Monarch butterflies (Danaus plexippus) use bright orange coloration to warn off predators as well... more Monarch butterflies (Danaus plexippus) use bright orange coloration to warn off predators as well as for sexual selection. Surprisingly the underlying pigment compounds have not been previously characterized. We used LCMS and fragmentation MS (including MSMS and MSn) of extracted pigments from nonmigratory summer-generation female monarch forewings to identify and provide relative quantitation of various orange pigments from D. plexippus. We observed seven ommochrome pigments, with xanthommatin and decarboxylated xanthommatin being the most abundant followed by xanthommatin methyl ester. Among the seven pigments, we also observed molecules that correspond to deaminated forms of these three amine-containing pigments. To the best of our knowledge, these deaminated compounds have not been previously discovered. A seventh pigment that we observed was α-hydroxyxanthommatin methyl ester, previously described in other nymphalid butterflies. We also show that chemical reduction of pigment extracts results in a change of their color from yellow to red, concomitant with the appearance of dihydro-xanthommatin and similarly reduced forms of the other pigment compounds. These findings indicate that monarchs may employ differences in the redox states of these pigments in order to achieve different hues of orange.
The coat protein from the MS2 bacteriophage plays a dual role by encapsidating viral RNA and also... more The coat protein from the MS2 bacteriophage plays a dual role by encapsidating viral RNA and also by binding RNA as a translational repressor. In order to study the isolated dimer in a conformation not influenced by capsid interactions, a mutant molecule was crystallized that is defective in capsid assembly but is an active repressor. The unassembled dimer crystallized in the space group P2]2]2 with a = 76.2, b = 55.7, and c = 28.4 A. In these crystals, monomers were related by twofold symmetry. When this dimer was co-crystallized with 5-bromouridine, crystals formed in space group R3 with a = b = 155.9 A, c = 29.9 A, y = 120"; the dimer was the asymmetric unit.
Proteomic biomarker discovery has been called into question. Diamandis hypothesized that seemingl... more Proteomic biomarker discovery has been called into question. Diamandis hypothesized that seemingly trivial factors, such as eating a hamburger, may cause sufficient proteomic change as to confound proteomic differences. This has been termed the hamburger effect. Little is known about the variability of complex proteomes in response to the environment. Two methods-two-dimensional gel electrophoresis (2DGE) and capillary liquid chromatography-electrospray ionization time-of-flight mass spectrometry (LCMS)-were used to study the hamburger effect in two cross-sections of the soluble fruit fly proteome. 2DGE measured abundant proteins, whereas LCMS measured small proteins and peptides. Proteomic differences between males and females were first evaluated to assess the discriminatory capability of the methods. Likewise, wild-type and white-eyed flies were analyzed as a further demonstration that genetically based proteomic differences could be observed above the background analytical variation. Then dietary interventions were imposed. Ethanol was added to the diet of some populations without significant proteomic effect. However, after a 24-h fast, proteomic differences were found using LCMS but not 2DGE. Even so, only three of approximately 1000 molecular species were altered significantly, suggesting that the influence of even an extreme diet change produced only modest proteomic variability, and that much of the fruit fly proteome remains relatively constant in response to diet. These experiments suggest that proteomics can be a viable approach to biomarker discovery.
Human furin catalyzes the proteolytic maturation of many proproteins in the exocytic and endocyti... more Human furin catalyzes the proteolytic maturation of many proproteins in the exocytic and endocytic secretory pathways by cleavage at the C-terminal side of the consensus sequence-ArgXaaLys/ArgArglk-. Both the trans-Golgi network (TGN) concentration and intracellular routing of furin require sequences in its 56 amino acid cytoplasmic tail. Here, we show that the furin cytoplasmic tail contains multiple trafficking signals. Localization to the TGN requires a cluster of acidic amino acids that, together with a pair of serine residues, forms a casein kinase II (CK II) phosphorylation site. We show that CK II efficiently phosphorylates these serines in vitro, and using a permeabilized cell system we provide evidence that CK II is the in vivo furin kinase. Analysis by mass spectrometry shows that, in vivo, furin exists as di-, mono-and nonphosphorylated forms. Finally, employing (i) furin constructs that mimic either non-phosphorylated or phosphorylated furin and (ii) the phosphatase inhibitor tautomycin, we show that the phosphorylation state of the furin cytoplasmic tail modulates retrieval of the endoprotease to the TGN. Thus, routing of furin is a two-tiered process combining a set of trafficking signals comprised of the primary amino acid sequence of the tail with its phosphorylation state.
The four Trp dipoles in the gramicidin A (gA) channel modulate channel conductance, and their sid... more The four Trp dipoles in the gramicidin A (gA) channel modulate channel conductance, and their side chain conformations should therefore be important, but the energies of different conformations are unknown. A conformational search for the right-handed helix based on molecular mechanics in vacuo yielded 46 conformations within 20 kcal/mol of the lowest energy conformation. The two lowest energy conformations correspond to the solid-state and solution-state NMR conformations, suggesting that interactions within the peptide determine the conformation. For representative conformations, the electrostatic potential of the Trp side chains on the channel axis was computed. A novel application of the image-series method of Neumcke and La ¨uger (1969. Biophys. J. 9:1160 -1170) was introduced to simulate the polarization of bulk water by the Trp side chains. For the experimentally observed structures, the CHARm toph19 potential energy (PE) of a cation in the channel center is Ϫ1.65 kcal/mol without images. With images, the PE is Ϫ1.9 kcal/mol, demonstrating that the images further enhance the direct dipole effect. Nonstandard conformations yielded less favorable PEs by 0.4 -1.1 kcal/mol.
Rapid communications in mass spectrometry : RCM, 2009
The low-abundance, low molecular weight serum proteome has high potential for the discovery of ne... more The low-abundance, low molecular weight serum proteome has high potential for the discovery of new biomarkers using mass spectrometry (MS). Because the serum proteome is large and complex, defining relative quantitative differences for a molecular species between comparison groups requires an approach with robust separation capability, high sensitivity, as well as high mass resolution. Capillary liquid chromatography (cLC)/MS provides both the necessary separation technique and the sensitivity to observe many low-abundance peptides. Subsequent identification of potential serum peptide biomarkers observed in the cLC/MS step can in principle be accomplished by in series cLC/MS/MS without further sample preparation or additional instrumentation. In this report a novel cLC/MS/MS method for peptide sequencing is described that surpasses previously reported size limits for amino acid sequencing accomplished by collisional fragmentation using a tandem time-of-flight MS instrument. As a dem...
Journal of Automated Methods and Management …, 2008
Foodborne illness presents a public health challenge in USA. There is an urgent need for the fede... more Foodborne illness presents a public health challenge in USA. There is an urgent need for the federal government and food industries to expand efforts to prevent any food contamination that potentially could be harmful to human health. The Food Safety Laboratory (FSL), ARS, USDA, is one of the leading laboratories for the development of optoelectronic sensing technologies and methodologies, successfully demonstrating several cutting-edge systems for detection and inspection of food quality, safety, sanitation, and security. The sensing technologies and systems include Raman, fluorescence, and visible/near infrared reflectance spectroscopies, as well as hyperspectral and multispectral imaging. A brief overview of the FSL approaches for food safety research and development in addition to applications of rapid hyperspectral and multispectral image-based online safety inspection for apples and chicken carcasses is presented.
Protein phosphorylation is a common post-translational modification of enormous biological import... more Protein phosphorylation is a common post-translational modification of enormous biological importance. Analysis of phosphorylation at the global level should shed light on the use of this modification to regulate metabolism, signal transduction, and other processes. We have begun a proteomic analysis of phosphorylation using two-dimensional gel electrophoresis. Chinese hamster ovary (CHO) cells were metabolically labeled using 32P-orthophosphate. The proteins were extracted and run on two-dimensional electrophoresis. Gels were stained using colloidal Coomassie stain, dried, and phosphorimaged. The Coomassie stain allowed the observation of 468 individual protein spots. The phosphorimage showed 181 spots. The phosphoproteome of CHO cells therefore comprises around one third as many proteins as the CHO cell abundance proteome. However, the most intense spots in the phosphoproteome usually do not correlate with intense spots in the abundance proteome. We investigated the effects of lab...
To detect diseases early in the general population, new diag-nostic approaches are needed that ha... more To detect diseases early in the general population, new diag-nostic approaches are needed that have adequate sensitivity and specificity. Recent studies have used mass spectrometry to identify a serum proteomic pattern for breast and ovarian cancer. Serum contains 60–80 mg/mL protein, but 57–71 % of this is serum albumin, and 8–26 % are -globulins.These large proteins must be depleted before smaller, less-abundant pro-teins can be detected using mass spectrometry, but because serum albumin is known to act as a carrier for smaller pro-teins, removal of these molecules using columns or filtration may result in the loss of molecules of interest.The objective of this study was to develop a reproducible method to deplete serum samples of high-abundance proteins in order to analyze the less-abundant proteins present in serum.We used organic solvents to precipitate the large proteins out of
Because blood interacts with almost all tissues of the body, it is likely that changes in the ove... more Because blood interacts with almost all tissues of the body, it is likely that changes in the overall health of an organism will be reflected in the quantities of specific serum peptides and proteins, making them biomarkers. Due to the complexity of serum, pre-analytical sample simplification and separation are needed prior to mass spectrometric analysis. Use of a reverse-phase capillary column coupled to a mass spectrometer allows for separation and analysis of serum as part of efforts to discover biomarkers. Even after sample simplification by organic solvent precipitation, data files for a single sample typically exceed one gigabyte, making it difficult to analyze complete serum mass spectrometry profiles with currently available software. However, with adequate safeguards, it appears possible to consider portions of mass spectra to find differences in peak intensities between clinical comparison groups visually. To facilitate this, the elution profile was divided into 2-min inte...
To detect diseases early in the general population, new diagnostic approaches are needed that hav... more To detect diseases early in the general population, new diagnostic approaches are needed that have adequate sensitivity and specificity. Recent studies have used mass spectrometry to identify a serum proteomic pattern for breast and ovarian cancer. Serum contains 60-80 mg/mL protein, but 57-71% of this is serum albumin, and 8-26% are gamma-globulins. These large proteins must be depleted before smaller, less-abundant proteins can be detected using mass spectrometry, but because serum albumin is known to act as a carrier for smaller proteins, removal of these molecules using columns or filtration may result in the loss of molecules of interest. The objective of this study was to develop a reproducible method to deplete serum samples of high-abundance proteins in order to analyze the less-abundant proteins present in serum. We used organic solvents to precipitate the large proteins out of solution. We also predicted that this would cause many smaller proteins to dissociate from their ...
Purpose: To elucidate the origins of biologically active retinal lipofuscin (RLF) by examining it... more Purpose: To elucidate the origins of biologically active retinal lipofuscin (RLF) by examining its protein composition. Methods: Total protein and total lipid were extracted and quantified. Proteins in this lipoprotein granule were identified by limited-scale proteomic analysis using both two-dimensional (2D) gel electrophoresis and SDS-PAGE coupled with MALDI-QqToF MSMS and automated LCMSMS, respectively. Results: RLF granules were 44% protein and 50% lipid. Proteomic analyses identified 41 constituent proteins. Hydrophobic proteins and several proteins specific to photoreceptors, including rhodopsin, that have not previously been reported, were identified. Extensive protein modification, especially oxidative damage, was observed. Conclusions: Proteins identified support the model that RLF accumulates in RPE cells as a result of the buildup of undigested material from the phagocytosis of photoreceptor outer segments. Perhaps oxidative damage renders some of these proteins indigestible and thus leads to the accumulation of RLF granules.
Monarch butterflies (Danaus plexippus) use bright orange coloration to warn off predators as well... more Monarch butterflies (Danaus plexippus) use bright orange coloration to warn off predators as well as for sexual selection. Surprisingly the underlying pigment compounds have not been previously characterized. We used LCMS and fragmentation MS (including MSMS and MSn) of extracted pigments from nonmigratory summer-generation female monarch forewings to identify and provide relative quantitation of various orange pigments from D. plexippus. We observed seven ommochrome pigments, with xanthommatin and decarboxylated xanthommatin being the most abundant followed by xanthommatin methyl ester. Among the seven pigments, we also observed molecules that correspond to deaminated forms of these three amine-containing pigments. To the best of our knowledge, these deaminated compounds have not been previously discovered. A seventh pigment that we observed was α-hydroxyxanthommatin methyl ester, previously described in other nymphalid butterflies. We also show that chemical reduction of pigment extracts results in a change of their color from yellow to red, concomitant with the appearance of dihydro-xanthommatin and similarly reduced forms of the other pigment compounds. These findings indicate that monarchs may employ differences in the redox states of these pigments in order to achieve different hues of orange.
The coat protein from the MS2 bacteriophage plays a dual role by encapsidating viral RNA and also... more The coat protein from the MS2 bacteriophage plays a dual role by encapsidating viral RNA and also by binding RNA as a translational repressor. In order to study the isolated dimer in a conformation not influenced by capsid interactions, a mutant molecule was crystallized that is defective in capsid assembly but is an active repressor. The unassembled dimer crystallized in the space group P2]2]2 with a = 76.2, b = 55.7, and c = 28.4 A. In these crystals, monomers were related by twofold symmetry. When this dimer was co-crystallized with 5-bromouridine, crystals formed in space group R3 with a = b = 155.9 A, c = 29.9 A, y = 120"; the dimer was the asymmetric unit.
Proteomic biomarker discovery has been called into question. Diamandis hypothesized that seemingl... more Proteomic biomarker discovery has been called into question. Diamandis hypothesized that seemingly trivial factors, such as eating a hamburger, may cause sufficient proteomic change as to confound proteomic differences. This has been termed the hamburger effect. Little is known about the variability of complex proteomes in response to the environment. Two methods-two-dimensional gel electrophoresis (2DGE) and capillary liquid chromatography-electrospray ionization time-of-flight mass spectrometry (LCMS)-were used to study the hamburger effect in two cross-sections of the soluble fruit fly proteome. 2DGE measured abundant proteins, whereas LCMS measured small proteins and peptides. Proteomic differences between males and females were first evaluated to assess the discriminatory capability of the methods. Likewise, wild-type and white-eyed flies were analyzed as a further demonstration that genetically based proteomic differences could be observed above the background analytical variation. Then dietary interventions were imposed. Ethanol was added to the diet of some populations without significant proteomic effect. However, after a 24-h fast, proteomic differences were found using LCMS but not 2DGE. Even so, only three of approximately 1000 molecular species were altered significantly, suggesting that the influence of even an extreme diet change produced only modest proteomic variability, and that much of the fruit fly proteome remains relatively constant in response to diet. These experiments suggest that proteomics can be a viable approach to biomarker discovery.
Human furin catalyzes the proteolytic maturation of many proproteins in the exocytic and endocyti... more Human furin catalyzes the proteolytic maturation of many proproteins in the exocytic and endocytic secretory pathways by cleavage at the C-terminal side of the consensus sequence-ArgXaaLys/ArgArglk-. Both the trans-Golgi network (TGN) concentration and intracellular routing of furin require sequences in its 56 amino acid cytoplasmic tail. Here, we show that the furin cytoplasmic tail contains multiple trafficking signals. Localization to the TGN requires a cluster of acidic amino acids that, together with a pair of serine residues, forms a casein kinase II (CK II) phosphorylation site. We show that CK II efficiently phosphorylates these serines in vitro, and using a permeabilized cell system we provide evidence that CK II is the in vivo furin kinase. Analysis by mass spectrometry shows that, in vivo, furin exists as di-, mono-and nonphosphorylated forms. Finally, employing (i) furin constructs that mimic either non-phosphorylated or phosphorylated furin and (ii) the phosphatase inhibitor tautomycin, we show that the phosphorylation state of the furin cytoplasmic tail modulates retrieval of the endoprotease to the TGN. Thus, routing of furin is a two-tiered process combining a set of trafficking signals comprised of the primary amino acid sequence of the tail with its phosphorylation state.
The four Trp dipoles in the gramicidin A (gA) channel modulate channel conductance, and their sid... more The four Trp dipoles in the gramicidin A (gA) channel modulate channel conductance, and their side chain conformations should therefore be important, but the energies of different conformations are unknown. A conformational search for the right-handed helix based on molecular mechanics in vacuo yielded 46 conformations within 20 kcal/mol of the lowest energy conformation. The two lowest energy conformations correspond to the solid-state and solution-state NMR conformations, suggesting that interactions within the peptide determine the conformation. For representative conformations, the electrostatic potential of the Trp side chains on the channel axis was computed. A novel application of the image-series method of Neumcke and La ¨uger (1969. Biophys. J. 9:1160 -1170) was introduced to simulate the polarization of bulk water by the Trp side chains. For the experimentally observed structures, the CHARm toph19 potential energy (PE) of a cation in the channel center is Ϫ1.65 kcal/mol without images. With images, the PE is Ϫ1.9 kcal/mol, demonstrating that the images further enhance the direct dipole effect. Nonstandard conformations yielded less favorable PEs by 0.4 -1.1 kcal/mol.
Rapid communications in mass spectrometry : RCM, 2009
The low-abundance, low molecular weight serum proteome has high potential for the discovery of ne... more The low-abundance, low molecular weight serum proteome has high potential for the discovery of new biomarkers using mass spectrometry (MS). Because the serum proteome is large and complex, defining relative quantitative differences for a molecular species between comparison groups requires an approach with robust separation capability, high sensitivity, as well as high mass resolution. Capillary liquid chromatography (cLC)/MS provides both the necessary separation technique and the sensitivity to observe many low-abundance peptides. Subsequent identification of potential serum peptide biomarkers observed in the cLC/MS step can in principle be accomplished by in series cLC/MS/MS without further sample preparation or additional instrumentation. In this report a novel cLC/MS/MS method for peptide sequencing is described that surpasses previously reported size limits for amino acid sequencing accomplished by collisional fragmentation using a tandem time-of-flight MS instrument. As a dem...
Journal of Automated Methods and Management …, 2008
Foodborne illness presents a public health challenge in USA. There is an urgent need for the fede... more Foodborne illness presents a public health challenge in USA. There is an urgent need for the federal government and food industries to expand efforts to prevent any food contamination that potentially could be harmful to human health. The Food Safety Laboratory (FSL), ARS, USDA, is one of the leading laboratories for the development of optoelectronic sensing technologies and methodologies, successfully demonstrating several cutting-edge systems for detection and inspection of food quality, safety, sanitation, and security. The sensing technologies and systems include Raman, fluorescence, and visible/near infrared reflectance spectroscopies, as well as hyperspectral and multispectral imaging. A brief overview of the FSL approaches for food safety research and development in addition to applications of rapid hyperspectral and multispectral image-based online safety inspection for apples and chicken carcasses is presented.
Protein phosphorylation is a common post-translational modification of enormous biological import... more Protein phosphorylation is a common post-translational modification of enormous biological importance. Analysis of phosphorylation at the global level should shed light on the use of this modification to regulate metabolism, signal transduction, and other processes. We have begun a proteomic analysis of phosphorylation using two-dimensional gel electrophoresis. Chinese hamster ovary (CHO) cells were metabolically labeled using 32P-orthophosphate. The proteins were extracted and run on two-dimensional electrophoresis. Gels were stained using colloidal Coomassie stain, dried, and phosphorimaged. The Coomassie stain allowed the observation of 468 individual protein spots. The phosphorimage showed 181 spots. The phosphoproteome of CHO cells therefore comprises around one third as many proteins as the CHO cell abundance proteome. However, the most intense spots in the phosphoproteome usually do not correlate with intense spots in the abundance proteome. We investigated the effects of lab...
To detect diseases early in the general population, new diag-nostic approaches are needed that ha... more To detect diseases early in the general population, new diag-nostic approaches are needed that have adequate sensitivity and specificity. Recent studies have used mass spectrometry to identify a serum proteomic pattern for breast and ovarian cancer. Serum contains 60–80 mg/mL protein, but 57–71 % of this is serum albumin, and 8–26 % are -globulins.These large proteins must be depleted before smaller, less-abundant pro-teins can be detected using mass spectrometry, but because serum albumin is known to act as a carrier for smaller pro-teins, removal of these molecules using columns or filtration may result in the loss of molecules of interest.The objective of this study was to develop a reproducible method to deplete serum samples of high-abundance proteins in order to analyze the less-abundant proteins present in serum.We used organic solvents to precipitate the large proteins out of
Because blood interacts with almost all tissues of the body, it is likely that changes in the ove... more Because blood interacts with almost all tissues of the body, it is likely that changes in the overall health of an organism will be reflected in the quantities of specific serum peptides and proteins, making them biomarkers. Due to the complexity of serum, pre-analytical sample simplification and separation are needed prior to mass spectrometric analysis. Use of a reverse-phase capillary column coupled to a mass spectrometer allows for separation and analysis of serum as part of efforts to discover biomarkers. Even after sample simplification by organic solvent precipitation, data files for a single sample typically exceed one gigabyte, making it difficult to analyze complete serum mass spectrometry profiles with currently available software. However, with adequate safeguards, it appears possible to consider portions of mass spectra to find differences in peak intensities between clinical comparison groups visually. To facilitate this, the elution profile was divided into 2-min inte...
To detect diseases early in the general population, new diagnostic approaches are needed that hav... more To detect diseases early in the general population, new diagnostic approaches are needed that have adequate sensitivity and specificity. Recent studies have used mass spectrometry to identify a serum proteomic pattern for breast and ovarian cancer. Serum contains 60-80 mg/mL protein, but 57-71% of this is serum albumin, and 8-26% are gamma-globulins. These large proteins must be depleted before smaller, less-abundant proteins can be detected using mass spectrometry, but because serum albumin is known to act as a carrier for smaller proteins, removal of these molecules using columns or filtration may result in the loss of molecules of interest. The objective of this study was to develop a reproducible method to deplete serum samples of high-abundance proteins in order to analyze the less-abundant proteins present in serum. We used organic solvents to precipitate the large proteins out of solution. We also predicted that this would cause many smaller proteins to dissociate from their ...
Purpose: To elucidate the origins of biologically active retinal lipofuscin (RLF) by examining it... more Purpose: To elucidate the origins of biologically active retinal lipofuscin (RLF) by examining its protein composition. Methods: Total protein and total lipid were extracted and quantified. Proteins in this lipoprotein granule were identified by limited-scale proteomic analysis using both two-dimensional (2D) gel electrophoresis and SDS-PAGE coupled with MALDI-QqToF MSMS and automated LCMSMS, respectively. Results: RLF granules were 44% protein and 50% lipid. Proteomic analyses identified 41 constituent proteins. Hydrophobic proteins and several proteins specific to photoreceptors, including rhodopsin, that have not previously been reported, were identified. Extensive protein modification, especially oxidative damage, was observed. Conclusions: Proteins identified support the model that RLF accumulates in RPE cells as a result of the buildup of undigested material from the phagocytosis of photoreceptor outer segments. Perhaps oxidative damage renders some of these proteins indigestible and thus leads to the accumulation of RLF granules.
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Papers by Craig Thulin