bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double‐stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease
Authors: Cheng Hua , Shen Nan , Pei Jimin , Grishin Nick V. 
Published: July 2004

AbstractDouble‐stranded DNA bacteriophages and herpesviruses assemble their heads in a similar fashion; a pre‐formed precursor called a prohead or procapsid undergoes a conformational transition to give rise to a mature head or capsid. A virus‐encoded prohead or procapsid protease is often required in this maturation process. Through computational analysis, we infer homology between bacteriophage prohead proteases (MEROPS families U9 and U35) and herpesvirus protease (MEROPS family S21), and unify them into a procapsid protease superfamily. We also extend this superfamily to include an uncharacterized cluster of orthologs (COG3566) and many other phage or bacteria‐encoded hypothetical proteins. On the basis of this homology and the herpesvirus protease structure and catalytic mechanism, we predict that bacteriophage prohead proteases adopt the herpesvirus protease fold and exploit a conserved Ser and His residue pair in catalysis. Our study provides further support for the proposed evolutionary link between dsDNA bacteriophages and herpesviruses.
The C‐terminal domain of dimeric serine hydroxymethyltransferase plays a key role in stabilization of the quaternary structure and cooperative unfolding of protein: Domain swapping studies with enzymes having high sequence identity
Authors: Bhatt Anant Narayan , Khan M. Yahiya , Bhakuni Vinod 
Published: July 2004

AbstractThe serine hydroxymethyltransferase from Bacillus subtilis (bsSHMT) and B. stearothermophilus (bstSHMT) are both homodimers and share ∼77% sequence identity; however, they show very different thermal stabilities and unfolding pathways. For investigating the role of N‐ and C‐terminal domains in stability and unfolding of dimeric SHMTs, we have swapped the structural domains between bs‐ and bstSHMT and generated the two novel chimeric proteins bsbstc and bstbsc, respectively. The chimeras had secondary structure, tyrosine, and pyridoxal‐5′‐phosphate microenvironment similar to that of the wild‐type proteins. The chimeras showed enzymatic activity slightly higher than that of the wild‐type proteins. Interestingly, the guanidium chloride (GdmCl)–induced unfolding showed that unlike the wild‐type bsSHMT, which undergoes dissociation of native dimer into monomers at low guanidium chloride (GdmCl) concentration, resulting in a non‐cooperative unfolding of enzyme, its chimera bsbstc, having the C‐terminal domain of bstSHMT was resistant to low GdmCl concentration and showed a GdmCl‐induced cooperative unfolding from native dimer to unfolded monomer. In contrast, the wild‐type dimeric bstSHMT was resistant to low GdmCl concentration and showed a GdmCl‐induced cooperative unfolding, whereas its chimera bstbsc, having the C‐ terminal domain of bsSHMT, showed dissociation of native dimer into monomer at low GdmCl concentration and a GdmCl‐induced non‐cooperative unfolding. These results clearly demonstrate that the C‐terminal domain of dimeric SHMT plays a vital role in stabilization of the oligomeric structure of the native enzyme hence modulating its unfolding pathway.
Insights into the DNA repair process by the formamidopyrimidine‐DNA glycosylase investigated by molecular dynamics
Authors: Amara Patricia , Serre Laurence , Castaing Bertrand , Thomas Aline 
Published: July 2004

AbstractFormamidopyrimidine‐DNA glycosylase (Fpg) identifies and removes 8‐oxoguanine from DNA. All of the X‐ray structures of Fpg complexed to an abasic site containing DNA exhibit a common disordered region present in the C‐terminal domain of the enzyme. However, this region is believed to be involved in the damaged base binding site when the initial protein/DNA complex is formed. The dynamic behavior of the disordered polypeptide (named Loop) in relation to the supposed scenario for the DNA repair mechanism was investigated by molecular dynamics on different models, derived from the X‐ray structure of Lactococcus lactis Fpg bound to an abasic site analog‐containing DNA and of Bacillus stearothermophilus Fpg bound to 8‐oxoG. This study shows that the presence of the damaged base influences the dynamics of the whole enzyme and that the Loop location is dependent on the presence and on the conformation of the 8‐oxoG in its binding site. In addition, from our results, the conformation of the 8‐oxoG seems to be favored in syn in the L. lactis models, in agreement with the available X‐ray structure from B. stearothermophilus Fpg and with a possible catalytic role of the flexibility of the Loop region.
Proteome‐wide functional classification and identification of prokaryotic transmembrane proteins by transmembrane topology similarity comparison
Authors: Arai Masafumi , Okumura Kosuke , Satake Masanobu , Shimizu Toshio 
Published: July 2004

AbstractWe propose a new method for classifying and identifying transmembrane (TM) protein functions in proteome‐scale by applying a single‐linkage clustering method based on TM topology similarity, which is calculated simply from comparing the lengths of loop regions. In this study, we focused on 87 prokaryotic TM proteomes consisting of 31 proteobacteria, 22 gram‐positive bacteria, 19 other bacteria, and 15 archaea. Prior to performing the clustering, we first categorized individual TM protein sequences as “known,” “putative” (similar to “known” sequences), or “unknown” by using the homology search and the sequence similarity comparison against SWISS‐PROT to assess the current status of the functional annotation of the TM proteomes based on sequence similarity only. More than three‐quarters, that is, 75.7% of the TM protein sequences are functionally “unknown,” with only 3.8% and 20.5% of them being classified as “known” and “putative,” respectively. Using our clustering approach based on TM topology similarity, we succeeded in increasing the rate of TM protein sequences functionally classified and identified from 24.3% to 60.9%. Obtained clusters correspond well to functional superfamilies or families, and the functional classification and identification are successfully achieved by this approach. For example, in an obtained cluster of TM proteins with six TM segments, 109 sequences out of 119 sequences annotated as “ATP‐binding cassette transporter” are properly included and 122 “unknown” sequences are also contained.
Orientation and helical conformation of a tissue‐specific hunter‐killer peptide in micelles
Authors: Plesniak Leigh A. , Parducho Jonathan I. , Ziebart Angie , Geierstanger Bernhard H. , Whiles Jennifer A. , Melacini Guiseppe , Jennings Patricia A. 
Published: July 2004

AbstractHunter‐killer peptides are chimeric synthetic peptides that selectively target specific cell types for an apoptotic death. These peptides, which are models for potential therapeutics, contain a homing sequence for receptor‐mediated interactions and a pro‐apoptotic sequence. Homing domains have been designed to target angiogenic tumor cells, prostate cells, arthritic tissue and, most recently, adipose tissue. After a receptor‐mediated internalization, the apoptotic sequence, which contains D‐enantiomer amino acids, initiates apoptosis through mitochondrial membrane disruption. We have begun structure and functional studies on a peptide (HKP1) that specifically targets angiogenic tumor cells for apoptosis. As a model for mitochondrial membrane disruption, we have examined peptide‐induced leakage of a calcein fluorophore from large unilamellar vesicles. These experiments demonstrate more potent leakage activity by HKP1 than the peptide lacking the homing domain. Circular dichroism and 2D homonuclear NMR experiments demonstrate that this tumor‐specific HKP adopts a left‐handed amphipathic helix in association with dodecylphosphorylcholine micelles in a parallel orientation to the lipid–water interface with the homing domain remaining exposed to solvent. The amphipathic helix of the apoptotic domain orients with nonpolar leucine and alanine residues inserting most deeply into the lipid environment.
Sexual Orientation and Demand for the Arts*
Authors: Lewis Gregory B. , Seaman Bruce A. 
Published: July 2004

Objective. We establish and try to explain a gay affinity for the arts.Methods. Using logit analysis on the General Social Survey, we test whether demographics, creativity, gender nonconformity, and sexual repression can explain differences between lesbians, gay men, and bisexuals (LGBs) and others in attendance at art museums, classical music concerts, and dance performances.Results. LGBs' higher education and probability of being childless city‐dwellers explain one‐third of the substantial attendance differences. However, LGBs do not demonstrate higher innate creativity through greater amateur production of art; gay men's affinity for the arts appears no stronger than lesbians', casting doubt on the gender nonconformity explanation; and LGB‐straight attendance differences are as large among young as older respondents, despite supposed declines in the special functions of arts attendance since gay liberation.Conclusions. LGBs are much more likely to attend the arts than demographically similar heterosexuals, but we find little support for three conventional explanations.
Knowledge Variables in Cross‐National Social Inquiry*
Authors: Mondak Jeffery J. , Canache Damarys 
Published: July 2004

Objectives. This article examines the impact of “don't know” responses on cross‐national measures of knowledge regarding science and the environment. Specifically, we explore cross‐national variance in aggregate knowledge levels and the gender gap in knowledge in each of 20 nations to determine whether response‐set effects contribute to observed variance.Methods. Analyses focus on a 12‐item true‐false knowledge battery asked as part of a 1993 International Social Survey Program environmental survey. Whereas most research on knowledge codes incorrect and “don't know” responses identically, we differentiate these response forms and develop procedures to identify and account for systematic differences in the tendency to guess.Results. Substantial cross‐national variance in guessing rates is identified, variance that contributes markedly to variance in observed “knowledge” levels. Also, men are found to guess at higher rates than women, a tendency that exaggerates the magnitude of the observed gender gap in knowledge.Conclusions. Recent research has suggested that “don't know” responses pose threats to the validity of inferences derived from measures of political knowledge in the United States. Our results indicate that a similar risk exists with cross‐national measures of knowledge of science and the environment. It follows that considerable caution must be exercised when comparing data drawn from different nations and cultures.
Faction in Movement: The Impact of Inclusivity on the Anti‐Globalization Movement*
Authors: Brooks D. Christopher 
Published: July 2004

Objectives.This research examines and evaluates the reasons why the anti‐globalization movement has yet to make significant progress in achieving its primary goals of democratizing international trade negotiation processes.Methods.Data on anti‐globalization protest cycles were collected from news sources for a time period of up to one month that encapsulated the protest events. From these, I constructed brief case narratives of the major events in Seattle, Washington, DC, Prague, Quebec City, Genoa, and Doha to illustrate my argument.Results.I find that the democratic master frame employed by the movement results in two important limitations: (1) the movement cannot exclude participants without undermining its legitimacy, and (2) its lack of a centralized organizational framework makes it impossible to police the actions of participants during major protests. Recognizing these limitations, states hosting global economic summits have demonstrated increasingly a willingness to utilize repressive measures against the movement thereby undermining the movement's ability to achieve its goals.Conclusion.I conclude that the inability of the anti‐globalization movement to exclude violent participants will continue to limit its effectiveness given states' increasing willingness to employ repressive tactics indiscriminately.
Apportioning the House of Representatives in 2000: The Effects of Alternative Policy Scenarios*
Authors: Baumle Amanda K. , Poston Dudley L. 
Published: July 2004

Objective. The goal of this article is to develop and examine eight different scenarios in which the U.S. House of Representatives is reapportioned for the year 2000 on the basis of eight scenarios in which the apportionment population is differentially defined. In each scenario we adjust the 2000 apportionment population of each of the 50 states on the basis of various aspects of immigration, eligibility to vote, the overseas population, and statistical sampling.Method. The method we use to apportion the House under each of the eight scenarios is the method of Equal Proportions, a divisor method that has been used to apportion the House since 1940. It endeavors to assign equitably to the 50 states, on the basis of population size, the 385 House seats that are available to be apportioned. Not all 435 House seats are assigned to the states using this method because each state automatically gets one seat.Results. We show that when the House of Representatives is reapportioned on the basis of any of the eight scenarios, there is a varying amount of redistribution of seats among the states. Many states end up gaining or losing seats, but not all are affected.Conclusion. There have been several legal challenges following the 2000 and earlier apportionments. The results of our analyses suggest that there will continue to be legal challenges to the 2000 and later apportionments. Since it is not likely that the Congress will permit a larger number of representatives than 435, apportionment challenges are really a zero‐sum game. Some states will gain political power, and others will lose it. This redistribution of power and its politically relevant consequences lead us to expect that apportionment challenges regarding the kinds of political and demographic issues raised in this article are not at all unlikely in the future.
Reinforcing Stereotypes? Race and Local Television News Coverage of Congress*
Authors: Schaffner Brian F. , Gadson Mark 
Published: July 2004

Objective. Despite the increasingly diverse legislative records of African‐American members of Congress, much of the population continues to believe that African‐American legislators are interested only in minority issues. If African‐American House members are becoming more like their nonblack colleagues, then why do many citizens continue to hold these stereotypes about African‐American legislators?Methods. We examine local television news coverage of House members and compare the coverage received by African‐American and nonblack incumbents.Results. We find that local television newscasts devote more coverage to African‐American members of Congress but this coverage is also more race oriented, especially in less diverse markets. In fact, local television stations produce more race‐oriented coverage of African‐American legislators regardless of their legislative records on minority issues.Conclusions. Local television news stations may be partially responsible for the prevailing stereotype of African‐American House members who are narrowly focused on race‐oriented issues.
Participation in Voluntary Youth‐Serving Associations and Early Adult Voting Behavior*
Authors: Frisco Michelle L. , Muller Chandra , Dodson Kyle 
Published: July 2004

Objective. We investigate adolescent membership in voluntary associations and whether participation in these activities influences voting behavior during early adulthood.Methods. Weighted logistic regression models predicting membership in voluntary associations and voting behavior were estimated using data from the National Educational Longitudinal Study of 1988–1994 (NELS).Results. Our findings suggest that membership in voluntary associations varies by race and socioeconomic status (SES). In addition, membership in organizations historically rooted in moral development and civic socialization positively predict voter‐registration status and whether or not young adults participated in the first national election that they were eligible to vote in, but this relationship is moderated by both race and SES.Conclusions. Our findings suggest that a large proportion of U.S. teenagers still participate in community‐based programs, many of which foster later civic participation, but that all youth do not equally benefit from participation.
Cross‐National Gender Variation in Environmental Behaviors*
Authors: Hunter Lori M. , Hatch Alison , Johnson Aaron 
Published: July 2004

Objective. This article presents a cross‐national examination of gender variations in environmental behaviors. Research on environmental concern reveals modest distinctions between men and women, with women typically displaying higher levels of environmental concern and behavioral adjustments relative to men. Additionally, some prior research suggests that women appear more engaged in household‐oriented (private) pro‐environment behaviors (e.g., recycling), and men in community/society‐oriented (public) pro‐environment behaviors (e.g., protests). The analysis provided here offers an important extension to existing research through its cross‐cultural, comparative perspective.Method. We make use of the 1993 International Social Survey to explore gender differences in “private” and “public” environmentally‐oriented behaviors across 22 nations.Results. It is shown that women tend to engage in more environmental behaviors than men in many nations, particularly private behaviors. In addition, both women and men tend to engage in relatively more private environmental behaviors as opposed to public ones.Conclusion. The cross‐national analysis provides support for gender distinctions with regard to some environmental behaviors within most of the incorporated 22 national contexts. Gender differences in level of private environmental behaviors tend to be more consistent within nations at the upper end of the wealth distribution.
Christian Fundamentalists and Public Opinion Toward the Middle East: Israel's New Best Friends?*
Authors: Mayer Jeremy D. 
Published: July 2004

Objectives.Although Christian fundamentalist elites have become increasingly vocal in their support for Israel in the ongoing conflict in the Middle East, it is not clear that this rhetoric has produced differing attitudes about U.S. foreign policy in public opinion. This article examines whether such differences exist, and whether they are rooted in aspects of fundamentalist eschatology.Methods.Data from a national telephone survey on attitudes toward the Middle East conflict and U.S. policy were examined using multivariate regression and means comparisons.Results.These results demonstrate that Christian fundamentalists are the strongest supporters of Israel in America today. Fundamentalists have greater sympathy for Israel, oppose policies to pressure Israel, and are distinctive from all other groups in their high levels of support for continuing Israeli settlements in occupied Palestinian territories, as well as complete Israeli control of Jerusalem.Conclusion.Christian fundamentalists in America are distinctive on this vital issue in American foreign policy because of their literal interpretation of the Bible or their leaders' increased cues on Middle East policies, or both. This suggests that religion is now an important factor in understanding public opinion on U.S. foreign policy in the region.
Expanding Discrimination Research: Beyond Ethnicity and to the Web*
Authors: Kuran Timur , McCaffery Edward J. 
Published: July 2004

Objective. This article aims to expand research about perceptions of discrimination both substantively and methodologically beyond the domains of race and ethnicity, relying partly on web‐based surveys.Methods. We conducted parallel surveys over the telephone and the World‐Wide Web, using standard random‐digit dial (RDD) techniques for the former, and a large volunteer panel for the latter.Results. Both modes, phone and web, revealed that respondents consider discrimination based on physical appearance and economic status to be more prevalent than discrimination based on ethnicity. Respondents also reported that they themselves have been victimized more by physical appearance and economic‐status discrimination than by ethnic discrimination. Significant differences emerged between the phone and web respondent pools, even after controlling for such independent variables as age, race, education level, and gender.Conclusions. People perceive discrimination across many aspects of social life, and appear more willing to reveal knowledge about controversial social phenomena on the web than on the phone.
The Impact of Church Activities and Socialization on African‐American Religious Commitment*
Authors: Wielhouwer Peter W. 
Published: July 2004

Objective. This article examines religious commitment (church involvement, private devotionalism, and religious salience) among African Americans as a function of being served by a religious congregation, perception of the historical role of the church in relation to the group, and religious and racial socialization.Methods. Drawing on traditional Christian expectations of the church, hypotheses are tested using the 1979–1980 National Survey of Black Americans. Three alternative models are tested that explicitly compare the effects of church activities with conventional socialization and demographic models of religious commitment.Results. The results show that the church's fulfillment of its normative roles of discipleship and ministry is profoundly important for understanding religiosity, even controlling for other conventional predictors.Conclusions. The analysis illustrates a central, and previously unaddressed, link between religious institutions and individual religiosity. The results have consequences for churches that might consider reprioritizing their activities in response to faith‐based initiatives because social‐service types of church activities influence religious commitment to a lesser degree than activities that emphasize spiritual growth.
The Intersection of Race and Gender: An Examination of Black Feminist Consciousness, Race Consciousness, and Policy Attitudes*
Authors: Simien Evelyn M. , Clawson Rosalee A. 
Published: July 2004

Objective. In this article, we investigate black feminist consciousness, its relationship to race consciousness, and its impact on policy attitudes. Unlike scholars and activists who argue that black feminist consciousness detracts from race consciousness, we argue that the two go hand in hand.Methods. Using confirmatory factor analysis, we examine public opinion survey data from the 1993 National Black Politics Study.Results. We find that both black women and men have fairly high levels of support for black feminist ideals. Also, we provide evidence that black feminist consciousness is positively related to the components of race consciousness and demonstrate the influence of black feminist consciousness on support for abortion rights.Conclusions. Our research is important because it uses a measure of black feminist consciousness true to its theoretical origins.