Decaheme Cytochrome MtrF Adsorption and Electron Transfer on Gold Surface

Emergent electrical properties of multiheme cytochromes have promising applications. We performed hybrid simulations (molecular dynamics, free energy computation, and kinetic Monte Carlo) to study decaheme cytochrome, MtrF adsorption on an Au (111) surface in water and the electron transfer (ET) efficiency. Our results reveal that the gold surface’s dehydration serves as a crucial driving force for protein adsorption due to large surface tension. The most possible adsorption orientation is with the ET terminal (heme5) approaching the gold surface, which yields a pathway for ET between the substrate and the aqueous environment. Upon adsorption, protein’s secondary structures and central domains (II and IV) bonded with heme-residues remain relatively stable. MtrF surface mobility is dictated by thiol-gold interaction and strong binding between Au(111) and peptide aromatic groups. ET transfer rate across protein heme-network along the solvent-to-surface direction is slightly larger than that of the reverse direction, but lower than that of the solvation structure

Lysozyme Adsorption on Polyethylene Surfaces: Why Are Long Simulations Needed?

The adsorption of lysozyme onto a polyethylene (PE) surface in an aqueous environment was investigated via molecular dynamics (MD) simulation. The adsorption can be divided into three processes: diffusion to the surface, dehydration induced by hydrophobic surface–protein interactions, and denaturation. The dehydration process is very long, around 70 ns. Structural deformations start soon after the protein reaches the surface and continue during the whole trajectory. The hydrophobic residues are slowly driven toward the surface, inducing changes in the protein’s secondary structure. The protein’s secondary structural components near the surface are more disturbed than those farther away from the surface. The lysozyme is adsorbed with its long axis parallel to the surface and displays an anisotropic mobility on the surface that is probably due to the intrinsic structure of the PE surface. Our study demonstrates the need for long-time atomistic simulation in order to gain a complete understanding of the adsorption process

Visualization 1: Digitally controlled chirped pulse laser for sub-terahertz-range fiber structure interrogation

real-time temperature distribution measurement Originally published in Optics Letters on 01 March 2017 (ol-42-5-1007

Multiscale Simulation of Protein Corona Formation on Silver Nanoparticles: Study of Ovispirin‑1 Peptide Adsorption

The exposure of nanoparticles (NPs) to biofluids leads to the rapid coverage of proteins, named protein corona, which alters the NPs’ chemicophysical and biological properties. Fundamental studies of the protein corona are thus critical to the increasing applications of NPs in nanotechnology and nanomedicines. The present work utilizes multiscale simulations of a model biological system, small ovispirin-1 peptides, and bare silver nanoparticles (AgNPs) to examine the NPs’ size and surface hydrophilicity effects on formation dynamics and the structure of the peptide corona. Our simulations revealed the different adsorption dynamics of ovispirin-1 peptides on the NPs, including the direct adsorption of a single peptide and peptide aggregates and multistep adsorption, as well as an intermediate cycle of desorption and readsorption. Notably, the whole process of peptide adsorption on hydrophilic AgNP surfaces can be generalized as three stages: diffusion to the surface, initial landing via hydrophilic residues, and the final attachment. The decrease in AgNP’s size leads to faster adsorption with more heterogeneous peptide interfacial dynamics, a denser and inhomogeneous peptide packing structure, and a wider distribution of adsorption orientations. Subsequent atomistic molecular dynamics simulations demonstrated that on the hydrophilic AgNP surfaces, adsorbed peptides display moderate changes in their secondary structure, resulting in further changes of corona composition, i.e., amino acid residue distribution on the surface

Novel circular RNA circATRNL1 accelerates the osteosarcoma aerobic glycolysis through targeting miR-409-3p/LDHA

In recent researches, circular RNAs (circRNAs) have been shown to exert critical functions in osteosarcoma biology. Nevertheless, the contribution of circRNAs to osteosarcoma remains largely unclear. Results indicated that expression of circATRNL1 was higher in osteosarcoma tissues and cells. The high-expression of circATRNL1 was significantly correlated with aggressive features and acted as an independent risk factor for osteosarcoma patients’ overall survival. Functionally, our findings demonstrate that circATRNL1 promotes the osteosarcoma aerobic glycolysis in vitro. Mechanistically, circATRNL1 up-regulated the expression level of LDHA, which was also targeted by miR-409-3p. Therefore, circATRNL1 exerted the accelerative roles of osteosarcoma aerobic glycolysis through miR-409-3p/LDHA axis. In conclusion, circATRNL1 promoted osteosarcoma progression by enhancing glycolysis via circATRNL1/miR-409-3p/LDHA axis, which may inspire a novel therapeutic target for osteosarcoma.</p

Dynamic Covalent Assembly of Peptoid-Based Ladder Oligomers by Vernier Templating

Dynamic covalent chemistry, in conjunction with template-directed assembly, enables the fabrication of extended nanostructures that are both precise and tough. Here we demonstrate the dynamic covalent assembly of peptoid-based molecular ladders with up to 12 rungs via scandium­(III)-catalyzed imine metathesis by employing the principle of Vernier templating, where small precursor units with mismatched numbers of complementary functional groups are coreacted to yield larger structures with sizes determined by the respective precursor functionalities. Owing to their monomer diversity and synthetic accessibility, sequence-specific oligopeptoids bearing dynamic covalent pendant groups were employed as precursors for molecular ladder fabrication. The generated structures were characterized using matrix-assisted laser desorption/ionization mass spectrometry and gel permeation chromatography, confirming successful molecular ladder fabrication

DataSheet_1_Development and Validation of Ferroptosis- and Immune-Related lncRNAs Signatures for Breast Infiltrating Duct and Lobular Carcinoma.pdf

BackgroundHeterogeneity of breast cancer (BRCA) is significantly correlated with its prognosis. Target therapy for ferroptosis and immunity is a new cancer treatment option discovered in recent years. In the present study, we aimed to identify ferroptosis- and immune-related long non-coding RNAs (lncRNAs) to accurately predict the prognosis and diagnosis of patients with breast infiltrating duct and lobular carcinoma by integrated analyses.MethodsThe corresponding data for the patients with breast infiltrating duct and lobular carcinoma by integrated analyses were obtained from The Cancer Genome Atlas (TCGA). Analyses of univariate and multivariate Cox regressions were used to identify the suitable candidate biomarkers.ResultsWe found that seven ferroptosis- and immune-related differentially expressed lncRNAs (FI-DELs) (AC007686.3, AC078883.1, ADAMTS9-AS1, AL035661.1, CBR3-AS1, FTX, and TMEM105) were correlated with the overall survival of patients with breast infiltrating duct and lobular carcinoma. The areas under the receiver operating characteristic (AUCs) value of the prognosis model were all over 0.6 in training, validation, and entire groups. The sensitivity and specificity of the diagnosis model was 87.84% and 97.06%, respectively.ConclusionsThrough a series of bioinformatics analyses, we found that the seven FI-DELs could serve as prognostic and diagnostic biomarkers for patients with breast infiltrating duct and lobular carcinoma. However, whether these seven biomarkers could be really applied to the clinic requires further investigations.</p

Table_1_Development and Validation of Ferroptosis- and Immune-Related lncRNAs Signatures for Breast Infiltrating Duct and Lobular Carcinoma.xlsx

BackgroundHeterogeneity of breast cancer (BRCA) is significantly correlated with its prognosis. Target therapy for ferroptosis and immunity is a new cancer treatment option discovered in recent years. In the present study, we aimed to identify ferroptosis- and immune-related long non-coding RNAs (lncRNAs) to accurately predict the prognosis and diagnosis of patients with breast infiltrating duct and lobular carcinoma by integrated analyses.MethodsThe corresponding data for the patients with breast infiltrating duct and lobular carcinoma by integrated analyses were obtained from The Cancer Genome Atlas (TCGA). Analyses of univariate and multivariate Cox regressions were used to identify the suitable candidate biomarkers.ResultsWe found that seven ferroptosis- and immune-related differentially expressed lncRNAs (FI-DELs) (AC007686.3, AC078883.1, ADAMTS9-AS1, AL035661.1, CBR3-AS1, FTX, and TMEM105) were correlated with the overall survival of patients with breast infiltrating duct and lobular carcinoma. The areas under the receiver operating characteristic (AUCs) value of the prognosis model were all over 0.6 in training, validation, and entire groups. The sensitivity and specificity of the diagnosis model was 87.84% and 97.06%, respectively.ConclusionsThrough a series of bioinformatics analyses, we found that the seven FI-DELs could serve as prognostic and diagnostic biomarkers for patients with breast infiltrating duct and lobular carcinoma. However, whether these seven biomarkers could be really applied to the clinic requires further investigations.</p

Five Isolated Pentagon Rule Isomers of Higher Fullerene C₉₄ Captured as Chlorides and CF₃ Derivatives: C₉₄(34)Cl₁₄, C₉₄(61)Cl₂₀, C₉₄(133)Cl₂₂, C₉₄(42)(CF₃)₁₆, and C₉₄(43)(CF₃)₁₈

High-temperature chlorination and trifluoromethylation of C94 isomeric mixtures followed by single-crystal X-ray diffraction with the use of synchrotron radiation resulted in the structure determination of C94(34)­Cl14, C94(61)­Cl20, C94(133)­Cl22, C94(42)­(CF3)16, and C94(43)­(CF3)18. Their addition patterns are stabilized by the formation of isolated CC bonds and aromatic substructures. Four cage isomers of C94 (nos. 34, 42, 43, and 133) have been experimentally confirmed for the first time