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Many proteins lack stable 3D structures. These intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains with intrinsically disordered protein regions (IDPRs) often carry out regulatory functions related to molecular recognition and signal transduction. IDPs/IDPRs constitute a substantial portion of the human proteome and are termed "the unfoldome". Herein, we probe the human breast cancer unfoldome and investigate relations between IDPs and key disease genes and pathways. We utilized bottom-up proteomics, MudPIT (Multidimensional Protein Identification Technology), to profile differentially expressed IDPs in human normal (MCF-10A) and breast cancer (BT-549) cell lines. Overall, we identified 2271 protein groups in the unfoldome of normal and cancer proteomes, with 148 IDPs found to be significantly differentially expressed in cancer cells. Further analysis produced annotations of 140 IDPs, which were then classified to GO (Gene Ontology) categories and pathways. In total, 65% (91 of 140) IDPs were related to various diseases, and 20% (28 of 140) mapped to cancer terms. A substantial portion of the differentially expressed IDPs contained disordered regions, confirmed by in silico characterization. Overall, our analyses suggest high levels of interactivity in the human cancer unfoldome and a prevalence of moderately and highly disordered proteins in the network. [ABSTRACT FROM AUTHOR]

Mapping volcanic flow deposits can be achieved by considering backscattering characteristics as a metric of surface roughness. In this study, we developed an approach to extract a measure of surface roughness from dual-band airborne Synthetic Aperture Radar (ASAR) backscattering data to characterize and map various volcanic flow deposits—namely, debris avalanches, lahars, lava flows, and pyroclastic density currents. We employed ASAR and Indian Space Research Organization (ISRO) airborne SAR datasets, from a joint project (ASAR-ISRO), acquired in December 2019 at 2 m spatial resolution, to assess the role and importance of incorporating dual-band data, i.e., L-band and S-band, into surface roughness models. Additionally, we derived and analyzed surface roughness from a digital surface model (DSM) generated from unoccupied aircraft systems (UAS) acquisitions using Structure from Motion (SfM) photogrammetry techniques. These UAS-derived surface roughness outputs served as meter-scale calibration products to validate the radar roughness data over targeted areas. Herein, we applied our method to a region in the United States over the Mount St. Helens volcano in the Cascade Range of Washington state. Our results showed that dual-band systems can be utilized to characterize different types of volcanic deposits and range of terrain roughness. Importantly, we found that a combination of radar wavelengths (i.e., 9 and 24 cm), in tandem with high-spatial-resolution backscatter measurements, yields improved surface roughness maps, compared to single-band, satellite-based approaches at coarser resolution. The L-band (24 cm) can effectively differentiate small, medium, and large-scale structures, namely, blocks/boulders from fine-grained lahar deposits and hummocks from debris avalanche deposits. Additionally, variation in the roughness estimates of lahar and debris avalanche deposits can be identified and quantified individually. In contrast, the S-band (9 cm) can distinguish different soil moisture conditions across variable terrain; for example, identify wet active channels. In principle, this dual-band approach can also be employed with time series of various other SAR data of higher coherence (such as satellite SAR), using different wavelengths and polarizations, encompassing a wider range of surface roughness, and ultimately enabling additional applications at other volcanoes worldwide and even beyond volcanology. [ABSTRACT FROM AUTHOR]

[Display omitted] • Evaluated the secondary p53 binding site of MDM2/X with heat capacity measurements. • Estimated conformational entropy changes with ITC. • Estimated conformational entropy changes with NMR relaxation. • NMR titration experiments used for chemical shift mapping. • Molecular dynamics simulations used to determine structure. The thermodynamics of secondary p53 binding sites on MDM2 and MDMX were evaluated using p53 peptides containing residues 16–29, 17–35, and 1–73. All the peptides had large, negative heat capacity (Δ C p), consistent with the burial of p53 residues F19, W23, and L26 in the primary binding sites of MDM2 and MDMX. MDMX has a higher affinity and more negative Δ C p than MDM2 for p53 17-35 , which is due to MDMX stabilization and not additional interactions with the secondary binding site. Δ C p measurements show binding to the secondary site is inhibited by the disordered tails of MDM2 for WT p53 but not a more helical mutant where proline 27 is changed to alanine. This result is supported by all-atom molecular dynamics simulations showing that p53 residues 30–35 turn away from the disordered tails of MDM2 in P27A 17-35 and make direct contact with this region in p53 17-35. Molecular dynamics simulations also suggest that an intramolecular methionine-aromatic motif found in both MDM2 and MDMX structurally adapts to support multiple p53 binding modes with the secondary site. Δ C p measurements also show that tighter binding of the P27A mutant to MDM2 and MDMX is due to increased helicity, which reduces the energetic penalty associated with coupled folding and binding. Our results will facilitate the design of selective p53 inhibitors for MDM2 and MDMX. [ABSTRACT FROM AUTHOR]

Simulations of porous gaseous flows are routinely used to investigate membrane permeation in catalytic adsorption and separation problems. Although basic continuum equations are supposed to breakdown in these nanoscale pores, many studies of force/flow relations assume flow to be linear in chemical potential or pressure differences. This work tests common assumptions using simulations of an atomistic, Lennard-Jones pore flow with distant, Langevin forcing at densities stretching through the transition and free flow regimes. Using NVE dynamics in very large boundary reservoirs, we find local equilibrium is established in the steady-state, but also identify two new finite-size effects. First, there is a steady flow of heat from the high-pressure reservoir backward to the thermostat region, and second, a significant proportion of the channel flow originates from the monolayer adsorbed to the flat outer wall. All walls are shown to obey a simple Langmuir adsorption isotherm at these low (< 400 kPa) pressures, even in the presence of flow. Despite multi-layer formation on the inner pore walls as density increases, the current carried by atoms at the wall has the same proportion to current carried through the channel center under nearly all conditions tested (with constant pore diameter). Comparing our flow rates to Fickian and Knudsen linear relations shows that the difference in reservoir pressure is significantly more predictive than the difference in chemical potential for this size regime. [ABSTRACT FROM AUTHOR]

Background: Cancer stem cells' (CSCs) self-maintenance is regulated via the pluripotency pathways promoting the most aggressive tumor phenotype. This study aimed to use the activity of these pathways for the CSCs' subpopulation enrichment and separating cells characterized by the OCT4 and SOX2 expression. Methods: To select and analyze CSCs, we used the SORE6x lentiviral reporter plasmid for viral transduction of colon adenocarcinoma cells. Additionally, we assessed cell chemoresistance, clonogenic, invasive and migratory activity and the data of mRNA-seq and intrinsic disorder predisposition protein analysis (IDPPA). Results: We obtained the line of CSC-like cells selected on the basis of the expression of the OCT4 and SOX2 stem cell factors. The enriched CSC-like subpopulation had increased chemoresistance as well as clonogenic and migration activities. The bioinformatic analysis of mRNA seq data identified the up-regulation of pluripotency, development, drug resistance and phototransduction pathways, and the downregulation of pathways related to proliferation, cell cycle, aging, and differentiation. IDPPA indicated that CSC-like cells are predisposed to increased intrinsic protein disorder. Conclusion: The use of the SORE6x reporter construct for CSCs enrichment allows us to obtain CSC-like population that can be used as a model to search for the new prognostic factors and potential therapeutic targets for colon cancer treatment. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS- CoV-2) with an estimated fatality rate of less than 1%. The SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 possess putative functions to manipulate host immune mechanisms. These involve interferons, which appear as a consensus function, immune signaling receptor NLRP3 (NLR family pyrin domain-containing 3) inflammasome, and inflammatory cytokines such as interleukin 1 β (IL-1 β) and are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins were observed across six continents of all complete SARS-CoV-2 proteomes based on the data reported before November 2020. A decreasing order of percentage of unique variations in the accessory proteins was determined as ORF3a > ORF8 > ORF7a > ORF6 > ORF10 > ORF7b across all continents. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. These findings suggest that the wide variations in accessory proteins seem to affect the pathogenicity of SARS-CoV-2. [ABSTRACT FROM AUTHOR]

Moonlighting proteins, known for their ability to perform multiple, often unrelated functions within a single polypeptide chain, challenge the traditional "one gene, one protein, one function" paradigm. As organisms evolved, their genomes remained relatively stable in size, but the introduction of post-translational modifications and sub-strategies like protein promiscuity and intrinsic disorder enabled multifunctionality. Enzymes, in particular, exemplify this phenomenon, engaging in unrelated processes alongside their primary catalytic roles. This study employs a systematic, quantitative informatics approach to shed light on human moonlighting protein sequences. Phylogenetic analyses of human moonlighting proteins are presented, elucidating the distal-proximal relationships among these proteins based on sequence-derived quantitative features. The findings unveil the captivating world of human moonlighting proteins, urging further investigations in the emerging field of moonlighting proteomics, with the potential for significant contributions to our understanding of multifunctional proteins and their roles in diverse cellular processes and diseases. [ABSTRACT FROM AUTHOR]