Specific Structural Contexts Research Articles

ELUCIDATING THE DIFFERENTIAL IMPACTS OF EQUIVALENT GATING-CHARGE MUTATIONS IN VOLTAGE-GATED SODIUM CHANNELS.

Voltage-gated sodium (Nav) channels are pivotal for cellular signaling and mutations in Nav channels can lead to excitability disorders in cardiac, muscular, and neural tissues. A major cluster of pathological mutations localizes in the voltage-sensing domains (VSDs), resulting in either gain-of-function (GoF), loss-of-function (LoF) effects, or both. However, the mechanism behind this functional divergence of mutations at equivalent positions remains elusive. Through hotspot analysis, we identified three gating charges (R1, R2, and R3) as major mutational hotspots in VSDs. The same amino-acid substitutions at equivalent gating-charge positions in VSDI and VSDII of the cardiac sodium channel Nav1.5 show differential gating-property impacts in electrophysiology measurements. We conducted 120 μs molecular dynamics (MD) simulations on wild-type and six mutants to elucidate the structural basis of their differential impacts. Our μs-scale MD simulations with applied external electric fields captured VSD state transitions and revealed the differential structural dynamics between equivalent R-to-Q mutants. Notably, we observed transient leaky conformations in some mutants during structural transitions, offering a detailed structural explanation for gating-pore currents. Our salt-bridge network analysis uncovered VSD-specific and state-dependent interactions among gating charges, countercharges, and lipids. This detailed analysis elucidated how mutations disrupt critical electrostatic interactions, thereby altering VSD permeability and modulating gating properties. By demonstrating the crucial importance of considering the specific structural context of each mutation, our study represents a significant leap forward in understanding structure-function relationships in Nav channels. Our work establishes a robust framework for future investigations into the molecular basis of ion channel-related disorders.

Structural Mapping of the Base Stacks Containing Post-transcriptionally Modified Bases in RNA.

Post-transcriptionally modified bases play vital roles in many biochemical processes involving RNA. Analysis of the non-covalent interactions associated with these bases in RNA is crucial for providing a more complete understanding of the RNA structure and function; however, the characterization of these interactions remains understudied. To address this limitation, we present a comprehensive analysis of base stacks involving all crystallographic occurrences of the most biologically relevant modified bases in a large dataset of high-resolution RNA crystal structures. This is accompanied by a geometrical classification of the stacking contacts using our established tools. Coupled with quantum chemical calculations and an analysis of the specific structural context of these stacks, this provides a map of the stacking conformations available to modified bases in RNA. Overall, our analysis is expected to facilitate structural research on altered RNA bases.

Organizational narratives in rehabilitation-focused dementia care - Negotiating identities, interventions and personhood.

Rehabilitation is increasingly being introduced in dementia care but studies highlight extensive heterogeneity in practices, conceptual confusion and divergent perceptions of its relevance across care organizations and national contexts. As this have implications for development of dementia care as well as for people with dementia's access to care it is important to study the organizational narratives and practices in rehabilitation-oriented dementia care organizations. The study build on qualitative interviews (individual and group interviews) with health professionals (N = 26) engaged with dementia care and rehabilitation in two Danish municipalities. The interviews were conducted in 2018-2019. The empirical data was analyzed using abductive analysis and theory-based narrative analysis, using Loseke's conceptualizations of and approach to analyzing formula stories. Four dominant organizational narratives were constructed from the data. Each narrative produced a specific organizational narrative of client identity: the active participant in individualized rehabilitation, the inactive individual benefitting from enhanced social environments, the disengaging self and the vulnerable self. Introducing rehabilitation in dementia care may amplify the organizational polyphonic and provide a plurality of organizational identities each expressing different perceptions of personhood and agency for people with dementia. The organizational narratives were negotiated within a specific structural context where national regulation and dominant discourses on economic challenges and ageing gave precedence to some narratives more than others. In Danish elder care, the first narrative is the most influential but risks excluding people with dementia. Instead, rehabilitation in dementia care is positioned within a social and relational perspective, which may silence important discussion of agency and resistance.

Thinking through the integration of corporate reporting: exploring the interplay between integrative and integrated thinking

PurposeThis paper aims to introduce an analytical focus on an individual’s integrative thinking capacity to further understand integrated thinking within the organisation. Integrated thinking is an elusive concept, gaining in prominence through its use by the International Integrated Reporting Council (IIRC), without specific guidance or a commonly understood framework. To date, the academic debate on integrated thinking addresses the organisational level only. However, thinking is a process occurring within the mind of an individual and therefore the prerequisites for integrated thinking at the individual level needs to be considered. Critical reflection is, therefore, provided on the interplay between integrative and integrated thinking.Design/methodology/approachThis paper draws on conceptual systems theory and case site analysis to reflect how integrative thinking can be encouraged and supported within the individual and how integrated thinking can hence be fostered within organisations.FindingsThe paper analyses and discusses four sites of integrative thinking: the Athenian democracy; the Minangkabau community; the Quakers and consensus decision-making; and the Apis Mellifera and the hive mind. The findings from these different sites illustrate that integrative thinking can be supported by specific structural, organisational and individual contexts and stimuli.Originality/valueExtending the context of integrated thinking analysis outside of the organisation and analysing these sites through components of integrative thought, this article provides further insights into how integrated thinking can be fostered within different organisations. The implications of these findings for accounting and professional institutions, organisations and the ongoing professional development of accountants are discussed.

An introduction to cryo-FIB-SEM cross-sectioning of frozen, hydrated Life Science samples.

SummaryThe introduction of cryo‐techniques to the focused ion‐beam scanning electron microscope (FIB‐SEM) has brought new opportunities to study frozen, hydrated samples from the field of Life Sciences. Cryo‐techniques have long been employed in electron microscopy. Thin electron transparent sections are produced by cryo‐ultramicrotomy for observation in a cryo‐transmission electron microscope (TEM). Cryo‐TEM is presently reaching the imaging of macromolecular structures. In parallel, cryo‐fractured surfaces from bulk materials have been investigated by cryo‐SEM.Both cryo‐TEM and cryo‐SEM have provided a wealth of information, despite being 2D techniques. Cryo‐TEM tomography does provide 3D information, but the thickness of the volume has a maximum of 200–300 nm, which limits the 3D information within the context of specific structures. FIB‐milling enables imaging additional planes by creating cross‐sections (e.g. cross‐sectioning or site‐specific X‐sectioning) perpendicular to the cryo‐fracture surface, thus adding a third imaging dimension to the cryo‐SEM. This paper discusses how to produce suitable cryo‐FIB‐SEM cross‐section results from frozen, hydrated Life Science samples with emphasis on ‘common knowledge’ and reoccurring observations.Lay DescriptionLife Sciences studies life down to the smallest details. Visualising the smallest details requires electron microscopy, which utilises high‐vacuum chambers. One method to maintain the integrity of Life Sciences samples under vacuum conditions is freezing. Frozen samples can remain in a suspended state. As a result, research can be carried out without having to change the chemistry or internal physical structure of the samples.Two types of electron microscopes equipped with cryo‐sample handling facilities are used to investigate samples: The scanning electron microscope (SEM) which investigates surfaces and the transmission electron microscope (TEM) which investigates thin electron transparent sections (called lamellae). A third method of investigation combines a SEM with a focused ion beam (FIB) to form a cryo‐FIB‐SEM, which is the basis of this paper. The electron beam images the cryo‐sample surface while the ion beam mills into the surface to expose the interior of the sample. The latter is called cross‐sectioning and the result provides a way of investigating the 3rd dimension of the sample. This paper looks at the making of cross‐sections in this manner originating from knowledge and experience gained with this technique over many years. This information is meant for newcomers, and experienced researchers in cryo‐microscopy alike.

Lessons from pressure denaturation of proteins.

Although it is now relatively well understood how sequence defines and impacts global protein stability in specific structural contexts, the question of how sequence modulates the configurational landscape of proteins remains to be defined. Protein configurational equilibria are generally characterized by using various chemical denaturants or by changing temperature or pH. Another thermodynamic parameter which is less often used in such studies is high hydrostatic pressure. This review discusses the basis for pressure effects on protein structure and stability, and describes how the unique mechanisms of pressure-induced unfolding can provide unique insights into protein conformational landscapes.

Exploring the importance of inter-departmental women’s friendship in geography as resistance in the neoliberal academy

ABSTRACTFriendship has potential as a key coping and self-care strategy among early career researchers (ECR’s) and has been shown to be crucial to overall well-being and sense of belonging, but its importance as a response to career pressures is not well studied. For ECR’s, friendships within the university are situated in a specific structural and institutional context, and formigrant women, this includes an additional aspect of gendered complexity. At the same time friendships may prove difficult as heightened neoliberal metrics emphasize competition forfunding, positions and teaching requirements. Using autoethnographic intra-reflections on the authors’ own friendship, bridging human geography and physical geography, this paper examines friendship of two ECR women from a homosocial perspective where institutional hierarchies and structures may be somewhat equalized. Drawing on the exploration of the authors’ friendship during their PhD years and into their post-doc positions, we reflect on the importance of friendship as an act of support, self-care and resistance. We argue for heightening importance for examining the way friendship creates safe social spaces and offer new insights into the importance of friendships in career paths. Friendship in the neoliberal academy has transformative potential for creating a culture of well-being in geography.

Understanding Enemy Images in Central and Eastern European Politics

In recent years, Europe has experienced a rise in politics based on antagonism, often discussed from the perspectives of populism and the mainstreaming of the ideologies of the radical right. In this study, we argue that there is a need for an interdisciplinary, theoretically broader and more empirically focused approach that fosters understanding of these developments. To explore the causal factors, we focus on the enemy images that are constructed and diffused by politicians, and their specific historical and structural contexts. The paper thus has two main components: First, we review what political theory, research on populism and on the extreme right and social psychology say about the functions of the use and development of enemy images. Second, we highlight the contextual factors that we consider make the success of a politics based on enemy images more likely in Central and Eastern Europe.

Structural landscape of base pairs containing post-transcriptional modifications in RNA.

Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA.

SIRT2 inactivation reveals a subset of hyperacetylated perinuclear microtubules inaccessible to HDAC6.

Deacetylation of α-tubulin at lysine 40 is catalyzed by two enzymes, the NAD-dependent deacetylase SIRT2 and the NAD-independent deacetylase HDAC6, in apparently redundant reactions. In the present study, we tested whether these two enzymes might have distinguishable preferences for the deacetylation of different microtubule structures. Using various agents, we induced tubulin hyperacetylation and analyzed the ensuing formation of distinct microtubule structures. HDAC6 inhibition led to general hyperacetylation of the microtubule network throughout the cell, whereas hyperacetylation induced by SIRT2 inactivation was limited to perinuclear microtubules. Hyperacetylation of these perinuclear microtubules was undiminished following HDAC6 overexpression, whereas reactivation of SIRT2 restored the basal acetylation level and a normal microtubule network. By contrast, SIRT2 and HDAC6 acted similarly on the morphologically different, hyperacetylated microtubule structures induced by taxol, MAP2c overexpression or hyperosmotic stress. These results indicate overlapping and distinct functions of HDAC6 and SIRT2. We propose that the differential activity of the two deacetylases, which target the same acetylated lysine residue, might be related to the recognition of specific structural contexts.

Unpacking the ‘structural’ in a structural approach for HIV prevention among female sex workers: A case study from China

Interventions for HIV prevention among female sex workers (FSWs) in China focus on HIV/sexually transmitted infection (STI) and individual behaviour change. An occupational health framework facilitates intervention across an array of health issues FSWs face including HIV/STI, violence, reproductive health, stigma and substance use. Through a case study of a community-based Jiaozhou (JZ) FSW programme, we developed a conceptual framework incorporating global discussions of structural approaches to HIV prevention with the specific social and structural contexts identified among FSWs in China. Based on ethnographic fieldwork between August 2010 and May 2013, we describe the evolution of this programme to its current occupational health focus and unpack the intervention strategies. We describe the critical features of the programme that have fostered success among FSWs including high-quality clinical services provided within a welcoming setting, responsive outreach work through staff and trained FSW peers, interpersonal and community-level engagement aimed at changing the local social and structural environments of sex work and tailored health education materials. This intervention differs from other projects in China by adopting a more holistic approach to FSW health that incorporates social issues. It also demonstrates the feasibility of structural interventions among FSWs even within an environment that has strong anti-prostitution policies.

Religious Public Discourses and Institutional Structures

This article examines the public claims-making and institutional arrangements of the Catholic Church through a comparative-historical study of the Catholic leadership conferences of Chile, Ireland, and Nigeria. Guided by theories from the sociology of religion and organizations, and drawing on historical and documentary sources including a content analysis of forty-two national-level pastoral letters, I document three empirical findings. First, the church appeals to national belonging more in missionary contexts than in traditionally Catholic settings. Second, Catholic religious leaders rely on secular and Catholic sources of legitimacy, but Catholic legitimations tend to predominate. Third, national hierarchies experience dissimilar resource opportunity structures in varying world geo-cultural regions. The theoretical contribution to the study of religious institutions and organizations in general is discussed in terms of taking account of specific local cultural conditions and structural contexts as well as globally resonant ideas and forms in understanding how religious power-holders respond to modernity at the national level.

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP–RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts. CapR is available at https://sites.google.com/site/fukunagatsu/software/capr.

‘Islam does not change’: young people narrating negotiations of religion and identity

There is growing interest in how diasporic Islam may be embraced by young people as a way of carving out space and identity in migratory contexts. Islamic identity may facilitate a critical stance in relation to both the ‘host’ society and also to parental authority and ‘traditional’ ethnic practices. However, there have been recent critiques of the tendency to oversimplify and exaggerate the extent of homogeneity in diasporic Islamic beliefs. This paper draws on lively focus group narratives of young people in London to explore the interactive presentation of Islamic selves. While on the surface these young people present themselves through ‘true’, ‘universal’ Islamic identity, on closer reading subtleties of difference and contingency become more apparent. By bringing together young people who practise Islam in different ways, this paper offers a deeper insight into how claims to a universal identity are actively constructed and contested through particular social relationships and interactions in specific structural contexts. In so doing, the paper takes up recent calls for more research on the personal meaning of religion for Muslim youngsters. I conclude by considering how religious identities can be understood as processes of youth identity formations.

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA

Prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. In many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal RNA, but also to a motif localized within their own mRNA, and thereby regulate expression of the operon. In this study, we computationally predicted an RNA motif present in many bacterial phyla within the 5' untranslated region of operons encoding ribosomal proteins S6 and S18. We demonstrated that the S6:S18 complex binds to this motif, which we hereafter refer to as the S6:S18 complex-binding motif (S6S18CBM). This motif is a conserved CCG sequence presented in a bulge flanked by a stem and a hairpin structure. A similar structure containing a CCG trinucleotide forms the S6:S18 complex binding site in 16S ribosomal RNA. We have constructed a 3D structural model of a S6:S18 complex with S6S18CBM, which suggests that the CCG trinucleotide in a specific structural context may be specifically recognized by the S18 protein. This prediction was supported by site-directed mutagenesis of both RNA and protein components. These results provide a molecular basis for understanding protein-RNA recognition and suggest that the S6S18CBM is involved in an auto-regulatory mechanism.

Stabilizing Impact of N-Glycosylation on the WW Domain Depends Strongly on the Asn-GlcNAc Linkage

N-glycans play important roles in many cellular processes and can increase protein conformational stability in specific structural contexts. Glycosylation (with a single GlcNAc) of the reverse turn sequence Phe-Yyy-Asn-Xxx-Thr at Asn stabilizes the Pin 1 WW domain by -0.85 ± 0.12 kcal mol(-1). Alternative methods exist for attaching carbohydrates to proteins; some occur naturally (e.g., the O-linkage), whereas others use chemoselective ligation reactions to mimic the natural N- or O-linkages. Here, we assess the energetic consequences of replacing the Asn linkage in the glycosylated WW domain with a Gln linkage, with two natural O-linkages, with two unnatural triazole linkages, and with an unnatural α-mercaptoacetamide linkage. Of these alternatives, only glycosylation of the triazole linkages stabilizes WW, and by a smaller amount than N-glycosylation, highlighting the need for caution when using triazole- or α-mercaptoacetamide-linked carbohydrates to mimic native N-glycans, especially where the impact of glycosylation on protein conformational stability is important.

Nucleosome-Nucleosome Stacking: A Major Element of Chromatin Structure

Interactions between nucleosome core particles (NCP) are key features of chromatin folding and are inherently related to regulation of DNA replication, transcription and repair. However, little is known about structures of NCP-NCP contacts as well as about the nature and scale of the forces involved. The NCP and chromatin are polyelectrolytes which show a sensitivity of folding and self-association both to ionic environment and to position, sequence and modifications of histone N-termini (tails). Combining experimental and computer modeling approaches, we study nucleosome-nucleosome interaction in both general polyelectrolyte and specific structural context. using native chemical ligation methods, large quantities of H4 histones containing acetylated and methylated lysines were synthesized. The influence of these posttranslational modifications on folding and intermolecular association of the NCPs and model chromatin arrays was studied as a function of the nature and concentration of monovalent and multivalent cations (K+, Na+, Mg2+, Co(NH3)63+, spermine4+). Additionally, computational modelling was used to investigate NCP-NCP interaction. A coarse-grained model of the NCP takes into account the details of its structure, based on the single crystal structure at atomic resolution and adequately describes the strong electrostatic forces acting in chromatin by explicit modelling of ions. Most experimental data is well-described by this electrostatic model. However, NCP-NCP close contact (stacking) shows sensitivity to the presence of the H4 histone tail and to acetylation of lysine 16 and other modifications in this histone which is beyond electrostatics. We suggest a structural model explaining the mechanism of these combined modification factors.

Local Agency and Structural Continuity: Views from an SHG-based Microcredit Scheme in Western India

This article uses Bourdieu and Giddens’ perspective of agency to investigate an anti-poverty programme of the Indian government that relies on self-help groups for the disbursal of microcredit. Multiple actors impact and refract away from the official agenda of the Swarnajayanti Gram Swarozgar Yojana (SGSY) scheme in Gujarat. Instead of working towards entrepreneurialism through self-help, actors use the SGSY as a vehicle for populism, rent-seeking and as a saving scheme for children's weddings. Through the agency of these actors, practised within a specific historical, structural and dispositional context, the structures of patriarchy and neo-liberalism are reproduced in everyday socio-economic and political life. However, hints of structural change, for example in women's control over earnings via access to banks, are also evident. Evidence from the SGSY scheme is used to highlight the ways in which microcredit can simultaneously empower and restrict the lives of female beneficiaries.

From gatekeeper to friend and back again: embracing the world of the street drug user

PurposeEthnographic research with street drug users is becoming increasingly difficult to undertake. In the main, it is perceived as “too risky” and frequently raises practical, ethical and emotional issues for ethnographers, however, this doesn't mean it is impossible. Indeed, one of the most challenging areas is the management of field relations – especially with gatekeepers. The main aim of this article is to provide an account of how gatekeeper field relations are developed and experienced in the context of researching street drug users.Design/methodology/approachThe article is based on a reflexive account to comment upon the experience of the researcher engaged in ethnographic research.FindingsThe author examines how field relations are influenced by the specific social and structural contexts in which the project took place and makes critical reflections on how these relationships impacted on him – professionally, personally and emotionally.Originality/valueThe article is useful for academics or researchers who are looking to study similar social groups.

Zivile Kontrolle des Militärs in jungen Demokratien: Agency, Struktur und institutioneller Wandel

This article integrates insights from historical institutionalism and arguments of strategic action in order to develop a new conceptual and theoretical approach to explaining changes in civil-military relations. In order to enforce civilian control over the military in new democracies, civilian decision-makers need to “break” stabilizing mechanisms of path dependence in civil-military relations. The ability of ‘change agents’ to overcome ‘path dependence’ depends on the concrete approach civilians take to reduce military power. Civilian choices, however, are structured by the specific structural, institutional and ideational contexts in which civil-military interaction takes place. These contextual factors also provide the constraints and resources for civilian actions. The civilian choices and the success of their control strategies are thus conditioned by the resources to which civilians have access and which allow them to initiate and consolidate changes vis-a-vis those actors opposing change in civil-military relations.