Modulation of Global Low-Frequency Motions Underlies Allosteric Regulation: Demonstration in CRP/FNR Family Transcription Factors

Allostery is a fundamental process by which ligand binding to a protein alters its activity at a distinct site. There is growing evidence that allosteric cooperativity can be communicated by modulation of protein dynamics without conformational change. The mechanisms, however, for communicating dynamic fluctuations between sites are debated. We provide a foundational theory for how allostery can occur as a function of low-frequency dynamics without a change in structure. We have generated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcription factors, CAP of Escherichia coli and GlxR of Corynebacterium glutamicum. The latter we demonstrate as a new exemplar for allostery without conformation change. We observe that binding the first molecule of cAMP ligand is correlated with modulation of the global normal modes and negative cooperativity for binding the second cAMP ligand without a change in mean structure. The theory makes key experimental predictions that are tested through an analysis of variant proteins by structural biology and isothermal calorimetry. Quantifying allostery as a free energy landscape revealed a protein ‘‘design space’’ that identified the inter- and intramolecular regulatory parameters that frame CRP/FNR family allostery. Furthermore, through analyzing CAP variants from diverse species, we demonstrate an evolutionary selection pressure to conserve residues crucial for allosteric control. This finding provides a link between the position of CRP/FNR transcription factors within the allosteric free energy landscapes and evolutionary selection pressures. Our study therefore reveals significant features of the mechanistic basis for allostery. Changes in low-frequency dynamics correlate with allosteric effects on ligand binding without the requirement for a defined spatial pathway. In addition to evolving suitable three-dimensional structures, CRP/FNR family transcription factors have been selected to occupy a dynamic space that fine-tunes biological activity and thus establishes the means to engineer allosteric mechanisms driven by low-frequency dynamics

Reemergence of anthropogenic carbon into the ocean's mixed layer strongly amplifies transient climate sensitivity

A positive marine chemistry‐climate feedback was originally proposed by Revelle and Suess (1957, https://doi.org/10.3402/tellusa.v9i1.9075), whereby the invasion flux of anthropogenic carbon into the ocean serves to inhibit future marine CO2 uptake through reductions to the buffering capacity of surface seawater. Here we use an ocean circulation‐carbon cycle model to identify an upper limit on the impact of reemergence of anthropogenic carbon into the ocean's mixed layer on the cumulative airborne fraction of CO2 in the atmosphere. We find under an RCP8.5 emissions pathway (with steady circulation) that the cumulative airborne fraction of CO2 has a sevenfold reduction by 2100 when the CO2 buffering capacity of surface seawater is maintained at preindustrial levels. Our results indicate that the effect of reemergence of anthropogenic carbon into the mixed layer on the buffering capacity of CO2 amplifies the transient climate sensitivity of the Earth system

Building an immune-mediated coagulopathy consensus: early recognition and evaluation to enhance post-surgical patient safety

Topical hemostats, fibrin sealants, and surgical adhesives are regularly used in a variety of surgical procedures involving multiple disciplines. Generally, these adjuncts to surgical hemostasis are valuable means for improving wound visualization, reducing blood loss or adding tissue adherence; however, some of these agents are responsible for under-recognized adverse reactions and outcomes. Bovine thrombin, for example, is a topical hemostat with a long history of clinical application that is widely used alone or in combination with other hemostatic agents. Hematologists and coagulation experts are aware that these agents can lead to development of an immune-mediated coagulopathy (IMC). A paucity of data on the incidence of IMC contributes to under-recognition and leaves many surgeons unaware that this clinical entity, originating from normal immune responses to foreign antigen exposure, requires enhanced post-operative vigilance and judicious clinical judgment to achieve best outcomes

Sialidases Affect the Host Cell Adherence and Epsilon Toxin-Induced Cytotoxicity of Clostridium perfringens Type D Strain CN3718

Clostridium perfringens type B or D isolates, which cause enterotoxemias or enteritis in livestock, produce epsilon toxin (ETX). ETX is exceptionally potent, earning it a listing as a CDC class B select toxin. Most C. perfringens strains also express up to three different sialidases, although the possible contributions of those enzymes to type B or D pathogenesis remain unclear. Type D isolate CN3718 was found to carry two genes (nanI and nanJ) encoding secreted sialidases and one gene (nanH) encoding a cytoplasmic sialidase. Construction in CN3718 of single nanI, nanJ and nanH null mutants, as well as a nanI/nanJ double null mutant and a triple sialidase null mutant, identified NanI as the major secreted sialidase of this strain. Pretreating MDCK cells with NanI sialidase, or with culture supernatants of BMC206 (an isogenic CN3718 etx null mutant that still produces sialidases) enhanced the subsequent binding and cytotoxic effects of purified ETX. Complementation of BMC207 (an etx/nanH/nanI/nanJ null mutant) showed this effect is mainly attributable to NanI production. Contact between BMC206 and certain mammalian cells (e.g., enterocyte-like Caco-2 cells) resulted in more rapid sialidase production and this effect involved increased transcription of BMC206 nanI gene. BMC206 was shown to adhere to some (e.g. Caco-2 cells), but not all mammalian cells, and this effect was dependent upon sialidase, particularly NanI, expression. Finally, the sialidase activity of NanI (but not NanJ or NanH) could be enhanced by trypsin. Collectively these in vitro findings suggest that, during type D disease originating in the intestines, trypsin may activate NanI, which (in turn) could contribute to intestinal colonization by C. perfringens type D isolates and also increase ETX action

Buses, cars, bicycles and walkers the influence of the type of human transport on the flight responses of waterbirds

One way to manage disturbance to waterbirds in natural areas where humans require access is to promote the occurrence of stimuli for which birds tolerate closer approaches, and so cause fewer responses. We conducted 730 experimental approaches to 39 species of waterbird, using five stimulus types (single walker, three walkers, bicycle, car and bus) selected to mimic different human management options available for a controlled access, Ramsar-listed wetland. Across species, where differences existed (56% of 25 cases), motor vehicles always evoked shorter flight-initiation distances (FID) than humans on foot. The influence of stimulus type on FID varied across four species for which enough data were available for complete cross-stimulus analysis. All four varied FID in relation to stimuli, differing in 4 to 7 of 10 possible comparisons. Where differences occurred, the effect size was generally modest, suggesting that managing stimulus type (e.g. by requiring people to use vehicles) may have species-specific, modest benefits, at least for the waterbirds we studied. However, different stimulus types have different capacities to reduce the frequency of disturbance (i.e. by carrying more people) and vary in their capacity to travel around important habita

A structured review of reasons for ecstasy use and related behaviours: pointers for future research

Abstract Background While the health risks of using ecstasy warrant intervention development, a recent meta-analysis of determinants of ecstasy use identified a number of lacunae in the literature. Specifically, no studies were included that address behaviours other than 'using ecstasy' (e.g. 'trying out ecstasy' or 'ceasing ecstasy use'). However, because meta-analyses aim to integrate study results quantitatively, the resulting rigid exclusion criteria cause many studies to be discarded on the basis of their qualitative methodology. Such qualitative studies may nonetheless provide valuable insights to guide future research. To provide an overview of these insights regarding ecstasy use, the current study summarizes and combines what is known from qualitative and exploratory quantitative literature on ecstasy use. Methods The databases PsycINFO and MedLine were searched for publications reporting reasons for ecstasy use and related behaviour, and the results were structured and discussed per behaviour and compared over behaviours. Results Two main categories of reasons were found. The first category comprised reasons to start using ecstasy, use ecstasy, use ecstasy more often, and refrain from ceasing ecstasy use. The second category comprised reasons to refrain from starting to use ecstasy, use less ecstasy, and cease using ecstasy. Reasons for related behaviours within each of these two categories appear to differ, but not as substantially as between the two categories. A large number of reasons that were not yet explored in quantitative research emerged. Conclusion The current summary and combination of exploratory studies yields useful lists of reasons for each behaviour. Before these lists can inform interventions, however, they beg quantitative verification. Also, similarity of determinant configurations of different behaviours can be assessed by addressing determinants of several behaviours in one study. Another important finding is that meta-analytical integration of the literature may overlook important findings and implications. Thus, qualitative reviews remain useful instruments in setting the research agenda.</p