Using explicit solvent molecular dynamics simulations, we were able to obtain direct observations of shifts in the hydrogen-bonding register of an intermolecular β-sheet protein-peptide complex. The β-sheet is formed between the FHA domain of cancer marker protein Ki67 (Ki67FHA) and a peptide fragment of the hNIFK signaling protein. Potential encounter complexes of the Ki67FHA receptor and hNIFK peptide are misregistered states of the β-sheet. Rearrangements of one of these misregistered states to the native state were captured in three independent simulations. All three rearrangements occurred by a common mechanism: an aromatic residue of the peptide (F263) anchors into a transient hydrophobic pocket of the receptor to facilitate the formation of native hydrogen bonds. To our knowledge, these simulations provide the first atomically detailed visualizations of a mechanism by which nature might correct for errors in the alignment of intermolecular β-sheets.
This paper curates four experiential narratives and poetry by the five co-authors that illustrate epistemic and ontic shift from the Modern Western (ModWest) mindset to a holistic, embodied and animistic mindset. Coming from different cultural backgrounds, yet having been systemically influenced by the dominant ModWest views and values, each author has initiated an ongoing shift in consciousness, demonstrating how such transformations are possible. Affirming that a shift in consciousness is not simply a matter of cognitive change but is a thoroughly holistic process, the authors write in autobiographical narratives and poetry to capture and convey embodied and emplaced, experiential understanding and feelings, or ‘felt sense.’ Deep changes in the consciousness, such as these epistemic shifts, take the whole ensemble of “body + mind + heart + soul + spirit + the world” as the unit of change for learning. Through these writings, they sensuously and feelingly, existentially-and-spiritually and discursively explore possibilities of becoming one-bodied with the animate Earth. They call this the re-bonding project through which they address humanity’s first-order bonding rupture between Humans and the Earth community.
This article addresses the significance of paradox as a steady presence in our lives. Contradictions and ambiguities often lead to aversive states of anxious uncertainty where straightforward answers are often unavailable yet sought after to alleviate existential insecurities. In conditions where narratives of ambivalence intensify, such as during the worldwide COVID-19 crises, our traditional socio-evolutionary inclinations to avoid them either through denial or active resistance become more noticeable. It also leads to distress in intersubjective spaces especially when uncertainty and perceptions of threat stand as correlates, and we start to fear what we do not understand. In this paper, I consider wisdom responses from a Buddhist perspective to help us acknowledge the value of paradox, highlighting how changes in the formulation of our self-concept can help with that. I draw upon select principles and insights from the Diamond Sutra and the Heart Sutra, two texts within the Mahaprajnaparamita sutras of Mahayana Buddhism. Through these, I examine some inherent paradoxes as vital components of a larger ontological unity, the recognition of which can act as an enabler to the Bodhisattva path. This path is worthy of exploration, allowing us to move past the need for closure and instead focus on reconciliation, disclosure, and epistemic humility.
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