Evolutionarily distinct and sperm-specific supersized chromatin loops are marked by Helitron transposons in Xenopus tropicalis.

Transposable elements (TEs) are abundant in metazoan genomes and have multifaceted effects on host fitness. However, the mechanisms underlying the functions of TEs are still not fully understood. Here, we combine Hi-C, ATAC-seq, and ChIP-seq assays to report the existence of multimegabase supersized loop (SSL) clusters in the Xenopus tropicalis sperm. We show that SSL anchors are inaccessible and devoid of the architectural protein CTCF, RNA polymerase II, and modified histones. Nearly all SSL anchors are marked by Helitrons, a class II DNA transposon. Molecular dynamics simulations indicate that SSL clusters are likely formed via a molecular agent-mediated chromatin condensation process. However, only slightly more SSL anchor-associated genes are expressed at late embryo development stages, suggesting that SSL anchors might only function in sperm. Our work shows an evolutionarily distinct and sperm-specific genome structure marked by a subset of Helitrons, whose establishment and function remain to be explored.

Liposomes embedded with PEGylated iron oxide nanoparticles enable ferroptosis and combination therapy in cancer.

Ferroptosis, an iron-dependent regulated cell death process driven by excessive lipid peroxides, can enhance cancer vulnerability to chemotherapy, targeted therapy and immunotherapy. As an essential upstream process for ferroptosis activation, lipid peroxidation of biological membranes is expected to be primarily induced by intrabilayer reactive oxygen species (ROS), indicating a promising strategy to initiate peroxidation by improving the local content of diffusion-limited ROS in the lipid bilayer. Herein, liposomes embedded with PEG-coated 3 nm γ-Fe2O3 nanoparticles in the bilayer (abbreviated as Lp-IO) were constructed to promote the intrabilayer generation of hydroxyl radicals (•OH) from hydrogen peroxide (H2O2), and the integration of amphiphilic PEG moieties with liposomal bilayer improved lipid membrane permeability to H2O2 and •OH, resulting in efficient initiation of lipid peroxidation and thus ferroptosis in cancer cells. Additionally, Lp-IO enabled traceable magnetic resonance imaging and pH/ROS dual-responsive drug delivery. Synergistic antineoplastic effects of chemotherapy and ferroptosis, and alleviated chemotherapeutic toxicity, were achieved by delivering doxorubicin (capable of xCT and glutathione peroxidase inhibition) with Lp-IO. This work provides an efficient alternative for triggering therapeutic lipid peroxidation and a ferroptosis-activating drug delivery vehicle for combination cancer therapies.

Intramembrane Nanoaggregates of Antimicrobial Peptides Play a Vital Role in Bacterial Killing.

Recent developments in antimicrobial peptides (AMPs) have focused on the rational design of short sequences with less than 20 amino acids due to their relatively low synthesis costs and ease of correlation of the structure-function relationship. However, gaps remain in the understanding of how short cationic AMPs interact with the bacterial outer and inner membranes to affect their antimicrobial efficacy and dynamic killing. The membrane-lytic actions of two designed AMPs, G(IIKK)3 I-NH2 (G3 ) and G(IIKK)4 I-NH2 (G4 ), and previously-studied controls GLLDLLKLLLKAAG-NH2 (LDKA, biomimetic) and GIGAVLKVLTTGLPALISWIKRKR-NH2 (Melittin, natural) are examined. The mechanistic processes of membrane damage and the disruption strength of the four AMPs are characterized by molecular dynamics simulations and experimental measurements including neutron reflection and scattering. The results from the combined studies are characterized with distinctly different intramembrane nanoaggregates formed upon AMP-specific binding, reflecting clear influences of AMP sequence, charge and the chemistry of the inner and outer membranes. G3 and G4 display different nanoaggregation with the outer and inner membranes, and the smaller sizes and further extent of insertion of the intramembrane nanoaggregates into bacterial membranes correlate well with their greater antimicrobial efficacy and faster dynamic killing. This work demonstrates the crucial roles of intramembrane nanoaggregates in optimizing antimicrobial efficacy and dynamic killing.

Hierarchical Assembly of Flexible Biopolymer Polyphosphate-Manganese into Nanosheets.

Polyphosphate (polyP) is one of the most compact inorganic polyanionic biopolymers that participates in various physiological processes. However, the development of polyP-based nanomaterials is still in its infancy. Here, biocompatible polyphosphate-manganese nanosheets are designed and synthesized by a hierarchical assembly strategy. The thickness and the lateral size of the resulting polyP-Mn nanosheets (PMNSs) are 5 nm and 120-130 nm, respectively. Molecular dynamics simulations suggested that the polyP-hexadecyl trimethyl ammonium bromide flat structure possesses a strong aggregating capacity and serves as the template for the 2D assembly of polyP-Mn. The PMNSs can activate the inflammatory response of macrophages resulting in the recovery of innate immunological functions to inhibit tumor proliferation. This work has initiated a new direction in constructing layered polyP-based nanomaterials and provides guidance for biocompatible and biodegradable biopolymer-based materials in the regulation of innate responses.

Orientation and Conformation of Hydrophobin at the Oil-Water Interface: Insights from Molecular Dynamics Simulations.

Hydrophobins, a new class of potential protein emulsifiers, have been extensively employed in the food, pharmaceutical, and chemical industries. However, the knowledge of the underlying molecular mechanism of protein adsorption at the oil-water interface remains elusive. In this study, all-atom molecular dynamics simulations were performed to probe the adsorption orientation and conformation change of class II hydrophobin HFBI at the cyclohexane-water interface. It was proposed that a hydrophobic dipole of the protein could be used to quantitatively predict the orientation of the adsorbed HFBI. Simulation results revealed that HFBI adsorbed at the interface with the patch-up orientation toward the oil phase, regardless of its initial orientations. HFBI's secondary structure was maintained to be intact in the course of simulations despite relatively significant variations in the tertiary structure observed, which could well preserve the bioactivity of HFBI. From the energy analysis, the driving force for interface adsorption was primarily determined by van der Waals interactions between HFBI and cyclohexane. Further analysis indicated that the adsorption orientation and conformation of HFBI at the oil-water interface were typically regulated by the hydrophobic patch and some key residues. This study provides some insights into the orientation, conformation, and adsorption mechanism of proteins at the oil-water interface and theoretical guidelines for the design and development of novel biological emulsifiers involved in the food, pharmaceutical, and chemical industries.

The interplay between surface-functionalized gold nanoparticles and negatively charged lipid vesicles.

The comprehensive understanding of the interactions between gold nanoparticles (AuNPs) and phospholipid vesicles has important implications in various biomedical applications; however, this is not yet well understood. Here, coarse-grained molecular dynamics (CGMD) simulations were performed to study the interactions between functionalized AuNPs and negatively charged lipid vesicles, and the effects of the surface chemistry and surface charge density (SCD) of AuNPs were analyzed. It is revealed that AuNPs with different surface ligands adhere to the membrane surface (anionic AuNPs) or get into the vesicle bilayer (hydrophobic and cationic AuNPs). Due to the loose arrangement of lipid molecules, AuNPs penetrate curved vesicle membranes more easily than planar lipid bilayers. Cationic AuNPs present three different interaction modes with the vesicle, namely insertion, partial penetration and complete penetration, which are decided by the SCD difference. Both hydrophobic interaction and electrostatic interaction play crucial roles in the interplay between cationic AuNPs and lipid vesicles. For the cationic AuNP with a low SCD, it gets into the lipid bilayer without membrane damage through the hydrophobic interaction, and it is finally stabilized in the hydrophobic interior of the vesicle membrane in a thermodynamically stable "snorkeling" configuration. For the cationic AuNP with a high SCD, it crosses the vesicle membrane and gets into the vesicle core through a membrane pore induced by strong electrostatic interaction. In this process, the membrane structure is destroyed. These findings provide a molecular-level understanding of the interplay between AuNPs and lipid vesicles, which may further expand the application of functional AuNPs in modern biomedicine.

Lysozyme Adsorption on Different Functionalized MXenes: A Multiscale Simulation Study.

Recently, MXenes, due to their abundant advantages, have been widely applied in energy storage, separation, catalysis, biosensing, et al. In this study, parallel tempering Monte Carlo and molecular dynamics methods were performed to investigate lysozyme adsorption on different functionalized Ti3C2Tx (-O, -OH, and -F). The simulation results show that lysozyme can adsorb effectively on Ti3C2Tx surfaces, and the order of interaction strength is Ti3C2O2 > Ti3C2F2 > Ti3C2(OH)2. Electrostatics together with van der Waals interactions control protein adsorption. The orientation distributions of lysozyme adsorbed on the Ti3C2O2 and Ti3C2F2 surfaces are more concentrated than that on the Ti3C2(OH)2 surface. During adsorption, the conformation of lysozyme remains stable, suggesting the good biocompatibility of Ti3C2Tx. Besides, the distribution of the interfacial water layer on the Ti3C2Tx surface has a certain impact on protein adsorption. This study provides theoretical insights for understanding the biocompatibility of 2D Ti3C2Tx materials and may help us evaluate the engineering of their surfaces for future biorelated applications.

Simulation Insight into the Synergic Role of Citrate and Polyaspartic Peptide in Biomineralization.

Hydroxyapatite (HAP) is one of the most important inorganic components in biological minerals such as bones and teeth. More than 90% of the total citrate is accumulated in human bones and other biomineralized tissues. In addition, mineralizing proteins are enriched in glutamate and aspartate residues, which are important for their mineral-regulating properties. However, how citrate ions (CITs) and/or acidic amino acids regulate the formation of HAP is still unclear. In this work, molecular dynamics simulations were performed to study how CIT regulates the adsorption behavior of polyaspartic acid (PASP) on the HAP surface in the calcium phosphate solution. The simulation results indicate that PASP can be used as an ion chelator to complex Ca2+ and can serve as templates for HAP mineralization by templating the distribution of Ca2+ on its surface, which are attributed to the -COO- and α-helix structure. Most importantly, the orientation distributions of PASP in all systems are narrower with the help of CIT, thereby PASP can be adsorbed on the HAP surface stably with a "lying-down" orientation. This indicates that CIT can be used as a bridging agent to bond the acidic peptide to the HAP surface in biomineralization. Thus, the synergic role of CIT and the acidic peptide on the HAP surface were revealed in this work, which can provide new insights into the interfacial phenomena during the biomineralization.

Computer Simulations on a pH-Responsive Anticancer Drug Delivery System Using Zwitterion-Grafted Polyamidoamine Dendrimer Unimolecular Micelles.

Unimolecular micelles have attracted wide attention in the field of drug delivery because of their thermodynamic stability and uniform size distribution. However, their drug loading/release mechanisms at the molecular level have been poorly understood. In this work, the stability and drug loading/release behaviors of unimolecular micelles formed using generation-5 polyamidoamine-graft-poly(carboxybetaine methacrylate) (PAMAM(G5)-PCBMA) were studied by dissipative particle dynamics simulations. In addition, the unimolecular micelles formed using generation-5 polyamidoamine-graft-poly(ethyleneglycol methacrylate) (PAMAM(G5)-PEGMA) were used as a comparison. The simulation results showed that PAMAM(G5)-PCBMA can spontaneously form core-shell unimolecular micelles. The PAMAM(G5) dendrimer constitutes a hydrophobic core to load the doxorubicin (DOX), while the zwitterionic PCBMA serves as a protective shell to improve the stability of the unimolecular micelle. The DOX can be encapsulated into the cavity of PAMAM(G5) at the physiological pH 7.4. The drug loading efficiency and drug loading content showed some regularities with the increase in the drug concentration. At the acidic pH 5.0, the loaded DOX can be released gradually from the hydrophobic core. The comparison of DOX-loaded morphologies between the PAMAM(G5)-PCBMA system and PAMAM(G5)-PEGMA system showed that the former has better monodisperse stability. This work could offer theoretical guidance for the design and development of promising unimolecular micelles for drug delivery.

Molecular mechanism of HIV-1 TAT peptide and its conjugated gold nanoparticles translocating across lipid membranes.

The trans-acting activator of transcription (TAT) peptide, which is derived from human immunodeficiency virus-1 (HIV-1), has been widely used as an effective nanocarrier to transport extracellular substances into cells. However, the underlying translocation mechanism of TAT peptide across cell membranes still remains controversial. Besides, the molecular process of TAT peptide facilitating the transport of extracellular substances into cells is largely unknown. In this study, we explore the interactions of TAT peptides and their conjugated gold nanoparticles with lipid membranes by coarse-grained molecular dynamics simulations. It is found that the TAT peptides can hardly penetrate through the membrane at low peptide concentrations; after the concentration increases to a threshold value, they can cross the membrane through an induced nanopore due to the transmembrane electrostatic potential difference. The translocation of TAT peptides is mainly caused by the overall structural changes of membranes. Furthermore, we demonstrate that the translocation of gold nanoparticles (AuNPs) across the membrane is significantly affected by the number of grafted TAT peptides on the particle surface. The transmembrane efficiency of AuNPs may even be reduced when a small number of peptides modify them; whereas, when the number of grafted peptides increases to a certain value, the TAT-AuNP complex can translocate across the membrane in a pore-mediated way. Based on our findings, an effective strategy has been proposed to enhance the delivery efficiency of AuNPs. The present study can improve our understanding of the interactions between TAT peptides and cell membranes; it may also give some insightful suggestions on the design and development of nanocarriers with high efficiency for the delivery of nanoparticles and drugs.

Computer simulations of the adsorption of an N-terminal peptide of statherin, SN15, and its mutants on hydroxyapatite surfaces.

Statherin is a 43 amino acid long protein, which plays an important role in the process of biomineralization of enamel. In this work, we investigated the solvent effect on the adsorption of a peptide from the N-terminus of statherin, SN15, and its mutants SNA15 and SNS15 on the (001) face of hydroxyapatite [Ca10(PO4)6(OH)2, or HAP] with molecular dynamics simulations. The simulation results showed that the adsorption of the three peptides onto the HAP(001) surface was primarily driven by salt-bridge and electrostatic attraction in calcium phosphate (Ca/P) and sodium chloride (NaCl) solutions, respectively. SN15 adsorbs on the HAP surface with the strongest electrostatic interaction, while SNS15 is the weakest. Besides, Ca2+ around SN15 can form an equilateral triangle, which resembles the structure formed by Ca(2) ions in the HAP(001) crystal face, and this looks like the initial stage of HAP nucleation. The conformational changes of SN15 on HAP are analyzed by the root-mean-square deviation. It shows that SN15 is more stable in Ca/P solution while SNS15 is more stable in NaCl solution; the stability of SNA15 is almost the same in both solutions. This work reveals the adsorption mechanism of a series of SN peptides on the HAP surface and provides guidelines for the design of biomaterials for restoring etched enamel and regulating biomineralization.

Bilirubin Oxidase Adsorption onto Charged Self-Assembled Monolayers: Insights from Multiscale Simulations.

The efficient immobilization and orientation of bilirubin oxidase (BOx) on different solid substrates are essential for its application in biotechnology. The T1 copper site within BOx is responsible for the electron transfer. In order to obtain quick direct electron transfer (DET), it is important to keep the distance between the T1 copper site and electrode surface small and to maintain the natural structure of BOx at the same time. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of BOx from Myrothecium verrucaria (MvBOx) adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH2-SAM with different surface charge densities (±0.05 and ±0.19 C·m-2). The results show that MvBOx adsorbs on negatively charged surfaces with a "back-on" orientation, whereas on positively charged surfaces, MvBOx binds with a "lying-on" orientation. The locations of the T1 copper site are closer to negatively charged surfaces. Furthermore, for negatively charged surfaces, the T1 copper site prefers to orient closer to the surface with lower surface charge density. Therefore, the negatively charged surface with low surface charge density is more suitable for the DET of MvBOx on electrodes. Besides, the structural changes primarily take place on the relatively flexible turns, coils, and α-helix. The native structure of MvBOx is well preserved when it adsorbs on both charged surfaces. This work sheds light on the controlling orientation and conformational information on MvBOx on charged surfaces at the atomistic level. This understanding would certainly promote our understanding of the mechanism of MvBOx immobilization and provide theoretical support for BOx-based bioelectrode design.

Understanding the Cellular Uptake of pH-Responsive Zwitterionic Gold Nanoparticles: A Computer Simulation Study.

Surface functionalization of nanoparticles (NPs) with stealth polymers (e.g., hydrophilic and zwitterionic polymers) has become a common strategy to resist nonspecific protein adsorption recently. Understanding the role of surface decoration on NP-biomembrane interactions is of great significance to promote the application of NPs in biomedical fields. Herein, using coarse-grained molecular dynamics (CGMD) simulations, we investigate the interactions between stealth polymer-coated gold nanoparticles (AuNPs) and lipid membranes. The results show that AuNPs grafted with zwitterionic polymers can more easily approach the membrane surface than those coated with hydrophilic poly(ethylene glycol) (PEG), which can be explained by the weak dipole-dipole interaction between them. For zwitterionic AuNPs which can undergo pH-dependent charge conversion, different interaction modes which depend on the polymer protonation degree are found. When the protonation degree is low, the particles just adsorb on the membrane surface; at moderate protonation degrees, the particles can directly translocate across the lipid membrane through a transient hydrophilic pore formed on the membrane surface; the particles are fully wrapped by the curved lipid membrane at high protonation degrees, which may lead to endocytosis. Finally, the effect of polymer chain length on the cellular uptake of zwitterionic polymer-coated AuNPs is considered. The results demonstrate that longer polymer chain length will block the translocation of AuNPs across the lipid membrane when the protonation degree is not high; however, it can improve the transmembrane efficiency of AuNPs at high protonation degrees. We expect that these findings are of immediate interest to the design and synthesis of pH-responsive nanomaterials based on zwitterionic polymers and can prompt their further applications in the field of biomedicine.

Computer simulations on the pH-sensitive tri-block copolymer containing zwitterionic sulfobetaine as a novel anti-cancer drug carrier.

In this work, dissipative particle dynamics (DPD) simulations were performed to study the self-assembled microstructures and doxorubicin (DOX) loading/release properties of pH-sensitive amphiphilic triblock copolymer: poly(ε-caprolactone)-b-poly(diethylaminoethyl methacrylate)-b-poly(sulfobetaine methacrylate) or poly (ethylene glycol methacrylate) (PCL-PDEA-PSBMA/PEGMA). Our results show that both copolymers can self-assemble into core-shell-corona micelles in aqueous environment. However, the corona structures are quite different for the two copolymer micelles. The shell layers formed by PEGMA have heterogeneous sizes while the shell layers in PCL-PDEA-PSBMA micelles are homogenous. This is mainly attributed to the stronger hydrophilicity of PSBMA than PEGMA. As the mole concentration of copolymer is increased from 10% to 50%, the microstructures formed by PCL-PDEA-PSBMA and DOX remains spherical micelles whereas PCL-PDEA-PEGMA undergoes structural transition from spherical to cylindrical and finally to lamellar micelles. Interestingly, the studied micelles have a pH-responsive drug release property, owing to the protonation of the PDEA block. The drug release process follows a "swelling-demicellization-release" mode. The multi-scale simulations demonstrate an avenue to the optimal design of nanomaterials for drug delivery with desired properties.

Molecular Understanding of the Penetration of Functionalized Gold Nanoparticles into Asymmetric Membranes.

In this work, the interactions between surface-functionalized gold nanoparticles (AuNPs) and asymmetric membranes and the associated cytotoxicity were explored by coarse-grained molecular dynamics simulations. Simulation results show that the surface chemistry of AuNPs and the asymmetry of lipid membranes play significant roles. AuNPs with different signs of charges spontaneously adhere to the membrane surface or penetrate the membrane core. Also, the asymmetric distribution of charged lipids in membranes can facilitate the penetration of cationic AuNPs. Increasing the surface charge density (SCD) of AuNPs can not only improve the penetration efficiency but also lead to more disruption of the membrane structure. Moreover, the flip-flop of charged lipids in the inner leaflet can be observed during the translocation of AuNPs with a high SCD. The breakdown of membrane asymmetry may hinder the cellular internalization of AuNPs in a direct penetration mechanism. More importantly, we demonstrate that the hydrophobic contact between protruding solvent-exposed lipid tails and the hydrophobic moieties of ligands can mediate the insertion of AuNPs with a low SCD into cell membranes, which will exhibit less cytotoxicity in most in vivo applications. This may open a new exciting avenue to developing nanocarriers with a higher translocation efficiency and a lower toxicity simultaneously for biomedical applications.

Structural properties of polymer-brush-grafted gold nanoparticles at the oil-water interface: insights from coarse-grained simulations.

In this work, the structural properties of amphiphilic polymer-brush-grafted gold nanoparticles (AuNPs) at the oil-water interface were investigated by coarse-grained simulations. The effects of grafting architecture (diblock, mixed and Janus brush-grafted AuNPs) and hydrophilicity of polymer brushes are discussed. Simulation results indicate that functionalized AuNPs present abundant morphologies including typical core-shell, Janus-type, jellyfish-like, etc., in a water or oil-water solvent environment. It is found that hydrophobic/weak hydrophilic polymer-brush-grafted AuNPs have better phase transfer performance, especially for AuNPs modified with hydrophobic chains as outer blocks and weak hydrophilic chains as inner blocks. This kind of AuNP can cross the interface region and move into the oil phase completely. For hydrophobic/strong hydrophilic polymer-brush-grafted AuNPs, they are trapped in the interface region instead of moving into any phase. The mechanism of phase transfer is ascribed to the flexibility and mobility of outer blocks. Besides, we study the desorption energy by PMF analysis. The results demonstrate that Janus brush-grafted AuNPs show the highest interfacial stability and activity, which can be further strengthened by increasing the hydrophilicity of grafted polymer brushes. This work will promote the industrial applications of polymer-brush-grafted NPs such as phase transfer catalysis and Pickering emulsion catalysis.