Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue’s effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict ¹³C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve the identification of small populations of transient structure in disordered proteins.     

Pichia pastoris-produced mucin-type fusion proteins with multivalent O-glycan substitution as targeting molecules for mannose-specific receptors of the immune system

Mannose-binding proteins like the macrophage mannose receptor (MR), the dendritic cell-specific intercellular adhesion molecule-3 grabbing non-integrin (DC-SIGN) and mannose-binding lectin (MBL) play crucial roles in both innate and adaptive immune responses. Immunoglobulin fusion proteins of the P-selectin glycoprotein ligand-1 (PSGL-1/mIgG(2b)) carrying mostly O-glycans and, as a control, the α1-acid glycoprotein (AGP/mIgG(2b)) carrying mainly N-linked glycans were stably expressed in the yeast Pichia pastoris. Pichia pastoris-produced PSGL-1/mIgG(2b) was shown to carry O-glycans that mediated strong binding to mannose-specific lectins in a lectin array and were susceptible to cleavage by α-mannosidases including an α1,2- but not an α1,6-mannosidase. Electrospray ionization ion-trap mass spectrometry confirmed the presence of O-glycans containing up to nine hexoses with the penta- and hexasaccharides being the predominant ones. α1,2- and α1,3-linked, but not α1,6-linked, mannose residues were detected by (1)H-nuclear magnetic resonance spectroscopy confirming the results of the mannosidase cleavage. The apparent equilibrium dissociation constants for binding of PNGase F-treated mannosylated PSGL-1/mIgG(2b) to MR, DC-SIGN and MBL were shown by surface plasmon resonance to be 126, 56 and 16 nM, respectively. In conclusion, PSGL-1/mIgG(2b) expressed in P. pastoris carried O-glycans mainly comprised of α-linked mannoses and with up to nine residues. It bound mannose-specific receptors with high apparent affinity and may become a potent targeting molecule for these receptors in vivo.     

Correction to: Characterization of anisotropic turbulence behavior in pulsatile blood flow

Turbulent-like hemodynamics with prominent cycle-to-cycle flow variations have received increased attention as a potential stimulus for cardiovascular diseases. These turbulent conditions are typically evaluated in a statistical sense from single scalars extracted from ensemble-averaged tensors (such as the Reynolds stress tensor), limiting the amount of information that can be used for physical interpretations and quality assessments of numerical models. In this study, barycentric anisotropy invariant mapping was used to demonstrate an efficient and comprehensive approach to characterize turbulence-related tensor fields in patient-specific cardiovascular flows, obtained from scale-resolving large eddy simulations. These techniques were also used to analyze some common modeling compromises as well as MRI turbulence measurements through an idealized constriction. The proposed method found explicit sites of elevated turbulence anisotropy, including a broad but time-varying spectrum of characteristics over the flow deceleration phase, which was different for both the steady inflow and Reynolds-averaged Navier–Stokes modeling assumptions. Qualitatively, the MRI results showed overall expected post-stenotic turbulence characteristics, however, also with apparent regions of unrealizable or conceivably physically unrealistic conditions, including the highest turbulence intensity ranges. These findings suggest that more detailed studies of MRI-measured turbulence fields are needed, which hopefully can be assisted by more comprehensive evaluation tools such as the once described herein.

     

Central Asian origin of and strong genetic differentiation among populations of the rare and disjunct Carex atrofusca (Cyperaceae) in the Alps

Aim Carex atrofusca has an arctic–alpine distribution in the Northern Hemisphere, with only a few, disjunct localities known in the European Alps. These alpine populations are declining in number and size. In contrast, C. atrofusca has a wide circumpolar distribution range and is abundant in large parts of the Arctic. The degree of genetic differentiation of the alpine populations and their importance for the conservation of the intraspecific genetic variation of the species is unknown. Location Eurasia and Greenland, with emphasis on the European Alps. Methods We applied amplified fragment length polymorphism (AFLP) fingerprinting and sequences of chloroplast DNA to determine the position of the alpine populations in a circumpolar phylogeography of C. atrofusca and to unravel the patterns of genetic diversity and differentiation within the Alps. Results Two distinct major groups were detected in a neighbour‐joining analysis of AFLP data and in parsimony analysis of chloroplast DNA sequences: one consisting of the populations from Siberia and Greenland and one consisting of all European populations as sister to the populations from Central Asia. Within Europe, the populations from the Tatra Mountains and those from Scotland and Scandinavia formed two well‐supported groups, whereas the alpine populations did not constitute a group of their own. The genetic variation in the Alps was almost completely partitioned among the populations, and the populations were almost invariable. Main conclusions The alpine populations possibly originated due to immigration from Central Asia. The strong differentiation among them suggests that genetic drift has been strongly acting on the populations, either as a consequence of founder events during colonization or due to subsequent reduction of population sizes during warm stages of the Holocene.     

Analytical quantification of low‐density lipoprotein using europium tetracycline indicator

Low‐density lipoprotein (LDL) is known as ‘bad’ cholesterol. If too much LDL circulates in the blood it can be retained in the walls of the arteries, causing atherosclerosis. In this paper we showed an alternative method to quantify LDL using the europium tetracycline (EuTc) indicator. The optical properties of the EuTc complex were investigated in aqueous solutions containing LDL. An enhancement was observed of the europium luminescence in the solutions with LDL compared those without the lipoprotein. A method to quantify the amount of LDL in a sample, based on EuTc enhanced luminescence, is proposed. The enhancement mechanism is also discussed. Copyright © 2009 John Wiley & Sons, Ltd.     

Active site mutants of Drosophila melanogaster multisubstrate deoxyribonucleoside kinase.

The multisubstrate deoxyribonucleoside kinase of Drosophila melanogaster (Dm-dNK) is sequence-related to three human deoxyribonucleoside kinases and to herpes simplex virus type-1 thymidine kinase. Dm-dNK phosphorylates both purine and pyrimidine deoxyribonucleosides and nucleoside analogues although it has a preference for pyrimidine nucleosides. We performed site-directed mutagenesis on residues that, based on structural data, are involved in substrate recognition. The aim was to increase the phosphorylation efficiency of purine nucleoside substrates to create an improved enzyme to be used in suicide gene therapy. A Q81N mutation showed a relative increase in deoxyguanosine phosphorylation compared with the wild-type enzyme although the efficiency of deoxythymidine phosphorylation was 10-fold lower for the mutant. In addition to residue Q81 the function of amino acids N28, I29 and F114 was investigated by different substitutions. All of the mutated enzymes showed decreased efficiency of thymidine phosphorylation in comparison with the wild-type enzyme supporting their importance for substrate binding and/or catalysis as proposed by the recently solved structure of Dm-dNK.     

Concomitant Socioeconomic,Behavioral, and Biological Factors Associated with the Disproportionate HIV Infection Burden among Black Men Who Have Sex with Men in 6 U.S. Cities

Background

American Black men who have sex with men (MSM) are disproportionately affected by HIV, but the factors associated with this concentrated epidemic are not fully understood.

Methods

Black MSM were enrolled in 6 US cities to evaluate a multi-component prevention intervention, with the current analysis focusing on the correlates of being newly diagnosed with HIV compared to being HIV-uninfected or previously diagnosed with HIV.

Results

HPTN 061 enrolled 1553 Black MSM whose median age was 40; 30% self-identified exclusively as gay or homosexual, 29% exclusively as bisexual, and 3% as transgender. About 1/6^th (16.2%) were previously diagnosed with HIV (PD); of 1263 participants without a prior HIV diagnosis 7.6% were newly diagnosed (ND). Compared to PD, ND Black MSM were younger (p<0.001); less likely to be living with a primary partner (p<0.001); more likely to be diagnosed with syphilis (p<0.001), rectal gonorrhea (p = 0.011) or chlamydia (p = 0.020). Compared to HIV-uninfected Black MSM, ND were more likely to report unprotected receptive anal intercourse (URAI) with a male partner in the last 6 months (p<0.001); and to be diagnosed with syphilis (p<0.001), rectal gonorrhea (p = 0.004), and urethral (p = 0.025) or rectal chlamydia (p<0.001). They were less likely to report female (p = 0.002) or transgender partners (p = 0.018). Multivariate logistic regression analyses found that ND Black MSM were significantly more likely than HIV-uninfected peers to be unemployed; have STIs, and engage in URAI. Almost half the men in each group were poor, had depressive symptoms, and expressed internalized homophobia.

Conclusions

ND HIV-infected Black MSM were more likely to be unemployed, have bacterial STIs and engage in URAI than other Black MSM. Culturally-tailored programs that address economic disenfranchisement, increase engagement in care, screen for STIs, in conjunction with safer sex prevention interventions, may help to decrease further transmission in this heavily affected community.     

A1M/α1-Microglobulin Protects from Heme-Induced Placental and Renal Damage in a Pregnant Sheep Model of Preeclampsia

Preeclampsia (PE) is a serious pregnancy complication that manifests as hypertension and proteinuria after the 20^th gestation week. Previously, fetal hemoglobin (HbF) has been identified as a plausible causative factor. Cell-free Hb and its degradation products are known to cause oxidative stress and tissue damage, typical of the PE placenta. A1M (α₁-microglobulin) is an endogenous scavenger of radicals and heme. Here, the usefulness of A1M as a treatment for PE is investigated in the pregnant ewe PE model, in which starvation induces PE symptoms via hemolysis. Eleven ewes, in late pregnancy, were starved for 36 hours and then treated with A1M (n = 5) or placebo (n = 6) injections. After injections, the ewes were re-fed and observed for additional 72 hours. They were monitored for blood pressure, proteinuria, blood cell distribution and clinical and inflammation markers in plasma. Before termination, the utero-placental circulation was analyzed with Doppler velocimetry and the kidney glomerular function was analyzed by Ficoll sieving. At termination, blood, kidney and placenta samples were collected and analyzed for changes in gene expression and tissue structure. The starvation resulted in increased amounts of the hemolysis marker bilirubin in the blood, structural damages to the placenta and kidneys and an increased glomerular sieving coefficient indicating a defect filtration barrier. Treatment with A1M ameliorated these changes without signs of side-effects. In conclusion, A1M displayed positive therapeutic effects in the ewe starvation PE model, and was well tolerated. Therefore, we suggest A1M as a plausible treatment for PE in humans.     

Bilateral versus Single Internal Mammary Coronary Artery Bypass Grafting in Sweden from 1997–2008

Background

Prior observational studies have suggested better outcomes in patients who receive bilateral internal mammary arteries (BIMA) during coronary artery bypass grafting (CABG) compared with patients who receive a single internal mammary artery (SIMA). The aim of this study was to analyze the association between BIMA use and long-term survival in patients who underwent primary isolated CABG.

Methods and Results

Patients who underwent primary isolated non-emergent CABG in Sweden between 1997 and 2008 were identified. The SWEDEHEART registry and other national Swedish registers were used to acquire information about patient characteristics and outcomes. Unadjusted and multivariable adjusted regression models were used to estimate the association between BIMA use and early mortality, long-term survival, and a composite of death from any cause or rehospitalization for myocardial infarction, heart failure, or stroke in the overall cohort and in a propensity score-matched cohort. The study population consisted of 49702 patients who underwent CABG with at least one internal mammary artery, and 559 (1%) of those had BIMA grafting. In the adjusted analyses, BIMA use was not associated with better survival compared with SIMA use in the overall cohort (hazard ratio (HR) for death: 1.16, 95% confidence interval (CI): 0.97 to 1.37) or in the matched cohort (HR: 1.04, 95% CI: 0.78 to 1.40). The results were similar for early mortality and the composite endpoint. Reoperation for sternal wound complications was more common among BIMA patients (odds ratio: 1.71, 95% CI: 1.01 to 2.88).

Conclusions

BIMA grafting was performed infrequently and was not associated with better outcomes compared with SIMA grafting in patients undergoing non-emergent primary isolated CABG in Sweden during 1997–2008.