The effects of asymmetry in active noises on the efficiency of single colloidal Stirling engines with active noises.

Molecular machines, which operate in highly fluctuating environments far from equilibrium, may benefit from their non-equilibrium environments. It is, however, a topic of controversy how the efficiency of the microscopic engines can be enhanced. Recent experiments showed that microscopic Stirling engines in bacterial reservoirs could show high performance beyond the equilibrium thermodynamics. In this work, we perform overdamped Langevin dynamics simulations for microscopic Stirling heat engines in bacterial reservoirs and show that the temperature dependence of the magnitude of active noises should be responsible for such high efficiency. Only when we introduce temperature-dependent active noises, the efficiency of the microscopic Stirling engines is enhanced significantly as in experiments.

Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures.

Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics technologies have enabled the detection and generation of variants at an unprecedented scale. However, efficient tools and resources are needed to link these two disparate data types - to "map" variants onto protein structures, to better understand how the variation causes disease and thereby design therapeutics. Here we present the Genomics 2 Proteins Portal (G2P; g2p.broadinstitute.org/): a human proteome-wide resource that maps 19,996,443 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the G2P portal generalizes the capability of linking genomics to proteins beyond databases by allowing users to interactively upload protein residue-wise annotations (variants, scores, etc.) as well as the protein structure to establish the connection. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotype.

Characterizing proteomic and transcriptomic features of missense variants in amyotrophic lateral sclerosis genes.

Within recent years, there has been a growing number of genes associated with amyotrophic lateral sclerosis (ALS), resulting in an increasing number of novel variants, particularly missense variants, many of which are of unknown clinical significance. Here, we leverage the sequencing efforts of the ALS Knowledge Portal (3864 individuals with ALS and 7839 controls) and Project MinE ALS Sequencing Consortium (4366 individuals with ALS and 1832 controls) to perform proteomic and transcriptomic characterization of missense variants in 24 ALS-associated genes. The two sequencing datasets were interrogated for missense variants in the 24 genes, and variants were annotated with gnomAD minor allele frequencies, ClinVar pathogenicity classifications, protein sequence features including Uniprot functional site annotations, and PhosphoSitePlus post-translational modification site annotations, structural features from AlphaFold predicted monomeric 3D structures, and transcriptomic expression levels from Genotype-Tissue Expression. We then applied missense variant enrichment and gene-burden testing following binning of variation based on the selected proteomic and transcriptomic features to identify those most relevant to pathogenicity in ALS-associated genes. Using predicted human protein structures from AlphaFold, we determined that missense variants carried by individuals with ALS were significantly enriched in ß-sheets and α-helices, as well as in core, buried or moderately buried regions. At the same time, we identified that hydrophobic amino acid residues, compositionally biased protein regions and regions of interest are predominantly enriched in missense variants carried by individuals with ALS. Assessment of expression level based on transcriptomics also revealed enrichment of variants of high and medium expression across all tissues and within the brain. We further explored enriched features of interest using burden analyses and identified individual genes were indeed driving certain enrichment signals. A case study is presented for SOD1 to demonstrate proof-of-concept of how enriched features may aid in defining variant pathogenicity. Our results present proteomic and transcriptomic features that are important indicators of missense variant pathogenicity in ALS and are distinct from features associated with neurodevelopmental disorders.

Efficient calculation of the free energy for protein partitioning using restraining potentials.

An approach for the efficient simulation of phase-separated lipid bilayers, for use in the calculation of equilibrium free energies of partitioning between lipid domains, is proposed. The methodology exploits restraint potentials and rectangular aspect ratios that enforce lipid phase separation, allowing for the simulation of smaller systems that approximately reproduce bulk behavior. The utility of this approach is demonstrated through the calculation of potentials of mean force for the translation of a transmembrane protein between lipid domains. The impact of the imposed restraints on lipid tail ordering and lipid packing are explored, providing insight into how restraints can best be employed to compute accurate free-energy surfaces. This approach should be useful in the accurate calculation of equilibrium partition coefficients for transmembrane protein partitioning in heterogeneous membranes, providing insight into the thermodynamic driving forces that control this fundamental biophysical phenomenon.

On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes.

Protein association in lipid membranes is fundamental to membrane protein function and of great biomedical relevance. All-atom and coarse-grained models have been extensively used to understand the protein-protein interactions in the membrane and to compute equilibrium association constants. However, slow translational and rotational diffusion of protein in membrane presents challenges to the effective sampling of conformations defining the ensembles of free and bound states contributing to the association equilibrium and the free energy of dimerization. We revisit the homodimerization equilibrium of the TM region of glycophorin A. Conformational sampling is performed using umbrella sampling along previously proposed one-dimensional collective variables and compared with sampling over a two-dimensional collective variable space using the MARTINI v2.2 force field. We demonstrate that the one-dimensional collective variables suffer from restricted sampling of the native homodimer conformations leading to a biased free energy landscape. Conversely, simulations along the two-dimensional collective variable effectively characterize the thermodynamically relevant native and non-native interactions contributing to the association equilibrium. These results demonstrate the challenges associated with accurately characterizing binding equilibria when multiple poses contribute to the bound state ensemble.

History-dependent nonequilibrium conformations of a highly confined polymer globule in a sphere.

Chromatin undergoes condensation-decondensation processes repeatedly during its cell lifetime. The spatial organization of chromatin in nucleus resembles the fractal globule, of which structure significantly differs from an equilibrium polymer globule. There have been efforts to develop a polymer globule model to describe the fractal globulelike structure of tightly packed chromatin in nucleus. However, the transition pathway of a polymer toward a globular state has been often ignored. Because biological systems are intrinsically in nonequilibrium states, the transition pathway that the chromatin would take before reaching the densely packaged globule should be of importance. In this study, by employing a simple polymer model and Langevin dynamics simulations, we investigate the conformational transition of a single polymer from a swollen coil to a compact globule. We aim to elucidate the effect of transition pathways on the final globular structure. We show that a fast collapse induces a nonequilibrium structure even without a specific intramolecular interaction and that its relaxation toward an equilibrium globule is extremely slow. Due to a strong confinement, the fractal globule never relaxes into an equilibrium state during our simulations such that the globular structure becomes dependent on the transition pathway.

The non-classical kinetics and the mutual information of polymer loop formation.

The loop formation of a single polymer chain has served as a model system for various biological and chemical processes. Theories based on the Smoluchowski equation proposed that the rate constant (kloop) of the loop formation would be inversely proportional to viscosity (η), i.e., kloop ∼ η-1. Experiments and simulations showed, however, that kloop showed the fractional viscosity dependence of kloop ∼ η-ß with ß < 1 either in glasses or in low-viscosity solutions. The origin of the fractional viscosity dependence remains elusive and has been attributed to phenomenological aspects. In this paper, we illustrate that the well-known failure of classical kinetics of the loop formation results from the breakdown of the local thermal equilibrium (LTE) approximation and that the mutual information can quantify the breakdown of the LTE successfully.

Heterogeneous kinetics of the loop formation of a single polymer chain in crowded and disordered media.

The cytoplasmic volume of cells is occupied and crowded by a variety of macromolecules, such as proteins and cytoskeleton structures. Such diverse macromolecules make the cell cytoplasm not only structurally heterogeneous but also dynamically heterogeneous: Some macromolecules may diffuse freely inside cell cytoplasm at certain timescales while others hardly diffuse. Studies on the effects of the dynamic heterogeneity on reaction kinetics have been limited even though the effects of the crowdedness and structural heterogeneity were investigated extensively. In this study, we employ a simple model of mixtures of mobile and immobile matrix particles, tune the degree of dynamic heterogeneity by changing the fraction of immobile matrix particles, and investigate reaction kinetics in such heterogeneous media. We employ the loop formation of a single polymer chain as a model reaction and perform Langevin dynamics simulations. We find that the free-energy barrier of the loop formation is decreased as the systems become more crowded with matrix particles. But the free-energy barrier is not sensitive to the dynamic heterogeneity. As dynamic heterogeneity increases with an increase in the fraction of immobile matrix particles, however, the diffusivity of the system decreases significantly. The decrease in the diffusion (due to the dynamic heterogeneity) and the decrease in the free-energy barrier (due to the crowdedness) lead together to a complicated trend of the loop formation kinetics. As the volume fraction of immobile matrix particles reaches a critical value at the percolation transition, the reaction kinetics becomes significantly heterogeneous and the survival probability distribution of the chain loop formation becomes stretched-exponential. We also illustrate that the heterogeneous reaction rate near the percolation transition relates closely to the structures of local pores in which the polymer is located.

The breakdown of the local thermal equilibrium approximation for a polymer chain during packaging.

The conformational relaxation of a polymer chain often slows down in various biological and engineering processes. The polymer, then, may stay in nonequilibrium states throughout the process such that one may not invoke the local thermal equilibrium (LTE) approximation, which has been usually employed to describe the kinetics of various processes. In this work, motivated by recent single-molecule experiments on DNA packaging into a viral capsid, we investigate how the nonequilibrium conformations and the LTE approximation would affect the packaging of a polymer chain into small confinement. We employ a simple but generic coarse-grained model and Langevin dynamics simulations to investigate the packaging kinetics. The polymer segments (both inside and outside the confinement) stay away from equilibrium under strong external force. We devise a simulation scheme to invoke the LTE approximation during packaging and find that the relaxation of nonequilibrium conformations plays a critical role in regulating the packaging rate.

Blood concentrations of lipopolysaccharide-binding protein, high-sensitivity C-reactive protein, tumor necrosis factor-α, and Interleukin-6 in relation to insulin resistance in young adolescents.

BACKGROUND: We assessed the association of insulin resistance as indicated by the homeostatic model assessment of insulin resistance (HOMA-IR) with inflammatory molecules, lipopolysaccharide-binding protein (LBP), high sensitivity C-reactive protein (hs-CRP), Tumor necrosis factor-α (TNF-α), and Interleukin-6 (IL-6) in urban young adolescents. METHODS: Seventy-six adolescents (36 subjects with HOMA-IR ≥ 2.6 and 40 subjects with HOMA-IR < 2.6) were included in the study. We assessed anthropometric and laboratory measures, such as BMI, blood pressure, insulin sensitivity, liver enzymes, and lipid profiles along with the aforementioned inflammatory biomarkers. The diagnostic accuracy of LBP, hs-CRP, TNF-α, and IL-6 for insulin resistance was evaluated by using the receiver operating characteristic (ROC) curve analysis. RESULTS: The mean age of the study subjects was 12.0 [12.0-13.0] y. Circulating LBP plasma concentration and hs-CRP were significantly increased in subjects with HOMA-IR ≥ 2.6 when compared with those with HOMA-IR < 2.6 (P < .0001). There was no difference in TNF-α or IL-6 concentrations between groups. Comparisons based on the area under the ROC curve for LBP, hs-CRP, TNF-α, and IL-6 with regard to insulin resistance (HOMA-IR ≥ 2.6) were 0.8384 (95% CI: 0.7380 to 0.9388), 0.7907 (95% CI: 0.6701 to 0.9113), 0.6207 (95% CI: 0.4770 to 0.7643), and 0.5763 (95% CI: 0.4285 to 0.7241), respectively. CONCLUSIONS: Among LBP, hs-CRP, TNF-α, and IL-6, plasma LBP has the greatest diagnostic accuracy for insulin resistance in young adolescents. Prospective studies are warranted to delineate the value of LBP in the prediction of insulin resistance.

Ubiquitin-specific peptidase 5 and ovarian tumor deubiquitinase 6A are differentially expressed in p53+/+ and p53-/- HCT116 cells.

Most proteins undergo ubiquitination, a process by which ubiquitin proteins bind to their substrate proteins; by contrast, deubiquitination is a process that reverses ubiquitination. Deubiquitinating enzymes (DUBs) function to remove ubiquitin proteins from the protein targets and serve an essential role in regulating DNA repair, protein degradation, apoptosis and immune responses. Abnormal regulation of DUBs may affect a number of cellular processes and may lead to a variety of human diseases, including cancer. Therefore, it is important to identify abnormally expressed DUBs to identify DUB-related diseases and biological mechanisms. The present study aimed to develop a multiplex polymerase chain reaction screening platform comprising primers for various DUB genes. This assay was used to identify p53-related DUBs in HCT116 p53+/+ and p53-/- cells. The results demonstrated that ubiquitin-specific peptidase 5 (USP5) and ovarian tumor deubiquitinase 6A (OTUD6A) were differentially expressed in p53+/+ and p53-/- HCT116 cells. Based on the data obtained through DUB screening, the protein expression levels of USP5 and OTUD6A were examined by western blotting, which confirmed that both of these DUBs were also expressed differentially in p53+/+ and p53-/- HCT116 cells. In conclusion, results from the DUB screening performed by the present study revealed that the expression of USP5 and OTUD6A may be affected by p53, and this method may be useful for the rapid and cost-effective identification of possible biomarkers.

Effects of solvent quality and non-equilibrium conformations on polymer translocation.

The conformation and its relaxation of a single polymer depend on solvent quality in a polymer solution: a polymer collapses into a globule in a poor solvent, while the polymer swells in a good solvent. When one translocates a polymer through a narrow pore, a drastic conformational change occurs such that the kinetics of the translocation is expected to depend on the solvent quality. However, the effects of solvent quality on the translocation kinetics have been controversial. In this study, we employ a coarse-grained model for a polymer and perform Langevin dynamics simulations for the driven translocation of a polymer in various types of solvents. We estimate the free energy of polymer translocation using steered molecular dynamics simulations and Jarzynski's equality and find that the free energy barrier for the translocation increases as the solvent quality becomes poorer. The conformational entropy contributes most to the free energy barrier of the translocation in a good solvent, while a balance between entropy and energy matters in a poor solvent. Interestingly, contrary to what is expected from the free energy profile, the translocation kinetics is a non-monotonic function of the solvent quality. We find that for any type of solvent, the polymer conformation stays far away from the equilibrium conformation during translocation due to an external force and tension propagation. However, the degree of tension propagation differs depending on the solvent quality as well as the magnitude of the external force: the tension propagation is more significant in a good solvent than in a poor solvent. We illustrate that such differences in tension propagation and non-equilibrium conformations between good and poor solvents are responsible for the complicated non-monotonic effects of solvent quality on the translocation kinetics.

Fractional Viscosity Dependence of Reaction Kinetics in Glass-Forming Liquids.

The diffusion of molecules in complex systems such as glasses and cell cytoplasm is slow, heterogeneous, and sometimes nonergodic. The effects of such intriguing diffusion on the kinetics of chemical and biological reactions remain elusive. In this Letter, we report that the kinetics of the polymer loop formation reaction in a Kob-Andersen (KA) glass forming liquid is influenced significantly by the dynamic heterogeneity. The diffusion coefficient D of a KA liquid deviates from the Stokes-Einstein relation at low temperatures and D shows a fractional dependence on the solvent viscosity η_{s}, i.e., D∼η_{s}^{-ξ_{D}} with ξ_{D}=0.85. The dynamic heterogeneity of a KA liquid affects the rate constant k_{rxn} of the loop formation and leads to the identical fractional dependence of k_{rxn} on η_{s} with k_{rxn}∼η_{s}^{-ξ} and ξ=ξ_{D}, contrary to reactions in dynamically homogeneous solutions where k_{rxn}∼η_{s}^{-1}.

p53 stability is regulated by diverse deubiquitinating enzymes.

The tumor suppressor protein p53 has a variety of roles in responses to various stress signals. In such responses, p53 activates specific transcriptional targets that control cell cycle arrest, DNA repair, angiogenesis, autophagy, metabolism, migration, aging, senescence, and apoptosis. Since p53 has been identified as the most frequently altered gene in human cancers, regulation and stabilization of its normal functions are important. Stability of p53 is regulated by the ubiquitin-proteasome pathway (UPP). Furthermore, it is readjusted by deubiquitination via deubiquitinating enzymes (DUBs) that can eliminate ubiquitin from p53. Diverse DUBs directly or indirectly affect the ubiquitination of p53 and, consequently, regulate various cellular processes associated with p53. As maintenance of p53 is regulated by a variety of DUBs, the interaction of DUBs and p53 can affect diseases such as cancer. Currently, DUBs have a central role in our understanding of various cancers, and some have potential in the development of effective therapeutic strategies. This review summarizes the current knowledge of p53 and of the interconnection between p53 and DUBs.

RNPS1 is modulated by ubiquitin-specific protease 4.

RNA-binding protein with serine-rich domain 1 (RNPS1) is a component of pre-splicing and post-splicing multiprotein complexes, which activates constitutive and alternative splicing. RNPS1 participates in the formation of the spliceosome and activates the pre-mRNA splicing process. In the present study, we found that ubiquitin-specific protease 4 (USP4) is a binding partner of RNPS1. Although RNPS1 is polyubiquitinated by both K48- and K63-linkages, USP4 exclusively deubiquitinates K63-linked polyubiquitin chains of RNPS1. We also demonstrate that the catalytic activity of USP4 on ubiquitinated RNPS1 is elevated by squamous cell carcinoma antigen recognized by T cells 3 (Sart3).

Ubiquitin-specific protease 21 regulating the K48-linked polyubiquitination of NANOG.

NANOG, one of homeobox proteins, plays a crucial role in regulating self-renewal and pluripotency for embryonic stem cells (ESCs). Since the ubiquitin-mediated degradation of NANOG protein has been implicated in its cellular functions involved in not only maintenance of pluripotency and pluripotent epiblast, but also prevention of primitive endoderm differentiation, the identification of ubiquitin ligases and deubiquitinating enzymes (DUBs) for NANOG is required to elucidate its protein stability and the regulation of cellular functions in these processes. In this study, we have identified a novel deubiquitinating enzyme USP21 which interacts with NANOG by both yeast two hybrid screening for DUBs and immunoprecipitation analyses. These analyses revealed that USP21 specifically regulates the Lys48-linked polyubiquitination and stability of NANOG, providing a new way of maintaining the pluripotency of ESCs and induced pluripotent stem cells (iPSCs).

Effects of shape and flexibility of conductive fillers in nanocomposites on percolating network formation and electrical conductivity.

Nanocomposites consist of nanofillers and matrices, thus allowing one to design novel materials with desirable properties of both nanofillers and matrices. The percolating network formation of nanofillers in matrices is critical to such desired properties. Some nanofillers such as carbon nanotubes and graphene nanosheets are so flexible that they become either wavy or crumpled. Such a variability in the nanofiller conformation may affect the percolating network formation but has been often (but not always) ignored in the theoretical and computational investigation. In this work, we investigate how the flexibility of different kinds of nanofillers influences the formation of the percolating network by performing extensive Langevin dynamics simulations. We consider three kinds of nanofillers of different shape: nanospheres, nanorods, and nanoplates. When the sizes of nanofillers (or the radius of gyration, R(g)) are comparable, nanorods form a percolating network at a lower volume fraction than nanoplates while nanofillers require the highest volume fraction to form the percolating network, which is consistent with previous experiments. The percolation threshold concentration (ϕ(c)) of nanospheres increases with an increase in their R(g), while ϕ(c) of nanorods and nanoplates decrease with R(g). However, the effect of flexibility on the percolation threshold volume fraction is much more significant for nanoplates than nanorods. We also estimate the electric conductivity and find that the electric conductivity follows a scaling relation faithfully but with different critical exponents depending on the shape and flexibility.