Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion

Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have contributed significantly to insights into protein molecular mechanisms and function. However, despite a shared purpose of these approaches, the topological nature of rigidity analysis, and thereby the absence of motion modes, has impeded a direct comparison. Here, we present an alternative, kinematic approach to rigidity analysis, which circumvents these drawbacks. We introduce a novel protein hydrogen bond network spectral decomposition, which provides an orthonormal basis for collective motions modulated by non-covalent interactions, analogous to the eigenspectrum of normal modes, and decomposes proteins into rigid clusters identical to those from topological rigidity. Our kinematic flexibility analysis bridges topological rigidity theory and ENM, and enables a detailed analysis of motion modes obtained from both approaches. Our analysis reveals that collectivity of protein motions, reported by the Shannon entropy, is significantly lower for rigidity theory versus normal mode approaches. Strikingly, kinematic flexibility analysis suggests that the hydrogen bonding network encodes a protein-fold specific, spatial hierarchy of motions, which goes nearly undetected in ENM. This hierarchy reveals distinct motion regimes that rationalize protein stiffness changes observed from experiment and molecular dynamics simulations. A formal expression for changes in free energy derived from the spectral decomposition indicates that motions across nearly 40% of modes obey enthalpy-entropy compensation. Taken together, our analysis suggests that hydrogen bond networks have evolved to modulate protein structure and dynamics

Cultural activism and the politics of place-making

In this paper, we explore the relationship between creative practice, activism, and urban place-making by considering the role they play in the construction of meaning in urban spaces. Through an analysis of two activist groups based in Stokes Croft, Bristol (UK), we argue that cultural activism provides new political prospects within the wider context of global capitalism through the cultivation of a shared aesthetics of protest. By cultivating aspects of shared history and a mutual enthusiasm for creative practice as a form of resistance, Stokes Croft has emerged as a ‘space of nurturance’ for creative sensibilities. However, we note how Stokes Croft as an autonomous space remains open-ended and multiple for activists interested in promoting different visions of social justice

Social media, protest cultures and political subjectivities of the Arab spring

This article draws on phenomenological perspectives to present a case against resisting the objectification of cultures of protest and dissent. The generative, self-organizing properties of protest cultures, especially as mobilized through social media, are frequently argued to elude both authoritarian political structures and academic discourse, leading to new political subjectivities or ‘imaginaries’. Stemming from a normative commitment not to over-determine such nascent subjectivities, this view has taken on a heightened resonance in relation to the recent popular uprisings in the Middle East and North Africa. The article argues that this view is based on an invalid assumption that authentic political subjectivities and cultures naturally emerge from an absence of constraint, whether political, journalistic or academic. The valorisation of amorphousness in protest cultures and social media enables affective and political projection, but overlooks politics in its institutional, professional and procedural forms

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into ‘cumulus-type’, i.e., those similar to puffy (white) clouds, and ‘stratus-type’, i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher rigidity of the individual units; there the conformational changes can be described by an ‘energy transfer’ mechanism. In the second class, the topology presents a compact structure with significant overlap between the modules; there the conformational changes can be described by ‘multi-trajectories’; that is, multiple highly populated pathways. We further propose that disordered protein regions evolved to help other protein segments reach ‘rarely visited’ but functionally-related states. We also show the role of disorder in ‘spatial games’ of amino acids; highlight the effects of intrinsically disordered proteins (IDPs) on cellular networks and list some possible studies linking protein disorder and protein structure networks

Reading hospitality mutually

This article addresses debates in geography regarding the nature and significance of hospitality. Despite increasingly inhospitable policy landscapes across the Global North, grassroots hospitality initiatives stubbornly persist, including various global travel-based initiatives and networks. Drawing from research with these travel networks, we argue that hospitality is fundamentally based on a pervasive, mutualistic sociality in a multitude of forms. Such initiatives, and hospitality more generally, can be better understood in terms of their relationship to these wider mutualities. we therefore use Peter Kropotkin’s anarchist-geographic concept of mutual aid – in conversation with Jacques Derrida and other thinkers – to reimagine hospitality as ‘mutual hospitableness’; systemic, spatio-temporally expansive, and underpinned by a conception of self that is constituted through, and gains its vitality from, intertwinement with the other

Struggling to 'fit in': On belonging and the ethics of sharing in project teams

This paper explores the links between belonging and ethics, which remain largely underdeveloped in project studies and are overlooked in everyday practice of managing projects. It focuses on belonging as the process articulating identity-construction of an inter-organisational project team from a global management consulting firm that was working in IS design. As the team?s experienced ?sense of place?, belonging becomes the space which highlights preferred affiliations and exposes how ? individually and collectively ? ethics are played out in the context of the management of projects. Four in situ belonging-narratives (of opposition, pragmatism, reflexivity, and the habitual narrative) represent ethics as part of lived action and of a life-world that emerge from deconstructing and reconstructing ?the team? and an ideal worker in projects. The team?s struggles to ?fit in? were experienced both when resisting and when collaborating with the dominant collective narrative of belonging. Modes of belonging are constituted in the relationship between self, others, and ?otherness?, creating a situated ethical imagination of how to ?be professional?. Implications concern the politics of belonging and call for a renewed practical ethics that engages with the social nature of ?being?, to change the current view of professional identities in projects

Protest or Riot?: Interpreting Collective Action in Contemporary France

Although both events were fundamentally acts of contestation led by different segments of France’s youth, the fall 2005 riots and the spring 2006 CPE protests received very different treatment in French public opinion. Whereas the riots were overwhelmingly condemned, the protests were not only tolerated but also often celebrated. By examining dominant interpretations of these events circulated in the news media alongside those of young people collected during a year of fieldwork in the public housing projects of a medium-sized French city, this paper shines light on fundamental French values and beliefs about how society ought to work while also contributing to ongoing debates about the cultural identity of such youth. More generally, it demonstrates the usefulness of comparison in the analysis of acts of political dissent