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Publication Record


Functional analysis of human cytochrome P450 21A2 variants involved in congenital adrenal hyperplasia.
Wang C, Pallan PS, Zhang W, Lei L, Yoshimoto FK, Waterman MR, Egli M, Guengerich FP
(2017) J Biol Chem 292: 10767-10778
MeSH Terms: Adrenal Hyperplasia, Congenital, Circular Dichroism, Cytochromes b5, Deuterium Exchange Measurement, Enzyme Stability, Hot Temperature, Humans, Mutation, Protein Domains, Spectrophotometry, Ultraviolet, Steroid 21-Hydroxylase
Show Abstract · Added March 14, 2018
Cytochrome P450 (P450, CYP) 21A2 is the major steroid 21-hydroxylase, converting progesterone to 11-deoxycorticosterone and 17α-hydroxyprogesterone (17α-OH-progesterone) to 11-deoxycortisol. More than 100 variants give rise to congenital adrenal hyperplasia (CAH). We previously reported a structure of WT human P450 21A2 with bound progesterone and now present a structure bound to the other substrate (17α-OH-progesterone). We found that the 17α-OH-progesterone- and progesterone-bound complex structures are highly similar, with only some minor differences in surface loop regions. Twelve P450 21A2 variants associated with either salt-wasting or nonclassical forms of CAH were expressed, purified, and analyzed. The catalytic activities of these 12 variants ranged from 0.00009% to 30% of WT P450 21A2 and the extent of heme incorporation from 10% to 95% of the WT. Substrate dissociation constants () for four variants were 37-13,000-fold higher than for WT P450 21A2. Cytochrome , which augments several P450 activities, inhibited P450 21A2 activity. Similar to the WT enzyme, high noncompetitive intermolecular kinetic deuterium isotope effects (≥ 5.5) were observed for all six P450 21A2 variants examined for 21-hydroxylation of 21--progesterone, indicating that C-H bond breaking is a rate-limiting step over a 10-fold range of catalytic efficiency. Using UV-visible and CD spectroscopy, we found that P450 21A2 thermal stability assessed in bacterial cells and with purified enzymes differed among salt-wasting- and nonclassical-associated variants, but these differences did not correlate with catalytic activity. Our in-depth investigation of CAH-associated P450 21A2 variants reveals critical insight into the effects of disease-causing mutations on this important enzyme.
© 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
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11 MeSH Terms
Time-resolved Studies of IsdG Protein Identify Molecular Signposts along the Non-canonical Heme Oxygenase Pathway.
Streit BR, Kant R, Tokmina-Lukaszewska M, Celis AI, Machovina MM, Skaar EP, Bothner B, DuBois JL
(2016) J Biol Chem 291: 862-71
MeSH Terms: Ascorbic Acid, Chromatography, Liquid, Heme, Heme Oxygenase (Decyclizing), Humans, Hydrogen Peroxide, Isotopes, Kinetics, Mass Spectrometry, Oxygen, Oxygenases, Signal Transduction, Spectrophotometry, Ultraviolet, Staphylococcus aureus, Time Factors
Show Abstract · Added February 8, 2016
IsdGs are heme monooxygenases that break open the tetrapyrrole, releasing the iron, and thereby allowing bacteria expressing this protein to use heme as a nutritional iron source. Little is currently known about the mechanism by which IsdGs degrade heme, although the products differ from those generated by canonical heme oxygenases. A synthesis of time-resolved techniques, including in proteo mass spectrometry and conventional and stopped-flow UV/visible spectroscopy, was used in conjunction with analytical methods to define the reaction steps mediated by IsdG from Staphylococcus aureus and their time scales. An apparent meso-hydroxyheme (forming with k = 0.6 min(-1), pH 7.4, 10 mm ascorbate, 10 μm IsdG-heme, 22 °C) was identified as a likely common intermediate with the canonical heme oxygenases. Unlike heme oxygenases, this intermediate does not form with added H2O2 nor does it convert to verdoheme and CO. Rather, the next observable intermediates (k = 0.16 min(-1)) were a set of formyloxobilin isomers, similar to the mycobilin products of the IsdG homolog from Mycobacterium tuberculosis (MhuD). These converted in separate fast and slow phases to β-/δ-staphylobilin isomers and formaldehyde (CH2O). Controlled release of this unusual C1 product may support IsdG's dual role as both an oxygenase and a sensor of heme availability in S. aureus.
© 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
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15 MeSH Terms
Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory.
Norman P, Parello J, Polavarapu PL, Linares M
(2015) Phys Chem Chem Phys 17: 21866-79
MeSH Terms: Base Pairing, Circular Dichroism, DNA, B-Form, Electrons, Models, Molecular, Nucleosides, Nucleosomes, Quantum Theory, Spectrophotometry, Ultraviolet, Thermodynamics
Show Abstract · Added April 10, 2018
It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles. At the DFT/B3LYP level of theory, the ECD signal response is reduced by a factor of 6.7 in going from the B-DNA to the N-DNA form, and it is illustrated how more than 90% of the individual base-pair dimers contribute to this strong hypochromic effect. Of the several inter-base pair parameters, an increase in twist angles is identified as to strongly contribute to a reduced ellipticity. The present work provides first evidence that first-principles calculations can elucidate changes in DNA dichroism due to the supramolecular organization of the nucleoprotein particle and associates these changes with the local structural features of nucleosomal DNA.
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MeSH Terms
Base-Displaced Intercalated Conformation of the 2-Amino-3-methylimidazo[4,5-f]quinoline N(2)-dG DNA Adduct Positioned at the Nonreiterated G(1) in the NarI Restriction Site.
Stavros KM, Hawkins EK, Rizzo CJ, Stone MP
(2015) Chem Res Toxicol 28: 1455-68
MeSH Terms: Circular Dichroism, DNA, Deoxyguanosine, Deoxyribonucleases, Type II Site-Specific, Intercalating Agents, Magnetic Resonance Spectroscopy, Molecular Conformation, Nucleic Acid Conformation, Protons, Quinolines, Spectrophotometry, Ultraviolet
Show Abstract · Added January 7, 2016
The conformation of an N(2)-dG adduct arising from the heterocyclic amine 2-amino-3-methylimidazo[4,5-f]quinoline (IQ), a potent food mutagen, was determined in 5'-d(C(1)T(2)C(3)X(4)G(5)C(6)G(7)C(8)C(9)A(10)T(11)C(12))-3':5'-d(G(13)A(14)T(15)G(16)G(17)C(18)G(19)C(20)C(21)G(22)A(23)G(24))-3'; X = N(2)-dG-IQ, in which the modified nucleotide X(4) corresponds to G(1) in the 5'-d(G(1)G(2)CG(3)CC)-3' NarI restriction endonuclease site. Circular dichroism (CD) revealed blue shifts relative to the unmodified duplex, consistent with adduct-induced twisting, and a hypochromic effect for the IQ absorbance in the near UV region. NMR revealed that the N(2)-dG-IQ adduct adopted a base-displaced intercalated conformation in which the modified guanine remained in the anti conformation about the glycosidic bond, the IQ moiety intercalated into the duplex, and the complementary base C(21) was displaced into the major groove. The processing of the N(2)-dG-IQ lesion by hpol η is sequence-dependent; when placed at the reiterated G(3) position, but not at the G(1) position, this lesion exhibits a propensity for frameshift replication [Choi, J. Y., et al. (2006) J. Biol. Chem., 281, 25297-25306]. The structure of the N(2)-dG-IQ adduct at the nonreiterated G(1) position was compared to that of the same adduct placed at the G(3) position [Stavros, K. M., et al. (2014) Nucleic Acids Res., 42, 3450-3463]. CD indicted minimal spectral differences between the G(1) vs G(3) N(2)-dG-IQ adducts. NMR indicated that the N(2)-dG-IQ adduct exhibited similar base-displaced intercalated conformations at both the G(1) and G(3) positions. This result differed as compared to the corresponding C8-dG-IQ adducts placed at the same positions. The C8-dG-IQ adduct adopted a minor groove conformation when placed at position G(1) but a base-displaced intercalated conformation when placed at position G(3) in the NarI sequence. The present studies suggest that differences in lesion bypass by hpol η may be mediated by differences in the 3'-flanking sequences, perhaps modulating the ability to accommodate transient strand slippage intermediates.
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11 MeSH Terms
5'-O-Alkylpyridoxamines: Lipophilic Analogues of Pyridoxamine Are Potent Scavengers of 1,2-Dicarbonyls.
Amarnath V, Amarnath K, Avance J, Stec DF, Voziyan P
(2015) Chem Res Toxicol 28: 1469-75
MeSH Terms: Biocatalysis, Electron Spin Resonance Spectroscopy, Free Radical Scavengers, Free Radicals, Glucose, Horseradish Peroxidase, Hydrophobic and Hydrophilic Interactions, Membrane Proteins, Molecular Conformation, Muramidase, Pyridoxamine, Pyruvaldehyde, Spectrophotometry, Ultraviolet, Superoxide Dismutase
Show Abstract · Added June 9, 2017
Pyridoxamine (PM) is a prospective drug for the treatment of diabetic complications. In order to make zwitterionic PM more lipophilic and improve its tissue distribution, PM derivatives containing medium length alkyl groups on the hydroxymethyl side chain were prepared. The synthesis of these alkylpyridoxamines (alkyl-PMs) starting from pyridoxine offers high yields and is amenable to bulk preparations. Interestingly, alkyl-PMs were found to react with methylglyoxal (MGO), a major toxic product of glucose metabolism and autoxidation, several orders of magnitude faster than PM. This suggests the formation of nonionic pyrido-1,3-oxazine as the key step in the reaction of PM with MGO. Since the primary target of MGO in proteins is the guanidine side chain of arginine, alkyl-PMs were shown to be more effective than PM in reducing the modification of N-α-benzoylarginine by MGO. Alkyl-PMs in the presence of MGO also protected the enzymatic activity of lysozyme that contains several arginine residues next to its active site. Alkyl-PMs can be expected to trap MGO and other toxic 1,2-carbonyl compounds more effectively than PM, especially in lipophilic tissue environments, thus protecting macromolecules from functional damage. This suggests potential therapeutic uses for alkyl-PMs in diabetes and other diseases characterized by the elevated levels of toxic dicarbonyl compounds.
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14 MeSH Terms
ω-Alkynyl lipid surrogates for polyunsaturated fatty acids: free radical and enzymatic oxidations.
Beavers WN, Serwa R, Shimozu Y, Tallman KA, Vaught M, Dalvie ED, Marnett LJ, Porter NA
(2014) J Am Chem Soc 136: 11529-39
MeSH Terms: Animals, Arachidonate 15-Lipoxygenase, Arachidonic Acid, Carbon, Cell Line, Chromatography, High Pressure Liquid, Cyclooxygenase 1, Cyclooxygenase 2, Fatty Acids, Fatty Acids, Unsaturated, Free Radicals, Hydroxyeicosatetraenoic Acids, Linoleic Acid, Lipids, Lipoxygenases, Macromolecular Substances, Macrophages, Mice, Oxygen, Soybeans, Spectrophotometry, Ultraviolet, Tandem Mass Spectrometry
Show Abstract · Added February 22, 2016
Lipid and lipid metabolite profiling are important parameters in understanding the pathogenesis of many diseases. Alkynylated polyunsaturated fatty acids are potentially useful probes for tracking the fate of fatty acid metabolites. The nonenzymatic and enzymatic oxidations of ω-alkynyl linoleic acid and ω-alkynyl arachidonic acid were compared to that of linoleic and arachidonic acid. There was no detectable difference in the primary products of nonenzymatic oxidation, which comprised cis,trans-hydroxy fatty acids. Similar hydroxy fatty acid products were formed when ω-alkynyl linoleic acid and ω-alkynyl arachidonic acid were reacted with lipoxygenase enzymes that introduce oxygen at different positions in the carbon chains. The rates of oxidation of ω-alkynylated fatty acids were reduced compared to those of the natural fatty acids. Cyclooxygenase-1 and -2 did not oxidize alkynyl linoleic but efficiently oxidized alkynyl arachidonic acid. The products were identified as alkynyl 11-hydroxy-eicosatetraenoic acid, alkynyl 11-hydroxy-8,9-epoxy-eicosatrienoic acid, and alkynyl prostaglandins. This deviation from the metabolic profile of arachidonic acid may limit the utility of alkynyl arachidonic acid in the tracking of cyclooxygenase-based lipid oxidation. The formation of alkynyl 11-hydroxy-8,9-epoxy-eicosatrienoic acid compared to alkynyl prostaglandins suggests that the ω-alkyne group causes a conformational change in the fatty acid bound to the enzyme, which reduces the efficiency of cyclization of dioxalanyl intermediates to endoperoxide intermediates. Overall, ω-alkynyl linoleic acid and ω-alkynyl arachidonic acid appear to be metabolically competent surrogates for tracking the fate of polyunsaturated fatty acids when looking at models involving autoxidation and oxidation by lipoxygenases.
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22 MeSH Terms
Proteomic analysis of vitreous biopsy techniques.
Skeie JM, Brown EN, Martinez HD, Russell SR, Birkholz ES, Folk JC, Boldt HC, Gehrs KM, Stone EM, Wright ME, Mahajan VB
(2012) Retina 32: 2141-9
MeSH Terms: Adolescent, Aged, Biomarkers, Biopsy, Chromatography, Liquid, Electrophoresis, Polyacrylamide Gel, Eye Diseases, Eye Proteins, Female, Humans, Male, Middle Aged, Proteomics, Spectrophotometry, Ultraviolet, Tandem Mass Spectrometry, Vitrectomy, Vitreous Body, Young Adult
Show Abstract · Added August 31, 2017
PURPOSE - To compare vitreous biopsy methods using analysis platforms used in proteomics biomarker discovery.
METHODS - Vitreous biopsies from 10 eyes were collected sequentially using a 23-gauge needle and a 23-gauge vitreous cutter instrument. Paired specimens were evaluated by UV absorbance spectroscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and liquid chromatography tandem mass spectrometry (LC-MS/MS).
RESULTS - The total protein concentration obtained with a needle and vitrectomy instrument biopsy averaged 1.10 mg/mL (standard error of the mean = 0.35) and 1.13 mg/mL (standard error of the mean = 0.25), respectively. In eight eyes with low or medium viscidity, there was a very high correlation (R = 0.934) between the biopsy methods. When data from 2 eyes with high viscidity vitreous were included, the correlation was reduced (R = 0.704). The molecular weight protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis profiles of paired needle and vitreous cutter samples were similar, except for a minority of pairs with single band intensity variance. Using LC-MS/MS, equivalent peptides were identified with similar frequencies (R ≥ 0.90) in paired samples.
CONCLUSION - Proteins and peptides collected from vitreous needle biopsies are nearly equivalent to those obtained from a vitreous cutter instrument. This study suggests both techniques may be used for most proteomic and biomarker discovery studies of vitreoretinal diseases, although a minority of proteins and peptides may differ in concentration.
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18 MeSH Terms
Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH.
Krishna Kumar K, Jacques DA, Pishchany G, Caradoc-Davies T, Spirig T, Malmirchegini GR, Langley DB, Dickson CF, Mackay JP, Clubb RT, Skaar EP, Guss JM, Gell DA
(2011) J Biol Chem 286: 38439-47
MeSH Terms: Antigens, Bacterial, Bacterial Proteins, Crystallography, X-Ray, Hemoglobins, Humans, Iron, Ligands, Light, Molecular Conformation, Protein Binding, Protein Structure, Secondary, Protein Structure, Tertiary, Receptors, Cell Surface, Spectrophotometry, Ultraviolet, Staphylococcal Infections, Staphylococcus aureus
Show Abstract · Added February 11, 2016
Pathogens must steal iron from their hosts to establish infection. In mammals, hemoglobin (Hb) represents the largest reservoir of iron, and pathogens express Hb-binding proteins to access this source. Here, we show how one of the commonest and most significant human pathogens, Staphylococcus aureus, captures Hb as the first step of an iron-scavenging pathway. The x-ray crystal structure of Hb bound to a domain from the Isd (iron-regulated surface determinant) protein, IsdH, is the first structure of a Hb capture complex to be determined. Surface mutations in Hb that reduce binding to the Hb-receptor limit the capacity of S. aureus to utilize Hb as an iron source, suggesting that Hb sequence is a factor in host susceptibility to infection. The demonstration that pathogens make highly specific recognition complexes with Hb raises the possibility of developing inhibitors of Hb binding as antibacterial agents.
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16 MeSH Terms
Novel oxysterols observed in tissues and fluids of AY9944-treated rats: a model for Smith-Lemli-Opitz syndrome.
Xu L, Liu W, Sheflin LG, Fliesler SJ, Porter NA
(2011) J Lipid Res 52: 1810-20
MeSH Terms: Animals, Anticholesteremic Agents, Cholestenones, Cholesterol, Chromatography, High Pressure Liquid, Dehydrocholesterols, Disease Models, Animal, Hydroxycholesterols, Ketocholesterols, Lipid Peroxidation, Magnetic Resonance Spectroscopy, Mass Spectrometry, Mice, Rats, Rats, Sprague-Dawley, Smith-Lemli-Opitz Syndrome, Spectrophotometry, Ultraviolet, Sterols, trans-1,4-Bis(2-chlorobenzaminomethyl)cyclohexane Dihydrochloride
Show Abstract · Added March 7, 2014
Treatment of Sprague-Dawley rats with AY9944, an inhibitor of 3β-hydroxysterol-Δ(7)-reductase (Dhcr7), leads to elevated levels of 7-dehydrocholesterol (7-DHC) and reduced levels of cholesterol in all biological tissues, mimicking the key biochemical hallmark of Smith-Lemli-Opitz syndrome (SLOS). Fourteen 7-DHC-derived oxysterols previously have been identified as products of free radical oxidation in vitro; one of these oxysterols, 3β,5α-dihydroxycholest-7-en-6-one (DHCEO), was recently identified in Dhcr7-deficient cells and in brain tissues of Dhcr7-null mouse. We report here the isolation and characterization of three novel 7-DHC-derived oxysterols (4α- and 4β-hydroxy-7-DHC and 24-hydroxy-7-DHC) in addition to DHCEO and 7-ketocholesterol (7-kChol) from the brain tissues of AY9944-treated rats. The identities of these five oxysterols were elucidated by HPLC-ultraviolet (UV), HPLC-MS, and 1D- and 2D-NMR. Quantification of 4α- and 4β-hydroxy-7-DHC, DHCEO, and 7-kChol in rat brain, liver, and serum were carried out by HPLC-MS using d(7)-DHCEO as an internal standard. With the exception of 7-kChol, these oxysterols were present only in tissues of AY9944-treated, but not control rats, and 7-kChol levels were markedly (>10-fold) higher in treated versus control rats. These findings are discussed in the context of the potential involvement of 7-DHC-derived oxysterols in the pathogenesis of SLOS.
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19 MeSH Terms
Characterization of DNA with an 8-oxoguanine modification.
Singh SK, Szulik MW, Ganguly M, Khutsishvili I, Stone MP, Marky LA, Gold B
(2011) Nucleic Acids Res 39: 6789-801
MeSH Terms: Base Pairing, Calorimetry, DNA, Guanine, Nuclear Magnetic Resonance, Biomolecular, Oligonucleotides, Sodium Chloride, Spectrophotometry, Ultraviolet, Temperature, Water
Show Abstract · Added May 29, 2014
The oxidation of DNA resulting from reactive oxygen species generated during aerobic respiration is a major cause of genetic damage that, if not repaired, can lead to mutations and potentially an increase in the incidence of cancer and aging. A major oxidation product generated in cells is 8-oxoguanine (oxoG), which is removed from the nucleotide pool by the enzymatic hydrolysis of 8-oxo-2'-deoxyguanosine triphosphate and from genomic DNA by 8-oxoguanine-DNA glycosylase. Finding and repairing oxoG in the midst of a large excess of unmodified DNA requires a combination of rapid scanning of the DNA for the lesion followed by specific excision of the damaged base. The repair of oxoG involves flipping the lesion out of the DNA stack and into the active site of the 8-oxoguanine-DNA glycosylase. This would suggest that thermodynamic stability, in terms of the rate for local denaturation, could play a role in lesion recognition. While prior X-ray crystal and NMR structures show that DNA with oxoG lesions appears virtually identical to the corresponding unmodified duplex, thermodynamic studies indicate that oxoG has a destabilizing influence. Our studies show that oxoG destabilizes DNA (ΔΔG of 2-8 kcal mol(-1) over a 16-116 mM NaCl range) due to a significant reduction in the enthalpy term. The presence of oxoG has a profound effect on the level and nature of DNA hydration indicating that the environment around an oxoG•C is fundamentally different than that found at G•C. The temperature-dependent imino proton NMR spectrum of oxoG modified DNA confirms the destabilization of the oxoG•C pairing and those base pairs that are 5' of the lesion. The instability of the oxoG modification is attributed to changes in the hydrophilicity of the base and its impact on major groove cation binding.
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10 MeSH Terms