Biomedical subjects

Patrik Johansson

Publications and source records attributed to Patrik Johansson.

14 recordsLinked to original sources

PubMed2006

Raman spectroscopic studies of terthiophenes for molecular electronics.

The effect of thiol and selenol functionalization on the vibrational spectra and photochemical stability of terthiophene based molecular wires was investigated using surface-enhanced Raman scattering (SERS). The molecules were found to exhibit markedly different properties at the silver surface of the SERS substrate, despite having almost identical Raman spectra in solution and in the solid state. In contrast to terthiophene (3T), the bisthiolterthiophene (T3) and biselenol-terthiophene (Se3) molecules were stable against photoinduced structural changes when adsorbed to the metal surface at low concentrations. This indicates that the strong bonds to the silver surface, via S or Se terminal atoms, leads to a rapid decay of photoexcited states. Comparison with ab initio calculations shows that both T3 and Se3 bind with only one of the functional groups to the Ag surface.

Journal Article↗

PubMed2006

Intrinsic anion oxidation potentials.

Anions of lithium battery salts have been investigated by electronic structure calculations with the objective to find a computational measure to correlate with the observed (in)stability of nonaqueous lithium battery electrolytes vs oxidation often encountered in practice. Accurate prediction of intrinsic anion oxidation potentials is here made possible by computing the vertical free energy difference between anion and neutral radical (Delta Gv) and further strengthened by an empirical correction using only the anion volume as a parameter. The 6-311+G(2df,p) basis set, the VSXC functional, and the C-PCM SCRF algorithm were used. The Delta Gv calculations can be performed using any standard computational chemistry software.

Letter↗

PubMed2006

Vibrational spectroscopy and ab initio studies of lithium bis(oxalato)borate (LiBOB) in different solvents.

The effect of lithium ion coordination with the bis(oxalato)borate (BOB-) [B(C2O4)2]- anion in DMSO, PEG, PPG, and d-PPG has been studied in detail by IR and Raman spectroscopy. Ab initio calculations were performed to allow a consistent analysis of the experimental data. The main features observed in the IR and Raman spectra correspond to the presence of "free", un-coordinated, BOB- anions. Only with use of d-PPG as solvent a small amount of Li+...BOB- ion pairs were detected. The Raman spectra and the calculations together indicate that Li+ coordinates bidentately with two end-oxygen atoms of the BOB- anion. The identification of ion pairs can be used to reveal limitations of LiBOB based electrolytes. The results for LiBOB are compared with literature on other Li salts.

Journal Article↗

PubMed2006

Structure and function of Rv0130, a conserved hypothetical protein from Mycobacterium tuberculosis.

A large fraction of the Mycobacterium tuberculosis genome codes for proteins of unknown function. We here report the structure of one of these proteins, Rv0130, solved to a resolution of 1.8 å. The Rv0130 monomer features a single hotdog fold composed of a highly curved beta-sheet on top of a long and a short alpha-helix. Two monomers in turn pack to form a double-hotdog-folded homodimer, similar to a large group of enzymes that use thiol esters as substrates. Rv0130 was found to contain a highly conserved R-specific hydratase motif buried deeply between the two monomers. Our biochemical studies show that the protein is able to hydrate a short trans-2-enoyl-coenzyme A moiety with a k(cat) of 1.1 x 10(2) sec(-1). The importance of the side chains of D40 and H45 for hydratase activity is demonstrated by site-directed mutagenesis. In contrast to many hotdog-folded proteins, a proline residue distorts the central helix of Rv0130. This distortion allows the creation of a long, curved tunnel, similar to the substrate-binding channels of long-chain eukaryotic hydratase 2 enzymes.

Bacterial Proteins↗

PubMed2006

Photo-induced transformations in 2,2':5',2''-terthiophene thin films on silver.

We report on transient photo-induced structural changes of 2,2':5',2''-terthiophene (3T) adsorbed on silver nanoparticles. Surface-enhanced Raman scattering (SERS) data show that the film thickness predetermines the eventual course of these changes. In particular, for high molecular concentrations (thick adsorbate layers), illumination leads to a photoinduced polymerization of the 3T film. For thin layers ( approximately monolayer coverage), the photoinduced spectral evolution is qualitatively different. We interpret the latter process as a cleavage of the terthiophene molecule, resulting in isolated thiophene units. Calculations of excitation energies for 3T + 3Ag+ and 1T + Ag+ revealed visible transitions, while calculated Raman frequencies indicated 1T as a possible photoproduct. As no photoinduced transformations are observed for 3T in the solid or solution phases, it is likely that the processes reported here originate in surface-enhanced charge-transfer between the Ag-surface and the organic adsorbate.

Adsorption↗

PubMed2006

Perceived discrimination in health care among American Indians/Alaska natives.

OBJECTIVES: We compared the prevalence of, and reasons for, perceived discrimination in health care among American Indian/Alaska Natives (AI/ANs) and persons of AI/AN + White heritage to African Americans, Asian Americans, and Whites. DESIGN: Data on perceived discrimination were collected by the 2001 California Health Interview Survey (CHIS). We used chi-square tests to evaluate the prevalence of perceived discrimination and the reasons for perceived discrimination across racial groups. SETTING: The 2001 CHIS, a telephone survey, one of the largest cross-sectional surveys ever conducted in the United States. PARTICIPANTS: Participants in this analysis were adults > or = 18 years of age, interviewed from 55,000 households that took part in the survey. INTERVENTIONS: Participants in the 2001 CHIS were asked "Thinking of your experiences with receiving health care in the past 12 months, have you felt you were discriminated against for any reason?" Respondents who endorsed this item were asked about possible reasons for the discrimination. MAIN OUTCOME MEASURES: 1) Does the prevalence of perceived discrimination in health care differ between AI/ANs, AI/AN + Whites, African Americans, Asian Americans, and Whites? and 2) Do the reasons for perceived discrimination in health care vary by race or ethnicity? RESULTS: Discrimination was perceived by 7.1% of the AI/AN alone group, 8.8% of AI/AN + White respondents, 5.6% of African Americans, 4.3% of Whites, and 2.6% of Asian Americans. After adjusting for covariates, the odds of perceived discrimination were different for AI/AN + White (odds ratio [OR] =2.0, 95% confidence interval [CI] 1.5-2.5) and Asian American (OR = .5, 95% CI .4-.7) when compared to Whites. CONCLUSIONS: AI/ANs, and especially those who identify as AI/AN + White, were the most likely among racial groups to report discrimination in health care.

Adolescent↗

PubMed2005

Structure of an atypical epoxide hydrolase from Mycobacterium tuberculosis gives insights into its function.

Epoxide hydrolases are vital to many organisms by virtue of their roles in detoxification, metabolism and processing of signaling molecules. The Mycobacterium tuberculosis genome encodes an unusually large number of epoxide hydrolases, suggesting that they might be of particular importance to these bacteria. We report here the first structure of an epoxide hydrolase from M.tuberculosis, solved to a resolution of 2.5 A using single-wavelength anomalous dispersion (SAD) from a selenomethionine-substituted protein. The enzyme features a deep active-site pocket created by the packing of three helices onto a curved six-stranded beta-sheet. This structure is similar to a previously described limonene-1,2-epoxide hydrolase from Rhodococcus erythropolis and unlike the alpha/beta-hydrolase fold typical of mammalian epoxide hydrolases (EH). A number of changes in the mycobacterial enzyme create a wider and deeper substrate-binding pocket than is found in its Rhodococcus homologue. Interestingly, each structure contains a different type of endogenous ligand of unknown origin bound in its active site. As a consequence of its wider substrate-binding pocket, the mycobacterial EH is capable of hydrolyzing long or bulky lipophilic epoxides such as 10,11-epoxystearic acid and cholesterol 5,6-oxide at appreciable rates, suggesting that similar compound(s) will serve as its physiological substrate(s).

Amino Acid Sequence↗

PubMed2005

Enzymatic properties of native and deglycosylated hybrid aspen (Populus tremulaxtremuloides) xyloglucan endotransglycosylase 16A expressed in Pichia pastoris.

The cDNA encoding a xyloglucan endotransglycosylase, PttXET16A, from hybrid aspen (Populus tremulaxtremuloides) has been isolated from an expressed sequence tag library and expressed in the methylotrophic yeast Pichia pastoris. Sequence analysis indicated a high degree of similarity with other proteins in the XTH (xyloglucan transglycosylase/hydrolase) gene subfamily of GH16 (glycoside hydrolase family 16). In addition to the conserved GH16 catalytic sequence motif, PttXET16A contains a conserved N-glycosylation site situated proximal to the predicted catalytic residues. MS analysis indicated that the recombinant PttXET16A expressed in P. pastoris is heterogeneous due to the presence of variable N-glycosylation and incomplete cleavage of the alpha-factor secretion signal peptide. Removal of the N-glycan by endoglycosidase H treatment did not influence the catalytic activity significantly. Similarly, site-directed mutagenesis of Asn93 to serine to remove the N-glycosylation site resulted in an enzyme which was comparable with the wild-type enzyme in specific activity and thermal stability but had clearly reduced solubility. Hydrolytic activity was detected neither in wild-type PttXET16A before or after enzymatic deglycosylation nor in PttXET16A N93S (Asn93-->Ser) mutant.

Amino Acid Sequence↗

PubMed2005

Rv0216, a conserved hypothetical protein from Mycobacterium tuberculosis that is essential for bacterial survival during infection, has a double hotdog fold.

The Mycobacterium tuberculosis genome contains about 4000 genes, of which approximately a third code for proteins of unknown function or are classified as conserved hypothetical proteins. We have determined the three-dimensional structure of one of these, the rv0216 gene product, which has been shown to be essential for M. tuberculosis growth in vivo. The structure exhibits the greatest similarity to bacterial and eukaryotic hydratases that catalyse the R-specific hydration of 2-enoyl coenzyme A. However, only part of the catalytic machinery is conserved in Rv0216 and it showed no activity for the substrate crotonyl-CoA. The structure of Rv0216 allows us to assign new functional annotations to a family of seven other M. tuberculosis proteins, a number if which are essential for bacterial survival during infection and growth.

Acyl Coenzyme A↗

PubMed2004

Crystal structures of a poplar xyloglucan endotransglycosylase reveal details of transglycosylation acceptor binding.

Xyloglucan endotransglycosylases (XETs) cleave and religate xyloglucan polymers in plant cell walls via a transglycosylation mechanism. Thus, XET is a key enzyme in all plant processes that require cell wall remodeling. To provide a basis for detailed structure-function studies, the crystal structure of Populus tremula x tremuloides XET16A (PttXET16A), heterologously expressed in Pichia pastoris, has been determined at 1.8-A resolution. Even though the overall structure of PttXET16A is a curved beta-sandwich similar to other enzymes in the glycoside hydrolase family GH16, parts of its substrate binding cleft are more reminiscent of the distantly related family GH7. In addition, XET has a C-terminal extension that packs against the conserved core, providing an additional beta-strand and a short alpha-helix. The structure of XET in complex with a xyloglucan nonasaccharide, XLLG, reveals a very favorable acceptor binding site, which is a necessary but not sufficient prerequisite for transglycosylation. Biochemical data imply that the enzyme requires sugar residues in both acceptor and donor sites to properly orient the glycosidic bond relative to the catalytic residues.

Amino Acid Sequence↗

PubMed2004

Microarray technology for identification and distinction of hantaviruses.

DNA microarrays combine high-precision technology with advanced molecular biology to achieve high-throughput screening of DNA fragments. In this study, we investigated the potential of the cDNA microarray technique to identify and discriminate PCR derived amplicons from genetically highly similar viruses. The wide range of sequence variation among hantaviruses makes them suitable as a model for this purpose. The hantaviruses, carried by rodents, cause several hundred thousand cases of severe human disease every year in many parts of the world. A hantavirus-specific microarray, including DNA fragments from 12 viral isolates of six different hantaviruses, was designed. The S and M genome segments were represented by 500-nucleotide overlapping and 250-nucleotide non-overlapping fragments. A considerable ability to distinguish between different hantaviruses was demonstrated using a novel analysis method. Even different isolates of a single virus, were identified correctly despite 90% sequence similarity. The distinction ability was accompanied by a tolerance for smaller sequence differences, which makes the microarray suitable for testing samples containing unknown viruses. Viral genetic material found in samples from the lungs of bank voles caught in the wild was identified precisely, which demonstrated further the potential for this technology.

Animals↗

PubMed2004

Complete gene sequence of a human Puumala hantavirus isolate, Puumala Umeå/hu: sequence comparison and characterisation of encoded gene products.

Puumala virus is a member of the hantavirus genus in the Bunyaviridae family, and the major causative agent of haemorrhagic fever with renal syndrome in Europe. This study was conducted with a human Puumala virus isolate (PUUV Umeå/hu), and contains the determination of the first complete PUUV sequence from a human source. When the relationship to other Puumala viruses was analysed, a possible RNA segment exchange between two local strains of PUUV was noticed. Furthermore, the coding regions of PUUV Umeå/hu S- and M-segments were cloned, and a large set of gene products were expressed in mammalian cells. In addition, postulated N- and O-linked glycosylation sites in the two envelope proteins (Gn and Gc) were investigated individually by site-directed mutagenesis followed by gel-shift analysis. Our data demonstrate that N-linked glycosylation occurs at three sites in Gn (N142, N357 and N409), and at one site in Gc (N937). Also, one possible O-glycosylation site was identified in Gc (T985). We conclude that the diversity between different Puumala virus isolates is high, and consequently characterization of local PUUV isolates is important for clinical diagnostic work. Finally, the obtained results concerning the encoded gene products are of great importance for the design of new vaccines.

Animals↗

PubMed2004

X-ray structure of peptidyl-prolyl cis-trans isomerase A from Mycobacterium tuberculosis.

Peptidyl-prolyl cis-trans isomerases (EC 5.2.1.8) catalyse the interconversion of cis and trans peptide bonds and are therefore considered to be important for protein folding. They are also thought to participate in processes such as signalling, cell surface recognition, chaperoning and heat-shock response. Here we report the soluble expression of recombinant Mycobacterium tuberculosis peptidyl-prolyl cis-trans isomerase PpiA in Escherichia coli, together with an investigation of its structure and biochemical properties. The protein was shown to be active in a spectrophotometric assay, with an estimated kcat/Km of 2.0 x 10(6) m(-1).s(-1). The X-ray structure of PpiA was solved by molecular replacement, and refined to a resolution of 2.6 A with R and Rfree values of 21.3% and 22.9%, respectively. Comparisons to known structures show that the PpiA represents a slight variation on the peptidyl-prolyl cis-trans isomerase fold, previously not represented in the Protein Data Bank. Inspection of the active site suggests that specificity for substrates and cyclosporin A will be similar to that found for most other enzymes of this structural family. Comparison to the sequence of the second M. tuberculosis enzyme, PpiB, suggests that binding of peptide substrates as well as cyclosporin A may differ in that case.

Amino Acid Sequence↗

PubMed2003

Crystallization and preliminary X-ray analysis of a xyloglucan endotransglycosylase from Populus tremula x tremuloides.

Xyloglucan endotransglycosylases (XETs) cleave and religate xyloglucan polymers in plant cell walls. Recombinant XET from poplar has been purified from a Pichia pastoris expression system and crystallized. Two different crystal forms were obtained by vapour diffusion from potassium sodium tartrate and from an imidazole buffer using sodium acetate as a precipitant. Data were collected from these crystal forms to 3.5 and 2.1 A resolution, respectively. The first crystal form was found to belong to space group P3(1)21 or P3(2)21 (unit-cell parameters a = 98.6, b = 98.6, c = 98.5 A) and the second crystal form to space group P6(3) (unit-cell parameters a = 188.7, b = 188.7, c = 46.1 A).

Cloning, Molecular↗