Adsorption of Collagen-like Peptides onto Gold Nanosurfaces

The adsorption behavior of perfluorooctane sulphonate on diamane regulated by strain

The adsorption of per- and polyfluoroalkyl substances (PFAS), such as perfluorooctane sulfonate (PFOS), is currently a critical issue in the environmental domain, yet it is not fully understood. Diamane, as a stable monolayer adsorbent, has garnered significant research interest. Defects and strain are reported to play a crucial role in regulating its electronic structure. In this study, we employ density functional theory (DFT) calculations to investigate the adsorption of PFOS on both pristine and nitrogen-vacancy (N-V) defected diamane, respectively. Additionally, we systematically examine the effects of strain in diamane along both the a- and b-directions (two directions of a monolayer) on PFOS adsorption. This analysis involves studying the adsorption energy (Eads), electron transfer, and the partial density of states. Finally, we propose the synergistic effects of N-V defects and compression strain in diamane, which enhance PFOS adsorption. Diamane is considered a promising candidate for PFOS sensing or capture.

Targeting the COMMD4-H2B protein complex in lung cancer

BACKGROUND

Lung cancer is the biggest cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC) accounts for 85-90% of all lung cancers. Identification of novel therapeutic targets are required as drug resistance impairs chemotherapy effectiveness. COMMD4 is a potential NSCLC therapeutic target. The aims of this study were to investigate the COMMD4-H2B binding pose and develop a short H2B peptide that disrupts the COMMD4-H2B interaction and mimics COMMD4 siRNA depletion.

METHODS

Molecular modelling, in vitro binding and site-directed mutagenesis were used to identify the COMMD4-H2B binding pose and develop a H2B peptide to inhibit the COMMD4-H2B interaction. Cell viability, DNA repair and mitotic catastrophe assays were performed to determine whether this peptide can specially kill NSCLC cells.

RESULTS

Based on the COMMD4-H2B binding pose, we have identified a H2B peptide that inhibits COMMD4-H2B by directly binding to COMMD4 on its H2B binding binding site, both in vitro and in vivo. Treatment of NSCLC cell lines with this peptide resulted in increased sensitivity to ionising radiation, increased DNA double-strand breaks and induction of mitotic catastrophe in NSCLC cell lines.

CONCLUSIONS

Our data shows that COMMD4-H2B represents a novel potential NSCLC therapeutic target.

Characterizing polyproline II conformational change of collagen superhelix unit on adsorption on gold surface

The dynamic process of protein binding onto a metal surface is a frequent occurrence as gold nanoparticles are increasingly being used in biomedical applications, including wound treatment and drug transport. Collagen, as a major component of the extracellular matrix, has potentially advantageous biomedical applications, due to its excellent biocompatibility and elasticity properties. Therefore, a mechanistic comprehension of how and which species in collagen interact with gold nanoparticles is a prerequisite for collagen-gold complexes in clinical application. However, the dynamic behavior of collagen with the polyproline II (PPII) conformation on gold sheets at the molecular level is too complex to capture under current experimental conditions. Here, using molecular dynamics simulations, we investigate the adsorption process and conformational behavior of the tripeptide Gly-Pro-Hyp with the repetitive unit of the collagen superhelix on the gold surface as a function of number of repeating units from 1 to 10. The different numbers of repeating units all prefer to approach the gold surface and adsorb via charged residues at the C-terminal or N-terminal ends, tending to form arch structures on the gold surface. Compared with the various tripeptide units in solution still retaining the native PPII conformation, the presence of the gold surface affects the formation of hydrogen bonds between the protein and water molecules, thus disrupting the PPII conformation of collagen. Specifically, the interaction between the gold surface and HYP limits the rotation of the dihedral angle of collagen, resulting in a tendency for the PPII conformation of the gold surface to transform to the β-sheet conformation. The results provide an indication of how to improve the interaction between the terminal groups and the gold surface for the design of a bioavailable protein-gold material for medicinal purposes.

Mono-phosphorylation at Ser4 of barrier-to-autointegration factor (Banf1) significantly reduces its DNA binding capability by inducing critical changes in its local conformation and DNA binding surface

Barrier-to-autointegration factor (Banf1) is a small DNA-bridging protein. The binding status of Banf1 to DNA is regulated by its N-terminal phosphorylation and dephosphorylation, which plays a critical role in cell proliferation. Banf1 can be phosphorylated at Ser4 into mono-phosphorylated Banf1, which is further phosphorylated at Thr3 to form di-phosphorylated Banf1. It was observed decades ago that mono-phosphorylated Banf1 cannot bind to DNA. However, the underlying molecular- and atomic-level mechanisms remain unclear. A clear understanding of these mechanisms will aid in interfering with the cell proliferation process for better global health. Herein, we explored the detailed atomic bases of unphosphorylated Banf1-DNA binding and how mono- and di-phosphorylation of Banf1 impair these atomic bases to eliminate its DNA-binding capability, followed by exploring the DNA-binding capability of mono- and di-phosphorylation Banf1, using comprehensive and systematic molecular modelling and molecular dynamics simulations. This work presented in detail the residue-level binding energies, hydrogen bonds and water bridges between Banf1 and DNA, some of which have not been reported. Moreover, we revealed that mono-phosphorylation of Banf1 causes its N-terminal secondary structure changes, which in turn induce significant changes in Banf1's DNA binding surface, thus eliminating its DNA-binding capability. At the atomic level, we also uncovered the alterations in interactions due to the induction of mono-phosphorylation that result in the N-terminal secondary structure changes of Banf1. Additionally, our modelling showed that phosphorylated Banf1 with their dominant N-terminal secondary structures bind to DNA with a significantly lower affinity and the docked binding pose are not stable in MD simulations. These findings help future studies in predicting effect of mutations in Banf1 on its DNA-binding capability and open a novel avenue for the development of therapeutics such as cancer drugs, targeting cell proliferation by inducing conformational changes in Banf1's N-terminal domain.

An exploration of enhancing thermal stability of leather by hydrophilicity regulation: effect of hydrophilicity of phenolic syntan

Effect of retanning on the thermal stability of leather is eliciting increasing attention. However, the relationship between the hydrophilicity of retanning agents and the heat resistance of leather and the corresponding mechanism remain unclear. Herein, phenolic formaldehyde syntans (PFSs) were selected as models to explore the effect of the hydrophilicity of retanning agents on the thermal stability of retanned leather. The thermal stability of leather was closely correlated to the hydrophilic group content (sulfonation degree) of PFSs. As the sulfonation degree increased, the water absorption rate of PFSs and their retanned leathers decreased, whereas the thermal stability of leather increased. Molecular dynamics simulation results proved that the introduction of PFSs could reduce the binding ability of collagen molecules with water and thus decreased the water molecules around the PFS-treated collagen. These results may provide guidance for the tanners to select retanning agents reasonably to improve the thermal stability of leather.

Graphical Abstract

Conducting polymer hydrogels with electrically-tuneable mechanical properties as dynamic cell culture substrates

Hydrogels are a popular substrate for cell culture due to their mechanical properties closely resembling natural tissue. Stimuli-responsive hydrogels are a good platform for studying cell response to dynamic stimuli. Poly(N-isopropylacrylamide) (pNIPAM) is a thermo-responsive polymer that undergoes a volume-phase transition when heated to 32 °C. Conducting polymers can be incorporated into hydrogels to introduce electrically responsive properties. The conducting polymer, polypyrrole (PPy), has been widely studied as electrochemical actuators due to its electrochemical stability, fast actuation and high strains. We determine the volume-phase transition temperature of pNIPAM hydrogels with PPy electropolymerised with different salts as a film within the hydrogel network. We also investigate the electro-mechanical properties at the transition temperature (32 °C) and physiological temperature (37 °C). We show statistically significant differences in the Young's modulus of the hybrid hydrogel at elevated temperatures upon electrochemical stimulation, with a 5 kPa difference at the transition temperature. Furthermore, we show a three-fold increase in actuation at transition temperature compared to room temperature and physiological temperature, attributed to the movement of ions in/out of the PPy film that induce the volume-phase transition of the pNIPAM hydrogel. Furthermore, cell adhesion to the hybrid hydrogel was demonstrated with mouse articular chondrocytes.

Influence of the second phase on protein adsorption on biodegradable Mg alloys' surfaces: Comparative experimental and molecular dynamics simulation studies

The effect of the second phase on the mechanical properties and corrosion resistance of Mg alloys has been systematically studied. However, there is limited information on the effect of the second phase on protein adsorption behavior. In the present study, the effect of the second phase on protein adsorption on the surfaces of biodegradable Mg alloys was investigated using experimental methods and molecular dynamics (MD) simulations. The experimental results showed that the effect of the second phase on fibrinogen adsorption was type-dependent. Fibrinogen preferentially adsorbed on Y-, Ce-, or Nd-involved second phases, while the second phase containing Zn inhibited its adsorption. MD simulations revealed the mechanism of the second phase that influenced protein adsorption in terms of charge distribution, surface-protein interaction energy, and water molecule distribution. Our studies proposed a deep understanding of the design of Mg-based biomaterials with superior biocompatibility. STATEMENT OF SIGNIFICANCE: Mechanical properties, uniform degradation, and biocompatibility must be considered while designing biomedical Mg alloys. To improve the mechanical properties and corrosion resistance of Mg alloys, the second phase is usually required. However, the effects of the second phase on biocompatibility of Mg alloys have been rarely reported. Here, the influence of the second phase on protein adsorption was experimentally studied by designing Mg alloys with different types of second phase. The first principle calculation and MD simulation were used to reveal the mechanism by which the second phase influences protein adsorption. This work could be used to better elucidate the protein adsorption mechanisms and design principles to improve the biocompatibility of Mg alloys.

A new mechanism for reduced cell adhesion: Adsorption dynamics of collagen on a nanoporous gold surface

Nanostructured materials such as nanoparticles and nanoporous materials strongly affect cell behaviors such as cell viability. Because cellular uptake of nanoporous materials does not occur, mechanisms for the effects of nanoporous materials on cells are different from those of nanoparticles. The effects of nanoporous materials on cells are thought to result from large conformational changes in the extracellular matrix (ECM) induced by the nanoporous materials, although the mechanotransduction and the critical focal adhesion cluster size also have an effect on the cell response. However, we show that the adhesion of mesenchymal stem cells to a gold surface is reduced for nanoporous gold (NPG), despite the conformational changes in collagen induced by NPG being below the detection limits of the experimental analyses. The adsorption dynamics of collagen on NPG are investigated by molecular dynamics simulations to determine the origin of the reduced cell adhesion to NPG. The adsorption energy of collagen on NPG is lower than that on flat gold (FG) despite there being little difference between the global conformation of collagen segments adsorbed on NPG compared with FG. This finding is related to the surface strain of NPG and the limited movement of collagen amino acids owing to interchain hydrogen bonds. The results obtained in this study provide new insight into the interactions between nanostructured materials and the ECM.

Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study

Collagen undergoes many types of post-translational modifications (PTMs), including intracellular modifications and extracellular modifications. Among these PTMs, glycosylation of hydroxylysine (Hyl) is the most complicated. Experimental studies demonstrated that this PTM ceases once the collagen triple helix is formed and that Hyl-O-glycosylation modulates collagen fibrillogenesis. However, the underlying atomic-level mechanisms of these phenomena remain unclear. In this study, we first adapted the force field parameters for O-linkages between Hyl and carbohydrates and then investigated the influence of Hyl-O-glycosylation on the structure of type I collagen molecule, by performing comprehensive molecular dynamic simulations in explicit solvent of collagen molecule segment with and without the glycosylation of Hyl. Data analysis demonstrated that (i) collagen triple helices remain in a triple-helical structure upon glycosylation of Hyl; (ii) glycosylation of Hyl modulates the peptide backbone conformation and their solvation environment in the vicinity and (iii) the attached sugars are arranged such that their hydrophilic faces are well exposed to the solvent, while their hydrophobic faces point towards the hydrophobic portions of collagen. The adapted force field parameters for O-linkages between Hyl and carbohydrates will aid future computational studies on proteins with Hyl-O-glycosylation. In addition, this work, for the first time, presents the detailed effect of Hyl-O-glycosylation on the structure of human type I collagen at the atomic level, which may provide insights into the design and manufacture of collagenous biomaterials and the development of biomedical therapies for collagen-related diseases.