Aqueous-phase mechanism for secondary organic aerosol formation from isoprene: application to the Southeast United States and co-benefit of SO2 emission controls

Isoprene emitted by vegetation is an important precursor of secondary organic aerosol (SOA), but the mechanism and yields are uncertain. Aerosol is prevailingly aqueous under the humid conditions typical of isoprene-emitting regions. Here we develop an aqueous-phase mechanism for isoprene SOA formation coupled to a detailed gas-phase isoprene oxidation scheme. The mechanism is based on aerosol reactive uptake coefficients (γ) for water-soluble isoprene oxidation products, including sensitivity to aerosol acidity and nucleophile concentrations. We apply this mechanism to simulation of aircraft (SEAC⁴RS) and ground-based (SOAS) observations over the Southeast US in summer 2013 using the GEOS-Chem chemical transport model. Emissions of nitrogen oxides (NO_x ≡ NO + NO₂) over the Southeast US are such that the peroxy radicals produced from isoprene oxidation (ISOPO₂) react significantly with both NO (high-NO_x pathway) and HO₂ (low-NO_x pathway), leading to different suites of isoprene SOA precursors. We find a mean SOA mass yield of 3.3 % from isoprene oxidation, consistent with the observed relationship of total fine organic aerosol (OA) and formaldehyde (a product of isoprene oxidation). Isoprene SOA production is mainly contributed by two immediate gas-phase precursors, isoprene epoxydiols (IEPOX, 58% of isoprene SOA) from the low-NO_x pathway and glyoxal (28%) from both low- and high-NO_x pathways. This speciation is consistent with observations of IEPOX SOA from SOAS and SEAC⁴RS. Observations show a strong relationship between IEPOX SOA and sulfate aerosol that we explain as due to the effect of sulfate on aerosol acidity and volume. Isoprene SOA concentrations increase as NO_x emissions decrease (favoring the low-NO_x pathway for isoprene oxidation), but decrease more strongly as SO₂ emissions decrease (due to the effect of sulfate on aerosol acidity and volume). The US EPA projects 2013-2025 decreases in anthropogenic emissions of 34% for NO_x (leading to 7% increase in isoprene SOA) and 48% for SO₂ (35% decrease in isoprene SOA). Reducing SO₂ emissions decreases sulfate and isoprene SOA by a similar magnitude, representing a factor of 2 co-benefit for PM_2.5 from SO₂ emission controls.

Aqueous-phase mechanism for secondary organic aerosol formation from isoprene: application to the Southeast United States and co-benefit of SO2 emission controls

Isoprene emitted by vegetation is an important precursor of secondary organic aerosol (SOA), but the mechanism and yields are uncertain. Aerosol is prevailingly aqueous under the humid conditions typical of isoprene-emitting regions. Here we develop an aqueous-phase mechanism for isoprene SOA formation coupled to a detailed gas-phase isoprene oxidation scheme. The mechanism is based on aerosol reactive uptake coefficients (γ) for water-soluble isoprene oxidation products, including sensitivity to aerosol acidity and nucleophile concentrations. We apply this mechanism to simulation of aircraft (SEAC⁴RS) and ground-based (SOAS) observations over the Southeast US in summer 2013 using the GEOS-Chem chemical transport model. Emissions of nitrogen oxides (NO_x ≡ NO + NO₂) over the Southeast US are such that the peroxy radicals produced from isoprene oxidation (ISOPO₂) react significantly with both NO (high-NO_x pathway) and HO₂ (low-NO_x pathway), leading to different suites of isoprene SOA precursors. We find a mean SOA mass yield of 3.3 % from isoprene oxidation, consistent with the observed relationship of total fine organic aerosol (OA) and formaldehyde (a product of isoprene oxidation). Isoprene SOA production is mainly contributed by two immediate gas-phase precursors, isoprene epoxydiols (IEPOX, 58% of isoprene SOA) from the low-NO_x pathway and glyoxal (28%) from both low- and high-NO_x pathways. This speciation is consistent with observations of IEPOX SOA from SOAS and SEAC⁴RS. Observations show a strong relationship between IEPOX SOA and sulfate aerosol that we explain as due to the effect of sulfate on aerosol acidity and volume. Isoprene SOA concentrations increase as NO_x emissions decrease (favoring the low-NO_x pathway for isoprene oxidation), but decrease more strongly as SO₂ emissions decrease (due to the effect of sulfate on aerosol acidity and volume). The US EPA projects 2013-2025 decreases in anthropogenic emissions of 34% for NO_x (leading to 7% increase in isoprene SOA) and 48% for SO₂ (35% decrease in isoprene SOA). Reducing SO₂ emissions decreases sulfate and isoprene SOA by a similar magnitude, representing a factor of 2 co-benefit for PM_2.5 from SO₂ emission controls.

Organic nitrate chemistry and its implications for nitrogen budgets in an isoprene- and monoterpene-rich atmosphere: constraints from aircraft (SEAC4RS) and ground-based (SOAS) observations in the Southeast US

Formation of organic nitrates (RONO₂) during oxidation of biogenic volatile organic compounds (BVOCs: isoprene, monoterpenes) is a significant loss pathway for atmospheric nitrogen oxide radicals (NO_x), but the chemistry of RONO₂ formation and degradation remains uncertain. Here we implement a new BVOC oxidation mechanism (including updated isoprene chemistry, new monoterpene chemistry, and particle uptake of RONO₂) in the GEOS-Chem global chemical transport model with ∼25 × 25 km² resolution over North America. We evaluate the model using aircraft (SEAC⁴RS) and ground-based (SOAS) observations of NO_x, BVOCs, and RONO₂ from the Southeast US in summer 2013. The updated simulation successfully reproduces the concentrations of individual gas- and particle-phase RONO₂ species measured during the campaigns. Gas-phase isoprene nitrates account for 25-50% of observed RONO₂ in surface air, and we find that another 10% is contributed by gas-phase monoterpene nitrates. Observations in the free troposphere show an important contribution from long-lived nitrates derived from anthropogenic VOCs. During both campaigns, at least 10% of observed boundary layer RONO₂ were in the particle phase. We find that aerosol uptake followed by hydrolysis to HNO₃ accounts for 60% of simulated gas-phase RONO₂ loss in the boundary layer. Other losses are 20% by photolysis to recycle NO_x and 15% by dry deposition. RONO₂ production accounts for 20% of the net regional NO_x sink in the Southeast US in summer, limited by the spatial segregation between BVOC and NO_x emissions. This segregation implies that RONO₂ production will remain a minor sink for NO_x in the Southeast US in the future even as NO_x emissions continue to decline.

Beneficial effects of judo training on bone mineral density of high-school boys in Korea

Bone mineralization is strongly stimulated by weight-bearing exercise during growth and development. Judo, an Olympic combat sport, is a well-known form of strenuous and weight-bearing physical activity. Therefore, the primary goal of this study was to determine the effects of Judo practice on the bone health of male high school students in Korea. The secondary goal of this study was to measure and compare the bone mineral density (BMD) of the hands of Judo players and sedentary control subjects. Thirty Judo players (JDP) and 30 sedentary high school boys (CON) voluntarily participated in the present study, and all of the sedentary control subjects were individually matched to the Judo players by body weight. BMD was determined by using dual-energy X-ray absorptiometry (Hologic, Bedford, MA, USA). The lumbar spine, femur and forearm BMD in the JDP group were significantly greater by 22.7%, 24.5%, and 18.3%, respectively, than those in the CON group. In addition, a significant difference in the CON group was observed between the dominant hand (DH) radius (0.710 ± 0.074 g/cm(2)) and the non-dominant hand (NDH) radius (0.683 ± 0.072 g/cm(2)), but this was not observed in the JDP group (DH = 0.819 ± 0.055 g/cm(2); NDH = 810 ± 0.066 g/cm(2)) (P < 0.05). Therefore, the results of this study suggest that Judo practice during the growth period significantly improves bone health in high school male students. In addition, it seems that Judo practice could eliminate the effect of increased BMD in the dominant hand.

Abstract P2-06-13: Pathway Profiling of Signal Transduction Proteins in Paired Tumor and Adjacent Normal Tissues Obtained from Breast Cancer Patients

Background: Targeted therapeutic strategies are currently limited to patients with hormone receptors and/or HER2 positive disease in breast cancer (BCA) treatment. However, patients often develop resistance to these therapies. The ability to functionally profile a whole spectrum of pathway proteins (and their variants) in tumor may provide valuable information about the potential mechanism for drug resistance and evidence for rational selection of suitable targeted therapies. Here we report a comprehensive profile of HER1, HER2, p95HER2, HER3, cMET, IGF1R, PI3K, Shc, AKT and other signal transduction pathway proteins in BCA tissues and their matched adjacent normal tissues (ANTs). Methods: A multiplexed Collaborative Proximity ImmunoAssay (COPIA), antibody-microarray platform requiring co-localization of 2 detector antibodies on captured biomarker proteins has been used for comprehensive pathway analysis. Channeling events between 2 detector enzymes (glucose oxidase & horse radish peroxidase) in proximity enabled the profiling of the target biomarkers with extreme sensitivity and specificity, and a direct comparison to electrochemiluminescence based immunoassay platform (MSD) was performed for pathway proteins in tumor vs. ANTs for their expression and activation in samples collected from 20 BCA patients. Results: Three dilutions of lysate (10ug, 1ug, 0.1ug) were analyzed for quantitative differential pathway modulation for COPIA.

- Substantially higher cytokeratin (CK) levels were found in 16/20 tumor samples when compared to paired-ANT; 3/20 samples showed high levels of CK in ANTs. Substantial levels of HER3 and IGF1R expression was detected in 9 and 5 tumor samples respectively.

- Over-expression of HER2 with high degree of activation was found in 2 patients. In one of the HER2-overexpressing patients, HER3 was also highly expressed and moderately phosphorylated. Co-expression of cMET and IGF1R was evident as well.

- A significant degree of HER2 phosphorylation was found in many patients with low level HER2 expression; this may be due to co-expression of high level of HER3 and other RTKs with trans-activational potential. Evidence of activated PI3K complex will be reported.

- In direct comparison to MSD, COPIA detected activated pathway proteins in samples that were not detectable with MSD. MSD was sensitive enough to detect the very extreme cases. COPIA appeared to be a more desirable method for detection of protein expression and activation for samples with limited availability. The distinct pathway modulation in each patient (detected by COPIA) will be reported.

Discussion: COPIA was used to detect the differential expression and phosphorylation of HER2, other RTKs and pathway proteins in 20 paired tumor and matched ANTs. As this platform requires magnitudes lower amounts of specimen, it can be used to profile tumors at different metastatic sites and could provide comprehensive metastatic profiles. The comprehensive functional pathway profiling of tumor specimen may provide insightful information for potential drug-resistant mechanisms and may guide appropriate selection of targeted drug-combinations or drug-sequencing.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-06-13.

Arginase induction by sodium phenylbutyrate in mouse tissues and human cell lines

Hyperargininemia is a urea cycle disorder caused by mutations in the gene for arginase I (AI) resulting in elevated blood arginine and ammonia levels. Sodium phenylacetate and a precursor, sodium phenylbutyrate (NaPB) have been used to lower ammonia, conjugating glutamine to produce phenylacetylglutamine which is excreted in urine. The elevated arginine levels induce the second arginase (AII) in patient kidney and kidney tissue culture. It has been shown that NaPB increases expression of some target genes and we tested its effect on arginase induction. Eight 9-week old male mice fed on chow containing 7.5 g NaPB/kg rodent chow and drank water with 10 g NaPB/L, and four control mice had a normal diet. After one week all mice were sacrificed. The arginase specific activities for control and NaPB mice, respectively, were 38.2 and 59.4 U/mg in liver, 0.33 and 0.42 U/mg in kidney, and 0.29 and 1.19 U/mg in brain. Immunoprecipitation of arginase in each tissue with AI and AII antibodies showed the activity induced by NaPB is mostly AI. AII may also be induced in kidney. AI accounts for the fourfold increased activity in brain. In some cell lines, NaPB increased arginase activity up to fivefold depending on dose (1-5 mM) and exposure time (2-5 days); control and NaPB activities, respectively, are: erythroleukemia, HEL, 0.06 and 0.31 U/mg, and K562, 0.46 and 1.74 U/mg; embryonic kidney, HEK293, 1.98 and 3.58 U/mg; breast adenocarcinoma, MDA-MB-468, 1.11 and 4.06 U/mg; and prostate adenocarcinoma, PC-3, 0.55 and 3.20 U/mg. In MDA-MB-468 and HEK most, but not all, of the induced activity is AI. These studies suggest that NaPB may induce AI when used to treat urea cycle disorders. It is relatively less useful in AI deficiency, although it could have some effect in those patients with missense mutations.

Diffusion-weighted MRI and ADC mapping in FK506 neurotoxicity

FK506 is a newly developed potent immunosuppressant for preventing rejection after organ transplantation. However, FK506 can induce central nervous system toxicity. Until now the pathogenic mechanism of FK506 neurotoxicity was unclear. We report the findings of diffusion-weighted MRI and apparent diffusion coefficient (ADC) mapping of a FK506 neurotoxicity patient who showed increased signal intensities in both parieto-occipital lobes on T(2) weighted images, diffusion-weighted images and ADC maps. These findings suggest that a vasogenic oedema rather than a cytotoxic oedema may play a pivotal role in FK506 neurotoxicity pathogenesis.

Mechanisms of viral membrane fusion and its inhibition

Viral envelope glycoproteins promote viral infection by mediating the fusion of the viral membrane with the host-cell membrane. Structural and biochemical studies of two viral glycoproteins, influenza hemagglutinin and HIV-1 envelope protein, have led to a common model for viral entry. The fusion mechanism involves a transient conformational species that can be targeted by therapeutic strategies. This mechanism of infectivity is likely utilized by a wide variety of enveloped viruses for which similar therapeutic interventions should be possible.

Efficient assembly of an HIV-1/MLV Gag-chimeric virus in murine cells

In human cells infected by HIV type 1 (HIV-1), the viral Gag protein directs the assembly of nascent viral particles at the plasma membrane. In murine cells, HIV-1 Gag fails to reach the plasma membrane and instead forms nonfunctional intracellular aggregates. The viral determinants of this species incompatibility are previously undefined. To address this problem, we replaced a region of HIV-1 Gag known to direct its localization, the matrix (MA) domain, with functionally homologous regions from Moloney murine leukemia virus (MLV), a murine retrovirus. An HIV-1 clone carrying such a chimeric Gag protein, designated murine HIV (MHIV), assembled more efficiently than nonchimeric HIV-1 and restored plasma membrane localization of Gag in murine cells. Increased efficiency of viral assembly in murine cells was observed from MHIV constructs carrying MLV MA in place of HIV-1 MA. Efficient processing of the HIV-1 capsid protein from the chimeric Gag polyprotein and subsequent infectivity of MHIV required the presence of MLV p12 in addition to MLV MA. These findings strongly suggest that the HIV-1 MA domain of HIV-1 Gag is responsible for the assembly defect in mouse cells. Although these MHIV do not recruit native HIV-1 Env efficiently, they are capable of single-round infection when produced by high-efficiency transfection of human 293 cells and provided with an HIV-1 Env lacking its cytoplasmic tail. With further adaptation, this chimeric MHIV approach may provide the basis for creating an infectious mouse model for HIV/AIDS.

Side-chain repacking calculations for predicting structures and stabilities of heterodimeric coiled coils

An important goal in biology is to predict from sequence data the high-resolution structures of proteins and the interactions that occur between them. In this paper, we describe a computational approach that can make these types of predictions for a series of coiled-coil dimers. Our method comprises a dual strategy that augments extensive conformational sampling with molecular mechanics minimization. To test the performance of the method, we designed six heterodimeric coiled coils with a range of stabilities and solved x-ray crystal structures for three of them. The stabilities and structures predicted by the calculations agree very well with experimental data: the average error in unfolding free energies is <1 kcal/mol, and nonhydrogen atoms in the predicted structures superimpose onto the experimental structures with rms deviations <0.7 A. We have also tested the method on a series of homodimers derived from vitellogenin-binding protein. The predicted relative stabilities of the homodimers show excellent agreement with previously published experimental measurements. A critical step in our procedure is to use energy minimization to relax side-chain geometries initially selected from a rotamer library. Our results show that computational methods can predict interaction specificities that are in good agreement with experimental data.

Design of potent inhibitors of HIV-1 entry from the gp41 N-peptide region

The HIV-1 gp41 envelope glycoprotein promotes fusion of the virus and cell membranes through the formation of a trimer-of-hairpins structure, in which the amino- and carboxyl-terminal regions of the gp41 ectodomain are brought together. Synthetic peptides derived from these two regions (called N and C peptides, respectively) inhibit HIV-1 entry. In contrast to C peptides, which inhibit in the nanomolar range, N peptides are weak inhibitors with IC(50) values in the micromolar range. To test the hypothesis that the weak inhibition of N peptides results from their tendency to aggregate, we have constructed chimeric variants of the N-peptide region of gp41 in which soluble trimeric coiled coils are fused to portions of the gp41 N peptide. These molecules, which present the N peptide in a trimeric coiled-coil conformation, are remarkably more potent inhibitors than the N peptides themselves and likely target the carboxyl-terminal region of the gp41 ectodomain. The best inhibitors described here inhibit HIV-1 entry at nanomolar concentrations.

Buried polar residues in coiled-coil interfaces

Coiled coils, estimated to constitute 3-5% of the encoded residues in most genomes, are characterized by a heptad repeat, (abcdefg)(n), where the buried a and d positions form the interface between multiple alpha-helices. Although generally hydrophobic, a substantial fraction ( approximately 20%) of these a- and d-position residues are polar or charged. We constructed variants of the well-characterized coiled coil GCN4-p1 with a single polar residue (Asn, Gln, Ser, or Thr) at either an a or a d position. The stability and oligomeric specificity of each variant were measured, and crystal structures of coiled-coil trimers with threonine or serine at either an a or a d position were determined. The structures show how single polar residues in the interface affect not only local packing, but also overall coiled-coil geometry as seen by changes in the Crick supercoil parameters and core cavity volumes.

A designed protein with packing between left-handed and right-handed helices

A common motif in protein structures is the assembly of alpha-helices. Natural alpha-helical assemblies, such as helical bundles and coiled coils, consist of multiple right-handed alpha-helices. Here we design a protein complex containing both left-handed and right-handed helices, with peptides of D- and L-amino acids, respectively. The two peptides, D-Acid and L-Base, feature hydrophobic heptad repeats and are designed to pack against each other in a "knobs-into-holes" manner. In solution, the peptides form a stable, helical heterotetramer with tight packing in the most solvent-protected core. This motif may be useful for designing protease-resistant, helical D-peptide ligands against biological protein targets.

The trimer-of-hairpins motif in membrane fusion: Visna virus

Structural studies of viral membrane fusion proteins suggest that a "trimer-of-hairpins" motif plays a critical role in the membrane fusion process of many enveloped viruses. In this motif, a coiled coil (formed by homotrimeric association of the N-terminal regions of the protein) is surrounded by three C-terminal regions that pack against the coiled coil in an oblique antiparallel manner. The resulting trimer-of-hairpins structure serves to bring the viral and cellular membranes together for fusion. learncoil-vmf, a computational program developed to recognize coiled coil-like regions that form the trimer-of-hairpins motif, predicts these regions in the membrane fusion protein of the Visna virus. Peptides corresponding to the computationally identified sequences were synthesized, and the soluble core of the Visna membrane fusion protein was reconstituted in solution. Its crystal structure at 1.5-A resolution demonstrates that a trimer-of-hairpins structure is formed. Remarkably, despite less than 23% sequence identity, the ectodomains in Visna and HIV-1 envelope glycoproteins show detailed structural conservation, especially within the area of a hydrophobic pocket in the central coiled coil currently being targeted for the development of new anti-HIV drugs.

A multiethnic study of Delta32ccr5 and ccr2b-V64I allele distribution in four Los Angeles populations

Mutant alleles of the chemokine receptors CCR5 and CCR2 affect the susceptibility to HIV infection as well as the rate of disease progression. In this article the authors report the results of a survey for presence of the common Delta32ccr5 and ccr2b-V64I mutant alleles in 472 individuals of a multiethnic cohort. Hispanic Americans had the highest observed frequency of the Delta32ccr5 allele (3.57%), whereas African Americans had a lower frequency (1.55%). The mutant allele was absent in Asian Americans and Native Americans. Thus, the Delta32ccr5 allele segregates in populations with a significant white admixture and is rare in genetically distant non-European groups. Native Americans had the highest occurrence of the ccr2b-V64I allele (31.13%), whereas African Americans, Asian Americans, and Hispanic Americans had much lower frequencies (14.36%, 11.94%, and 14.37% respectively). This mutation is probably an ancient one, occurring before the migration of the ancestors of Native Americans across the Bering Straits to the Americas. The twofold greater frequency of ccr2b-V64I in modern Native Americans probably reflects a founder effect. The observed population differences in Delta32ccr5 and ccr2b-V64I frequencies, considered together with their documented effects on sensitivity to HIV infection and rate of disease progression, have implications for HIV transmission patterns in the United States, as well as for AIDS prediction, monitoring, and treatment.

Radiofrequency sacroiliac joint denervation for sacroiliac syndrome

BACKGROUND AND OBJECTIVES

Radiofrequency (RF) denervation of the sacroiliac (SI) joint has been advocated for the treatment of sacroiliac syndrome, yet no clinical studies or case series support its use.

METHODS

We report the results of a consecutive series of 50 SI joint RF denervations performed in 33 patients with sacroiliac syndrome. All patients underwent diagnostic SI joint injections with local anesthetic before denervation. Changes in visual analog pain scores (VAS), pain diagrams, physical examination (palpation tenderness over the joint, myofascial trigger points overlying the joint, SI joint pain provocation tests, and range of motion of the lumbar spine), and opioid use were assessed pre- and postdenervation.

RESULTS

The criteria for successful RF denervation were at least a 50% decrease in VAS for a period of at least 6 months; 36.4% of patients (12 of 33) met these criteria. Failure of denervation correlated with the presence of disability determination and pain on lateral flexion to the affected side. The average duration of pain relief was 12.0 +/- 1.2 months in responders versus 0.9 +/- 0.2 months in nonresponders (P < or = 0.0001). A positive response was associated with an atraumatic inciting event. Successful denervation was associated with a change in the pain diagram and a reduction in the pattern of referred pain, a normalization of SI joint pain provocation tests, and a reduction in the use of opioids.

CONCLUSIONS

This study suggests that RF denervation of the SI joint can significantly reduce pain in selected patients with sacroiliac syndrome for a protracted time period. Moreover, certain abnormal physical findings (i.e., SI joint pain provocation tests) revert to normal for the duration of the analgesia.

Protein design of an HIV-1 entry inhibitor

Human immunodeficiency virus type-1 (HIV-1) membrane fusion is promoted by the formation of a trimer-of-hairpins structure that brings the amino- and carboxyl-terminal regions of the gp41 envelope glycoprotein ectodomain into close proximity. Peptides derived from the carboxyl-terminal region (called C-peptides) potently inhibit HIV-1 entry by binding to the gp41 amino-terminal region. To test the converse of this inhibitory strategy, we designed a small protein, denoted 5-Helix, that binds the C-peptide region of gp41. The 5-Helix protein displays potent (nanomolar) inhibitory activity against diverse HIV-1 variants and may serve as the basis for a new class of antiviral agents. The inhibitory activity of 5-Helix also suggests a strategy for generating an HIV-1 neutralizing antibody response that targets the carboxyl-terminal region of the gp41 ectodomain.

Savinin, a lignan from Pterocarpus santalinus inhibits tumor necrosis factor-alpha production and T cell proliferation

Two lignans were isolated from the heartwood of Pterocarpus santalinus by activity-guided fractionation and investigated for their biological properties and molecular mechanism of action. On the basis of their spectroscopic data, these compounds were identified as savinin (1) and calocedrin (2), dibenzyl butyrolactone-type lignan compounds having an alpha-arylidene gamma-lactone structure. These lignans significantly inhibited tumor necrosis factor (TNF)-a production in lipopolysaccharide (LPS)-stimulated RAW264.7 cells, and T cell proliferation elicited by concanavalin (Con A), without displaying cytotoxicity. The molecular inhibitory mechanism of compound 1 was confirmed to be mediated by the non-polar butyrolactone ring, according to a structure-relationship study with structurally related and unrelated compounds, such as arctigenin (a dibenzyl butyrolactone type lignan), eudesmin (a furofuran type lignan), isolariciresinol (a dibenzylbutane type lignan), and cynaropicrin (a sesquiterpene lactone). The results suggest that savinin may act as an active principle in the reported biological activities of P. santalinus, such as antiinflammatory effect, by mediation of the butyrolactone ring as a valuable pharmacophore.

Structural characterization of the human respiratory syncytial virus fusion protein core

Human respiratory syncytial virus (HRSV) is a major cause of a number of severe respiratory diseases, including bronchiolitis and pneumonia, in infants and young children. The HRSV F protein, a glycoprotein essential for viral entry, is a primary target for vaccine and drug development. Two heptad-repeat regions within the HRSV F sequence were predicted by the computer program learncoil-vmf. These regions are thought to form trimer-of-hairpins-like structures, similar to those found in the fusion proteins of several enveloped viruses. The hairpin structure likely brings the viral and cellular membranes into close apposition, thereby facilitating membrane fusion and subsequent viral entry. Here, we show that peptides, denoted HR-N and HR-C, corresponding to the heptad-repeat regions from the N-terminal and C-terminal segments of the HRSV F protein, respectively, form a stable alpha-helical trimer of heterodimers. The HRSV N/C complex was crystallized and its x-ray structure was determined at 2.3-A resolution. As anticipated, the complex is a six-helix bundle in which the HR-N peptides form a three-stranded, central coiled coil, and the HR-C peptides pack in an antiparallel manner into hydrophobic grooves on the coiled-coil surface. There is remarkable structural similarity between the HRSV N/C complex and the fusion protein core of other viruses, including HIV-1 gp41. In addition, earlier work has shown that HRSV HR-C peptides, like the HIV-1 gp41 C peptides, inhibit viral infection. Thus, drug discovery and vaccine development strategies aimed at inhibiting viral entry by blocking hairpin formation may be applied to the inhibition of HRSV.

Palmitoylation of the HIV-1 envelope glycoprotein is critical for viral infectivity

Recent studies suggest that HIV-1 budding occurs selectively from detergent-insoluble membrane domains, referred to as lipid rafts. Palmitoylation is thought to be one of the factors responsible for targeting membrane proteins to lipid rafts. The cytoplasmic domain of the HIV-1 envelope glycoprotein (gp160) contains two palmitoylated cysteine residues. In this work, we studied the solubility of gp160 after detergent extraction. We show that wild-type gp160 is mostly insoluble after ice-cold Triton X-100 extraction, but that it becomes almost completely soluble at 37 degrees C. In contrast, we find that a mutant gp160, in which the two palmitoylated cysteine residues are replaced by serine, is Triton X-100 soluble even under ice-cold extraction. These findings are consistent with the properties of proteins that localize to lipid rafts and strongly suggest that gp160 is associated with lipid rafts. Further, removal of both palmitoylation sites results in the formation of virus with low levels of gp160 incorporation as well as a decrease in viral infectivity by 60-fold. Our results strongly support the suggestion that HIV-1 buds from lipid rafts and point to a role for rafts as a viral assembly hub.

A missense mutation G2320R in the thyroglobulin gene causes non-goitrous congenital primary hypothyroidism in the WIC-rdw rat

A convincing line of evidence is being developed that the congenital nongoitrous hypothyroidism and dwarfism observed in the WIC-rdw rat may indeed be caused by a primary defect in thyroid hormonogenesis. In support of this hypothesis, several recent reports have shown the presence of elevated molecular chaperone levels in the WIC-rdw thyrocytes, the endoplasmic reticulum of which was markedly dilated, suggesting a defect in intracellular protein transport. Here the studies were undertaken to identify the precise molecular defect in the WIC-rdw rat. First, the genetic linkage analysis revealed that the rdw locus was on rat chromosome 7 and was identical to the thyroglobulin (Tg) gene locus. Moreover, the Tg protein level was reduced in the WIC-rdw thyroid despite a similar level of the Tg gene transcripts that were indistinguishable in their size from the normal. Next, the complete sequencing of the rdw and the normal rat Tg cDNAs revealed a single nucleotide change, G6958C, resulting in a G2320R missense mutation in a highly conserved region of the Tg molecule. Finally, transient expression of the intact Tg cDNA containing the rdw mutation in the COS-7 cells showed no detectable Tg in the secreted media, indicating a severe defect in the export of the mutant Tg. Together, our observations suggest that a missense mutation, G2320R, in the Tg gene is responsible for the rdw mutation in the WIC-rdw rat.

Overexpression of c-H-ras p21 is correlated with vascular endothelial growth factor expression and neovascularization in advanced gastric carcinoma

BACKGROUND AND AIMS

ras Gene and its product (p21) have been reported to be associated with vascular endothelial growth factor (VEGF), which is one of the most important angiogenic factors, and tumor-associated angiogenesis. We tried to evaluate the correlation between the expression of c-H-ras gene product p21 and angiogenesis in advanced gastric carcinoma.

METHODS

Immunohistochemical expression of c-H-ras p21 and VEGF was examined in 49 advanced gastric adenocarcinomas. In addition, double immunohistochemical staining was performed using anti-CD34 and anti-Ki-67 antibodies, and the intratumoral microvessel densities and their endothelial proliferative labeling indices were then counted to evaluate the degree of angiogenesis.

RESULTS

The expression of c-H-ras p21 was demonstrated in 43 out of 49 gastric adenocarcinomas (87.8%). It did not correlate with histologic type, depth of invasion or metastasis. However, the degree of c-H-ras p21 expression was correlated with VEGF. In addition, the degree of c-H-ras p21 expression was correlated with increased intratumoral microvascular density and endothelial proliferative activity.

CONCLUSIONS

We suggest that c-H-ras oncogene product p21 contributes to the upregulation of tumor-associated angiogenesis by the increased production of VEGF in advanced gastric carcinomas. Therefore, treatment involving the targeting of ras oncogene could inhibit solid tumor growth by suppressing tumor-associated angiogenesis.

A computationally directed screen identifying interacting coiled coils from Saccharomyces cerevisiae

Computational methods can frequently identify protein-interaction motifs in otherwise uncharacterized open reading frames. However, the identification of candidate ligands for these motifs (e.g., so that partnering can be determined experimentally in a directed manner) is often beyond the scope of current computational capabilities. One exception is provided by the coiled-coil interaction motif, which consists of two or more alpha helices that wrap around each other: the ligands for coiled-coil sequences are generally other coiled-coil sequences, thereby greatly simplifying the motif/ligand recognition problem. Here, we describe a two-step approach to identifying protein-protein interactions mediated by two-stranded coiled coils that occur in Saccharomyces cerevisiae. Coiled coils from the yeast genome are first predicted computationally, by using the multicoil program, and associations between coiled coils are then determined experimentally by using the yeast two-hybrid assay. We report 213 unique interactions between 162 putative coiled-coil sequences. We evaluate the resulting interactions, focusing on associations identified between components of the spindle pole body (the yeast centrosome).

Folding of bovine pancreatic trypsin inhibitor (BPTI) variants in which almost half the residues are alanine

Recent studies indicate that a fraction of the information contained in an amino acid sequence may be sufficient for specifying a native protein structure. An earlier alanine-scanning experiment conducted on bovine pancreatic trypsin inhibitor (BPTI; 58 residues) suggested that if cumulative mutations have additive effects on protein stability, a native protein structure could be built from BPTI sequences that contained many alanine residues distributed throughout the protein. To test this hypothesis, we designed and produced six BPTI mutants containing from 21 to 29 alanine residues. We found that the melting temperature of mutants containing up to 27 alanine residues (48 % of the total number of residues) could be predicted quite well by the sum of the change in melting temperature for the single mutations. Additionally, these same mutants folded into a native-like structure, as judged by their cooperative thermal denaturation curves and heteronuclear multiple quantum correlation (HMQC) NMR spectra. A BPTI mutant containing 22 alanine residues was further shown by 2D and 3D-NMR to fold into a structure very similar to that of native BPTI, and to be a functional trypsin inhibitor. These results provide insight into the extent to which native protein structure and function can be achieved with a highly simplified amino acid sequence.

Inhibitor of tumor necrosis factor-alpha production in lipopolysaccharide-stimulated RAW264.7 cells from Amorpha fruticosa

Certain flavonoids were reported to show an immunoregulatory activity against lymphocyte proliferation and cytokine production. In the course of a search for tumor necrosis factor (TNF)-alpha inhibitory compounds from natural plants, we also isolated a prenylfavanone type of flavonoid, amoradicin, from the extract of Amorpha fruticosa by activity-guided fractionation. This compound significantly inhibited TNF-alpha production in lipopolysaccharide (LPS)-stimulated RAW264.7 cells with an IC(50) value of 28.5 microM. The activity was comparable or higher than those of standard flavonoid compounds, genistein and silybin with IC(50) of 24.9 and 140.3 microM, respectively.

NOF-11: a one-year pediatric randomized double-blind comparison of neoral versus sandimmune in orthotopic liver transplantation

BACKGROUND

Although cyclosporine (CsA) has been a mainstay in liver transplantation immunosuppression the original formulation [Sandimmune (SIM)] has variable absorption, particularly in children. Neoral is a new formulation of CsA that may have improved biovailability that would be advantageous in children. This study was undertaken to assess the pharmacokinetics (PK) and effects on outcome of Neoral versus Sandimmune (SIM) in primary pediatric liver transplant recipients.

METHODS

Thirty-two patients were randomized to receive Neoral (17 patients) or SIM (15 patients) in the early posttransplant period (days 1-7) in a double-blind fashion. Intravenous CsA was instituted immediately posttransplant followed by Neoral or SIM as soon as the patient was tolerating oral fluids (days 1-7). PK were compared after the first dose (1-7 days), 3 weeks, and 6 and 12 months posttransplant. In addition, side effects, effect of age and food on absorption, and rejection episodes were assessed by intent to treat analysis. Notable characteristics of this study include the use of a central laboratory for all sample analyses and the assessment of renal function using radioisotopic evaluation of glomerular filtration rates.

RESULTS

At baseline the two groups were comparable. Neoral resulted in higher peak levels of CsA and total drug exposure with comparable time to peak drug levels at days 1-7 and week 3. This trend was maintained at 6 and 12 months. Time on i.v. CsA was reduced in the Neoral group (8.4 vs. 11.1 days) and the weight adjusted daily dose of SIM required to achieve target trough levels was about 2-fold more than Neoral from day 22 onward. In addition, biopsy proven and treated and steroid-resistant rejection episodes were fewer in the Neoral group (6 vs. 12; P=0.01 and 1 vs. 8: P=0.004, respectively). Side effects were comparable in both treatment groups.

CONCLUSIONS

Neoral was well tolerated and had greater biovailability than SIM without any increase in the incidence of side effects. In addition fewer episodes of rejection were observed with Neoral versus SIM. We conclude that Neoral is the CsA formulation of choice for use in pediatric liver transplant recipients.

Optimum duration of treatment with 6-mercaptopurine for Crohn's disease

OBJECTIVE

6-Mercaptopurine (6MP) and azathioprine are immunomodulators used in the treatment of refractory Crohn's disease. Studies have confirmed their efficacy and value in maintenance of remission, but it is our purpose to determine how long 6MP/azathioprine should be continued once remission has been accomplished.

METHODS

Careful follow-up was accomplished in patients with Crohn's disease seen at one medical center who were treated with 6MP for > or = 6 months, who achieved remission within 1 yr of initiation of therapy, and who were in prolonged clinical remission (> or = 6 months without steroids). The time-to-relapse was calculated in those who continued treatment, in those who stopped treatment for reasons other than a relapse, and in the whole sample, taking into account that they could be treated with the drug, or could not, as a function of time. The influence of concomitant variables on the time-to-relapse rate was evaluated.

RESULTS

A total of 120 patients met the inclusion criteria. The cumulative probabilities of relapse at 1, 2, 3, and 5 yr for those who continued to take 6MP and for those who stopped the therapy for reasons other than a relapse are as follows: Patients maintained on 6MP (n = 84): 1 yr, 29%; 2 yr, 45%; 3 yr, 55%; 5 yr, 61%. Patients who terminated 6MP (n = 36): 1 yr, 36%; 2 yr, 71%; 3 yr, 85%; 5 yr, 85%. Sex, distribution of disease, duration of disease, time to remission on 6MP, and concomitant 5-ASA use did not influence the relapse rates. Younger age was associated with a higher rate of relapse in patients who were maintained on 6MP. A higher daily dose of 6MP was associated with a higher relapse rate.

CONCLUSIONS

Discontinuation of 6MP, while Crohn's disease is in remission, leads to higher relapse rates and continuation of 6MP reduces the likelihood of relapse. Therefore, we favor the indefinite use of 6MP once remission has been achieved.

Gastric malignant stromal tumor with long stalk impacted into duodenum

Most GIST have traditionally been classified as submucosal origin by upper gastrointestinal series (UGIS) or endoscopy. However, we experienced a gastrointestinal mesenchymal origin tumor expressed by polypoid mass with a long stalk. The gastric outlet was obstructed by the polypoid mass on the duodenum. The microscopic findings of the resected mass showed a stromal cell component by immunohistochemical stain. We experienced gastric stromal tumor found as a polypoid mass with long stalk which was easily detected by endoscopy. It would not have been suspected as a stromal tumor as a result of endoscopic findings only.

Alpha-lactalbumin forms a compact molten globule in the absence of disulfide bonds

Human alpha-lactalbumin (alpha-LA) is a four disulfide-bonded protein that adopts partially structured conformations under a variety of mildly denaturing conditions. At low pH, the protein is denatured but compact, with a high degree of secondary structure and a native-like fold. This is commonly referred to as a molten globule. A variant of alpha-LA, in which all eight cysteines have been mutated to alanine (all-Ala alpha-LA), has been studied using NMR spectroscopy. At low pH all-Ala alpha-LA is nearly as compact as wild type alpha-LA. Urea-induced unfolding experiments reveal that the residues that remain compact in the absence of disulfide bonds are those that are most resistant to unfolding in the wild-type alpha-LA molten globule. This is particularly remarkable because this stable core is formed by segments of the polypeptide chain from both the N- and C-termini. These results show that the overall architecture of the protein fold of alpha-LA is determined by the polypeptide sequence itself, and not as the result of cross-linking by disulfide bonds, and provide insight into the way in which the sequence codes for the fold.

Inhibiting HIV-1 entry: discovery of D-peptide inhibitors that target the gp41 coiled-coil pocket

The HIV-1 gp41 protein promotes viral entry by mediating the fusion of viral and cellular membranes. A prominent pocket on the surface of a central trimeric coiled coil within gp41 was previously identified as a potential target for drugs that inhibit HIV-1 entry. We designed a peptide, IQN17, which properly presents this pocket. Utilizing IQN17 and mirror-image phage display, we identified cyclic, D-peptide inhibitors of HIV-1 infection that share a sequence motif. A 1.5 A cocrystal structure of IQN17 in complex with a D-peptide, and NMR studies, show that conserved residues of these inhibitors make intimate contact with the gp41 pocket. Our studies validate the pocket per se as a target for drug development. IQN17 and these D-peptide inhibitors are likely to be useful for development and identification of a new class of orally bioavailable anti-HIV drugs.

Large sessile colonic adenomas: use of argon plasma coagulator to supplement piecemeal snare polypectomy

BACKGROUND

Residual adenoma is frequently found at the site of endoscopically resected large sessile adenomas on follow-up examination. We evaluated the efficacy of a thermal energy source, the argon plasma coagulator, to destroy visible residual adenoma after piecemeal resection of sessile polyps.

METHODS

Seventy-seven piecemeal polypectomies with or without the use of argon plasma coagulator were analyzed retrospectively. All polyps were sessile, 20 mm or greater in size. The results from three groups of patients were compared. The study group was composed of patients who had visible residual adenoma after piecemeal polypectomy and had the base of the polypectomy site treated with the argon plasma coagulator. The first comparison group consisted of patients who underwent standard piecemeal polypectomy in whom the colonoscopist thought that all adenomatous tissue was removed and no further treatment was necessary. The second comparison group included patients in whom visible residual adenoma was left at the base after piecemeal resection of large adenomas. Follow-up colonoscopy was performed approximately 6 months after the initial procedure to check for recurrent/residual adenomatous tissue.

RESULTS

The argon plasma coagulator was used after 30 piecemeal polypectomies in an attempt to eradicate visible residual adenomatous tissue; at follow-up, 50% of these cases had complete eradication of adenoma. The group in whom all visible tumor was removed by piecemeal polypectomy alone had an adenoma eradication rate of 54% on follow-up colonoscopy. In the patients in whom visible residual adenoma was left at the site the recurrence rate was 100% on the follow-up examination. Bleeding necessitating endoscopic therapy occurred once (3.3%) in the argon plasma coagulator group; there were four (12.5%) bleeding episodes and one (3.1%) confined retroperitoneal perforation in the complete piecemeal polypectomy group and no complications in the group in which polypectomy was incomplete.

CONCLUSIONS

Argon plasma coagulator ablation of residual adenomatous tissue at the polypectomy base is safe and useful. It helps to complete the eradication of large sessile polyps when there is visible evidence of residual polyp.

pRb is required for MEF2-dependent gene expression as well as cell-cycle arrest during skeletal muscle differentiation

BACKGROUND

The onset of differentiation-specific gene expression in skeletal muscle is coupled to permanent withdrawal from the cell cycle. The retinoblastoma tumor-suppressor protein (pRb) is a critical regulator of this process, required for both cell-cycle arrest in G0 phase and high-level expression of late muscle-differentiation markers. Although the cell-cycle defects that are seen in pRb-deficient myocytes can be explained by the well-described function of pRb as a negative regulator of the transition from G1 to S phase, it remains unclear how pRb positively affects late muscle-gene expression.

RESULTS

Here, we show that the myogenic defect in Rb-/- cells corresponds to a deficiency in the activity of the transcription factor MEF2. Without pRb, MyoD induces the accumulation of nuclear-localized MEF2 that is competent to bind DNA yet transcriptionally inert. When pRb is present, MyoD stimulates the function of the MEF2C transcriptional activation domain and the activity of endogenous MEF2-type factors. Co-transfection of MyoD together with an activated form of MEF2C containing the Herpesvirus VP16 transcriptional activation domain partially bypasses the requirement for pRb and induces late muscle-gene expression in replicating cells. This ectopic myogenesis is nevertheless significantly augmented by co-expression of an E2F1-pRb chimeric protein that blocks the cell cycle.

CONCLUSION

These findings indicate that pRb promotes the expression of late-stage muscle-differentiation markers by both inhibiting cell-cycle progression and cooperating with MyoD to promote the transcriptional activation activity of MEF2.

High-performance liquid chromatographic analysis of the 2-chloroprocaine metabolite, diethylaminoethanol, in blood and serum

BACKGROUND AND OBJECTIVES

2-Chloroprocaine is rapidly metabolized in the blood to yield 2-chloro-para-aminobenzoic acid (an inactive metabolite) and diethylaminoethanol (DEAE). DEAE possesses local anesthetic activity. The only reported assay for DEAE is a colorimetric method.

METHODS

Clinical samples of whole blood and serum were obtained from patients receiving stepped intravenous infusions of 3% 2-chloroprocaine. A high pH-dependent liquid-liquid extraction step with diethyl ether was used to eliminate interfering peaks in high-pressure liquid chromatography (HPLC) analysis. Separation and quantitation were performed using HPLC on a polymeric-reversed phase column with a mobile phase consisting of 10% or 20% acetonitrile (for whole blood or serum analysis, respectively) in 50 mm aqueous sodium phosphate buffer, pH = 11.50. The elution order of DEAE and its analogues was tested to interpret the HPLC separation mechanism.

RESULTS

Extraction recovery of DEAE from whole blood was 67 +/- 13.5%, from serum, 71 +/- 12.2%, and from water, 75 +/- 2.9%. The high pH value of the mobile phase resulted in sharp, well-resolved peaks with run times of approximately 8 minutes using 20% acetonitrile. The lower limit of detection was 5 ng/mL of DEAE from a 1-mL sample. The elution order of DEAE and its analogues indicated that separation was based on the hydrophobicity of the analytes rather than polar group interactions occurring with silica-based stationary phase.

CONCLUSIONS

A new, simple and rapid HPLC method for extraction and measurement of DEAE in whole blood or serum samples is reported here.

Core structure of the envelope glycoprotein GP2 from Ebola virus at 1.9-A resolution

Ebola virions contain a surface transmembrane glycoprotein (GP) that is responsible for binding to target cells and subsequent fusion of the viral and host-cell membranes. GP is expressed as a single-chain precursor that is posttranslationally processed into the disulfide-linked fragments GP1 and GP2. The GP2 subunit is thought to mediate membrane fusion. A soluble fragment of the GP2 ectodomain, lacking the fusion-peptide region and the transmembrane helix, folds into a stable, highly helical structure in aqueous solution. Limited proteolysis studies identify a stable core of the GP2 ectodomain. This 74-residue core, denoted Ebo-74, was crystallized, and its x-ray structure was determined at 1.9-A resolution. Ebo-74 forms a trimer in which a long, central three-stranded coiled coil is surrounded by shorter C-terminal helices that are packed in an antiparallel orientation into hydrophobic grooves on the surface of the coiled coil. Our results confirm the previously anticipated structural similarity between the Ebola GP2 ectodomain and the core of the transmembrane subunit from oncogenic retroviruses. The Ebo-74 structure likely represents the fusion-active conformation of the protein, and its overall architecture resembles several other viral membrane-fusion proteins, including those from HIV and influenza.

Combinatorial codons: a computer program to approximate amino acid probabilities with biased nucleotide usage

Using techniques from optimization theory, we have developed a computer program that approximates a desired probability distribution for amino acids by imposing a probability distribution on the four nucleotides in each of the three codon positions. These base probabilities allow for the generation of biased codons for use in mutational studies and in the design of biologically encoded libraries. The dependencies between codons in the genetic code often makes the exact generation of the desired probability distribution for amino acids impossible. Compromises are often necessary. The program, therefore, not only solves for the "optimal" approximation to the desired distribution (where the definition of "optimal" is influenced by several types of parameters entered by the user), but also solves for a number of "sub-optimal" solutions that are classified into families of similar solutions. A representative of each family is presented to the program user, who can then choose the type of approximation that is best for the intended application. The Combinatorial Codons program is available for use over the web from http://www.wi.mit.edu/kim/computing.html.

Evidence that a prominent cavity in the coiled coil of HIV type 1 gp41 is an attractive drug target

Synthetic C peptides, corresponding to the C helix of the HIV type 1 (HIV-1) gp41 envelope protein, are potent inhibitors of HIV-1 membrane fusion. One such peptide is in clinical trials. The crystal structure of the gp41 core, in its proposed fusion-active conformation, is a trimer of helical hairpins in which three C helices pack against a central coiled coil. Each C helix shows especially prominent contacts with one of three symmetry-related, hydrophobic cavities on the surface of the coiled coil. We show that the inhibitory activity of the C peptide C34 depends on its ability to bind to this coiled-coil cavity. Moreover, examining a series of C34 peptide variants with modified cavity-binding residues, we find a linear relationship between the logarithm of the inhibitory potency and the stability of the corresponding helical-hairpin complexes. Our results provide strong evidence that this coiled-coil cavity is a good drug target and clarify the mechanism of C peptide inhibition. They also suggest simple, quantitative assays for the identification and evaluation of analogous inhibitors of HIV-1 entry.

Crystal structure of GCN4-pIQI, a trimeric coiled coil with buried polar residues

Coiled coils consist of two or more alpha-helices wrapped around each other with a superhelical twist. The interfaces between helices of a coiled coil are formed by hydrophobic amino acid residues packed in a "knobs-into-holes" arrangement. Most naturally occurring coiled coils, however, also contain buried polar residues, as do the cores of the majority of naturally occurring globular proteins. Two common buried polar residues in both dimeric and trimeric coiled coils are asparagine and glutamine. In dimeric coiled coils, buried asparagine, but not glutamine, residues have been shown to confer specificity of oligomerization. We have placed a glutamine residue in the otherwise hydrophobic interior of a stable trimeric coiled coil, GCN4-pII, to study the effect of this buried polar residue in a trimeric coiled-coil environment. The resulting peptide, GCN4-pIQI, is a discrete, trimeric coiled coil with a lower stability than GCN4-pII. The crystal structure determined to 1.8 A shows that GCN4-pIQI is a trimeric coiled coil with a chloride ion coordinated by one buried glutamine residue from each monomer.

High-resolution protein design with backbone freedom

Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.