequence tags almost always contain errors. Additional difficulties arise from actual protein sequence variation and post-translational modifications. We present a search engine named PepTiger which is capable of correctly matching de novo sequence tags with errors to protein sequences in a protein database. The algorithm is based on approximate string matching followed by a novel scoring procedure which takes into account mass differences and the string distance between de novo sequence and matched peptides and similarities between theoretical and experimental MS/MS spectra. Comparison of PepTiger with other protein identification software shows that PepTiger is better able to assign de novo sequence tags with errors to the correct peptide sequences.","PeriodicalId":88758,"journal":{"name":"The open spectroscopy journal","volume":"1 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2007-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68069541","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}
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