Search

Marine spatial planning (MSP) was developed as a place-based, integrated marine governance approach to address sectoral and fragmented management issues and has seen significant evolvement over the past two decades. MSP has rapidly become the most commonly endorsed management regime for sustainable development in the marine environment, with initiatives being implemented across multiple regions of the globe. Despite its broad and growing acceptance and use, there are several key challenges that remain, both conceptual and practical, that are negatively impacting the realization of MSP’s potential. These include institutional shortcomings, the exclusion of stakeholders, a failure to account for the human and social dimensions of marine regions, the marginalization of different types of knowledge, and the growing need to adapt to global environmental change. Although studies have examined the emergence of MSP in different geographical and institutional contexts, there is a lack of comparative analysis of how initiatives are progressing and if the foundational aims of MSP are being achieved. There is a need to analyze the degree to which MSP initiatives are responding to the environmental challenges that they have been set up to tackle and, as marine plans are setting out long-term visions for marine management, to understand if current initiatives are fit for purpose. This article responds to these concerns and reviews the evolution of MSP within 12 regional ocean areas. We utilize the term regional ocean areas to illustrate the geographical spread of MSP, with examinations conducted of the approach to MSP that specific nations within each of the 12 chosen clusters have followed. By critically assessing how MSP is progressing, it is possible to shed light on the opportunities and challenges that are facing current initiatives. This can help to reveal learning lessons that can inform future MSP systems and guide initiatives along more sustainable pathways.

The expansion of prescribing rights in Aotearoa New Zealand has enabled registered nurse prescribers (RN prescribers) working in primary care and specialty teams, to enhance nursing care, by prescribing medicines to their patient population. This widening of prescribing rights was to improve the population’s access to medicines and health care; however, little is known about the medications prescribed by RN prescribers. This paper reports on a descriptive survey of self-reported RN prescribers prescribing in a single district health board. The survey tool used was a Microsoft Excel spreadsheet to record nurse’s area of practice, patient demographic details, health conditions seen, and medicines prescribed and deprescribed. Simple data descriptions and tabulations were used to report the data. Eleven RN prescribers consented to take part in the survey and these nurses worked in speciality areas of cardiology, respiratory, diabetes, and primary care. Findings from the survey demonstrated that RN prescribers prescribe medicines within their area of practice and within the limits of the list of medicines for RN prescribers. Those working in primary care saw a wider range of health conditions and therefore prescribed a broader range of medications. This survey revealed that the list of medications available for RN prescribers needs to be updated regularly to align with the release of evidence-based medications on the New Zealand Pharmaceutical Schedule. It is also a useful record for both educational and clinical settings of the types of medications prescribed by RN prescribers.

Abstract: The BCL‐2 family is a challenging group of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL‐2 family regulators of apoptosis are useful as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non‐antibody‐binding proteins based on a conserved scaffold) to identify ligands for MCL‐1, BCL‐xL, BCL‐2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective recognition of their target BCL‐2 protein. For anti‐apoptotic targets BCL‐xL and MCL‐1, competitive inhibition of their canonical protein‐protein interactions is demonstrated. Co‐crystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug‐bound‐like conformation. These proof‐of‐concept studies indicate that Affimers could be used as alternative templates to inspire the design of selective BCL‐2 family modulators and more generally other protein‐protein interaction inhibitors., Affimer reagents (non‐antibody binding proteins) are identified that bind selectively to the anti‐apoptotic proteins BCL‐xL and MCL‐1. Crystallographic studies reveal an unprecedented mode of molecular recognition in which flexible loops from the Affimer dock into the BH3 binding cleft as opposed to a canonical α‐helix. Furthermore the Affimers induce changes in the target proteins towards desirable drug‐bound‐like conformations.

Marine spatial planning (MSP) has become the most adopted approach for sustainable marine governance. While MSP has transformative capacity, evaluations of its implementation illustrate large gaps between how it is conceptualised and how it is practiced. We argue that these gaps arise from MSP being implemented through post-political processes. Although MSP has been explored through post-political lenses, these evaluations are incomplete and do not provide sufficient detail about the complex nature of the post-political condition. Drawing on seminal literature, we conceptualise the post-political as consisting of highly interconnected modalities of depoliticisation, including: neoliberalism; choreographed participation; path dependency; technocratic-managerialism; and the illusion of progressive change. Using these modalities as an analytical framework, we evaluate English MSP and find that it focuses on entrenching neoliberal logic through: tokenistic participation; wholescale adoption of path-dependent solutions; obstructionist deployment of inactive technological solutions; and promising progressive change. We do not, however, view the post-political condition as unresolvable and we develop a suite of suggestions for the re-politicisation of MSP which, collectively, could form the basis for more radical forms of MSP.

This article focuses on the promotion of equal rights feminism in the journals of the Old Comrades Associations (OCAs), which were organizations set up to support women who had served with one of t...

The endogenous inhibitor of ATP synthase in mitochondria, called IF1, conserves cellular energy when the proton-motive force collapses by inhibiting ATP hydrolysis. Around neutrality, the 84-amino-acid bovine IF1 is thought to self-assemble into active dimers and, under alkaline conditions, into inactive tetramers and higher oligomers. Dimerization is mediated by formation of an antiparallel α-helical coiled-coil involving residues 44–84. The inhibitory region of each monomer from residues 1–46 is largely α-helical in crystals, but disordered in solution. The formation of the inhibited enzyme complex requires the hydrolysis of two ATP molecules, and in the complex the disordered region from residues 8–13 is extended and is followed by an α-helix from residues 14–18 and a longer α-helix from residue 21, which continues unbroken into the coiled-coil region. From residues 21–46, the long α-helix binds to other α-helices in the C-terminal region of predominantly one of the β-subunits in the most closed of the three catalytic interfaces. The definition of the factors that influence the self-association of IF1 is a key to understanding the regulation of its inhibitory properties. Therefore, we investigated the influence of pH and salt-types on the self-association of bovine IF1 and the folding of its unfolded region. We identified the equilibrium between dimers and tetramers as a potential central factor in the in vivo modulation of the inhibitory activity and suggest that the intrinsically disordered region makes its inhibitory potency exquisitely sensitive and responsive to physiological changes that influence the capability of mitochondria to make ATP.

The rheological behavior of an epoxidized natural rubber (ENR) nanocomposite containing 10 wt.% of silica particles was examined by time-resolved mechanical spectroscopy (TRMS), exploiting the unique capability of this technique for monitoring the time-dependent characteristics of unstable polymer melts. The resulting storage modulus curve has revealed a progressive evolution of the elastic component of the composite, associated with slower relaxations of the ENR macromolecular chains. Two major events were identified and quantified: one is associated with the absorption of the epoxidized rubber macromolecules onto the silica surface, which imposes further restrictions on the motions of the chains within the polymer phase, the second is related to gelation and the subsequent changes in rheological behavior resulting from the simultaneous occurrence cross-linking and chain scission reactions within the ENR matrix. These were quantified using two parameters related to changes in the storage and loss modulus components.

Physical inactivity is a risk factor for numerous chronic diseases, and a mounting global health problem. It is likely that the outdoor physical environment, together with social environmental factors, has a tendency to either promote or discourage physical activity, not least in cities and other urban areas. However, the evidence base on this is sparse, making it hard to identify the best policy interventions to make, at the local or city level. This study seeks to assess the impact of one such intervention, the Connswater Community Greenway CCG), in Belfast, in Northern Ireland, UK. To do that it uses innovative methodologies, ‘Walk-along’ and ‘Cycle-along’ that involve wearable sensors and video footages, to improve our understanding of the impact of the CCG on local residents. The findings suggest that four characteristics of the CCG affect people’s activity and the benefits that the CCG created. These are physical factors, social factors, policy factors and individual factors. Each of these has many elements, with different impacts on different people using the greenway.

Funder: Lundbeckfonden; doi: http://dx.doi.org/10.13039/501100003554, Funder: Villum Fonden (DK), Understanding the interplay between sequence, structure and function of proteins has been complicated in recent years by the discovery of intrinsically disordered proteins (IDPs), which perform biological functions in the absence of a well-defined three-dimensional fold. Disordered protein sequences account for roughly 30% of the human proteome and in many proteins, disordered and ordered domains coexist. However, few studies have assessed how either feature affects the properties of the other. In this study, we examine the role of a disordered tail in the overall properties of the two-domain, calcium-sensing protein neuronal calcium sensor 1 (NCS-1). We show that loss of just six of the 190 residues at the flexible C-terminus is sufficient to severely affect stability, dynamics, and folding behavior of both ordered domains. We identify specific hydrophobic contacts mediated by the disordered tail that may be responsible for stabilizing the distal N-terminal domain. Moreover, sequence analyses indicate the presence of an LSL-motif in the tail that acts as a mimic of native ligands critical to the observed order–disorder communication. Removing the disordered tail leads to a shorter life-time of the ligand-bound complex likely originating from the observed destabilization. This close relationship between order and disorder may have important implications for how investigations into mixed systems are designed and opens up a novel avenue of drug targeting exploiting this type of behavior.

The health of a cell depends on accurate translation and proper protein folding, whereas misfolding can lead to aggregation and disease. The first opportunity for a protein to fold occurs during translation, when the ribosome and surrounding environment can affect the nascent chain energy landscape. However, quantifying these environmental effects is challenging because ribosomal proteins and rRNA preclude most spectroscopic measurements of protein energetics. Here, we have applied two gel-based approaches, pulse proteolysis and force-profile analysis, to probe the folding and unfolding pathways of RNase H (RNH) nascent chains stalled on the prokaryotic ribosome in vitro. We found that ribosome-stalled RNH has an increased unfolding rate compared with free RNH. Because protein stability is related to the ratio of the unfolding and folding rates, this increase completely accounts for the observed change in protein stability and indicates that the folding rate is unchanged. Using arrest peptide–based force-profile analysis, we assayed the force generated during the folding of RNH on the ribosome. Surprisingly, we found that population of the RNH folding intermediate is required to generate sufficient force to release a stall induced by the SecM stalling sequence and that readthrough of SecM directly correlates with the stability of the RNH folding intermediate. Together, these results imply that the folding pathway of RNH is unchanged on the ribosome. Furthermore, our findings indicate that the ribosome promotes RNH unfolding while the nascent chain is proximal to the ribosome, which may limit the deleterious effects of RNH misfolding and assist in folding fidelity.

The evolution of antifreeze glycoproteins has enabled notothenioid fish to flourish in the freezing waters of the Southern Ocean. Whilst successful at the biodiversity level to life in the cold, paradoxically at the cellular level these stenothermal animals have problems producing, folding and degrading proteins at their ambient temperatures of down to −1.86°C. In this first multi-species transcriptome comparison of the amino acid composition of notothenioid proteins with temperate teleost proteins, we show that, unlike psychrophilic bacteria, Antarctic fish provide little evidence for the mass alteration of protein amino acid composition to enhance protein folding and reduce protein denaturation in the cold. The exception was the significant over-representation of positions where leucine in temperate fish proteins was replaced by methionine in the notothenioid orthologues. Although methionine may increase stability in critical proteins, we hypothesise that a more likely explanation for the extra methionines is that they have been preferentially assimilated into the genome because they act as redox sensors. This redox hypothesis is supported by the enrichment of duplicated genes within the notothenioid transcriptomes which centre around Mapk signalling, a major pathway in the cellular cascades associated with responses to environmental stress. Whilst notothenioid fish show cold-associated problems with protein homeostasis, they may have modified only a selected number of biochemical pathways to work efficiently below 0°C. Even a slight warming of the Southern Ocean might disrupt the critical functions of this handful of key pathways with considerable impacts for the functioning of this ecosystem in the future.

The BCL-2 family of proteins plays a central role in regulating cell survival and apoptosis. Disordered BH3-only proteins bind promiscuously to a number of different BCL-2 proteins, with binding affinities that vary by orders of magnitude. Here we investigate the basis for these differences in affinity. We show that eight different disordered BH3 proteins all bind to their BCL-2 partner (MCL-1) very rapidly, and that the differences in sequences result in different dissociation rates. Similarly, mutation of the binding surface of MCL-1 generally affects association kinetics in the same way for all BH3 peptides but has significantly different effects on the dissociation rates. Importantly, we infer that the evolution of homologous, competing interacting partners has resulted in complexes with significantly different lifetimes.

This book offers a wide-ranging and detailed analysis of the history of the Women's Royal Naval Service (WRNS) from its foundation in 1917 to the end of the Second World War. Adopting an inter-disc...

Fibres were electrospun from blends of an epoxidized natural rubber (ENR) with a minor amount of a crystalline grade of polylactic acid (PLA), using a graft copolymer compatibilizer (ENR-g-JM) produced by reaction processing of a mixture of PLA and monoamine terminated polypropylene glycol (Jeffamine M600). The incorporation of PLA into the elastomer spinning solution in the form of a blend was necessary to obtain the required solution properties and to establish the appropriate operational conditions for the successful electrospinning of fibres. The addition of a small quantity of compatibilizer to the ENR/PLA blend reduced the severity of surface roughness of the fibres. Moreover, the use of monoamine terminated polypropylene glycol alone, as a plasticizer, was also found to exert a control on the development of surface texture during electrospinning. The rate of solvent induced crystallization in the swollen fibres jet was identified as the factor determining the surface topography.

How do the key features of protein folding, elucidated from studies on native, isolated proteins, manifest in cotranslational folding on the ribosome? Using a well-characterized family of homologous α-helical proteins with a range of biophysical properties, we show that spectrin domains can fold vectorially on the ribosome and may do so via a pathway different from that of the isolated domain. We use cryo-EM to reveal a folded or partially folded structure, formed in the vestibule of the ribosome. Our results reveal that it is not possible to predict which domains will fold within the ribosome on the basis of the folding behavior of isolated domains; instead, we propose that a complex balance of the rate of folding, the rate of translation and the lifetime of folded or partly folded states will determine whether folding occurs cotranslationally on actively translating ribosomes.

BCL-2 proteins control the intrinsic pathway of programmed cell death. Composed of anti- and pro-apoptotic members, their network of interactions forms a molecular switch that controls mitochondrial outer-membrane permeability. Apoptotic stimulation leads to BAK/BAX oligomerization and pore formation, yet the molecular details of this pivotal step remain poorly understood, and controversy persists regarding the activation mechanism. Here we use native mass spectrometry and kinetics to show that the homo-oligomerization of BAK and BAX is spontaneous in hydrophobic environments. This process is abrogated by hetero-dimerization of both BAK and BAX with the anti-apoptotic BCL-2 protein MCL-1. Pro-apoptotic BH3-only proteins disrupt these hetero-dimers by binding competitively to MCL-1, releasing BAK/BAX for homo-oligomerization. Thus, we infer that their oligomeric states are thermodynamically favored at the membrane. Our approach provides the framework for future quantitative biophysical characterizations of the BCL-2 network, and advances our molecular understanding of apoptosis.

The BCL-2 family is a challenging set of proteins to target selectively due to sequence and structural homologies across the family. Selective ligands for the BCL-2 family regulators of apoptosis are desirable as probes to understand cell biology and apoptotic signalling pathways, and as starting points for inhibitor design. We have used phage display to isolate Affimer reagents (non-antibody binding proteins based on a conserved scaffold) to identify ligands for MCL-1, BCL-xL, BCL-2, BAK and BAX, then used multiple biophysical characterisation methods to probe the interactions. We established that purified Affimers elicit selective and potent recognition of their target BCL-2 protein. For anti-apoptotic targets, competitive inhibition of their canonical protein-protein interactions is demonstrated. Co-crystal structures reveal an unprecedented mode of molecular recognition; where a BH3 helix is normally bound, flexible loops from the Affimer dock into the BH3 binding cleft. Moreover, the Affimers induce a change in the target proteins towards a desirable drug bound like conformation. These results indicate Affimers can be used as alternative templates to inspire design of selective BCL-2 family modulators, and provide proof-of-concept for the elaboration of selective non-antibody binding reagents for use in cell-biology applications.

The endogenous inhibitor of ATP synthase in mitochondria, called IF(1), conserves cellular energy when the proton-motive force collapses by inhibiting ATP hydrolysis. Around neutrality, the 84-amino-acid bovine IF(1) is thought to self-assemble into active dimers and, under alkaline conditions, into inactive tetramers and higher oligomers. Dimerization is mediated by formation of an antiparallel α-helical coiled-coil involving residues 44–84. The inhibitory region of each monomer from residues 1–46 is largely α-helical in crystals, but disordered in solution. The formation of the inhibited enzyme complex requires the hydrolysis of two ATP molecules, and in the complex the disordered region from residues 8–13 is extended and is followed by an α-helix from residues 14–18 and a longer α-helix from residue 21, which continues unbroken into the coiled-coil region. From residues 21–46, the long α-helix binds to other α-helices in the C-terminal region of predominantly one of the β-subunits in the most closed of the three catalytic interfaces. The definition of the factors that influence the self-association of IF(1) is a key to understanding the regulation of its inhibitory properties. Therefore, we investigated the influence of pH and salt-types on the self-association of bovine IF(1) and the folding of its unfolded region. We identified the equilibrium between dimers and tetramers as a potential central factor in the in vivo modulation of the inhibitory activity and suggest that the intrinsically disordered region makes its inhibitory potency exquisitely sensitive and responsive to physiological changes that influence the capability of mitochondria to make ATP.

Marine spatial planning (MSP) has been lauded as a remedy to unsuitable marine management. There is, however, growing MSP research illustrating that it is failing to foster paradigm shifts towards sustainable governance. The gap between MSP theory and practice is due to its asocial and apolitical implementation. This narrow version of MSP has been advanced through post-political planning and uncritical rationalities. The result is a choreographed form of MSP, with clearly defined outcomes that serve the needs of elite actors rather than the public interest. This chapter argues that to recapture its democratising potential, MSP requires explicit engagement with politics and power. We highlight the use of the boundary object lens and citizen science as two potential avenues to facilitate this engagement.

In this work, time-resolved mechanical spectroscopy (TRMS) was used to accurately characterize the rheological behavior of an epoxidized natural rubber (ENR) containing 25 mol% of epoxy groups. Conventional rheological tests are not suitable to characterize with accuracy the frequency-dependent linear viscoelastic behavior of materials, such as ENR, in a transient configurational state. For this reason, TRMS was used to determine the true rheological behavior of ENR, as well as to gain some insights into the changes of its macromolecular architecture under the dynamic conditions experienced during the measurements. The constructed master curves for the moduli revealed a gradual transition of the ENR rheological state from liquid-like to solid-like through the formation of an &ldquo, elastic gel&rdquo, throughout the bulk of the polymer. Furthermore, the evolution of the stress relaxation modulus revealed a slow relaxation mechanism, resulting from thermally activated reactions in the molten state attributed to the formation of crosslinks. Finally, the crosslink density evolution was estimated from the TRMS data and compared with results derived from equilibrium solvent-swelling measurements. These demonstrated the accuracy of the TRMS data in the prediction of the structural changes that can take place in polymers during processing.

Significance Most proteins need to fold into a specific 3D structure to function. The mechanism by which isolated proteins fold has been thoroughly studied by experiment and theory. However, in the cell proteins do not fold in isolation but are synthesized as linear chains by the ribosome during translation. It is therefore natural to ask at which point during synthesis proteins fold, and whether this differs from the folding of isolated protein molecules. By studying folding of a well-characterized protein domain, titin I27, stalled at different points during translation, we show that it already folds in the mouth of the ribosome exit tunnel and that the mechanism is almost identical to that of the isolated protein., Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ribosome, affect the folding pathway of a protein? Previous studies have shown that the cotranslational folding process for many proteins, including small, single domains, is directly affected by the ribosome. Here, we investigate the cotranslational folding of an all-β Ig domain, titin I27. Using an arrest peptide-based assay and structural studies by cryo-EM, we show that I27 folds in the mouth of the ribosome exit tunnel. Simulations that use a kinetic model for the force dependence of escape from arrest accurately predict the fraction of folded protein as a function of length. We used these simulations to probe the folding pathway on and off the ribosome. Our simulations—which also reproduce experiments on mutant forms of I27—show that I27 folds, while still sequestered in the mouth of the ribosome exit tunnel, by essentially the same pathway as free I27, with only subtle shifts of critical contacts from the C to the N terminus.

The energy landscape theory and the funnel description have had remarkable success in describing protein folding mechanisms and function. However, there are experimental results that are not understood using this approach. Among the puzzling examples are the α-spectrin results, in which the R15 domain folds 3 orders of magnitude more rapidly than the homologous R16 and R17, even though they are structurally very similar to each other. Such anomalous observations are usually attributed to the influence of internal friction on protein folding rates, but this is not a satisfactory explanation. In this study, this phenomenon is addressed by focusing on non-native interactions that could account for this effect. We carried out molecular dynamics simulations with structure-based C α models, in which the folding process of α-spectrin domains was investigated. The simulations take into account the hydrophobic and electrostatic contributions separately. The folding time results have shown qualitative agreement with the experimental data. We have also investigated mutations in R16 and R17, and the simulation folding time results correlate with the observed experimental ones. We suggest that the origin of the internal friction, at least in this case, might emerge from a cooperativity effect of these non-native interactions.

Understanding and control of structures and rates involved in protein ligand binding are essential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot directly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment 25–109Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescale using simulations of an all-atom MD model, with high accuracy and precision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissociation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale., Binding and unbinding kinetics are important determinants of protein-protein or small molecule protein functional interactions that can guide drug development. Here the authors exploit the multi-ensemble Markov model framework to develop a computational approach that allows the estimation of binding kinetics reaching into the seconds timescale.

Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ribosome, affect the folding pathway of a protein? Previous studies have shown that the cotranslational folding process for many proteins, including small, single domains, is directly affected by the ribosome. Here, we investigate the cotranslational folding of an all-b immunoglobulin domain, titin I27. Using an arrest peptide-based assay and structural studies by cryo-EM, we show that I27 folds in the mouth of the ribosome exit tunnel. Simulations that use a kinetic model for the force-dependence of escape from arrest, accurately predict the fraction of folded protein as a function of length. We used these simulations to probe the folding pathway on and off the ribosome. Our simulations - which also reproduce experiments on mutant forms of I27 - show that I27 folds, while still sequestered in the mouth of the ribosome exit tunnel, by essentially the same pathway as free I27, with only subtle shifts of critical contacts from the C to the N terminus.Significance StatementMost proteins need to fold into a specific three-dimensional structure in order to function. The mechanism by which isolated proteins fold has been thoroughly studied by experiment and theory. However, in the cell proteins do not fold in isolation, but are synthesized as linear chains by the ribosome during translation. It is therefore natural to ask at which point during synthesis proteins fold, and whether this differs from the folding of isolated protein molecules. By studying folding of a well characterized protein domain, titin I27, stalled at different points during translation, we show that it already folds in the mouth of the ribosome exit tunnel, and that the mechanism is almost identical to that of the isolated protein.

Pregelled mixes of an epoxidized natural rubber, known as ENR50, containing dodecenyl succinic anhydride (DDSA) as cross-linking agent and dimethyl benzyl amine (DMBA) as catalyst, were cured isothermally at 160 °C, and the progress of the reactions was followed by both thermal analysis (differential scanning calorimetry and thermogravimetric analysis [TGA]) and infrared spectroscopy (Fourier transform near-infrared and attenuated total reflection). The curing reactions were found to be approximately first order for both heat of reaction associated with cross-linking and the disappearance of the epoxy groups, even though the reduction of epoxy group concentration was found to be substantially greater than the amount expected from reactions with the anhydride, because of the formation of large quantities of vicinal OH groups. The TGA data have indicated that the pregelled mixes undergo more extensive anaerobic degradation at higher temperatures than the un–cross-linked elastomer, which is accelerated by the presence of the DMBA catalyst.

Diagnostic testing is used by biosecurity officers for the detection and identification of plant and animal pathogens, often informing high-consequence decisions such as restricting the entry of trade goods. It is rare that such tests can be considered gold standards; however, uncertainty can be reduced by using the results of other tests, measuring performance on samples of known status and incorporating prior knowledge from expert judgement. This article presents an extension to the methods of Joseph et al. (Am J Epidemiol 141:263–272, 1995), and Dendukuri and Joseph (Biometrics 57:158–167, 2001) for Bayesian estimation in the absence of a gold standard test, which allows for the use of incomplete test data. This extension is demonstrated with a novel application: the case study of myrtle rust from Holliday et al. (Plant Dis 97:828–834, 2013), which involves samples from potential biosecurity risk material on importation pathways to Australia. The samples were tested at two laboratories, and prior estimates for pathway prevalence were obtained by expert elicitation. The Bayesian estimation was based on a model with and without covariances for the test results to assess the assumption of conditional independence. The results show that pathogen prevalence, diagnostic sensitivity and diagnostic specificity can be estimated using all available data even where some samples have been subject to only one of two available tests. The results also indicate the importance of consideration of the assumption of conditional independence. The findings enable diagnostic testing laboratories and decision makers to make use of all test results and to explicitly incorporate prior knowledge to estimate pathogen prevalence and test accuracy.

Summary The mechanisms by which intrinsically disordered proteins engage in rapid and highly selective binding is a subject of considerable interest and represents a central paradigm to nuclear pore complex (NPC) function, where nuclear transport receptors (NTRs) move through the NPC by binding disordered phenylalanine-glycine-rich nucleoporins (FG-Nups). Combining single-molecule fluorescence, molecular simulations, and nuclear magnetic resonance, we show that a rapidly fluctuating FG-Nup populates an ensemble of conformations that are prone to bind NTRs with near diffusion-limited on rates, as shown by stopped-flow kinetic measurements. This is achieved using multiple, minimalistic, low-affinity binding motifs that are in rapid exchange when engaging with the NTR, allowing the FG-Nup to maintain an unexpectedly high plasticity in its bound state. We propose that these exceptional physical characteristics enable a rapid and specific transport mechanism in the physiological context, a notion supported by single molecule in-cell assays on intact NPCs., Graphical Abstract, Highlights • Integrative structural biology reveals the basis of rapid nuclear transport • Transient binding of disordered nucleoporins leaves their plasticity unaffected • Multiple minimalistic low-affinity binding motifs create a polyvalent complex • A highly reactive and dynamic surface permits an ultrafast binding mechanism, Intrinsically disordered nucleoporins (Nups) engage rapidly with nuclear transport receptors through many minimalistic, weakly binding motifs. These Nups form polyvalent complexes while retaining conformational plasticity thus ensuring both rapid and specific transport.

Recent experimental and computational studies have shown the influence of internal friction in protein folding dynamics. However, uncertainty remains over its molecular origin. α-spectrin experimental results indicate that R15 domain folds three orders of magnitude faster than its homologous R16 and R17. Such anomalous observations are usually attributed to the influence of internal friction on protein folding rates. To study this phenomenon, we carried out molecular dynamics simulations with structure-based Cα models, in which the folding process of α-spectrin domains was investigated by adding non-native interactions. The simulations take into account the hydrophobic and the electrostatic contributions separately. The folding time results have shown a qualitative agreement with experimental data. We have also investigated mutations in R16 and R17, and the simulation folding time results correlate with the observed experimental ones. We suggest that the origin of the internal friction emerges from a cooperativity effect of these non-native interactions.

Intrinsically disordered proteins (IDPs) are characterized by a lack of defined structure. Instead, they populate ensembles of rapidly interconverting conformations with marginal structural stabilities. Changes in solution conditions such as temperature and crowding agents consequently affect IDPs more than their folded counterparts. Here we reveal that the residual structure content of IDPs is modulated both by ionic strength and by the type of ions present in solution. We show that these ion-specific structural changes result in binding affinity shifts of up to sixfold, which happen through alteration of both association and dissociation rates. These effects follow the Hofmeister series, but unlike the well-established effects on the stability of folded proteins, they already occur at low, hypotonic concentrations of salt. We attribute this sensitivity to the marginal stability of IDPs, which could have physiological implications given the role of IDPs in signaling, the asymmetric ion profiles of different cellular compartments, and the role of ions in biology.

Since the introduction of “Green Tyres” in the early 90’s, the use of silica as a reinforcing filler, along with a silane coupling agent, has spread and grown worldwide. The greatest advantage of using silica over carbon black as a reinforcing filler in a tyre tread compound is that a lower rolling resistance is achieved, while maintaining good wet traction. However, a previous study has shown that the wear resistance of a silica filled epoxidised natural rubber (ENR) compound was not as high as those of conventional Oil Extended Styrene Butadiene rubber (OESBR) and NR/BR compounds used in passenger car and truck tyre treads. In this work, with the aim of improving abrasion resistance, the effect of blending Butadiene rubber (BR) into a silica filled ENR compound was studied. Blends with 0 to 30 phr BR were prepared in a Polylab Haake internal mixer. The rheological properties of the compounds were measured using a Mooney viscometer and Oscilating Disc Rheometer. The hardness, tensile strength and DIN abrasion resistance were also measured. The results showed that the ENR/silica compound properties such as tensile strength and hardness were as good as those of the conventional compounds. However, the most important finding was that abrasion resistance increased significantly with BR content, exceeding that of the conventional compound at BR:ENR ratios of greater than 20:80.

Understanding and control of structures and rates involved in protein ligand binding are essential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot directly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment 25–109Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescale using simulations of an all-atom MD model, with high accuracy and precision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissociation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale.

Three homologous spectrin domains have remarkably different folding characteristics. We have previously shown that the slow-folding R16 and R17 spectrin domains can be altered to resemble the fast folding R15, in terms of speed of folding (and unfolding), landscape roughness and folding mechanism, simply by substituting five residues in the core. Here we show that, by contrast, R15 cannot be engineered to resemble R16 and R17. It is possible to engineer a slow-folding version of R15, but our analysis shows that this protein neither has a rougher energy landscape nor does change its folding mechanism. Quite remarkably, R15 appears to be a rare example of a protein with a folding nucleus that does not change in position or in size when its folding nucleus is disrupted. Thus, while two members of this protein family are remarkably plastic, the third has apparently a restricted folding landscape., Graphical Abstract, Highlights • Homologous spectrin domains have very different folding kinetics and mechanisms. • R15 has been engineered to fold and unfold slowly similar to R16 and R17. • The folding pathway is entirely unchanged. • R15 is a rare example of a protein with an inflexible transition state.

Association rates for interactions between folded proteins have been investigated extensively, allowing the development of computational and theoretical prediction methods. Less is known about association rates for complexes where one or more partner is initially disordered, despite much speculation about how they may compare to those for folded proteins. We have attached a fluorophore to the N-terminus of the 25 amino acid cMyb peptide used previously in NMR and equilibrium studies (termed FITC-cMyb), and used this to monitor the kinetics of its interaction with the KIX protein. We have investigated the ionic strength and temperature dependence of the kinetics, and conclude that the association process is extremely fast, apparently exceeding the rates predicted by formulations applicable to interactions between pairs of folded proteins. This is despite the fact that not all collisions result in complex formation (there is an observable activation energy for the association process). We propose that this is partially a result of the disordered nature of the FITC-cMyb peptide itself.