md simulation
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Nanomaterials ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 247
Hao Zhang ◽  
Ling Pan ◽  
Xuqing Xie

Droplets impinging on solid surfaces is a common phenomenon. However, the motion of surfaces remarkably influences the dynamical behaviors of droplets, and related research is scarce. Dynamical behaviors of water nanodroplets impinging on translation and vibrating solid copper surfaces were investigated via molecular dynamics (MD) simulation. The dynamical characteristics of water nanodroplets with various Weber numbers were studied at four translation velocities, four vibration amplitudes, and five vibration periods of the surface. The results show that when water nanodroplets impinge on translation surfaces, water molecules not only move along the surfaces but also rotate around the centroid of the water nanodroplet at the relative sliding stage. Water nanodroplets spread twice in the direction perpendicular to the relative sliding under a higher surface translation velocity. Additionally, a formula for water nanodroplets velocity in the translation direction was developed. Water nanodroplets with a larger Weber number experience a heavier friction force. For cases wherein water nanodroplets impinge on vibration surfaces, the increase in amplitudes impedes the spread of water nanodroplets, while the vibration periods promote it. Moreover, the short-period vibration makes water nanodroplets bounce off the surface.

E.I. Fatullaev ◽  
V.V. Bezrodnyi ◽  
I.M. Neelov

Biocompatible peptide dendrimers and dendrigrafts have useful properties for application in biomedicine. In previous papers the computational approach for study lysine dendrimers and dendrigrafts as well as their complexes with various medical peptides was used. In this paper the comparison of complex formation between molecules of therapeutic AEDG tetrapeptide and novel K2R peptide dendrimer or DG2 dendrigraft of near the same size and charge was fulfilled. The systems consisting of 16 therapeutic AEDG tetrapeptide molecules and one dendrimer or one dendrigraft were studied by molecular dynamics simulation. Full atomic models of these molecules in water with explicit counterions were used for this goal. First of all, the process of complex formation was studied. It was obtained that peptide molecules were attracted by both branched molecules and were quickly adsorbed by them. Times of complexes formation as well as size, anisotropy and structure of each complex were calculated. It was demonstrated that both K2R dendrimer and DG2 dendrigraft are effective for complexation of these peptide molecules but new dendrimer complex is more stable than dendrigraft complex because it has almost twice more hydrogen bonds with peptide molecules and 33% more ion pairs with their charged groups.

2022 ◽  
Yohei Harada ◽  
Akemi Sato ◽  
Mitsugu Araki ◽  
Shigeyuki Matsumoto ◽  
Yuta Isaka ◽  

Abstract Purpose Dealing with variants of unknown significance (VUS) is an important issue in the clinical application of NGS-based cancer gene panel tests. We detected a novel ERBB2 extracellular domain VUS, c.1157A > G p.(E401G), in a cancer gene panel test. Since the mechanisms of activation by ERBB2 extracellular domain (ECD) variants are not fully understood, we aimed to clarify those mechanisms and the biological functions of ERBB2 E401G. Methods ERBB2 E401G was selected as VUS for analysis because multiple software tools predicted its pathogenicity. We prepared ERBB2 expression vectors with the E401G variant as well as vectors with S310F and E321G, which are known to be activating mutations. On the basis of wild-type ERBB2 or mutant ERBB2 expression in cell lines without ERBB2 amplification or variants, we evaluated the phosphorylation of human epidermal growth factor receptor 2 and related proteins, and investigated with molecular dynamics (MD) simulation the mechanisms conferred by the variants. The biological effects of ERBB2 E401G were also investigated, both in vitro and in vivo. Results We found that ERBB2 E401G enhances C-terminal phosphorylation in a way similar to S310F. MD simulation analysis revealed that these variants maintain the stability of the EGFR-HER2 heterodimer in a ligand-independent manner. Moreover, ERBB2 E401G-transduced cells showed an increased invasive capacity in vitro and an increased tumor growth capacity in vivo. Conclusion Our results provide important information on the activating mechanisms of ERBB2 extracellular domain (ECD) variants and illustrate a model workflow integrating wet and dry bench processes for the analysis of VUS detected with cancer gene panel tests.

2022 ◽  
Vol 8 ◽  
Alexander A. Malär ◽  
Morgane Callon ◽  
Albert A. Smith ◽  
Shishan Wang ◽  
Lauriane Lecoq ◽  

Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from  240 copies of the Cp149 core protein. We measure both T1 and T1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.

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