How graphene affects the misfolding of human prion protein: A combined experimental and molecular dynamics simulation study

Zhu, Yafang; Guo, Jingjing; Ai, Zhang; Li, Lanlan; Liu, Xuewei; Liu, Huanxiang; Yao, Xiaojun

doi:10.1016/j.envres.2018.12.057

Cited by 8 publications

(7 citation statements)

References 70 publications

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“…Because of the inherent plane structure of the b-sheet, its structure remains largely unchanged after adsorption. 57,[60][61][62] Conversely, the denaturation of the a-helix protein structure was observed in the simulation, aligning with the findings observed with carbon nanotubes (CNTs) and GRA. [63][64][65] This indicates that the individual a-helix structure may undergo denaturation on GRA/h-BN, whereas the b-sheet structure remains intact.…”

Section: Structural Changes Of Protein On the Gra/h-bn Heterojunctionsupporting

confidence: 85%

Theoretical study of protein adsorption on graphene/h-BN heterostructures

Lan,

Peng,

Liang

et al. 2023

Phys. Chem. Chem. Phys.

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Section: Structural Changes Of Protein On the Gra/h-bn Heterojunctionsupporting

confidence: 85%

Theoretical study of protein adsorption on graphene/h-BN heterostructures

Lan,

Peng,

Liang

et al. 2023

Phys. Chem. Chem. Phys.

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“…85 This was attributed to high mobility of LPDMS that can inhibit heterogeneous nucleation on the substrate. Our methodology, a combination of AA and 40 2015 graphene lysozyme −320 Vilhena et al 41 2016 graphene BSA −236, −106 Vilhena et al 42 2016 graphene IgG −545, −1150 Samieegohar et al 43 2017 gold lysozyme −55 Zhu et al 44 2019 graphene PrP 117−231 −176, −297 a We assume the difference between the free energies of the protein on the surface and in bulk water as the adsorption free energy. The minimum and maximum values are listed for studies in which the free energy of the protein is calculated with different orientations on the surface.…”

Section: Discussionmentioning

confidence: 99%

High Antifouling Performance of Weakly Hydrophilic Polymer Brushes: A Molecular Dynamics Study

Yagasaki,

Matubayasi

2024

Langmuir

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The antifouling performance of polymer brushes usually improves with increasing hydrophilicity of the grafted polymer. However, in some cases, less hydrophilic polymers show comparable or better antifouling performance than do more hydrophilic polymers. We investigate the mechanism of this anomalous behavior using molecular dynamics (MD) simulations of coarse−grained (CG) models of weakly and strongly hydrophilic polymers. The antifouling performance is evaluated from the potential of mean force of a model protein.The strongly hydrophilic polymer exhibits a better antifouling performance than the weakly hydrophilic polymer when the substrate of the polymer brush is repulsive. However, when the substrate is sufficiently attractive, the weakly hydrophilic polymer brush becomes more effective than the strongly hydrophilic brush in a certain range of grafting density. This is because the weakly hydrophilic polymer chains form a tightly packed layer that prevents the adsorbate molecule from contacting the substrate. We also perform all-atom (AA) MD simulations for several standard polymers to examine the correspondence with the CG polymer models. The weakly hydrophilic CG polymer is found to be similar to poly[N-(2hydroxypropyl)methacrylamide] and poly(2-hydroxyethyl methacrylate), both of which have a hydroxyl group in a monomer unit. The strongly hydrophilic CG polymer resembles zwitterionic poly(carboxybetaine methacrylate). A discussion referring to the adsorption free energies of proteins on surfaces calculated in previous AA MD studies suggests that the higher antifouling performance of less hydrophilic polymer brushes can be realized for various combinations of protein and surface.

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“…All bonds comprising hydrogen atoms were constrained using the SHAKE algorithm during the MD simulations . The binding energies through MD simulations have been evaluated for the RBD interactions with surfaces of different metals using the molecular mechanics generalized born surface area (MM-GBSA) method. − Previous studies indicated that MM-GBSA can provide a remarkable estimation of the affinity of the proteins and biomolecules to different adsorbents including graphene, graphene oxide, gold surface, and gold self-assembled monolayer. − The binding energies were calculated from the final 5000 frames of the product step (50 ns). The details of the MM-GBSA method are presented in the Supporting Information.…”

Section: Methodsmentioning

confidence: 99%

“… 61 − 63 Previous studies indicated that MM-GBSA can provide a remarkable estimation of the affinity of the proteins and biomolecules to different adsorbents including graphene, graphene oxide, gold surface, and gold self-assembled monolayer. 64 − 69 The binding energies were calculated from the final 5000 frames of the product step (50 ns). The details of the MM-GBSA method are presented in the Supporting Information .…”

Section: Methodsmentioning

confidence: 99%

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study

Khavani

Mehranfar

Mofrad

2023

J. Chem. Inf. Model.

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The novel coronavirus disease and its complications have motivated the design of new sensors with the highest sensitivity, and affinity for the detection of the SARS-CoV-2 virus is considered in many research studies. In this research article, we employ full atomistic molecular dynamics (MD) models to study the interactions between the receptor binding domain (RBD) and spike protein of the coronavirus and different metals such as gold (Au), platinum (Pt), and silver (Ag) to analyze their sensitivity against this virus. The comparison between the RBD interactions with ACE2 (angiotensin-converting enzyme 2) and different metals indicates that metals have remarkable effects on the structural features and dynamical properties of the RBD. The binding site of the RBD has more affinity to the surfaces of gold, platinum, and silver than to the other parts of the protein. Moreover, the initial configuration of the RBD relative to the metal surface plays an important role in the stability of metal complexes with the RBD. The binding face of the protein to the metal surface has been changed in the presence of different metals. In other words, the residues of the RBD that participate in RBD interactions with the metals are different irrespective of the initial configurations in which the [Asn, Thr, Tyr], [Ser, Thr, Tyr], and [Asn, Asp, Tyr] residues of the protein have a greater affinity to Ag, Au, and Pt, respectively. The corresponding metals have a considerable affinity to the RBD, which due to strong interactions with the protein can change the secondary structure and structural features. Based on the obtained results during the complexation process between the protein and metals, the helical structure of the protein changes to the bend and antiparallel β-sheets. The calculated binding energies for the RBD complexes with silver, gold, and platinum are −95.03, −138.03, and −133.96 kcal·mol–1, respectively. The adsorption process of the spike protein on the surfaces of different metals represents similar results and indicates that the entire spike protein of the coronavirus forms a more stable complex with the gold surface compared with other metals. Moreover, the RBD of the spike protein has more interactions with the surfaces than with the other parts of the protein. Therefore, it is possible to predict the properties of the coronavirus on the metal surface based on the dynamical behavior of the RBD. Overall, our computational results confirm that the gold surface can be considered as an outstanding substrate for developing new sensors with the highest sensitivity against SARS-CoV-2.

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How graphene affects the misfolding of human prion protein: A combined experimental and molecular dynamics simulation study

Cited by 8 publications

References 70 publications

Theoretical study of protein adsorption on graphene/h-BN heterostructures

Theoretical study of protein adsorption on graphene/h-BN heterostructures

High Antifouling Performance of Weakly Hydrophilic Polymer Brushes: A Molecular Dynamics Study

On the Sensitivity and Affinity of Gold, Silver, and Platinum Surfaces against the SARS-CoV-2 Virus: A Comparative Computational Study

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