bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting hidden sequence propensity for amyloid fibril formation
Authors: Yoon Sukjoon , Welsh William J. 
Published: July 2004

AbstractThe preponderance of evidence implicates protein misfolding in many unrelated human diseases. In all cases, normal correctly folded proteins transform from their proper native structure into an abnormal β‐rich structure known as amyloid fibril. Here we introduce a computational algorithm to detect nonnative (hidden) sequence propensity for amyloid fibril formation. Analyzing sequence–structure relationships in terms of tertiary contact (TC), we find that the hidden β‐strand propensity of a query local sequence can be quantitatively estimated from the secondary structure preferences of template sequences of known secondary structure found in regions of high TC. The present method correctly pinpoints the minimal peptide fragment shown experimentally as the likely local mediator of amyloid fibril formation in β‐amyloid peptide, islet amyloid polypeptide (hIAPP), α‐synuclein, and human acetylcholinesterase (AChE). It also found previously unrecognized β‐strand propensities in the prototypical helical protein myoglobin that has been reported as amyloidogenic. Analysis of 2358 nonhomologous protein domains provides compelling evidence that most proteins contain sequences with significant hidden β‐strand propensity. The present method may find utility in many medically relevant applications, such as the engineering of protein sequences and the discovery of therapeutic agents that specifically target these sequences for the prevention and treatment of amyloid diseases.
NMR structure of CXCR3 binding chemokine CXCL11 (ITAC)
Authors: Booth Valerie , Clark‐Lewis Ian , Sykes Brian D. 
Published: July 2004

AbstractCXCL11 (ITAC) is one of three chemokines known to bind the receptor CXCR3, the two others being CXCL9 (Mig) and CXCL10 (IP‐10). CXCL11 differs from the other CXCR3 ligands in both the strength and the particularities of its receptor interactions: It has a higher affinity, is a stronger agonist, and behaves differently when critical N‐terminal residues are deleted. The structure of CXCL11 was determined using solution NMR to allow comparison with that of CXCL10 and help elucidate the source of the differences. CXCL11 takes on the canonical chemokine fold but exhibits greater conformational flexibility than has been observed for related chemokines under the same sample conditions. Unlike related chemokines such as IP‐10 and IL‐8, ITAC does not appear to form dimers at millimolar concentrations. The origin for this behavior can be found in the solution structure, which indicates a β‐bulge in β‐strand 1 that distorts the dimerization interface used by other CXC chemokines.
The Geography of Support for Open‐Space Initiatives: A Case Study of New Jersey's 1998 Ballot Measure*
Authors: Solecki William D. , Mason Robert J. , Martin Shannon 
Published: July 2004

Objectives. By a two to one margin, New Jersey voters in 1998 approved a ballot measure authorizing a 10‐year, 1‐billion dollar open‐space acquisition program. This article's principal objectives are to investigate and explain the spatial character of that vote.Methods. Our methods consists of regression and principal components analyses; we use municipal‐level data to define statewide patterns of voter support and participation in relation to a series of socioeconomic, political, and environmental variables.Results. The analyses yielded two major findings: (1) support for the ballot measure was widespread, but exceptionally strong in the “wealth belt” area of north‐central New Jersey, and (2) voter participation, defined as those voting on the measure as a proportion of all who voted, lagged in the core urban areas.Conclusions. Our conclusions point critically to the importance of socioeconomic status, urban residence, and presence of existing open‐space regulations—as well as rapid changes in the overall sociopolitical landscape—in explaining voter behavior.
Efficiency, Accountability, and Private Government: The Impact of Residential Community Associations on Residential Property Values*
Authors: Langbein Laura , Spotswood‐Bright Kim 
Published: July 2004

Objective. This study evaluates the impact of residential community associations (RCAs) on RCA property values by testing competing theoretical expectations about the efficiency and accountability of RCAs with empirical evidence.Method. We use pooled data on 195 units in six RCAs in one city, regressing sales price on RCA fees, a proxy for the importance of professional management compared to community involvement, previous property values, and other variables.Results. We find that increases in RCA fees (and services) depress average property values over what they would be otherwise, and that professional management somewhat mitigates this effect by raising property values.Conclusion. RCAs with horizontal, community controls act as if they are governed by a high‐demand, volunteer, review group by producing and charging too much, while professional management (i.e., hierarchical control) slightly reduces the tendency of RCAs to produce and charge too much. RCAs may not be the model of efficiency that proponents of private governments expect.
Options: Racial/Ethnic Identification of Children of Intermarried Couples*
Authors: Qian Zhenchao 
Published: July 2004

Objective.Whites of various European ethnic backgrounds usually have weak ethnic attachment and have options to identify their ethnic identity (Waters, 1990). What about children born to interracially married couples?Methods.I use 1990 Census data—the last census in which only one race could be chosen—to examine how African American‐white, Latino‐white, Asian American‐white, and American Indian‐white couples identify their children's race/ethnicity.Results.Children of African American‐white couples are least likely to be identified as white, while children of Asian American‐white couples are most likely to be identified as white. Intermarried couples in which the minority spouse is male, native born, or has no white ancestry are more likely to identify their children as minorities than are those in which the minority spouse is female, foreign born, or has part white ancestry. In addition, neighborhood minority concentration increases the likelihood that biracial children are identified as minorities.Conclusion.This study shows that choices of racial and ethnic identification of multiracial children are not as optional as for whites of various European ethnic backgrounds. They are influenced by race/ethnicity of the minority parent, intermarried couples' characteristics, and neighborhood compositions.
Fertility Changes Among Immigrants: Generations, Neighborhoods, and Personal Characteristics*
Authors: Hill Laura E. , Johnson Hans P. 
Published: July 2004

Objective. To understand how adaptation/assimilation, disruption, and diffusion interact to produce changes in fertility levels among successive generations of Mexicans and Central Americans in the United States.Method. Using restricted access data that link individual data (CPS) to neighborhood data (census tracts), we examine the role of generation, personal characteristics, and neighborhood characteristics in determining children ever born (CEB).Results. There are significant differences in fertility across generations and, to a lesser extent, between women who live in ethnic enclaves and those who do not. Once personal characteristics are considered, the independent effect of generation on fertility is nearly eliminated. Personal characteristics dominate neighborhood characteristics in their ability to predict fertility. The most consistent predictor of CEB at the neighborhood level is the percentage of Hispanic adults.Conclusions. Personal characteristics dominate fertility change across generation, and were it not for increases in educational attainment, fertility might be higher in successive generations rather than lower or unchanged.
Race/Ethnicity and Beliefs about Wealth and Poverty*
Authors: Hunt Matthew O. 
Published: July 2004

Objective. Lay explanations for “wealth” have been neglected in research on beliefs about social stratification. This study compares the nature and determinants of beliefs about the causes of both wealth and poverty, with special focus on race/ethnic differences.Methods. Using survey data collected from Los Angeles County residents in 2000, descriptive and multivariate procedures are used to analyze “individualistic” and “structuralist” beliefs about wealth and poverty. In addition, one “fatalistic” belief, asking about the role of “God's will” in shaping wealth and poverty, is examined. Analyses test (1) whether race/ethnicity and other social and political characteristics variables shape these stratification beliefs, and (2) whether African Americans, Latinos, and whites differ in the determinants of beliefs about wealth and poverty.Results. Respondents favor individualistic over structuralist reasons for wealth, but favor structuralist over individualistic beliefs in explaining poverty. Fatalistic beliefs are least popular. On beliefs about wealth, African Americans, Latinos, and whites show similar levels of support for individualistic explanations; however, the race/ethnic minorities are both more structuralist than whites on this issue. On beliefs about poverty, the race/ethnic minorities are simultaneously more structuralist and more individualistic than are whites. Social‐class identification and self‐reported conservatism both significantly impact beliefs about wealth and poverty, and do so differently across race/ethnic lines.Conclusions. Findings support the separate treatment and examination of beliefs about wealth and poverty, and reinforce recent calls for greater attention to “nonwhites” in studies of sociopolitical attitudes.
Kinetic Characterization of the Neutral Protease Vimelysin from Vibrio Sp. T1800
Authors: Kunugi Shigeru , Koyasu Akira , Kitayaki Moto , Takahashi Saori , Oda Kohei 
Published: July 2004

The kinetics of the hydrolysis of dipeptide and tripeptide substrates by the recently discovered neutral protease from Vibrio species T1800 (vimelysin) were studied. In the pH dependence of the apparent second‐order rate constant, the pKa2 value of vimelysin (≈6.5) was significantly lower than thermolysin (8.3). although the pKa2 (≈ 5.1) values were comparable (5.0). The kcat/Km(lim) parameter for hydrolysis of Fua‐Gly‐PheNH2 (Fua = furylacryloyl) was more than sevenfold greater than for Fua‐Gly‐LeuNH2. This higher specificity for Fua‐Gly‐PheNH2 was deduced for both kcat and Km parameters. Fua‐Phe‐PheNH2 showed the highest kcat/Km(app) value of the six substrates studied. The discrimination between Phe/Leu at the P1′ site was most evident when the P1 site was not sufficiently filled.Reflecting the characteristically high proteolytic activity of vimelysin at lower temperatures [Oda, K., Okayama, K., Okutomi, K., Shimada, M., Sato, R. & Takahashi, S. (1996)Biosci. Biotech. Biochem. 60, 463–467], the Arrhenius plot of the apparent second‐order rate constant for the hydrolysis of Fua‐Gly‐LeuNH2 showed an inverse temperature dependence; higher reaction rates were observed at lower temperatures. This was not merely due to the pKa shift nor to thermal denaturation of the enzyme coupling, but rather to the kcat(app) parameter, which alone showed an inverse temperature dependence. A model containing two temperature‐dependent forms of the active enzyme was postulated to explain this unique temperature dependence.
Refolding and Reassociation of Glycerol Dehydrogenase from Bacillus Stearothermophilus in the Absence and Presence of Groel
Authors: Krauss Oliver , Gore Michael G. 
Published: July 2004

The refolding of the tetrameric, metalloenzyme glycerol dehydrogenase (GDH) from Bacillus steurothermophilus has been investigated using stopped‐flow fluorescence and circular dichroism spectroscopy. The effects of metal ions on the refolding of the native enzyme and the refolding of a monomeric mutant ([A208]GDH) have also been studied. The refolding process of the wild‐type enzyme is at least biphasic; 70% of the respective signal changes occur in the first 2 ms followed by a slower process with a half‐life of 3 s. The presence of the metal ion does not affect the slowest biphasic refolding rate, which is virtually the same for all three versions of the enzyme. The presence of GroEL slows down the first phase of refolding.The reassociation of subunits was examined by measuring the regain in catalytic activity and the enhancement in the fluorescence emission from NADH on binding to the oligomeric form of the enzyme. The rate and extent of reassociation is dependent on enzyme concentration and the extent of reactivation is dependent on the presence of the metal ion. The reassociation process was more efficient in the presence of NADH particularly for the metal‐depleted enzyme (apo‐GDH). The presence of GroEL or GroEL plus ATP leads to a higher yield of reassociation and therefore catalytically active enzyme. The additional presence of Mg‐ATP does not affect the extent of reassociation, but has a small positive effect on the rate of reassociation. These data suggest that GDH is bound weakly to GroEL and that GroES is not required for release of the protein.
The Protein Conformation of Cd‐Substituted Horse Liver Alcohol Dehydrogenase and its Metal‐Site Coordination Geometry in Binary and Ternary Inhibitor Complexes
Authors: Hemmingsen Lars , Bauer Rogert , Bjerrum Morten Jannik , Adolph Hans Werner , Zeppezauer Michael , Cedergren‐Zeppezauer Eila 
Published: July 2004

The coordination geometry of the metal at the active site in Cd‐substituted horse liver alcohol dehydrogenase (LADH) has been investigated for the binary complexes of LADH with imidazole, isobutyramide, decanoic acid and C1−, and for the ternary complexes of LADH with NADH and imidazole, NADH and isobutyramide, NAD+ and decanoic acid and NAD+ and Cl−, by using the method of perturbed angular correlation of γ‐rays (PAC). The spectral results are consistent with a flexible structure around the metal for the binary complexes with inhibitors. For ternary complexes, however, a rigid structure is observed. An exception is the ternary complex between LADH, NADH and imidazole, in which the metal site is still flexible. Comparing with available structures determined by X‐ray crystallography, we found a correlation between open structures and flexible metal sites, and between closed structures and rigid metal sites. This indicates that the PAC technique can be applied to distinguish the two conformations in solution.The spectral parameters, ωo and η, of the experiments, except for the complexes with imidazole, fall into two groups: one with low ωo and one with high ωo, (η is relatively constant in all experiments). In this work it is clarified that the low ωo, values are connected with the presence of a negatively charged solvent ligand. Using an angular‐overlap approach to interpret the results, the low ωo values are found to be compatible with a coordination geometry where the S‐Cd‐S (Cys174 and Cys46 coordinate to the metal) angle is about 110° as suggested in [Hemmingsen, L., Bauer, R., Danielsen, E., Bjerrum, M. J., Zeppezauer, M., Adolph, H. W., Formicka, G. & Cedergren‐Zeppezauer, E. (1995)Biochemistry 34, 7145571531, whereas high ωo values are compatible with an S‐Cd‐S angle of 130°. The presence of a negatively charged metal ligand, therefore, might trigger the movement of the sulfur of Cys174. As it is believed that alcohols coordinate to the metal as alcoholate ions this could be important for catalysis.
α‐Crystallin Stabilizes Actin Filaments and Prevents Cytochalasin‐Induced Depolymerization in a Phosphorylation‐Dependent Manner
Authors: Wang Keyang , Spector Abraham 
Published: July 2004

α‐crystallin, a major lens protein of approximately 800 kDa with subunits of about 20 kDa has previously been shown to act as a chaperone protecting other proteins from stress‐induced damage and to share sequence similarity with small heat‐shock proteins, sHsp. It is now demonstrated that this chaperone effect extends to protection of the intracellular matrix component actin. It was found that the powerful depolymerization effect of cytochalasin D could be almost completely blocked by α‐crystallin, αA‐crystallin or αB‐crystallin. However, phosphorylation of α‐crystallin markedly decreased its protective effect. It is suggested that phosphorylation of α‐crystallin may contribute to changes in actin structure observed during cellular remodeling that occurs with the terminal differentiation of a lens epithelial cell to a fiber cell and contributes to cellular remodeling in other cell types that contain α‐crystallin species. This communication presents biochemical evidence clearly demonstrating that α‐crystallin is involved in actin polymerization‐depolymerization dynamics.It is also shown that α‐crystallin prevented heat‐induced aggregation of actin filaments. α‐crystallin was found to stabilize actin polymers decreasing dilution‐induced depolymerization rates up to twofold while slightly decreasing the critical concentration from 0.23 μM to 0.18 μM. Similar results were found with either α‐crystallin or its purified subunits αA‐crystallin and αB‐crystallin. In contrast to the experiments with cytochalasin D, phosphorylation had no effect. There does not appear to be an interaction between α‐crystallin and actin monomers since the effect of α‐crystallin in enhancing actin polymerization does not become apparent until some polymerization has occurred. Examination of the stoichiometry of the α‐crystallin effect indicates that 2‐3 α‐crystallin monomers/actin monomer give maximum actin polymer stabilization.
Complete NMR Structural Elucidation of the Capsular Polysaccharide Adjuvant from Klebsiella I‐714
Authors: Adam Olivier , Rivière Michel , Vercellone Alain , Monsan Pierre F. , Puzo Germain 
Published: July 2004

The capsular polysaccharide (CPS) produced by the non‐pathogenic Klebsiella strain 1–714, selected for its immunomodulating activity, has been purified and almost completely detoxified in a previous study [Adam, O., Vercellone, A., Paul, F., Monsan, P. F. & Puzo, G. (1995)Anal. Biochem. 225, 321–3271, The present report concerns the structural elucidation of this CPS by several one‐dimensional and two‐dimensional 1H‐NMR and 13C‐NMR experiments performed on the native molecule. It was found to be a high molecular‐mass branched polymer constituted by a hexasaccharide repeating unit of following structure:
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The presence of two glycosidic substitutions on the Galp residue resulted in a strong overlapping of its proton signals, preventing direct assignment of both proton and carbon resonances. However, assignment could be achieved using the two‐bond and three‐bond 1H‐13C heteronuclear coupling observed in the 1H‐13C heteronuclear multiple‐bond correlation (HMBC) spectrum.
Purification, Characterization and Biological Evaluation of Recombinant Leech‐Derived Tryptase Inhibitor (rLDTI) Expressed at High Level in the Yeast Saccharomyces Cerevisiae
Authors: Pohlig Gabriele , Fendrich Gabriele , Knecht Rene , Eder Beate , Piechottka Gerd , Sommerhoff Christian P. , Heim Jutta 
Published: July 2004

An efficient expressiordpurification procedure has been developed which allows the production of pure, biologically active recombinant leech‐derived tryptase inhibitor (rLDTI), originally found in the leech Hirudo medicinalis. The gene for LDTI was generated synthetically from three overlapping oligonu‐cleotides by PCR synthesis. LDTI was expressed in the yeast Saccharomyces cerevisiae under the control of the copper‐inducible CUPI promoter and fused to the invertase signal sequence (SUCZ). The entire expression cassette was inserted into the yeast high‐copy vector pDP34. Appropriate host strains transformed with the expression plasmid secreted rLDTI into the medium upon copper addition. Proteinchemi‐cal analysis of the secreted rLDTI revealed exclusively inhibitor with the correct N‐terminal sequence. Up to 60% of the rLDTI, however, appeared to be modified by glycosylation and the unglycosylated material showed heterogeneity at the C‐terminus. Besides full‐length rLDTI, truncated rLDTI species lacking either the terminal Asn46 or in addition the penultimate Leu45 were isolated. The C‐terminally truncated variants were eliminated using a S. cerevisiae host strain disrupted in the structural genes of carboxypeptidases yscY and yscα, thus identifying these proteases as being responsible for the degradation of rLDTI.Mature rLDTI was purified in high yields from the culture supernatant of the carboxypeptidase‐deficient yeast strain by cation‐exchange chromatography and reverse‐phase HPLC. The recombinant protein is at least 98% pure, based on HPLC and capillary electrophoresis, and is fully biologically active. Structural identity with the authentic leech protein was confirmed by sequence analysis and molecular‐mass determination. The purified protein was tested for its ability to inhibit tryptase and trypsin in vitro and to interfere with the tryptase‐induced proliferation of human fibroblasts and keratinocytes. Recombinant LDTI appears to be as potent as the authentic leech protein, exhibiting Ki‐values of ≈1.5 nM and ≈1.6 nM against human tryptase and bovine trypsin, respectively. The tryptase‐induced proliferation of human fibroblasts and keratinocytes was inhibited with half‐maximum values of ≈0.1 nM and ≈1 nM, respectively. The availability of the recombinant material will allow evaluation of the concept of tryptase inhibition in various disease models and to test the therapeutic potential of LDTI in mast‐cell‐related disorders.
Overproduction of a Foreign Membrane Protein in Escherichia Coli Stimulates and Depends on Phospholipid Synthesis
Authors: Nieboer Maarten , Vis Albert‐Jon , Witholt Bernard 
Published: July 2004

When the Pseudomonas oleovorans alk system, consisting of the alkBFGHJKL and alkST genes, is expressed in Escherichia coli W3110, significant changes in phospholipid metabolism of the host are observed. A major role seems to be played by the cytoplasmic membrane protein alkane hydroxylase (AlkB), which is synthesized as up to 10–15% of the total protein in this strain [Nieboer, M., Kingma, J. & Witholt, B. (1993) The alkane oxidation system of Pseudomonas oleovorans: induction of the alk genes in Escherichia coli W3110[pGEc47] affects membrane biogenesis and results in overexpression of alkane hydroxylase in a distinct cytoplasmic membrane subfraction, Mol. Microbiol. 8, 1039–1051]. In the present paper, we have studied the link between synthesis of the membrane protein and the synthesis of phospholipids and fatty acids by examining the kinetics of these processes.Using [35S]methionine labeling, it was shown that induction of AlkB was maximal within 30–60 min after addition of inducer, when up to 15% of all newly synthesized protein is AlkB. Phospholipid synthesis was followed by measuring the incorporation of 14C‐labeled acetate and 33P‐labeled phosphoric acid into phospholipids. Despite a negative effect of the inducer on the growth rate of W3110[pGEc47], net phospholipid synthesis was significantly enhanced as a result of the expression of alkB. Synthesis of all three major phospholipids were stimulated to comparable extents by the induction of alkB. Induction did not increase 33P incorporation into lipids in the control recombinant alk+ strain which lacked alkB.Simultaneous with AlkB synthesis, the conversion of unsaturated 9‐hexadecenoic acid (C,6:1) into 9,10‐methylene hexadecanoic acid (C17:ocyc) was reduced in the alk+ recombinant. Overall, these data show that the production of a foreign membrane protein in E. coli can engender a response of the phospholipid‐synthesizing system of the host. In the absence of such a response, induction of the alk system would be much more toxic to the cells. Apparently, the increased phospholipid synthesis plays an important role in enabling the AlkB overproducing strain to grow.