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Biomedical subjects

Alan G Marshall

Publications and source records attributed to Alan G Marshall.

At least 19 recordsLinked to original sources

De novo sequencing and disulfide mapping of a bromotryptophan-containing conotoxin by Fourier transform ion cyclotron resonance mass spectrometry.

T-1-family conotoxins belong to the T-superfamily and are composed of 10-17 amino acids. They share a common cysteine framework and disulfide connectivity and exhibit unusual posttranslational modifications, such as tryptophan bromination, glutamic acid carboxylation, and threonine glycosylation. We have isolated and characterized a novel peptide, Mo1274, containing 11 amino acids, that shows the same cysteine pattern, -CC-CC, and disulfide linkage as those of the T-1-family members. The complete sequence, GNWCCSARVCC, in which W denotes bromotryptophan, was derived from MS-based de novo sequencing. The FT-ICR MS/MS techniques of electron capture dissociation (ECD), infrared multiphoton dissociation, and collision-induced dissociation served to detect and localize the tryptophan bromination. The bromine contributes a distinctive isotopic distribution in all fragments that contain bromotryptophan. ECD fragmentation results in the loss of bromine and return to the normal isotopic distribution. Disulfide connectivity of Mo1274, between cysteine pairs 1-3 and 2-4, was determined by mass spectrometry in combination with chemical derivatization employing tris(2-carboxyethyl)phosphine, followed by differential alkylation with N-ethylmaleimide and iodoacetamide. The ECD spectra of the native and partially modified peptide reveal a loss of bromine in a process that requires the presence of a disulfide bond.

Amino Acid Sequence↗

Supercritical fluid chromatography reduction of hydrogen/deuterium back exchange in solution-phase hydrogen/deuterium exchange with mass spectrometric analysis.

The single biggest problem with solution-phase H/D exchange as a mass spectrometric probe of surface exposure in a protein (or protein complex) is back-exchange of H for D after the initial H/D exchange has been quenched. Back-exchange results in loss of pertinent data and also greatly hampers data analysis. Previously, very fast, cold (0-4 degrees C) HPLC was performed to help reduce back-exchange, but calculated back-exchange still averages approximately 30%. In this report, supercritical fluid chromatography replaces HPLC as the desalting/separation technique prior to mass analysis, providing a dramatic reduction in back-exchange compared to the fast, cold HPLC methods.

Amino Acid Sequence↗

Charge location directs electron capture dissociation of peptide dications.

The effect of peptide dication charge location on electron capture dissociation (ECD) fragmentation pattern is investigated. ECD fragmentation patterns are compared for peptides with amide and free acid C-terminal groups. ECD of free acid compared with C-terminally amidated peptides with basic residues near the N-terminus demonstrates increased formation of a-type ions. Similarly, ECD of free acid compared with C-terminally amidated peptides with basic residues near the C-terminus exhibits increased formation of y-type ions. Alteration of the peptide sequence to inhibit the formation of charged side chains (i.e., amino acid substitution and acetylation) provides further evidence for charge location effect on ECD. We propose that formation of zwitterionic peptide structures increases the likelihood of amide nitrogen protonation (versus basic side chains), which is responsible for the increase in a- and y-type ion formation.

Algorithms↗

Atmospheric pressure photoionization fourier transform ion cyclotron resonance mass spectrometry for complex mixture analysis.

We have coupled atmospheric pressure photoionization (APPI) to a home-built 9.4-T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. Analysis of naphtho[2,3-a]pyrene and crude oil mass spectra reveals that protonated molecules, deprotonated molecules, and radical molecular ions are formed simultaneously in the ion source, thereby complicating the spectra (>12 000 peaks per mass spectrum and up to 63 peaks of the same nominal mass), and eliminating the "nitrogen rule" for nominal mass determination of number of nitrogens. Nevertheless, the ultrahigh mass resolving power and mass accuracy of FT-ICR MS enable definitive elemental composition assignments, even for doublets as closely spaced as 1.1 mDa (SH3(13)C vs (12)C4). APPI efficiently ionizes nonpolar compounds that are unobservable by electrospray and allows nonpolar sulfur speciation of petrochemical mixtures.

Journal Article↗

Structural characterization of an unusually stable cyclic peptide, kalata B2 from Oldenlandia affinis.

Kalata peptides are isolated from an African medicinal plant, Oldenlandia affinis, an aqueous decoction of which can be ingested to accelerate uterine contraction during childbirth. The closely packed disulfide core of kalata peptides confers unusual stability against thermal, chemical, and enzymatic degradation. The molecular arrangement may hamper NMR-assisted disulfide connectivity assignment. We have combined NMR with high-resolution mass spectrometry (MS) and MS/MS of native and chemically derivatized kalata B2 to determine its amino acid sequence and disulfide connectivity. Infrared multiphoton dissociation establishes the disulfide bond linkages in kalata B2 as I-IV, II-V and III-VI.

Amino Acid Sequence↗

Reaction of hydrogen gas with C60 at elevated pressure and temperature: hydrogenation and cage fragmentation.

Products of the reaction of C(60) with H(2) gas have been monitored by high-resolution atmospheric pressure photoionization Fourier transform ion cyclotron resonance mass spectrometry (APPI FT-ICR MS), X-ray diffraction, and IR spectroscopy as a function of hydrogenation period. Samples were synthesized at 673 K and 120 bar hydrogen pressure for hydrogenation periods between 300 and 5000 min, resulting in the formation of hydrofullerene mixtures with hydrogen content ranging from 1.6 to 5.3 wt %. Highly reduced C(60)H(x) (x > 36-40) and products of their fragmentation were identified in these samples by APPI FT-ICR MS. A sharp change in structure was observed for samples with at least 5.0 wt % of hydrogen. Low-mass (300-500 Da) hydrogenation products not observed by prior field desorption (FD) FT-ICR MS were detected by APPI FT-ICR MS and their elemental compositions obtained for the first time. Synthetic and analytical fragmentation pathways are discussed.

Journal Article↗

Impact of environmental conditions on the marine natural product bryostatin 1.

Marine Natural Products (MNPs), such as bryostatin 1, are exposed to a range of physical and chemical conditions through the life cycle of the host organism. These include exposure to sunlight, oxidizing and reducing agents, cation binding, and adsorption to reactive metal oxide surfaces. Using Fourier Transform-Ion Cyclotron Resonance (FT-ICR), Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS), UV/Vis absorbance spectroscopy, and molecular modeling, we studied the impact of UV light, TiO2, I2, and reaction with FeCl3 on the structure of bryostatin 1. Our results demonstrate that natural conditions transform bryostatin to a number of structures, including one with a molar mass of 806 Da, which we have previously identified in the sediment collected from the Gulf of Mexico. To date, at least 20 different structures of bryostatin have been reported in the literature. This work suggests that these variations may be products of the chemical environment in which the bryozoa Bugula neritina resides and are not the result of genetic variations within Bugula.

Animals↗

Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage.

Many viruses employ molecular motors to package their genomes into preformed empty capsids (procapsids). In dsRNA bacteriophages the packaging motor is a hexameric ATPase P4, which is an integral part of the multisubunit procapsid. Structural and biochemical studies revealed a plausible RNA-translocation mechanism for the isolated hexamer. However, little is known about the structure and regulation of the hexamer within the procapsid. Here we use hydrogen-deuterium exchange and mass spectrometry to delineate the interactions of the P4 hexamer with the bacteriophage phi12 procapsid. P4 associates with the procapsid via its C-terminal face. The interactions also stabilize subunit interfaces within the hexamer. The conformation of the virus-bound hexamer is more stable than the hexamer in solution, which is prone to spontaneous ring openings. We propose that the stabilization within the viral capsid increases the packaging processivity and confers selectivity during RNA loading.

Adenosine Triphosphatases↗

Probing protein ligand interactions by automated hydrogen/deuterium exchange mass spectrometry.

Amide hydrogen/deuterium exchange is a powerful biophysical technique for probing changes in protein dynamics induced by ligand interaction. The inherent low throughput of the technology has limited its impact on drug screening and lead optimization. Automation increases the throughput of H/D exchange to make it compatible with drug discovery efforts. Here we describe the first fully automated H/D exchange system that provides highly reproducible H/D exchange kinetics from 130 ms to 24 h. Throughput is maximized by parallel sample processing, and the system can run H/D exchange assays in triplicate without user intervention. We demonstrate the utility of this system to differentiate structural perturbations in the ligand-binding domain (LBD) of the nuclear receptor PPARgamma induced upon binding a full agonist and a partial agonist. PPARgamma is the target of glitazones, drugs used for treatment of insulin resistance associated with type II diabetes. Recently it has been shown that partial agonists of PPARgamma have insulin sensitization properties while lacking several adverse effects associated with full agonist drugs. To further examine the mechanism of partial agonist activation of PPARgamma, we extended our studies to the analysis of ligand interactions with the heterodimeric complex of PPARgamma/RXRalpha LBDs. To facilitate analysis of H/D exchange of large protein complexes, we performed the experiment with a 14.5-T Fourier transform ion cyclotron resonance mass spectrometer capable of measuring mass with accuracy in the ppb range.

Amino Acid Sequence↗

Characterization of the capsid protein glycosylation of adeno-associated virus type 2 by high-resolution mass spectrometry.

Adeno-associated virus type 2 (AAV-2) capsid proteins have eight sequence motifs that are potential sites for O- or N-linked glycosylation. Three are in prominent surface locations, close to the sites of cellular receptor attachment and to neutralizing epitopes on or near protrusions surrounding the three-fold axes, raising the possibility that AAV-2 might use glycosylation as a means of immune escape or for preventing reattachment on release of progeny virus. Peptide mapping and structural analysis by Fourier transform ion cyclotron resonance mass spectrometry demonstrates, however, no glycosylation of the capsid protein for virus prepared in cultured HeLa cells.

Capsid Proteins↗

Magnetism, electron paramagnetic resonance, electrochemistry, and mass spectrometry of the pentacopper(II)-substituted tungstosilicate [Cu5(OH)4(H2O)2(A-alpha-SiW9O33)2]10-, a model five-spin frustrated cluster.

The dimeric, pentacopper(II)-substituted tungstosilicate [Cu(5)(OH)(4)(H(2)O)(2)(A-alpha-SiW(9)O(33))(2)](10)(-) (1) has been characterized by single-crystal X-ray diffraction, elemental analysis, IR, electrochemistry, magnetic measurements, electron paramagnetic resonance (EPR), and mass spectrometry (MS). Magnetization and high-field EPR measurements reveal that the pentameric copper core {Cu(5)(OH)(4)(H(2)O)(2)}(6+) of 1 exhibits strong antiferromagnetic interactions (J(a) = -51 +/- 6 cm(-)(1), J(b) = -104 +/- 1 cm(-)(1), and J(c) = -55 +/- 3 cm(-)(1)) resulting in a spin S(T) = (1)/(2) ground state. EPR data show that the unpaired electron spin density is localized on the spin-frustrated apical Cu(2+) ion with g(zz) = 2.4073 +/- 0.0005, g(yy) = 2.0672 +/- 0.0005, g(xx) = 2.0240 +/- 0.0005, and A(zz) = -340 +/- 20 MHz (-0.0113 cm(-)(1)). 1 can therefore be considered as a model system for a five-spin, electronically coupled, spin-frustrated system. Polyanion 1, which is stable over a wide pH domain (pH 1-7), was characterized by cyclic voltammetry (CV) in a pH 5 medium. Its CV was constituted by an initial two-step reduction of the Cu(2+) centers to Cu(0) through Cu(+), followed at more negative potential by the redox processes of the W centers. Controlled potential coulometry of 1 allows for the reduction of the five Cu(2+) centers, as seen by consumption of 10.05 +/- 0.05 electrons per molecule. Polyanion 1 triggers efficiently the electrocatalytic reduction of nitrate and nitrite, and it also catalyzes the reduction of N(2)O. To our knowledge, this is the first example of N(2)O catalytic reduction by a polyoxoanion. Fourier transform ion cyclotron resonance MS was used to unambiguously assign the molecular weight of the solution-phase species 1 and the oxidation states of the Cu atoms in the central {Cu(5)(OH)(4)(H(2)O)(2)}(6+) core. Infrared (IR) multiphoton dissociation MS/MS of 1 showed evidence of a condensation process similar to bronze formation at low irradiation intensity. Higher IR intensity resulted in the formation of stable fragments consistent with those previously observed in the solution chemistry of polyoxoanions.

Journal Article↗

Selective synthesis of the C3v isomer of C60h18.

[chemical structure: see text]. C60H18 has been produced by hydrogenation of C60 at 100 bar H2 pressure and 673 K for 10 h. We have investigated the crude material without any purification by use of 1H NMR, 13C NMR, and IR spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry. We show that the crude material consists of 95% of the C3v isomer of C60H18.

Journal Article↗

Multicomponent internal recalibration of an LC-FTICR-MS analysis employing a partially characterized complex peptide mixture: systematic and random errors.

In high-throughput proteomics, a promising current approach is the use of liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS) of tryptic peptides from complex mixtures of proteins. To apply this method, it is necessary to account for any systematic measurement error, and it is useful to have an estimate of the random error expected in the measured masses. Here, we analyze by LC-FTICR-MS a complex mixture of peptides derived from a sample previously characterized by LC-QTOF-MS. Application of a Bayesian probability model of the data and partial knowledge of the composition of the sample suffice to estimate both the systematic and random errors in measured masses.

Amino Acid Sequence↗

Combined top-down and bottom-up mass spectrometric approach to characterization of biomarkers for renal disease.

Here we describe a mass spectrometry (MS) approach for biomarker discovery and structural characterization, based on both top-down and bottom-up analyses. Capillary electrophoresis (CE) coupled to electrospray ionization (ESI) time-of-flight (TOF) MS serves to separate and mass-measure the thousands of polypeptides contained in human urine. Statistical analysis of the differences between healthy control samples and patients with focal-segmental glomerulosclerosis, membranous glomerulonephritis, minimal change disease, IgA nephropathy, and diabetic nephropathy validates multiple biomarkers for the control and each of the diseases. To identify those biomarkers, we employ preparative CE, enabling direct infusion ESI MS analysis, followed by sample manipulation and reanalysis where necessary. We show how tandem Fourier transform ion cyclotron resonance (FT-ICR) MS identifies these sometimes large (>8 kDa) biomarkers. Critically, we maintain connectivity between the CE TOF MS data and the ICR data used for biomarker identification.

Amino Acid Sequence↗

Fourier transform ion cyclotron resonance mass spectrometry for the analysis of small ubiquitin-like modifier (SUMO) modification: identification of lysines in RanBP2 and SUMO targeted for modification during the E3 autoSUMOylation reaction.

The attachment of the ubiquitin-like protein SUMO to target proteins is involved in a number of important cellular processes. Typically, SUMO modification occurs on lysine residues within the consensus sequence psiKxE/D (psi is a hydrophobic residue and x is any residue), although there are examples of modifications at nonconsensus sites. In most cases, sites of SUMO modification have been inferred from a combination of site-directed mutagenesis and functional analysis; however, these methods have two limitations. They do not directly identify the acceptor lysine, nor are they sufficient to identify acceptor lysine residues in SUMO polymers. Here, we use Fourier transform ion cyclotron resonance (FT-ICR) together with activated-ion electron capture dissociation (AI-ECD) or infrared multiphoton dissociation (IRMPD) mass spectrometry techniques to overcome these restrictions. These approaches were employed to analyze the autoSUMOylation reaction catalyzed by the SUMO E3 ligase RanBP2. Six sites of in vitro SUMOylation in RanBP2 along with four branch-point lysines in SUMO-1 and three in SUMO-2 were identified. In all but one case, SUMOylation occurred within the sequences KxE or KpsiK. These results demonstrate the utility of FT-ICR with AI-ECD or IRMPD mass spectrometry in detecting SUMOylation, and sites of SUMOylation, and their potential roles as complementary tools for proteomic and functional analysis, and provide significant insight into the modification of a SUMO ligase for which conventional techniques have been unsuccessful.

Amino Acid Sequence↗

Composition of hydrofullerene mixtures produced by C(60) reaction with hydrogen gas revealed by high-resolution mass spectrometry.

Complex solid hydrofulleride mixtures were synthesized by prolonged hydrogenation of C(60) at 120 bar hydrogen pressure, 673 K temperature, and different reaction periods. The high degree of hydrogenation was confirmed by infrared spectroscopy and X-ray diffraction. The identity of hydrogenation products was determined by high-resolution field desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry. Despite partial gas-phase fragmentation of hydrofullerene ions during mass analysis, the data suggest that the synthesized mixtures consist of mostly C(58-60)H(x) hydrofullerenes. Increasing the duration of hydrogenation results in synthesis of C(59)H(x) and C(58)H(x) as major products. Possible hydrofullerene fragmentation pathways during both material synthesis and mass spectrometric analysis are discussed. Gas-phase fragmentation in the mass spectrometer arises from hydrofullerene ions C(60)H(x)(+) with x > 40 and C(59)H(44)(+) with drastically decreased molecular stability relative to the known C(60)H(36).

Journal Article↗

Functional visualization of viral molecular motor by hydrogen-deuterium exchange reveals transient states.

Molecular motors undergo cyclical conformational changes and convert chemical energy into mechanical work. The conformational dynamics of a viral packaging motor, the hexameric helicase P4 of dsRNA bacteriophage phi8, was visualized by hydrogen-deuterium exchange and high-resolution mass spectrometry. Concerted changes of exchange kinetics revealed a cooperative unit that dynamically links ATP-binding sites and the central RNA-binding channel. The cooperative unit is compatible with a structure-based model in which translocation is mediated by a swiveling helix. Deuterium labeling also revealed the transition state associated with RNA loading, which proceeds via opening of the hexameric ring. The loading mechanism is similar to that of other hexameric helicases. Hydrogen-deuterium exchange provides an important link between time-resolved spectroscopic observations and high-resolution structural snapshots of molecular machines.

Adenosine Triphosphate↗