coarse grained molecular dynamics

  • 文章类型: Journal Article
    纳米材料的灵活性具有挑战性,但值得针对生物医学应用进行调整。生物相容性二氧化硅纳米材料正在进行广泛的探索,但尽管具有聚合物性质,但很少观察到表现出柔韧性。在这里,据报道,超薄柔性二氧化硅纳米片(NS)是一种简单的一步法路线,其低厚度和高直径厚度比使折叠。可以容易地调节厚度和直径以实现受控的柔性。机理研究表明,除了常用的表面活性剂,带有两个疏水尾巴的“不常见”在生产片状/层状/带壳结构中起指导作用,而乙醇的添加适当地减轻了组装的表面活性剂的强界面张力,否则会产生大卷曲的片状结构。有了这些超薄NS,进一步表明,细胞对颗粒形状和刚性的偏好高度依赖于纳米颗粒的表面化学:在高颗粒细胞亲和力下,NS,尤其是柔性的将被哺乳动物细胞优选用于内化或附着,而当亲和力较低时,此首选项基本上是无效的。因此,超薄二氧化硅NSs的性能可以通过表面化学有效地扩展和增强,以实现改进的生物传感或药物递送。
    Flexibility of nanomaterials is challenging but worthy to tune for biomedical applications. Biocompatible silica nanomaterials are under extensive exploration but are rarely observed to exhibit flexibility despite the polymeric nature. Herein, a facile one-step route is reported to ultrathin flexible silica nanosheets (NSs), whose low thickness and high diameter-to-thickness ratio enables folding. Thickness and diameter can be readily tuned to enable controlled flexibility. Mechanism study reveals that beyond the commonly used surfactant, the \"uncommon\" one bearing two hydrophobic tails play a guiding role in producing sheeted/layered/shelled structures, while addition of ethanol appropriately relieved the strong interfacial tension of the assembled surfactants, which will otherwise produce large curled sheeted structures. With these ultrathin NSs, it is further shown that the cellular preference for particle shape and rigidity is highly dependent on surface chemistry of nanoparticles: under high particle-cell affinity, NSs, and especially the flexible ones will be preferred by mammalian cells for internalization or attachment, while this preference is basically invalid when the affinity is low. Therefore, properties of the ultrathin silica NSs can be effectively expanded and empowered by surface chemistry to realize improved bio-sensing or drug delivery.
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  • 文章类型: Journal Article
    Serotonin (5-HT) receptors have been shown to homodimerize and heterodimerize with other G protein-coupled receptors (GPCRs), although the details of this process have not yet been elucidated. Here we use coarse-grained molecular dynamics on monomeric 5-HT2C receptors to predict the transmembrane (TM) helices involved in such associations. All these simulations were carried out both in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayers and in mixed composition POPC-Cholesterol ones, to show whether the presence of cholesterol could directly influence and drive the dimeric association. The goal is to get insights on the self-assembly pathway leading to GPCRs 5-HT2C oligomerization, which is supposed to be the basis of its constitutional activity. From the analysis of the molecular dynamics trajectories, we observed the formation of 5-HT2C oligomers through self-assembly and we identified the main domains involved in the receptor dimerization. In particular, dimers and oligomers from the two different environments show TM4-TM5 and TM1-TM7-H8 as the preferential dimerization interfaces. Nevertheless, substantial differences arise for oligomers in POPC and in POPC-Chol membranes: in POPC-Chol the variability of dimers interfaces is strictly limited to the TM1-TM7-H8 and TM4-TM5 interfaces and the dimorphism depends on cholesterol that directly participates in its formation. These results are in agreement with both experimental evidences and other computational studies conducted on other GPCRs oligomerization.
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  • 文章类型: Journal Article
    We performed an extensive computational study to obtain insight in the molecular mechanisms that take place prior to membrane fusion. We focused on membrane-anchored hybrid macromolecules (lipid-polymer-oligopeptide) that mimic biological SNARE proteins in terms of liposome fusion characteristics [H. Robson Marsden et al., 2009]; efficient micro-second simulation was enabled by combining validated MARTINI force fields for the molecular building blocks in coarse-grained molecular dynamics (CGMD). We find that individual peptide domains in the hybrid macromolecules bind and partially integrate parallel to the membrane surface, in agreement with experimental findings. By varying several experimental design parameters, we observe that peptide domains remain in the solvent phase only in two cases: (1) for solitary lipopeptides (low concentration), below a threshold area per lipid in the membrane, and (2) when the lipopeptide concentration is high enough for the peptide domains to self-assemble into tetrameric homo-complexes. The peptide-membrane binding is not affected by solvent-induced peptide unfolding, which we mimicked by relaxing the usual MARTINI helix constraints. Remarkably, in this case, a reverse transition to a helical secondary structure is observed after binding, highlighting the role of the membrane as a template (partitioning-folding coupling). Our findings undermine the current view of the initial stages towards fusion, in which membranes are thought to be kept in close apposition via dimerization of individual complementary peptides in the solvent phase. Although we did not study actual fusion, our simulations show that the formation of homomers, which is suppressed in experimental peptide-pair design and therefore believed to be insignificant for fusion, by peptides anchored to the same membrane does play a key role in this locking mechanism and potentially also in membrane destabilization that precede fusion.
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