Effects of molecular crowding and confinement on the spatial organization of a biopolymer

A chain molecule can be entropically collapsed in a crowded medium in a free or confined space. Here, we present a unified view of how molecular crowding collapses a flexible polymer in three distinct spaces: free, cylindrical, and (two-dimensional) slit-like. Despite their seeming disparities, a few general features characterize all these cases, even though the phi(c)-dependence of chain compaction differs between the two cases: a > a(c) and a a(c) (applicable to a coarse-grained model of bacterial chromosomes), chain size depends on the ratio a phi(c)/a(c), and "full'' compaction occurs universally at a phi(c)/a(c) approximate to 1; for a(c) > a (relevant for protein folding), it is controlled by phi(c) alone and crowding has a modest effect on chain size in a cellular environment (phi(c) approximate to 0.3). Also for a typical parameter range of biological relevance, molecular crowding can be viewed as effectively reducing the solvent quality, independent of confinement.NSERC (Canada)Korea Institute of Science and Technology Information (KISTI)Basic Science Research Program [2015R1D1A1A09057469]KIAS (Korea Institute for Advanced Study

How are molecular crowding and the spatial organization of a biopolymer interrelated

In a crowded cellular interior, dissolved biomolecules or crowders exert excluded volume effects on other biomolecules, which in turn control various processes including protein aggregation and chromosome organization. As a result of these effects, a long chain molecule can be phase-separated into a condensed state, redistributing the surrounding crowders. Using computer simulations and a theoretical approach, we study the interrelationship between molecular crowding and chain organization. In a parameter space of biological relevance, the distributions of monomers and crowders follow a simple relationship: the sum of their volume fractions rescaled by their size remains constant. Beyond a physical picture of molecular crowding it offers, this finding explains a few key features of what has been known about chromosome organization in an E. coli cell.NSERC (Canada)Korea Institute of Science and Technology Information (KISTI)Basic Science Research Program [2015R1D1A1A09057469]KIAS (Korea Institute for Advanced Study

Effect of Long-Range Interactions in the Conserved Kardar-Parisi-Zhang Equation

The conserved Kardar-Parisi-Zhang equation in the presence of long-range nonlinear interactions is studied by the dynamic renormalization group method. The long-range effect produces new fixed points with continuously varying exponents and gives distinct phase transitions, depending on both the long-range interaction strength and the substrate dimension $d$. The long-range interaction makes the surface width less rough than that of the short-range interaction. In particular, the surface becomes a smooth one with a negative roughness exponent at the physical dimension d=2.Comment: 4 pages(LaTex), 1 figure(Postscript

The ubiquitin-mediated degradation of Jak1 modulates osteoclastogenesis by limiting interferon-beta-induced inhibitory signaling.

Interferons (IFNs) have been shown to negatively regulate osteoclastogenesis. In a proteomic study to assess protein expression during osteoclastogenesis, we discovered that the expression level of Jak1 was significantly decreased during the early stage of osteoclast differentiation from mouse bone marrow macrophages (BMMs) upon stimulation with receptor activator of nuclear factor kappaB ligand (RANKL). RANKL induced Jak1 ubiquitination, and a proteasome inhibitor MG132 efficiently blocked the RANKL-induced degradation of Jak1. The expression level of Jak1 correlated with the susceptibility of osteoclast precursors to the negative regulatory effects of IFN-beta on osteoclastogenesis, since preosteoclasts (pOCs) in which Jak1 expression is significantly reduced could proceed with osteoclastogenesis in the presence of IFN-beta. Forced down-regulation of Jak1 by small interfering RNA (siRNA) resulted in the efficient osteoclast differentiation of BMMs in the presence of inhibitory IFN-beta, while overexpression of Jak1 in pOCs elicited IFN-beta-dependent inhibition of osteoclastogenesis. Furthermore, we found that the IFN-beta-induced inhibition of osteoclastogenesis required STAT3 downstream of Jak1. These data suggest that the regulation of Jak1 expression during osteoclast differentiation might serve as an intrinsic mechanism that determines osteoclast lineage commitment by modulating the negative regulation by IFN-beta

Prohibitin modulates periodontium differentiation in mice development

Introduction: Prohibitin (PHB) is an essential scaffold protein that modulates signaling pathways controlling cell survival, metabolism, inflammation, and bone formation. However, its specific role in periodontium development remains less understood. This study aims to elucidate the expression pattern and function of PHB in periodontium development and its involvement in alveolar bone formation.Methods: Immunolocalization of PHB in the periodontium of postnatal (PN) mice were examined. Phb morpholino was micro-injected into the right-side mandible at PN5, corresponding to the position where the alveolar bone process forms in relation to the lower first molar. The micro-injection with a scramble control (PF-127) and the left-side mandibles were used as control groups. Five days post-micro-injection, immunohistochemical analysis and micro-CT evaluation were conducted to assess bone mass and morphological changes. Additionally, expression patterns of signaling molecules were examined following Phb downregulation using 24-h in vitro cultivation of developing dental mesenchyme at E14.5.Results: The immunostaining of PHB showed its localization in the periodontium at PN5, PN8, and PN10. The in vitro cultivation of dental mesenchyme resulted in alterations in Bmps, Runx2, and Wnt signalings after Phb knock-down. At 5 days post-micro-injection, Phb knocking down showed weak immunolocalizations of runt-related transcription factor (RUNX2) and osteocalcin (OCN). However, knocking down Phb led to histological alterations characterized by decreased bone mass and stronger localizations of Ki67 and PERIOSTIN in the periodontium compared 1 to control groups. The micro-CT evaluation showed decreased bone volume and increased PDL space in the Phb knock-down specimens, suggesting its regulatory role in bone formation.Discussion: The region-specific localization of PHB in the margin where alveolar bone forms suggests its involvement in alveolar bone formation and the differentiation of the periodontal ligament. Overall, our findings suggest that Phb plays a modulatory role in alveolar bone formation by harmoniously regulating bone-forming-related signaling molecules during periodontium development

Human Cytomegalovirus UL18 Utilizes US6 for Evading the NK and T-Cell Responses

Human cytomegalovirus (HCMV) US6 glycoprotein inhibits TAP function, resulting in down-regulation of MHC class I molecules at the cell surface. Cells lacking MHC class I molecules are susceptible to NK cell lysis. HCMV expresses UL18, a MHC class I homolog that functions as a surrogate to prevent host cell lysis. Despite a high level of sequence and structural homology between UL18 and MHC class I molecules, surface expression of MHC class I, but not UL18, is down regulated by US6. Here, we describe a mechanism of action by which HCMV UL18 avoids attack by the self-derived TAP inhibitor US6. UL18 abrogates US6 inhibition of ATP binding by TAP and, thereby, restores TAP-mediated peptide translocation. In addition, UL18 together with US6 interferes with the physical association between MHC class I molecules and TAP that is required for optimal peptide loading. Thus, regardless of the recovery of TAP function, surface expression of MHC class I molecules remains decreased. UL18 represents a unique immune evasion protein that has evolved to evade both the NK and the T cell immune responses