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Batista APS, Teixeira ACSC, Cooper WJ, Cottrell BA. Correlating the chemical and spectroscopic characteristics of natural organic matter with the photodegradation of sulfamerazine. Water Res 2016; 93:20-29. [PMID: 26878479 DOI: 10.1016/j.watres.2015.11.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/10/2015] [Accepted: 11/14/2015] [Indexed: 06/05/2023]
Abstract
The role of aquatic natural organic matter (NOM) in the removal of contaminants of emerging concern has been widely studied. Sulfamerazine (SMR), a sulfonamide antibiotic detected in aquatic environments, is implicated in environmental toxicity and may contribute to the resistance of bacteria to antibiotics. In aquatic systems sulfonamides may undergo direct photodegradation, and, indirect photodegradation through the generation of reactive species. Because some forms of NOM inhibit the photodegradation there is an increasing interest in correlating the spectroscopic parameters of NOM as potential indicators of its degradation in natural waters. Under the conditions used in this study, SMR hydrolysis was shown to be negligible; however, direct photolysis is a significant in most of the solutions studied. Photodegradation was investigated using standard solutions of NOM: Suwannee River natural organic matter (SRNOM), Suwannee River humic acid (SRHA), Suwannee River fulvic acid (SRFA), and Aldrich humic acid (AHA). The steady-state concentrations and formation rates of the reactive species and the SMR degradation rate constants (k1) were correlated with NOM spectroscopic parameters determined using UV-vis absorption, excitation-emission matrix (EEM) fluorescence spectroscopy, and proton nuclear magnetic resonance ((1)H NMR). SMR degradation rate constants (k1) were correlated with steady-state concentrations of NOM triplet-excited state ([(3)NOM(∗)]ss) and the corresponding formation rates ((3)NOM*) for SRNOM, SRHA, and AHA. The efficiency of SMR degradation was highest in AHA solution and was inhibited in solutions of SRFA. The steady-state concentrations of singlet oxygen ([(1)O2]ss) and the SMR degradation rate constants with singlet oxygen (k1O2) were linearly correlated with the total fluorescence and inversely correlated with the carbohydrate/protein content ((1)H NMR) for all forms of NOM. The total fluorescence and EEMs Peak A were confirmed as indicators of (1)O2 formation. Specific ultraviolet absorbance at 254 nm (SUVA254) and aromaticity showed potential correlations with the steady-state concentrations of hydroxyl radical ([HO]ss) and the corresponding formation rates (HO).
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Affiliation(s)
- Ana Paula S Batista
- Chemical Engineering Department, School of Engineering, University of São Paulo, Av. Prof. Luciano Gualberto, 380, travessa 3, São Paulo, SP 05508-010, Brazil.
| | - Antonio Carlos S C Teixeira
- Chemical Engineering Department, School of Engineering, University of São Paulo, Av. Prof. Luciano Gualberto, 380, travessa 3, São Paulo, SP 05508-010, Brazil
| | - William J Cooper
- Department of Civil and Environmental Engineering, University of California, Irvine, Irvine, CA 92697-2175, USA
| | - Barbara A Cottrell
- Department of Civil and Environmental Engineering, University of California, Irvine, Irvine, CA 92697-2175, USA
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Lessard CB, Cottrell BA, Maruyama H, Suresh S, Golde TE, Koo EH. γ-Secretase Modulators and APH1 Isoforms Modulate γ-Secretase Cleavage but Not Position of ε-Cleavage of the Amyloid Precursor Protein (APP). PLoS One 2015; 10:e0144758. [PMID: 26678856 PMCID: PMC4683055 DOI: 10.1371/journal.pone.0144758] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/23/2015] [Indexed: 12/30/2022] Open
Abstract
The relative increase in Aβ42 peptides from familial Alzheimer disease (FAD) linked APP and PSEN mutations can be related to changes in both ε-cleavage site utilization and subsequent step-wise cleavage. Cleavage at the ε-site releases the amyloid precursor protein (APP) intracellular domain (AICD), and perturbations in the position of ε-cleavage are closely associated with changes in the profile of amyloid β-protein (Aβ) species that are produced and secreted. The mechanisms by which γ-secretase modulators (GSMs) or FAD mutations affect the various γ-secretase cleavages to alter the generation of Aβ peptides have not been fully elucidated. Recent studies suggested that GSMs do not modulate ε-cleavage of APP, but the data were derived principally from recombinant truncated epitope tagged APP substrate. Here, using full length APP from transfected cells, we investigated whether GSMs modify the ε-cleavage of APP under more native conditions. Our results confirmed the previous findings that ε-cleavage is insensitive to GSMs. In addition, fenofibrate, an inverse GSM (iGSM), did not alter the position or kinetics of ε-cleavage position in vitro. APH1A and APH1B, a subunit of the γ-secretase complex, also modulated Aβ42/Aβ40 ratio without any alterations in ε-cleavage, a result in contrast to what has been observed with PS1 and APP FAD mutations. Consequently, GSMs and APH1 appear to modulate γ-secretase activity and Aβ42 generation by altering processivity but not ε-cleavage site utilization.
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Affiliation(s)
- Christian B. Lessard
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Barbara A. Cottrell
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Hiroko Maruyama
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Suraj Suresh
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
| | - Todd E. Golde
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, College of Medicine, University of Florida, Florida, United States of America
| | - Edward H. Koo
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
- Departments of Medicine and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail:
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Batista APS, Cottrell BA, Nogueira RFP. Photochemical transformation of antibiotics by excitation of Fe(III)-complexes in aqueous medium. J Photochem Photobiol A Chem 2014. [DOI: 10.1016/j.jphotochem.2013.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cottrell BA, Timko SA, Devera L, Robinson AK, Gonsior M, Vizenor AE, Simpson AJ, Cooper WJ. Photochemistry of excited-state species in natural waters: a role for particulate organic matter. Water Res 2013; 47:5189-5199. [PMID: 23863383 DOI: 10.1016/j.watres.2013.05.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 05/28/2013] [Accepted: 05/31/2013] [Indexed: 06/02/2023]
Abstract
Laser flash photolysis (LFP) was used to characterize a triplet excited state species isolated from Black River and San Joaquin wetlands particulate organic matter (POM). The solubilized organic matter, isolated from POM by pH-independent diffusion in distilled water, was named PdOM. UV-visible absorption spectroscopy, excitation-emission matrix spectroscopy (EEMs), and (1)H NMR were used to characterize the PdOM. While LFP of dissolved organic matter (DOM) is known to generate the solvated electron, LFP of the PdOM transient in argon-, air-, and nitrous oxide-saturated solutions indicated that this was a triplet excited state species ((3)PdOM*). The lifetime and the reactivity of (3)PdOM* with sorbic acid, a triplet state quencher, were compared with that of the triplet excited state of benzophenone, a DOM proxy. A second excited state species (designated DOM*), with a longer lifetime, was reported in a number of previous studies but not characterized. The lifetime of DOM*, measured for seventeen organic matter isolates, lignin, tannic acid, and three wetlands plant extracts, was shown to differentiate allochthonous from autochthonous DOM. (3)POM* and DOM* were also observed in lake water and a constructed wetlands' water. Aqueous extracts of fresh and aged plant material from the same wetland were shown to be one source of these excited state species. This study provides evidence of a role for POM in the photochemistry of natural and constructed wetland waters.
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Affiliation(s)
- Barbara A Cottrell
- Department of Chemistry, University of Toronto Scarborough, Scarborough, ON M1C1A4, Canada.
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Cottrell BA, Cheng WR, Lam B, Cooper WJ, Simpson AJ. An enhanced capillary electrophoresis method for characterizing natural organic matter. Analyst 2013; 138:1174-9. [DOI: 10.1039/c2an36144b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Ayatollahi S, Kalnina D, Song W, Cottrell BA, Gonsior M, Cooper WJ. Recent advances in structure and reactivity of dissolved organic matter: radiation chemistry of non-isolated natural organic matter and selected model compounds. Water Sci Technol 2012; 66:1941-1949. [PMID: 22925867 DOI: 10.2166/wst.2012.404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The importance of natural organic matter (NOM) as a source of carbon in natural waters, as the source of reactive oxygen species, or for the complications its presence causes in treatment of natural waters, is undeniable. Recent studies have also pointed to the major photochemical role of triplet excited state of natural organic matter in the environmental fate of pharmaceutical and personal care products (PPCPs) in waters. However, the characterization of NOM is problematic due to its complex molecular structure. One approach to better understand NOM chemistry is the use of model compounds. As the condensation of a plant's phenolic compounds leads to humification and the formation of NOM, a structurally broad group of nine phenolic compounds were selected as model compounds for this study. With methods used in the discipline of radiation chemistry, the oxidative chemistry and transient spectra of these phenols were studied. In addition, the oxidative chemistry and transient spectra of a sample of NOM from the Black River, North Carolina, USA, was characterized. This natural water sample was used as received and represents the first studies of non-isolated NOM by pulsed radiolysis. The results of the transient spectra of the NOM revealed that the radical intermediates were very long lived. This phenomenon was not captured using the nine model compounds suggesting that more complex compounds are needed to further our understanding of the oxidation chemistry of NOM.
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Affiliation(s)
- Shakiba Ayatollahi
- Department of Civil and Environmental Engineering, Urban Water Research Center, University of California, Irvine, Irvine, CA 92697-2175, USA
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Kukar TL, Ladd TB, Robertson P, Pintchovski SA, Moore B, Bann MA, Ren Z, Jansen-West K, Malphrus K, Eggert S, Maruyama H, Cottrell BA, Das P, Basi GS, Koo EH, Golde TE. Lysine 624 of the amyloid precursor protein (APP) is a critical determinant of amyloid β peptide length: support for a sequential model of γ-secretase intramembrane proteolysis and regulation by the amyloid β precursor protein (APP) juxtamembrane region. J Biol Chem 2011; 286:39804-12. [PMID: 21868378 PMCID: PMC3220543 DOI: 10.1074/jbc.m111.274696] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 08/16/2011] [Indexed: 11/06/2022] Open
Abstract
γ-Secretase is a multiprotein intramembrane cleaving aspartyl protease (I-CLiP) that catalyzes the final cleavage of the amyloid β precursor protein (APP) to release the amyloid β peptide (Aβ). Aβ is the primary component of senile plaques in Alzheimer's disease (AD), and its mechanism of production has been studied intensely. γ-Secretase executes multiple cleavages within the transmembrane domain of APP, with cleavages producing Aβ and the APP intracellular domain (AICD), referred to as γ and ε, respectively. The heterogeneous nature of the γ cleavage that produces various Aβ peptides is highly relevant to AD, as increased production of Aβ 1-42 is genetically and biochemically linked to the development of AD. We have identified an amino acid in the juxtamembrane region of APP, lysine 624, on the basis of APP695 numbering (position 28 relative to Aβ) that plays a critical role in determining the final length of Aβ peptides released by γ-secretase. Mutation of this lysine to alanine (K28A) shifts the primary site of γ-secretase cleavage from 1-40 to 1-33 without significant changes to ε cleavage. These results further support a model where ε cleavage occurs first, followed by sequential proteolysis of the remaining transmembrane fragment, but extend these observations by demonstrating that charged residues at the luminal boundary of the APP transmembrane domain limit processivity of γ-secretase.
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Affiliation(s)
- Thomas L Kukar
- Emory University, School of Medicine, Department of Pharmacology, Center for Neurodegenerative Disease, Atlanta, Georgia 30322, USA.
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Czirr E, Cottrell BA, Serneels L, Leuchtenberger S, Schubenel R, Torpey JW, Esselmann H, Pietrzik CU, Wiltfang J, DeStrooper B, Baumann K, Koo EH, Weggen S. P4‐192: Mechanism of γ‐secretase cleavage: Evidence for independent generation of Aβ42 and Aβ38 peptide species. Alzheimers Dement 2008. [DOI: 10.1016/j.jalz.2008.05.2259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Eva Czirr
- University of DuesseldorfDuesseldorfGermany
| | | | - Lutgarde Serneels
- Flanders Interuniversity Institute for Biotechnology and Katholieke Universiteit LeuvenLeuvenBelgium
| | | | | | | | | | | | | | - Bart DeStrooper
- Flanders Interuniversity Institute for Biotechnology and Katholieke Universiteit LeuvenLeuvenBelgium
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Czirr E, Cottrell BA, Leuchtenberger S, Kukar T, Ladd TB, Esselmann H, Paul S, Schubenel R, Torpey JW, Pietrzik CU, Golde TE, Wiltfang J, Baumann K, Koo EH, Weggen S. Independent Generation of Aβ42 and Aβ38 Peptide Species by γ-Secretase. J Biol Chem 2008; 283:17049-54. [DOI: 10.1074/jbc.m802912200] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Cottrell BA, Galvan V, Banwait S, Gorostiza O, Lombardo CR, Williams T, Schilling B, Peel A, Gibson B, Koo EH, Link CD, Bredesen DE. A pilot proteomic study of amyloid precursor interactors in Alzheimer's disease. Ann Neurol 2005; 58:277-89. [PMID: 16049941 PMCID: PMC1847583 DOI: 10.1002/ana.20554] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Several approaches have been used in an effort to identify proteins that interact with beta-amyloid precursor protein (APP). However, few studies have addressed the identification of proteins associated with APP in brain tissue from patients with Alzheimer's disease. We report the results of a pilot proteomic study performed on complexes immunoprecipitated with APP in brain samples of patients with Alzheimer's disease and normal control subjects. The 21 proteins identified could be grouped into five functional classes: molecular chaperones, cytoskeletal and structural proteins, proteins involved in trafficking, adaptors, and enzymes. Among the proteins identified, six had been reported previously as direct, indirect, or genetically inferred APP interactors. The other 15 proteins immunoprecipitated with APP were novel potential partners. We confirmed the APP interaction by Western blotting and coimmunolocalization in brain tissues, for 5 of the 21 interactors. In agreement with previous studies, our results are compatible with an involvement of APP in axonal transport and vesicular trafficking, and with a potential association of APP with cellular protein folding/protein degradation systems.
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Abstract
Neurogenesis, which persists in the adult mammalian brain, may provide a basis for neuronal replacement therapy in neurodegenerative diseases like Alzheimer's disease (AD). Neurogenesis is increased in certain acute neurological disorders, such as ischemia and epilepsy, but the effect of more chronic neurodegenerations is uncertain, and some animal models of AD show impaired neurogenesis. To determine how neurogenesis is affected in the brains of patients with AD, we investigated the expression of immature neuronal marker proteins that signal the birth of new neurons in the hippocampus of AD patients. Compared to controls, Alzheimer's brains showed increased expression of doublecortin, polysialylated nerve cell adhesion molecule, neurogenic differentiation factor and TUC-4. Expression of doublecortin and TUC-4 was associated with neurons in the neuroproliferative (subgranular) zone of the dentate gyrus, the physiological destination of these neurons (granule cell layer), and the CA1 region of Ammon's horn, which is the principal site of hippocampal pathology in AD. These findings suggest that neurogenesis is increased in AD hippocampus, where it may give rise to cells that replace neurons lost in the disease, and that stimulating hippocampal neurogenesis might provide a new treatment strategy.
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Affiliation(s)
- Kunlin Jin
- Buck Institute for Age Research, Novato, CA 94945, USA
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Peel AL, Rao RV, Cottrell BA, Hayden MR, Ellerby LM, Bredesen DE. Double-stranded RNA-dependent protein kinase, PKR, binds preferentially to Huntington's disease (HD) transcripts and is activated in HD tissue. Hum Mol Genet 2001; 10:1531-8. [PMID: 11468270 DOI: 10.1093/hmg/10.15.1531] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fourteen neurological diseases have been associated with the expansion of trinucleotide repeat regions. These diseases have been categorized into those that give rise to the translation of toxic polyglutamine proteins and those that are untranslated. Thus far, compelling evidence has not surfaced for the inclusion of a model in which a common mechanism may participate in the pathobiology of both translated and untranslated trinucleotide diseases. In these studies we show that a double-stranded RNA-binding protein, PKR, which has previously been linked to virally-induced and stress-mediated apoptosis, preferentially binds mutant huntingtin RNA transcripts immobilized on streptavidin columns that have been incubated with human brain extracts. These studies also show, by immunodetection in tissue slices, that PKR is present in its activated form in both human Huntington autopsy material and brain tissue derived from Huntington yeast artificial chromosome transgenic mice. The increased immunolocalization of the activated kinase is more pronounced in areas most affected by the disease and, coupled with the RNA binding results, suggests a role for PKR activation in the disease process.
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Affiliation(s)
- A L Peel
- The Buck Institute, 8001 Redwood Boulevard, Novato, CA 94945, USA.
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Abstract
It has been hypothesized that a major factor in the progression of mitochondrial disease resulting from defects in oxidative phosphorylation (OXPHOS) is the stimulation of the mitochondrial production of reactive oxygen species (ROS) and the resulting damage to the mtDNA. To test this hypothesis, we examined the mitochondria from mice lacking the heart/muscle isoform of the adenine nucleotide translocator (Ant1), designated Ant1(tm2Mgr) (-/-) mice. The absence of Ant1 blocks the exchange of ADP and ATP across the mitochondrial inner membrane, thus inhibiting OXPHOS. Consistent with Ant1 expression, mitochondria isolated from skeletal muscle, heart, and brain of the Ant1-deficient mice produced markedly increased amounts of the ROS hydrogen peroxide, whereas liver mitochondria, which express a different Ant isoform, produced normally low levels of hydrogen peroxide. The increased production of ROS by the skeletal muscle and heart was associated with a dramatic increase in the ROS detoxification enzyme manganese superoxide dismutase (Sod2, also known as MnSod) in muscle tissue and muscle mitochondria, a modest increase in Sod2 in heart tissue, and no increase in heart mitochondria. The level of glutathione peroxidase-1 (Gpx1), a second ROS detoxifying enzyme, was increased moderately in the mitochondria of both tissues. Consistent with the lower antioxidant defenses in heart, the heart mtDNAs of the Ant1-deficient mice showed a striking increase in the accumulation of mtDNA rearrangements, whereas skeletal muscle, with higher antioxidant defenses, had fewer mtDNA rearrangements. Hence, inhibition of OXPHOS does increase mitochondrial ROS production, eliciting antioxidant defenses. If the antioxidant defenses are insufficient to detoxify the ROS, then an increased mtDNA mutation rate can result.
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Affiliation(s)
- L A Esposito
- Center for Molecular Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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Wang YZ, Patterson J, Gray JE, Yu C, Cottrell BA, Shimizu A, Graham D, Riley M, Doolittle RF. Complete sequence of the lamprey fibrinogen alpha chain. Biochemistry 1989; 28:9801-6. [PMID: 2611265 DOI: 10.1021/bi00451a039] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The complete amino acid sequence of the lamprey fibrinogen alpha chain has been determined by a combination of peptide sequencing and cDNA and genomic cloning. The chain, which has an apparent molecular weight by dodecyl sulfate-polyacrylamide gel electrophoresis of ca. 100,000, is composed of 961 amino acid residues and has a calculated molecular weight of 96,722. It is distinguished by a large number of 18-residue repeats in a region where mammalian fibrinogens have 13-residue repeats. The data are in accord with our previous finding that the lamprey alpha chain has a distinctive amino acid composition, almost half the residues being glycine, serine, or threonine. The chain differs from mammalian alpha chains in that there are no cysteines in the carboxy-terminal half, and thus no intrachain loop, nor are there any RGD sequences in the lamprey alpha chain. Taken together with previous data on the sequences of the beta and gamma chains, the findings bear significantly on our understanding of fibrin formation. The alpha chain also provides an interesting case of structural convergence during evolution.
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Affiliation(s)
- Y Z Wang
- Center for Molecular Genetics, University of California, San Diego, La Jolla 92093
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Strong DD, Moore M, Cottrell BA, Bohonus VL, Pontes M, Evans B, Riley M, Doolittle RF. Lamprey fibrinogen gamma chain: cloning, cDNA sequencing, and general characterization. Biochemistry 1985; 24:92-101. [PMID: 2581603 DOI: 10.1021/bi00322a014] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A cDNA library from lamprey liver was constructed in pBR322 and screened with a synthetic mixed oligonucleotide probe, the sequence of which was based on a partial amino acid sequence of the lamprey fibrinogen gamma chain determined by conventional procedures. Among the positive clones was one containing a 600-base insert that covered the carboxy-terminal third of the chain and another with a 1950-base insert that stretched more than full length. The two inserts were sequenced by the Maxam-Gilbert procedure. The DNA sequencing was corroborated by reference to the amino acid sequences of five cyanogen bromide peptides that compose the carboxy-terminal 130 amino acids, as well as to a number of tryptic peptides from elsewhere in the molecule. The clone with the smaller insert (6G) contained 594 nucleotides (not counting G and C tails), 435 of which are coding and correspond to residues 264-408 of the gamma chain. The remaining 159 nucleotides included the terminator codon followed by a noncoding segment. The larger clone (2E) coded for 408 amino acids that could be readily aligned with the 411-residue human gamma chain. A 24-residue signal peptide adjacent to the proposed amino terminal was also inferred. The amino acid sequence of the fibrinogen gamma chain has been differentially conserved during evolution, the lamprey and human sequences being more than 70% identical in certain key regions but dropping to less than 25% in other sections, including the segment thought to be a part of the "coiled coils". Overall, the resemblance amounts to 50% identity. Of the 10 cysteines found in mammalian chains, 9 are at identical positions, but the tenth, which in mammalian fibrinogens is a part of the interdimeric bridging, is absent in the lamprey.
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Hawiger J, Timmons S, Strong DD, Cottrell BA, Riley M, Doolittle RF. Identification of a region of human fibrinogen interacting with staphylococcal clumping factor. Biochemistry 1982; 21:1407-13. [PMID: 7074095 DOI: 10.1021/bi00535a047] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Abstract
Fragments E1, E2, and E3 are plasmic derivatives of fibrin encompassing the NH2-terminal region of the molecule. The first two species, but not the third, can bind to fragment DD, forming a (DD)E complex, and therefore probably contain binding sites involved in the polymerization of fibrin. For localization of these sites the structure of the fragments was determined by establishing the NH2- and COOH-terminal boundaries of the molecules and using the published amino acid sequence of fibrinogen. Fragment E1 encompasses Gly-alpha 17 to Lys-alpha 78, Gly-beta 15 to Lys-beta 122, and Tyr-gamma 1 to Lys-gamma 62, this representing the intact NH2-terminal region of fibrin. Fragment E2 is an asymmetric molecule which is lacking the sequence of Gly-beta 15 to Lys-beta 53 in one beta-chain remnant. This fragment E2 also lost Lys-beta 122 from the COOH terminal of the beta chain as compared with fragment E1. These cleavages did not affect the ability of fragment E2 to bind to fragment DD. Fragment E3 was heterogeneous, the main species encompassing Val-alpha 20 to Lys-alpha 78, Lys-beta 54 to Leu-beta 120, and Tyr-gamma 1 to Lys-gamma 53. Thus, the loss of the binding function involved in the formation of fibrin clot was associated with the removal of small fragments from all three polypeptide chains: alpha 17-19 (Gly-Pro-Arg), beta 15-53 from the remaining half of the molecule, beta 121 (Leu), and gamma 54-58 (Thr-Ser-Glu-Val-Lys).
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Cottrell BA, Strong DD, Watt KW, Doolittle RF. Amino acid sequence studies on the alpha chain of human fibrinogen. Exact location of cross-linking acceptor sites. Biochemistry 1979; 18:5405-10. [PMID: 518845 DOI: 10.1021/bi00591a023] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Human fibrinogen was clotted under conditions that promote latent factor XIII activity and in the presence of a radioactive substitute cross-linking donor ([14C]glycine ethyl ester). The labeled fibrin was reduced and alkylated in the presence of 6 M guanidinium chloride. After dialysis and freeze-drying, the preparation was separated into its constituent polypeptide subunits by chromatography on (carboxymethyl)cellulose in the presence of 8 M urea. Under the incorporation conditions used, the radioactivity was limited to gamma chains (one donor molecule/chain) and alpha chains (two donor molecules/chain). The labeled alpha chains were digested with cyanogen bromide and fractionated on Sephadex G-50. All the radioactivity was found in a fragment previously designated H alpha CNI, the largest of the cyanogen bromide fragments in the alpha chain. The fragment was further fragmented by digestion with plasmin, trypsin, chymotrypsin, and/or staphylococcal protease. The incorporated radioactivity was found to reside in equal amounts at two different sites located 38 residues apart. These were determined to be positions 88 and 126 in H alpha CNI, which correspond to glutamine-328 and glutamine-366 in the alpha chain.
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Watt KW, Cottrell BA, Strong DD, Doolittle RF. Amino acid sequence studies on the alpha chain of human fibrinogen. Overlapping sequences providing the complete sequence. Biochemistry 1979; 18:5410-6. [PMID: 518846 DOI: 10.1021/bi00591a024] [Citation(s) in RCA: 68] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The complete amino acid sequence of the alpha chain of human fibrinogen has been determined. It contains 610 amino acid residues and has a calculated molecular weight of 66,124. The chain has 10 methionines, and fragmentation with cyanogen bromide yields 11 peptides [Doolittle, R.F., Cassman, K.G., Cottrell, B.A., Friezner, S.J., Hucko, J.T., & Takagi, T. (1977) Biochemistry 16, 1703]. The arrangement of the 11 fragments was determined by the isolation of peptide overlaps from plasmic and staphylococcal protease digests of fibrinogen and/or alpha chains. In addition, certain of the cyanogen bromide fragments, preliminary reports of whose sequences have appeared previously, have been reexamined in order to resolve several discrepancies. The alpha chain is homologous with the beta and gamma chains of fibrinogen, although a large repetitive segment of unusual composition is absent from the latter two chains. The existence of this unusual segment divides the sequence of the alpha chain into three zones of about 200 residues each that are readily distinguishable on the basis of amino acid composition alone.
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Strong DD, Watt KW, Cottrell BA, Doolittle RF. Amino acid sequence studies on the alpha chain of human fibrinogen. Complete sequence of the largest cyanogen bromide fragment. Biochemistry 1979; 18:5399-404. [PMID: 518844 DOI: 10.1021/bi00591a022] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The largest fragment produced by complete cyanogen bromide digestion of the alpha chain of human fibrinogen contains 236 residues and has a calculated molecular weight of 23,949. The complete amino acid sequence of the fragment was determined by the isolation of peptides generated by plasmin, trypsin (including digestion of citraconylated material), staphylococcal protease, and chymotrypsin. In addition, some key subfragmentation was achieved by selective chemical cleavage at tryptophan residues. The fragment has an unusual amino acid composition, more than half of its residues being glycine, serine, threonine, and proline. There are very few nonpolar residues, although 7 of the alpha-chain's 10 tryptophans occur in this fragment. The fragment contains 2 cysteine residues located 30 residues apart which are connected by an intrachain disulfide bond in the native molecule. The tryptophans occur with a definite periodicity that highlights a series of 13-residue homology repeats. The fragment also contains the two principal alpha-chain cross-linking sites.
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Abstract
The amino acid sequence of the human fibrinogen alpha-chain reveals a structure that can be divided into three zones of unique amino acid composition. The middle of these contains the two primary alpha-chain cross-linking acceptor sites and consists of a remarkable series of internal duplications.
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Doolittle RF, Cottrell BA, Strong D, Watt KW. Sequence of amino acids comprising the single intra-chain disulfide loop in the alpha-chain of human fibrinogen. Biochem Biophys Res Commun 1978; 84:495-500. [PMID: 152630 DOI: 10.1016/0006-291x(78)90196-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Doolittle RF, Cassman KG, Cottrell BA, Friezner SJ, Hucko JT, Takagi T. Amino acid sequence studies on the alpha chain of human fibrinogen. Characterization of 11 cyanogen bromide fragments. Biochemistry 1977; 16:1703-9. [PMID: 856257 DOI: 10.1021/bi00627a028] [Citation(s) in RCA: 43] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The alpha chain of human fibrinogen consists of 600 +/- 25 amino acid residues, 10-11 of which are methionines. In this regard, we have identified and characterized 11 cyanogen bromide peptide fragments of 2, 3, 26, 28, 28, 37, 51, 56, 60 +/- 5, 64 +/- 5, and 260 +/- 20 residues, respectively. The sequences of five of these and a portion of a sixth have been reported previously. We now report the complete amino acid sequences of another of these fragments (56 residues), partial sequences for four others, and a preliminary characterization of the largest fragment. In a companion study (Doolittle, R. F., Cassman, K. G., Cottrell, B. A., Friezner, S. J., and Takagi, T. (1977), Biochemistry 16 (following paper in this issue)), we have obtained key overlap sequences from plasmic digests of fibrinogen which allow all but one of these cyanogen bromide peptides to be arranged in order. The sequences of some of these newly reported fragments have revealed an internal homology in the alpha chain, as well as structural similarities to the corresponding portions of the beta and gamma chains.
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Doolittle RF, Cassman KG, Cottrell BA, Friezner SJ, Takagi T. Amino acid sequence studies on the alpha chain of human fibrinogen. Covalent structure of the alpha-chain portion of fragment D. Biochemistry 1977; 16:1710-5. [PMID: 139916 DOI: 10.1021/bi00627a029] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The alpha-chain portion of fragment D has been purified from an exhaustive plasmic digest of human fibrinogen. The major polypeptide species has 91 amino acid residues, although a small amount of a 97-residue chain representing an earlier digestion stage remains. The amino acid sequence of the first 44 residues was determined by stepwise degradation with an automatic solid-phase sequencer. Another large stretch of sequence was revealed by the finding that the alpha chain of fragment D overlaps the cyanogen bromide fragments alphaCNIVA and alphaCNIII (Doolittle, R. F. Cassman, K. G., Cottrell, B. A., Friezner, S. J. Hucko, J. T., and Takagi, T. (1977), Biochemistry 16 (preceding paper in this issue)). The automatic sequencer results were confirmed and extended by the isolation and characterization of 18 of 19 expected tryptic peptides from the fragment D alpha chain. As a result, almost the entire sequence has been obtained. The overlap with key cyanogen bromide fragments has also allowed us to propose an order for the first 198 residues of the fibrinogen alpha chain. A striking homology with the gamma chain and beta chain is apparent which has interesting structural implications.
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Doolittle RF, Cassman KG, Cottrell BA, Friezner SJ. Amino acid sequence studies on the alpha chain of human fibrinogen. Isolation and characterization of two linked alpha-chained cyanogen bromide fragments from fully cross-linked fibrin. Biochemistry 1977; 16:1715-9. [PMID: 851527 DOI: 10.1021/bi00627a030] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fully cross-linked human fibrin was digested with cyanogen bromide and the resulting fragments were characterized and compared with the fragments produced upon cyanogen bromide treatment of fibrinogen alpha chains. The largest molecular-weight fraction isolated by gel filtration on Sephadex G-150 was reduced and alkylated, and upon rechromatography on Sephadex G-150 it eluted at the same place as the original material. This large molecular weight fraction was subjected to amino acid analysis and the amino-terminal sequences of its constituent chains were determined by both dimethylaminonaphthyl sulfonation (Dns) and thioacetylation procedures. The identified sequences corresponded to two cyanogen bromide fragments previously found in alpha chains isolated from fibrinogen, one of which has a molecular weight of about 30 000 and the other 6000. The latter is thought to be the carboxy-terminal penultimate cyanogen bromide fragment of the alpha chain.
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Cottrell BA, Doolittle RF. Amino acid sequences of lamprey fibrinopeptides A and B and characterizations of the junctions split by lamprey and mammalian thrombins. Biochim Biophys Acta 1976; 453:426-38. [PMID: 999898 DOI: 10.1016/0005-2795(76)90138-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The amino acid sequences of the fibrinopeptides A and B from lamprey fibrinogen have been determined. The fibrinopeptide A is the shortest fibrinopeptide ever isolated, being comprised of only six amino acids. The fibrinopeptide B, on the other hand, is the largest fibrinopeptide characterized to date, having 36 amino acid residues and a cluster of covalently bound carbohydrate. As reported previously, lamprey fibrinogen is readily clotted by mammalian thrombins, but only the fibrinopeptide B is released during the process. Lamprey fibrinopeptide A is not released by mammalian thrombins and could only be removed with the use of lamprey thrombin. Firm proof that the lamprey fibrinopeptides A and B are the amino segments of the alpha and beta-chains respectively was obtained by a series of stepwise degradations on lamprey fibrinogen and lamprey fibrins produced in turn by the action of mammalian thrombin (fibrin B) and lamprey thrombin (fibrin A). These studies were supplemented by stepwise degradations on the individual Aalpha and Bbeta-chains. It the case of the lamprey Aalpha-chain it was also possible to release the 6-residue fibrinopeptide A from the isolated chain with lamprey thrombin and demonstrate that the newly exposed amino-terminal sequence begins with the Gly-Pro-Arg sequence characteristic of mammalian fibrin alpha-chains. In fact, the sequences on the fibrin side of both of the junctions split by thrombin(s) are highly conserved and virtually identical with those found in mammalian alpha and beta-chains.
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Doolittle RF, Cottrell BA, Riley M. Amino acid compositions of the subunit chains of lamprey fibrinogen. Evolutionary significance of some structural anomalies. Biochim Biophys Acta 1976; 453:439-52. [PMID: 826275 DOI: 10.1016/0005-2795(76)90139-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Our original objective in studying lamprey fibrinogen was embodied in the notion that the proteins of this ancient vertebrate might themselves by more primitive. As such, it was possible that the subunits of lamprey fibrinogen might have been more similar, one to another, than is the case in higher vertebrates, or even identical. Amino acid analysis of the individual polypeptide chains indicates, however, that the alpha, beta and gamma-chains are instead more dissimilar from each other than are the corresponding chains from human fibrinogen. This finding was somewhat surprising because regions of homology have been detected recently among those three chains when isolated from human fibrinogen, suggesting that all three chains have indeed descended from a common ancestor. The paradox is especially evidenced by the unusual amino acid composition of the lamprey alpha-chain, 45% of which is composed of glycine, serine and threonine. This unusual amino acid distribution may be involved in the anomalous behavior of these chains on sodium dodecyl sulfate polyacrylamide gel electrophoresis.
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Cottrell BA, Doolittle RF. The amino acid sequence of a 27-residue peptide released from the alpha-chain carboxy-terminus during the plasmic digestion of human fibrinogen. Biochem Biophys Res Commun 1976; 71:754-61. [PMID: 134710 DOI: 10.1016/0006-291x(76)90895-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
Human platelet fibrinogen has been shown to be indistinguishable from plasma fibrinogen by a variety of criteria, including subunit composition and cross-linking characteristics as judged by sodium dodecyl sulfate-gel electro phoresis, quantitative amino terminal analysis of fibrin, and the amino acid compositions of fibrinopeptides released from platelet and plasma fibrinogens is products of the same gene or genes.
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Clarkson MJ, Cottrell BA, Enayat MS. The indirect haemagglutination test in the study of Trypanosoma vivax infections of sheep. Ann Trop Med Parasitol 1971; 65:335-40. [PMID: 5096375 DOI: 10.1080/00034983.1971.11686762] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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