Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide

Zeng, Songwei; Zhou, Guoquan; Guo, Jian-Zhong; Zhou, Feng; Chen, Junlang

doi:10.1038/srep24906

Cited by 22 publications

(17 citation statements)

References 40 publications

(44 reference statements)

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“…The action of GO was investigated more explicitly by representing the substrate using the Lerf-Klinowski model (Lerf et al, 1998 ), which describes the behavior of a standard oxidation process. Using this approach, two paradigmatic articles (Sun et al, 2014 ; Zeng et al, 2016 ) demonstrated that GO displays an enhanced adsorption of the attached protein. Firstly, in Sun et al ( 2014 ), an atomistic description of the inhibitory action of GO on the activity of α-chymotrypsin (ChT), has been provided.…”

Section: Computational Modeling and Simulations Of Graphene-interactimentioning

confidence: 99%

Interfacing Graphene-Based Materials With Neural Cells

Bramini

Alberini

Colombo

et al. 2018

Front. Syst. Neurosci.

105

114

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The scientific community has witnessed an exponential increase in the applications of graphene and graphene-based materials in a wide range of fields, from engineering to electronics to biotechnologies and biomedical applications. For what concerns neuroscience, the interest raised by these materials is two-fold. On one side, nanosheets made of graphene or graphene derivatives (graphene oxide, or its reduced form) can be used as carriers for drug delivery. Here, an important aspect is to evaluate their toxicity, which strongly depends on flake composition, chemical functionalization and dimensions. On the other side, graphene can be exploited as a substrate for tissue engineering. In this case, conductivity is probably the most relevant amongst the various properties of the different graphene materials, as it may allow to instruct and interrogate neural networks, as well as to drive neural growth and differentiation, which holds a great potential in regenerative medicine. In this review, we try to give a comprehensive view of the accomplishments and new challenges of the field, as well as which in our view are the most exciting directions to take in the immediate future. These include the need to engineer multifunctional nanoparticles (NPs) able to cross the blood-brain-barrier to reach neural cells, and to achieve on-demand delivery of specific drugs. We describe the state-of-the-art in the use of graphene materials to engineer three-dimensional scaffolds to drive neuronal growth and regeneration in vivo, and the possibility of using graphene as a component of hybrid composites/multi-layer organic electronics devices. Last but not least, we address the need of an accurate theoretical modeling of the interface between graphene and biological material, by modeling the interaction of graphene with proteins and cell membranes at the nanoscale, and describing the physical mechanism(s) of charge transfer by which the various graphene materials can influence the excitability and physiology of neural cells.

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Section: Computational Modeling and Simulations Of Graphene-interactimentioning

confidence: 99%

Interfacing Graphene-Based Materials With Neural Cells

Bramini

Alberini

Colombo

et al. 2018

Front. Syst. Neurosci.

105

114

View full text Add to dashboard Cite

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“…For example, an HIV-1 regulatory protein undergoes α-helix to β-sheet structural changes upon graphene association [18]. Similarly, VPR 13-33 adsorption on the graphene oxide surface caused the loss of secondary structure [42]. Strong dispersion interactions of the solvent-exposed basic residues and graphene can provide the major driving force [41] for protein structural changes.…”

Section: Resultsmentioning

confidence: 99%

Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments

Jeevan

Pokhrel

Bhattarai

et al. 2017

Biochemical and Biophysical Research Communications

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Ebola virus infections cause hemorrhagic fever that often results in very high fatality rates. In addition to exploring vaccines, development of drugs is also essential for treating the disease and preventing the spread of the infection. The Ebola virus matrix protein VP40 exists in various conformational and oligomeric forms and is a potential pharmacological target for disrupting the virus life-cycle. Here we explored graphene-VP40 interactions using molecular dynamics simulations and graphene pelleting assays. We found that graphene sheets associate strongly with VP40 at various interfaces. We also found that the graphene is able to disrupt the C-terminal domain (CTD-CTD) interface of VP40 hexamers. This VP40 hexamer-hexamer interface is crucial in forming the Ebola viral matrix and disruption of this interface may provide a method to use graphene or similar nanoparticle based solutions as a disinfectant that can significantly reduce the spread of the disease and prevent an Ebola epidemic.

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“…The solvent-accessible surface area was calculated with the Gromacs library [ 36]. The contacting surface area can be then calculated using the following formula: CSA = (SASA Peptide(s) + SASA DNA -SASA Peptide(s)-DNA)/2 [ 37]. Initially, the CSA was close to zero due to the distance between peptides and DNA.…”

Section: Contacting Surface Areamentioning

confidence: 99%

Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

Pirkhezranian

Tahmurespur

Daura

et al. 2019

Preprint

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Background: Lactoferrampin (LFampin), Lactoferricin (LFcin), and LFchimera are three well-known antimicrobial peptides derived from Lactoferrin and proposed as alternatives for antibiotics. Although the intracellular activity of these peptides has been previously demonstrated, their mode of action is not yet fully understood. Here, we performed a molecular dynamics simulation study to understand the molecular interactions between camel Lactoferrin derived peptides, including CLFampin, CLFcin, and CLFchimera, and DNA as an important intracellular target. Results: Our results indicate that all three peptides bind to DNA, albeit with different propensities, with CLFchimera showing the highest binding affinity. The secondary structures of the peptides, modeled on Lactoferrin, did not undergo significant changes during simulation, supporting their functional relevance. Main residues involved in the peptide-DNA interaction were identified based on binding free energy estimates calculated over 200 ns, which, as expected, confirmed strong electrostatic interactions between DNA phosphate groups and positively charged peptide side chains. Interaction between the different concentrations of CLFchimera and DNA revealed that after binding of four copies of CLFchimera to DNA, hydrogen bonds between the two strands of DNA start to break from one of the termini. Conclusions: Importantly, our results revealed that there is no DNA-sequence preference for peptide binding, in line with a broad antimicrobial activity. Moreover, the results showed that the strength of the interaction between DNA and CLFchimera is concentration dependent. The insight provided by these results can be used for the rational redesign of natural antimicrobial peptides targeting the bacterial DNA.

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Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide

Cited by 22 publications

References 40 publications

Interfacing Graphene-Based Materials With Neural Cells

Interfacing Graphene-Based Materials With Neural Cells

Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments

Interaction of camel Lactoferrin derived peptides with DNA: a molecular dynamics study

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