Quantification of Twist from the Central Lines of β-Strands

Since the discovery of right-handed twist of a β-strand, many studies have been conducted to understand the twist. Given the atomic structure of a protein, twist angles have been defined using atomic positions of the backbone. However, limited study is available to characterize twist when the atomic positions are not available, but the central lines of β-strands are. Recent studies in cryoelectron microscopy show that it is possible to predict the central lines of β-strands from a medium-resolution density map. Accurate measurement of twist angles is important in identification of β-strands from such density maps. We propose an effective method to quantify twist angles from a set of splines. In a data set of 55 pairs of β-strands from 11 β-sheets of 11 proteins, the spline measurement shows comparable results as measured using the discrete method that uses atomic positions directly, particularly in capturing twist angle change along a pair, different levels of twist among different pairs, and the average of twist angles. The proposed method provides an alternative method to characterize twist using the central lines of a β-sheet

Greater Engagement in Gender-Sexuality Alliances (GSAs) and GSA Characteristics Predict Youth Empowerment and Reduced Mental Health Concerns

Extracurricular groups can promote healthy development, yet the literature has given limited attention to indirect associations between extracurricular involvement and mental health or to sexual and gender minority youth. Among 580 youth (Mage = 15.59, range = 10–20 years) and adult advisors in 38 Gender-Sexuality Alliances (GSAs), multilevel structural equation models showed that greater engagement in GSAs over the school year predicted increased perceived peer validation, self-efficacy to promote social justice, and hope (baseline adjusted). Through increased hope, greater engagement indirectly predicted reduced depressive and anxiety symptoms at the year’s end (baseline adjusted). GSAs whose members had more mental health discussions and more meetings reported reduced mental health concerns. Findings suggest how groups addressing issues of equity and justice improve members’ health

Gay guys using gay language: Friendship, shared values and the intent-context-effect matrix

This article draws on in-depth interviews with 35 openly gay male undergraduates from four universities in England to develop an understanding of the changing nature of language related to homosexuality. In addition to finding a diminution in the prevalence of homophobic language, we demonstrate that participants maintain complex and nuanced understandings of phrases that do not use homophobic pejoratives, such as ‘that’s so gay’. The majority of participants rejected the notion that these phrases are inherently homophobic, instead arguing that the intent with which they are said and the context in which they are used are vital in understanding their meaning and effect. We conceptualize an intent-context-effect matrix to understand the interdependency of these variables. Highlighting the situated nature of this matrix, we also demonstrate the importance of the existence of shared norms between those saying and hearing the phrase when interpreting such language

Modelling Beta-sheets using Iterative Bézier Surface Fitting on Cryo-EM Density Maps

Cryo-electron microscopy is a powerful technique to produce 3-dimensional images for large molecular complexes. When the resolution of 3-dimensional images is not sufficient to derive atomic structure directly from the image, it is still challenging to interpret the image. In order to model β-strands from medium-resolution images, we propose the use of Bézier surface iteratively to fit a β-sheet image. The proposed method shows improved accuracy in fitting when it was tested using eight cases

Improving Detection of Secondary Structures within Medium Resolution Cryo-EM Density Maps

Cryo-electron microscopy is a biophysical technique in production of electron density maps that are 3-dimensional images. Although atomic structures can be derived from such images at high-resolution, it is still challenging to predict structures when the resolution of the image is at medium resolutions (5-10Å). Although computational methods are available to extract protein secondary structures from a medium-resolution image, they lack sufficient accuracy for structure prediction. This work aims to improve detection of secondary structures such as helices and β-sheets as compared to previous work SSETracer. Detection of these secondary structures is an important prior step for methods that perform further analysis, such as protein sequencing

An Iterative Bézier Method for Fitting Beta-Sheet Component of a Cryo-EM Density Map

Cryo-electron microscopy (Cryo-EM) is a powerful technique to produce 3-dimensional density maps for large molecular complexes. Although many atomic structures have been solved from cryo-EM density maps, it is challenging to derive atomic structures when the resolution of density maps is not sufficiently high. Geometrical shape representation of secondary structural components in a medium-resolution density map enhances modeling of atomic structures. We compare two methods in producing surface representation of the β-sheet component of a density map. Given a 3-dimensional volume of β-sheet that is segmented from a density map, the performance of a polynomial fitting was compared with that of an iterative Bézier fitting. The results suggest that the iterative Bézier fitting is more suitable for β-sheets, since it provides more accurate representation of the corners that are naturally twisted in a β-sheet

Comparison of Multiple Methods for Quantifying β-Strand Twist in a Protein Structure

Although proteins have a variety of atomic structures, they are often composed of secondary structures of helices, β-sheets, turns, and loops. β-sheet is a major type of secondary structures and was discovered in the 70’s that all β-sheets are twisted in nature. When images of proteins are produced at low resolutions, it is difficult to distinguish β-strands that are components of a β-sheet. Twist of a β-sheet was previously utilized to predict the position of β-strands in the image of a β-sheet. However, it is challenging to quantify the overall twist precisely. We studied multiple methods in quantifying the twist of a β-sheet. In a test consisting ten beta sheets, comparison shows that the best method varied with the size of the beta sheet. For sheets with three or less strands, overall twist calculated with the average twist angles of the two longest beta strands best fit the true protein structure. In sheets with four or five strands, the average of all angles provided the best fit, and in sheets with six or more strands, the average of all the angles except those on the edges of the beta sheet was the most accurate

Structural and environmental factors are associated with internalised homonegativity in men who have sex with men: findings from the European MSM Internet Survey (EMIS) in 38 countries.

Internalised homonegativity refers to a gay person's negative feelings about homosexuality and is believed to stem from negative societal stereotypes and attitudes towards homosexuality. Surprisingly, little research has centred on this link. In this research, we aimed to examine the associations between internalised homonegativity and structural forces, cultural influence, and access to sexual health promotion measures among a sample of 144,177 men who have sex with men (MSM) in 38 European countries. Participants were recruited as part of the European MSM Internet Survey (EMIS) during 2010. It was a self-completion, multilingual Internet-based survey for men living in Europe who have sex with men and/or feel attracted to men. Assumed causal relations were tested through multiple regression models. Variables at the structure of rule-systems (macro-level) that were significantly and negatively associated with internalised homonegativity were the presence of laws recognising same-sex relationships and same-sex adoption. In the meso-level model, greater proportions of the population expressing that they would not like to have homosexuals as neighbours predicted higher internalised homonegativity. In the last model, five variables were significantly and negatively associated with internalised homonegativity: being exposed to HIV/STI information for MSM, access to HIV testing, access to STI testing, access to condoms, and experience of gay-related hostility. In turn, men who had tested for HIV in the past year evidenced lower internalised homonegativity. This is the largest and certainly most geographically diverse study to date to examine structural and environmental predictors of internalised homonegativity among MSM. Our results show that one insidious consequence of society's stigma towards homosexuals is the internalisation of that stigma by gay and bisexual men themselves, thus, drawing attention to the importance of promoting social equity for self-acceptance around gay identity in building a positive sense of self