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Numerous enveloped viruses, such as coronaviruses, influenza, and respiratory syncytial virus (RSV), utilize class I fusion proteins for cell entry. During this process, the proteins transition from a prefusion to a postfusion state, undergoing substantial and irreversible conformational changes. The prefusion conformation has repeatedly shown significant potential in vaccine development. However, the instability of this state poses challenges for its practical application in vaccines. While non-native disulfides have been effective in maintaining the prefusion structure, identifying stabilizing disulfide bonds remains an intricate task. Here, we present a general computational approach to systematically identify prefusion-stabilizing disulfides. Our method assesses the geometric constraints of disulfide bonds and introduces a ranking system to estimate their potential in stabilizing the prefusion conformation. We hypothesized that disulfides restricting the initial stages of the conformational switch could offer higher stability to the prefusion state than those preventing unfolding at a later stage. The implementation of our algorithm on the RSV F protein led to the discovery of prefusion-stabilizing disulfides that supported our hypothesis. Furthermore, the evaluation of our top design as a vaccine candidate in a cotton rat model demonstrated robust protection against RSV infection, highlighting the potential of our approach for vaccine development. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) and multiple sclerosis (MS) are two CNS disorders affecting millions of people, for which no cure is available. AD is usually diagnosed in individuals age 65 and older and manifests with accumulation of beta amyloid in the brain. MS, a demyelinating disorder, is most commonly diagnosed in its relapsing-remitting (RRMS) form in young adults (age 20--40). The lack of success in a number of recent clinical trials of immune- or amyloid-targeting therapeutics emphasizes our incomplete understanding of their etiology and pathogenesis. Evidence is accumulating that infectious agents such as viruses may contribute either directly or indirectly. With the emerging recognition that demyelination plays a role in risk and progression of AD, we propose that MS and AD are connected by sharing a common environmental factor (a viral infection such as HSV-1) and pathology (demyelination). In the viral DEmyelinating Neurodegenerative Trigger (vDENT) model of AD and MS, the initial demyelinating viral (e.g., HSV-1) infection provokes the first episode of demyelination that occurs early in life, with subsequent virus reactivations/demyelination and associated immune/inflammatory attacks resulting in RRMS. The accumulating damage and/or virus progression deeper into CNS leads to amyloid dysfunction, which, combined with the inherent age-related defects in remyelination, propensity for autoimmunity, and increased blood-brain barrier permeability, leads to the development of AD dementia later in life. Preventing or diminishing vDENT event(s) early in life, thus, may have a dual benefit of slowing down the progression of MS and reducing incidence of AD at an older age. [ABSTRACT FROM AUTHOR]

Many respiratory viruses cause lung damage that may evolve into acute lung injury (ALI), a cytokine storm, acute respiratory distress syndrome, and ultimately, death. Peroxisome proliferator activated receptor gamma (PPARg), a member of the nuclear hormone receptor (NHR) family of transcription factors, regulates transcription by forming heterodimers with another NHR family member, Retinoid X Receptor (RXR). Each component of the heterodimer binds specific ligands that modify transcriptional capacity of the entire heterodimer by recruiting different co-activators/co-repressors. However, the role of PPARg/RXR ligands in the context of influenza infection is not well understood. PPARg is associated with macrophage differentiation to an anti-inflammatory M2 state. We show that mice lacking the IL-4Ra receptor, required for M2a macrophage differentiation, are more susceptible to mouseadapted influenza (A/PR/8/34; "PR8")-induced lethality. Mice lacking Ptgs2, that encodes COX-2, a key proinflammatory M1 macrophage mediator, are more resistant. Blocking the receptor for COX-2-induced Prostaglandin E2 (PGE2) was also protective. Treatment with pioglitazone (PGZ), a PPARg ligand, increased survival from PR8 infection, decreased M1 macrophage gene expression, and increased PPARg mRNA in lungs. Conversely, conditional knockout mice expressing PPARg-deficient macrophages were significantly more sensitive to PR8-induced lethality. These findings were extended in cotton rats: PGZ blunted lung inflammation and M1 cytokine gene expression after challenge with non-adapted human influenza. To study mechanisms by which PPARg/RXR transcription factors induce canonical M2a genes, WT mouse macrophages were treated with IL-4 in the absence or presence of rosiglitazone (RGZ; PPARg ligand), LG100754 (LG; RXR ligand), or both. IL-4 dose-dependently induced M2a genes Arg1, Mrc1, Chil3, and Retnla. Treatment of macrophages with IL-4 and RGZ and/or LG differentially affected induction of Arg1 and Mrc1 vs. Chil3 and Retnla gene expression. In PPARgdeficient macrophages, IL-4 alone failed to induce Arg1 and Mrc1 gene expression; however, concurrent treatment with LG or RGZ + LG enhanced IL-4-induced Arg1 and Mrc1 expression, but to a lower level than in WT macrophages, findings confirmed in the murine alveolar macrophage cell line, MH-S. These findings support a model in which PPARg/RXR heterodimers control IL-4-induced M2a differentiation, and suggest that PPARg/RXR agonists should be considered as important tools for clinical intervention against influenza-induced ALI. [ABSTRACT FROM AUTHOR]

The histone acetylase PCAF plays a bigger role in nuclear receptor function that it has been thought. Retinoid acid receptor and retinoid X receptor enlist the help of PCAF from mammalian cell extracts in a ligand-dependent manner. There is increased retinoid-responsive transcription when there is additional PCAF. The in vitro demonstration with PCAF also defines anew model of DNA binding.