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P Håkansson

Publications and source records attributed to P Håkansson.

At least 19 recordsLinked to original sources
PubMed2006

Improved diffusion Monte Carlo propagators for bosonic systems using Itô calculus.

The construction of importance sampled diffusion Monte Carlo (DMC) schemes accurate to second order in the time step is discussed. A central aspect in obtaining efficient second order schemes is the numerical solution of the stochastic differential equation (SDE) associated with the Fokker-Plank equation responsible for the importance sampling procedure. In this work, stochastic predictor-corrector schemes solving the SDE and consistent with Itô calculus are used in DMC simulations of helium clusters. These schemes are numerically compared with alternative algorithms obtained by splitting the Fokker-Plank operator, an approach that we analyze using the analytical tools provided by Ito; calculus. The numerical results show that predictor-corrector methods are indeed accurate to second order in the time step and that they present a smaller time step bias and a better efficiency than second order split-operator derived schemes when computing ensemble averages for bosonic systems. The possible extension of the predictor-corrector methods to higher orders is also discussed.

Journal Article↗
PubMed2006

A constant-momentum/energy-selector time-of-flight mass spectrometer.

A matrix assisted laser desorption/ionization time-of-flight mass spectrometer has been built with an ion source that can be operated in either constant-energy or constant-momentum acceleration modes. A decreasing electric field distribution in the ion-accelerating region makes it possible to direct ions onto a space-focal plane in either modes of operation. Ions produced in the constant-momentum mode have velocities and, thus, flight times that are linearly dependent on mass and kinetic energies that are inversely dependent on mass. The linear mass dispersion doubles mass resolving power of ions accelerated with space-focusing conditions in constant-momentum mode. The mass-dependent kinetic energy is exploited to disperse ions according to mass in a simple kinetic energy filter constructed from two closely spaced, oblique ion reflectors. Focusing velocity of ions of the same mass can substantially improve ion selection for subsequent post source decay or tandem time-of-flight analyses.

Angiotensin I↗
PubMed2004

Establishment and phenotypic characterization of human U937 cells with inducible P210 BCR/ABL expression reveals upregulation of CEACAM1 (CD66a).

Chronic myeloid leukemia (CML) is characterized by the expression of the P210 BCR/ABL fusion protein. The molecular mechanisms behind this oncogene-mediated hematological disease are, however, not fully understood. Here, we describe the establishment and phenotypic characterization of U937 cells in which P210 BCR/ABL can be conditionally expressed using tetracycline. The induction of BCR/ABL in the obtained clones resulted in a rapid phosphorylation of the STAT1, STAT3 and STAT5 molecules, consistent with the findings in other model systems. Phenotypic characterization of the clones revealed that BCR/ABL induces a slight decrease in the proliferation and viability, without a marked effect on cell cycle distribution, the rate of apoptosis or on cellular differentiation, as judged by several cell surface markers and capacity to reduce nitro blue tetrazolium. Interestingly, BCR/ABL was found to upregulate the expression of carcinoembryonic-related antigen (CEA)CAM1 (CD66a), which is a plasma membrane-linked glycoprotein belonging to the CEAs and involved in signal transduction and cellular adhesion. The expression of CEACAM1 was reversible upon imatinib treatment in BCR/ABL-expressing U937 cells as well as in BCR/ABL-positive K562 cells. The established cell lines may prove useful in further modeling and dissection of BCR/ABL-induced leukemogenesis.

Antigens, CD↗
PubMed2002

Ontogenetic development and spatial distribution of the ileal apical sodium-dependent bile acid transporter and the ileal lipid-binding protein in apoE knockout and C57BL/6 mice.

BACKGROUND: Although apoE-/- mice are characterized by hypercholesterolemia, the bile acid enterohepatic circulation, which plays a crucial role in cholesterol homeostasis, has not been examined in these mice. The differences between apoE-/- and C57BL/6 mice in expression of the ileal ASBT and ILBP and in intestinal bile acid absorption were studied. METHODS: The intestinal tissues of the fetal, neonatal and post-weaning mice were processed for immunohistochemistry. Body retention and fecal excretion of 75SeHCAT were measured. The bile acid pool size and its composition were analysed by HPLC. RESULTS: In apoE-/- and C57BL/6 mice, the bile acid pool size was 75 +/- 13 and 78 +/- 13 micromol/ 100 g body weight, respectively, while the ratio of cholic acid/beta-muricholic acid was 1.8 +/- 0.3 and 1.4 +/- 0.3 (P < 0.05), respectively. The daily body retention of 75SeHCAT was 48% = 1.8% in C57 black mice and 58.4% +/- 2.7% in apoE-/- mice (P < 0.05). In both mouse strains, ASBT expression in the small intestine was found in the near-term fetal and post-weaning mice, while ILBP expression was found in all postnatal mice. In the post-weaning mice, ILBP expression was limited to the distal 25%-30% of the small intestine, while ASBT expression was limited to the distal 18%. CONCLUSIONS: The bile acid enterohepatic circulation in apoE-/- mice probably does not differ greatly from that in C57BL/6 mice.

Animals↗
PubMed2001

Mammalian p53R2 protein forms an active ribonucleotide reductase in vitro with the R1 protein, which is expressed both in resting cells in response to DNA damage and in proliferating cells.

Recently, a homologue of the small subunit of mammalian ribonucleotide reductase (RNR) was discovered, called p53R2. Unlike the well characterized S phase-specific RNR R2 protein, the new form was induced in response to DNA damage by the p53 protein. Because the R2 protein is specifically degraded in late mitosis and absent in G0/G1 cells, the induction of the p53R2 protein may explain how resting cells can obtain deoxyribonucleotides for DNA repair. However, no direct demonstration of RNR activity of the p53R2 protein was presented and furthermore, no corresponding RNR large subunit was identified. In this study we show that recombinant, highly purified human and mouse p53R2 proteins contain an iron-tyrosyl free radical center, and both proteins form an active RNR complex with the human and mouse R1 proteins. UV irradiation of serum-starved, G0/G1-enriched mouse fibroblasts, stably transformed with an R1 promoter-luciferase reporter gene construct, caused a 3-fold increase in luciferase activity 24 h after irradiation, paralleled by an increase in the levels of R1 protein. Taken together, our data indicate that the R1 protein can function as the normal partner of the p53R2 protein and that an R1-p53R2 complex can supply resting cells with deoxyribonucleotides for DNA repair.

Amino Acid Sequence↗
PubMed2001

Improved low-energy electron injection systems for high rate electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry.

New low-energy electron injection systems based on indirectly heated dispenser cathodes facilitate electron capture dissociation (ECD) in Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. In this joint report, details are presented of the design and performance of these systems on two commercial FTICR instruments, 9.4 T Bruker BioAPEX in Uppsala and 4.7 T IonSpec Ultima in Odense. New results include obtaining meaningful one-scan MS/MS data for isolated precursor ions with millisecond irradiation times. The ECD rate improvement is not only due to the larger total electron current, but the larger emitting area as well.

Amino Acid Sequence↗
PubMed2001

Inter- and intra-molecular migration of peptide amide hydrogens during electrospray ionization.

The isotopic exchange of amide hydrogens in proteins in solution strongly depends on the surrounding protein structure, thereby allowing structural studies of proteins by mass spectrometry. However, during electrospray ionization (ESI), gas phase processes may scramble or deplete the isotopic information. These processes have been investigated by on-line monitoring of the exchange of labile deuterium atoms in homopeptides with hydrogens from a solvent suitable for ESI. The relative contribution of intra- and inter-molecular exchange in the gas phase could be studied from their distinct influence on the well-characterized exchange processes in the spraying solution. The deuterium content of individual labile hydrogens was assessed from the isotopic patterns of two consecutive collision-induced dissociation fragments, as observed with a 9.4 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Results demonstrate that gas phase exchange in the high-pressure region between the capillary and the skimmer cause substantial depletion of the isotopic information of penta-phenylalanine and penta-aspartic acid. For penta-alanine and hexa-tyrosine, the amide hydrogens located close to the N-terminus are depleted from deuterium during mass analysis. Amide hydrogens located close to the C-terminus still retain the information of the isotopic state in solution, but they are redistributed by intra-molecular exchange of the amide hydrogens with the C-terminal hydroxyl group.

Algorithms↗
PubMed2001

Automatic analysis of hydrogen/deuterium exchange mass spectra of peptides and proteins using calculations of isotopic distributions.

High mass-resolving power has been shown to be useful for studying the conformational dynamics of proteins by hydrogen/deuterium (H/D) exchange. A computer algorithm was developed that automatically identifies peptides and their extent of deuterium incorporation from H/D exchange mass spectra of enzymatic digests or fragment ions produced by collisionally induced dissociation (CID) or electron capture dissociation (ECD). The computer algorithm compares measured and calculated isotopic distributions and uses a fast calculation of isotopic distributions using the fast Fourier transform (FFT). The algorithm facilitates rapid and automated analysis of H/D exchange mass spectra suitable for high-throughput approaches to the study of peptide and protein structures. The algorithm also makes the identification independent on comparisons with undeuterated control samples. The applicability of the algorithm was demonstrated on simulated isotopic distributions as well as on experimental data, such as Fourier transform ion cyclotron resonance (FTICR) mass spectra of myoglobin peptic digests, and CID and ECD spectra of substance P.

Algorithms↗
PubMed2001

A test for cleaning and disinfection processes in a washer-disinfector.

Disinfection processes such as heat, aldehydes or alcohols kill vegetative microorganisms but do not necessarily remove other organic contamination. Organic residues impair the result of low-temperature sterilisation processes. Heat-stable organic residues may give rise to clinical symptoms in the patient. Standards are available in Britain and in Sweden for the examination of cleaning processes in washer-disinfectors. The test substances are artificial soil or blood. These standards are based on visual inspection of instruments or equipment. They cannot be used for examination of tubular instruments, nor can they be quantified. For validation of cleaning procedures a simple quantifiable method, which can be performed in an infection control laboratory is needed. We have used suspensions in horse blood of Enterococcus faecalis bacteria and Bacillus subtilis spores to test disinfection and cleaning in a washer-disinfector. Instruments used for laparoscopic surgery were contaminated with a blood bacteria suspension containing 10(7) organisms/ml and then dried and processed in a washer-disinfector using a regular process. Remaining microbial contamination was cultured quantitatively. Nineteen objects were investigated in 10 experiments each. Cleaning, measured as log reduction >5-6 of B. subtilis, was achieved on surfaces that were adequately in contact with the water flow in the machine. Disinfection (and cleaning) measured as log reduction >5-6 of E. faecalis was successful at all points examined. The test method is simple and quantifiable, and can be used to evaluate and to improve cleaning and disinfection processes.

Animals↗
PubMed2000

Analysis of enzymatically digested proteins and protein mixtures using a 9.4 Tesla Fourier transform ion cyclotron mass spectrometer.

A commercially available 9.4 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer was applied in the analysis of tryptic digests of protein mixtures without any separation. First, the method was demonstrated on a mixture of tryptic digests of equine cytochrome c, equine myoglobin and bovine serum albumin. The same method was then applied to human plasma from a healthy blood donor. Computer programs were employed to simplify analysis of the complex spectra. The 2745 peaks in the human plasma electrospray ionization FTICR spectrum could be reduced to 1165 isotopic clusters and 669 unique masses. Out of these, 82 masses matched tryptic fragments of serum albumin with mass measurement errors less than 10 ppm, covering 93% of the sequence. Another 16 masses were assigned to tryptic fragments of transferrin, covering 41% of the sequence on the 10 ppm mass measurement error level (14 within 2 ppm). The mass measurement errors were approximately normal distributed with a standard deviation of 1.7 ppm. This demonstrates the feasibility of combining the ultra-high mass resolving power and accuracy of FTICR mass spectrometry with automated computer analysis for investigating complex biological matrices.

Algorithms↗
PubMed2000

A new method for the accurate determination of the isotopic state of single amide hydrogens within peptides using Fourier transform ion cyclotron resonance mass spectrometry.

A new method is presented to accurately determine the probability of having a deuterium or hydrogen atom on a specific amide position within a peptide after deuterium/hydrogen (D/H) exchange in solution. Amide hydrogen exchange has been proven to be a sensitive probe for studying protein structures and structural dynamics. At the same time, mass spectrometry in combination with physical fragmentation methods is commonly used to sequence proteins based on an amino acid residue specific mass analysis. In the present study it is demonstrated that the isotopic patterns of a series of peptide fragment ions obtained with capillary-skimmer dissociation, as observed with a 9.4 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer, can be used to calculate the isotopic state of specific amide hydrogens. This calculation is based on the experimentally observed isotopic patterns of two consecutive fragments and on the isotopic binomial distributions of the atoms in the residue constituting the difference between these two consecutive fragments. The applicability of the method is demonstrated by following the sequence-specific D/H exchange rate in solution of single amide hydrogens within some peptides.

Amides↗
PubMed2000

Mechanistic studies of multipole storage assisted dissociation.

The degree and onset of fragmentation in multipole storage assisted dissociation (MSAD) have been investigated as functions of several hexapole parameters. Strict studies of hexapole charge density (number of ions injected) and hexapole storage time were made possible by placing a pulsed shutter in front of the entrance to the mass spectrometer. The results obtained show that the charge density is the most critical parameter, but also dependencies on storage time, radio-frequency (rf) -amplitude, and pressure are seen. From these data, and from simulations of the ion trajectories inside the hexapole, a mechanism for MSAD, similar to the ones for sustained off-resonance irradiation (SORI), and for low energy collisionally induced dissociation in the collision multipole of a triple quadrupole mass spectrometer, is proposed. It is believed that, at higher charge densities, ions are pushed to larger hexapole radii where the electric potential created by the rf field is higher, forcing the ions to oscillate radially to higher amplitudes and thereby reach higher (but still relatively low) kinetic energies. Multiple collisions with residual gas molecules at these elevated energies then heat up the molecules to their dissociation threshold. Further support for this mechanism is obtained from a comparison of MSAD and SORI spectra which are almost identical in appearance.

Mass Spectrometry↗
PubMed1999

Conformational stability of adsorbed insulin studied with mass spectrometry and hydrogen exchange.

A new method is described for direct monitoring of the conformational stability of proteins that are physically adsorbed from solution onto a solid substrate. The adsorption-induced conformational changes of insulin are studied using a combination of hydrogen/deuterium (H/D) exchange and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The effect of the surface hydrophobicity on the adsorption-induced conformational changes in the insulin structure is probed by adsorbing insulin on a hydrophilic silica and a hydrophobic methylated silica surface before subjecting the insulin molecules to the isotopic exchange process. The present study describes the experimental procedure of this new application of MALDI. Results show that insulin is more highly and more irreversibly adsorbed to a hydrophobic methylated silica surface than to a hydrophilic silica surface. Hydrogen-exchange experiments clearly demonstrate that the strong interaction of insulin with the hydrophobic surface is accompanied by a strong increase in the H/D-exchange rates and thus in a reduction in the insulin native structural stability. In contrast, H/D-exchange rates of insulin are somewhat reduced upon adsorption on silica from solution.

Adsorption↗
PubMed1999

Electron capture dissociation of substance P using a commercially available Fourier transform ion cyclotron resonance mass spectrometer.

Electron capture dissociation of the peptide Substance P is reported for the first time, with an unmodified, commercially available Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. The fragmentation pattern is compared with that obtained with collisionally induced dissociation of the ions in the electrospray ion source, and note that electron capture dissociation gives a more easily interpreted spectrum, showing mainly C-fragments. With the exception of the proline residues, which require cleavage of two chemical bonds, we observe all C-fragmental we find the bias voltage of the electron gun not to be very critical.

Amino Acid Sequence↗
PubMed1999

A high resolving power multiple reflection matrix-assisted laser desorption/ionization time-of-flight mass spectrometer.

Two electrostatic mirrors, mounted symmetrically on the same optical axis facing each other, are used to increase the time-of-flight of molecular ions produced in matrix-assisted laser desorption/ionization (MALDI). The mirrors, which are used in the non-compensating mode, are located between a MALDI ion source and a stop detector. The source is operated at 10.5 kV acceleration voltage using the delayed extraction technique. The high voltage for the mirror arrangement is switched on after the desorption event when the molecular ions have drifted into the region between the mirrors. The ions are trapped by successive reflections of the opposite electrostatic fields in the mirrors until the electric fields are switched off. The number of reflections depends on the speed of the ions when they enter the mirror trap and the ontime of the mirrors. When the electric fields are removed during the motion of the ions towards the stop detector, the ions penetrate the grids of the mirror and reach that detector. The extension of the flight path due to the number of reflections is used to increase the resolving power in time-of-flight spectra. Values of 55,000 for substance-P (MW 1346.7) and 31,000 for bovine insulin (MW 5734) were obtained for single laser shot spectra.

Algorithms↗
PubMed1999

Interaction between explosive and analyte layers in explosive matrix-assisted plasma desorption mass spectrometry.

An HMX/insulin two-layer system was chosen as a model for further investigation of the matrix properties of explosive materials for protein analytes in plasma desorption mass spectrometry. The dependencies of the molecular ion yield and average charge state as a function of the analyte thickness were studied. An increase in the charge state of multiply protonated molecular species was confirmed as the major matrix effect, with the average charge state z at the smallest thickness studied being higher than in matrix-assisted laser desorption/ionization and closer to the value obtained in electrospray ionization under standard acidic conditions. Observed charge state distributions are significantly narrower than the corresponding Poisson distributions, which suggests that the protonation of insulin is limited in plasma desorption by the number of basic sites in the molecule, similar to electrospray ionization. Both the curve displaying total molecular ion yield and the one showing the total charge (proton) yield as a function of the insulin thickness have maxima at a thickness different from an insulin monolayer. These observations diminish the significance of a matrix/analyte interface mechanism for the explosive matrix assistance. Instead, a mechanism related to the chemical energy release during conversion of the explosive after the ion impact is proposed. As additional mechanisms, enhanced protonation of the analyte through collisions with products of the explosive decay is considered, as well as electron scavenging by other products, which leads to a higher survival probability of positively charged protein molecular ions. Copyright 1999 John Wiley & Sons, Ltd.

Journal Article↗
PubMed1998

Combination of nozzle-skimmer fragmentation and partial acid hydrolysis in electrospray ionization time-of-flight mass spectrometry of synthetic peptides.

For reliable confirmation of peptide structures, nozzle-skimmer collisionally induced dissociation was found in many cases to be insufficient, and partial acid hydrolysis was employed as a complementary technique. The utility of combining these fragmentation methods is demonstrated in two examples where the complete sequences of two synthetic peptides (peptide I, MW 2290 and peptide II, MW 1482) were unambiguously determined. In a third example, three different valine deletions in a 2 kDa synthetic peptide were identified and their positions unambiguously established. A home-built electrospray ionization time-of-flight mass spectrometer with orthogonal extraction was used for these analyses. The performance of this instrument with a resolving power of up to 7500, a mass accuracy of < or = 10 ppm, and a detection limit of 1 fmol was shown to be well suited for such studies. As a substitution to conventional external calibration, a more convenient and equally accurate internal 3-point calibration is proposed, based on the low mass ions that are present in almost all peptide spectra.

Amino Acid Sequence↗