Topology- and size-dependent binding of DNA nanostructures to the DNase I

The susceptibility of DNA nanomaterials to enzymatic degradation in biological environments is a significant obstacle limiting their broad applications in biomedicine. While DNA nanostructures exhibit some resistance to nuclease degradation, the underlying mechanism of this resistance remains elusive. In this study, the interaction of tetrahedral DNA nanostructures (TDNs) and double-stranded DNA (dsDNA) with DNase I is investigated using all-atom molecular dynamics simulations. Our results indicate that DNase I can effectively bind to all dsDNA molecules, and certain key residues strongly interact with the nucleic bases of DNA. However, the binding of DNase I to TDNs exhibits a non-monotonic behavior based on size; TDN15 and TDN26 interact weakly with DNase I (∼ - 75 kcal/mol), whereas TDN21 forms a strong binding with DNase I (∼ - 110 kcal/mol). Furthermore, the topological properties of the DNA nanostructures are analyzed, and an under-twisting (∼32°) of the DNA helix is observed in TDN15 and TDN26. Importantly, this under-twisting results in an increased width of the minor groove in TDN15 and TDN26, which primarily explains their reduced binding affinity to DNase I comparing to the dsDNA. Overall, this study demonstrated a novel mechanism for local structural control of DNA at the nanoscale by adjusting the twisting induced by length.

Effect of Terahertz Waves on the Structure of the Aβ42 Monomer, Dimer, and Protofibril: Insights from Molecular Dynamics Simulations

Amyloid-β (Aβ) and its assemblies play important roles in the pathogenesis of Alzheimer's disease (AD). Recent studies conducted by experimental and computational researchers have extensively explored the structure, assembly, and influence of biomolecules and cell membranes on Aβ. However, the impact of terahertz waves on the structures of Aβ monomers and aggregates remains largely unexplored. In this study, we systematically investigate the molecular mechanisms by which terahertz waves affect the structure of the Aβ42 monomer, dimer, and tetramer through all-atom molecular dynamics (MD) simulations. Our findings indicate that terahertz waves at a specific frequency (42.55 THz) can enhance intramolecular and intermolecular interactions in the Aβ42 monomer and dimer, respectively, by resonating with the symmetric stretching mode of the -COO- groups and the symmetric bending/stretching mode of -CH3 groups. Consequently, the β-structure content of the Aβ42 monomer is greatly increased, and the binding energy between the monomers in the Aβ42 dimer is significantly enhanced. Additionally, our observations suggest that terahertz waves can mildly stabilize the structure of tetrameric protofibrils by enhancing the interactions among peripheral peptides. Furthermore, we also investigated the effect of the frequency of terahertz waves on the structure of Aβ42. The present study contributes to a better understanding of the impact of external fields on the biobehavior of Aβ42 peptides and may shed some light on the potential risks associated with electromagnetic field radiation.

Effect of maleylation and denaturation of human serum albumin on its interaction with scavenger receptors

The specific recognition of serum proteins by scavenger receptors is critical and fundamental in many biological processes. However, the underlying mechanism of scavenger receptor-serum protein interaction remains elusive. In this work, taking scavenger receptors class A1 (SR-A1) as an example, we systematically investigate its interaction with human serum albumin (HSA) at different states through a combination of molecular docking and all-atom molecular dynamics simulations. It is found that native HSA can moderately bind to collagen-like (CL) region or scavenger receptor cysteine-rich (SRCR) region, with both electrostatic (ELE) and van der Waals (VDW) interactions, playing important roles. After maleylation, the binding energy, particularly the ELE energy, between HSA and CL region is significantly enhanced, while the binding energy between HSA and SRCR region remains nearly unchanged. Additionally, we also observe that unfolding of the secondary structures in HSA leads to a larger contact surface area between denatured HSA and CL region, but has little impact on the HSA-SRCR region interaction. Therefore, similar to maleylated HSA, denatured HSA is also more likely to bind to the CL region of SR-A1.

Effect of the Graphene Nanosheet on Functions of the Spike Protein in Open and Closed States: Comparison between SARS-CoV-2 Wild Type and the Omicron Variant

The spread of coronavirus disease 2019 caused by SARS-CoV-2 and its variants has become a global health crisis. Although there were many attempts to use nanomaterials-based devices to fight against SARS-CoV-2, it still remains elusive as to how the nanomaterials interact with SARS-CoV-2 and affect its biofunctions. Here, taking the graphene nanosheet (GN) as the model nanomaterial, we investigate its interaction with the spike protein in both WT and Omicron by molecular simulations. In the closed state, the GN can insert into the region between the receptor binding domain (RBD) and the N-terminal domain (NTD) in both wild type (WT) and Omicron, which keeps the RBD in the down conformation. In the open state, the GN can hamper the binding of up RBD to ACE2 in WT, but it has little impact on up RBD and, even worse, stimulates the down-to-up transition of down RBDs in Omicron. Moreover, the GN can insert in the vicinity of the fusion peptide in both WT and Omicron and prevents the detachment of S1 from the whole spike protein. The present study reveals the effect of the SARS-CoV-2 variant on the nanomaterial-spike protein interaction, which informs prospective efforts to design functional nanomaterials against SARS-CoV-2.

Cancer risks among iron and steel workers in Anshan, China, Part II: Case-control studies of lung and stomach cancer

Nested case-control interview studies of lung cancer (610 incident cases), stomach cancer (292 incident cases), and 959 controls were conducted to follow up leads from a proportional mortality analysis of deaths among male workers in a large integrated iron-steel complex in Anshan, China. For lung cancer, after adjusting for the significant non-occupational risk factors (smoking, other pulmonary disease, family history of lung cancer, and low consumption of fruit or tea), risks were significantly elevated for those employed for 15 or more years in smelting and rolling (OR = 1.5, CI = 1.1-2.2), in the fire-resistant brick factory (OR = 2.9, CI = 1.4-5.9), in general loading (OR = 2.5, CI = 1.0-6.1), and as coke oven workers (OR = 3.4; CI = 1.4-8.5). For stomach cancer, after adjusting for consumption of pickled vegetables, prior gastric diseases, family history of stomach cancer, low intake of fruits and vegetables, and education, risks were significantly elevated for those employed for 15 or more years in ore sintering and transportation (OR = 2.1, CI = 1.0-4.4), in the fire-resistant brick factory (OR = 2.5, CI = 1.1-5.8), in general loading (OR = 3.2, CI = 1.2-8.9), as boilerworkers and cooks (OR = 2.6, CI = 1.2-5.6), and as coke oven workers (OR = 5.4, CI = 1.8-16.0). For both lung and stomach cancers, significant dose-response gradients were observed for exposure to total dust and benzo(a)pyrene, but not for specific chemical components of dust. Overall, long-term steel workers with exposure to workplace pollutants had a 40% increased risk of both lung and stomach cancers. These case-control studies confirm many of the occupational findings reported in the proportionate mortality analysis, and suggest avenues for further work to evaluate the carcinogenicity of individual components of dust.

The application of leukocyte adherence inhibition assay to patients with colorectal cancer. Comparison with serum level of carcinoembryonic antigen and sialic acid

Antitumor immune response to colorectal cancer extracts was tested by leukocyte adherence inhibition (LAI) assay. Of 38 colorectal cancer patients, 26 (68.4 percent) were LAI positive. The sensitivity of LAI assay was found to be inversely related to the stage of the disease. In contrast, 2 of 50 (4 percent) healthy individuals, 2 of 37 (5.4 percent) patients with nonmalignant gastrointestinal diseases, and 2 of 32 (6.3 percent) patients with malignancies other than colorectal cancer were LAI positive. Serum carcinoembryonic antigen (CEA) and serum sialic acid (SA) also were determined in 38 colorectal cancer patients. Using LAI assay in combination with CEA determination could improve the detection rate of colorectal cancer.