Rotavirus VP6 protein as a bio-electrochemical scaffold: Molecular dynamics and experimental electrochemistry

García-García, Wendy I.; Vidal-Limón, Abraham; Arrocha-Arcos, A.A.; Palomares, Laura A.; Ramı́rez, Octavio T.; Miranda-Hernández, M.

doi:10.1016/j.bioelechem.2019.02.012

Cited by 9 publications

(7 citation statements)

References 27 publications

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“…However, we did not observe the charge transfer reaction of potassium ferricyanide when this protein was encapsulated (Figure 2). These results demonstrated that VP6 protein could be used as conductive scaffold for the development of different BEI applications [41].…”

Section: Molecular Dynamics As a Tool To Predict The Electrochemical mentioning

confidence: 74%

“…Therefore, our previous data on viral capsids can serve as a workflow to identify candidate proteins or enzymes for construction of BEI devices. Altogether, theoretical and experimental reports on BEI [41][42][43] are examples of how structural information could help to elucidate the behavior of biological systems during electrochemical reactions. Nonetheless, the aforementioned studies depend on structural information from biomolecules, and certain biomolecules are very complex and highly labile, which difficult elucidation of atomic positions.…”

Section: Molecular Dynamics As a Tool To Predict The Electrochemical mentioning

confidence: 99%

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Design of Bioelectrochemical Interfaces Assisted by Molecular Dynamics Simulations

Vidal-Limón¹,

Huerta-Miranda²,

García-García³

et al. 2021

Homology Molecular Modeling - Perspectives and Applications

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The design of bioelectrochemical interfaces (BEI) is an interesting topic that recently demands attention. The synergy between biomolecules and chemical components is necessary to achieve high molecular selectivity and sensitivity for the development of biosensors, synthesis of different compounds, or catalytic processes. For most BEI, the charge transfer process occurs in environments with particular chemical conditions; modeling these environments is a challenging task and requires multidisciplinary efforts. These interfaces can be composed of biomolecules, such as proteins, DNA, or more complex systems like microorganisms. Oxidoreductases enzymes are good candidates, among others, due to their catalytic activities and structural characteristics. In BEI, enzymes are immobilized on conductive surfaces to improve charge transfer processes. Covalent immobilization is the most common method to prolong lifetime or modulate the detection process. However, it is necessary to implement new methodologies that allow the selection of the best candidates for a more efficient design. Homology modeling of oxidoreductases combined with Molecular Dynamics (MD) simulation methods are alternative and already routinely used tools to investigate the structure, dynamics, and thermodynamics of biological molecules. Our motivation is to show different techniques of molecular modeling (Homology Modeling, Gaussian accelerated molecular dynamics, directed adaptive molecular dynamics and electrostatic surface calculations), and using horseradish peroxidase as a model to understand the interactions between biomolecules and gold nanoclusters (as current collector). Additionally, we present our previous studies considering molecular simulations and we discuss recent advances in biomolecular simulations aimed at biosensor design.

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Section: Molecular Dynamics As a Tool To Predict The Electrochemical mentioning

confidence: 74%

Section: Molecular Dynamics As a Tool To Predict The Electrochemical mentioning

confidence: 99%

Design of Bioelectrochemical Interfaces Assisted by Molecular Dynamics Simulations

Vidal-Limón¹,

Huerta-Miranda²,

García-García³

et al. 2021

Homology Molecular Modeling - Perspectives and Applications

View full text Add to dashboard Cite

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“…( A ) Different expression systems from prokaryotic E. coli [ 2 , 72 , 126 ] to eukaryotic systems such as yeast [ 17 ], insect cell/baculovirus systems (IC-BV) [ 38 , 67 ], mammalian cells [ 38 ], HSV-1 [ 90 ], and plant cells [ 37 , 89 , 127 ] have been used successfully to produce assembled structures of VP6 tubes/VLPs. ( B ) Applications of VP6 tubes/VLPs, as vaccines (immunogenicity and protection) [ 15 , 44 , 54 , 55 , 64 – 66 , 70 , 95 , 108 ], adjuvants [ 15 , 16 , 55 , 76 – 78 , 108 – 110 ], immunological carriers [ 49 , 53 , 92 , 96 , 102 , 111 ], drug delivery tools [ 5 , 91 , 122 , 126 ], and nano-biomaterials [ 5 , 23 , 24 , 41 , 42 , 50 , 91 , 122 , 126 ] …”

Section: Vp6 Expression and Formation Of Structured Vp6 Tubes/vlpsmentioning

confidence: 99%

“…Some examples are insertion of (i) a peptide derived from the RV VP4 protein, (ii) a 14-amino-acid peptide derived from simian paramyxovirus 5 (V5 epitope), (iii) three epitopes of poliovirus type 1, (iv) three epitopes derived from the VP4 of RV, (v) two peptides (23 and 140 amino acids) derived from the M2 and HA genes of influenza A virus, and (vi) the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein (S) to the surface loops or N-terminus of VP6 [ 49 , 53 , 92 , 96 , 102 , 111 ] (iv) Drug delivery Biocompatible and biodegradable RV VP6 structured protein assemblies in the form of nanotubes/VLPs are capable of encapsulating therapeutic reagents for drug delivery and have been used successfully for treatment of diseases such as cancer. [ 5 , 91 , 122 , 126 ] (v) Nano-biomaterials The VP6 tubes/VLPs form multifunctional scaffolds that can be used to create bio-electrochemical interfaces for construction of organized metallic nano-biomaterials (silver, gold, platinum), and palladium (Pd) [ 5 , 23 , 24 , 41 , 42 , 50 , 91 , 122 , 126 ] …”

Section: Vp6 Expression and Formation Of Structured Vp6 Tubes/vlpsmentioning

confidence: 99%

Rotavirus VP6: involvement in immunogenicity, adjuvant activity, and use as a vector for heterologous peptides, drug delivery, and production of nano-biomaterials

et al. 2022

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The first-generation, live attenuated rotavirus (RV) vaccines, such as RotaTeq and Rotarix, were successful in reducing the number of RV-induced acute gastroenteritis (AGE) and child deaths globally. However, the low efficacy of these first-generation oral vaccines, coupled with safety concerns, required development of improved RV vaccines. The highly conserved structural protein VP6 is highly immunogenic, and it can generate self-assembled nano-sized structures, including tubes and spheres (virus-like particles; VLPs). Amongst the RV proteins, only VP6 shows these features. Interestingly, VP6-assembled structures, in addition to being highly immunogenic, have several other useful characteristics that could allow them to be used as adjuvants, immunological carriers, and drug-delivery vehicles as well as acting a scaffold for production of valuable nano-biomaterials. This review provides an overview of the self-assembled nano-sized structures of VP6-tubes/VLPs and their various functions.

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“…An interesting feature of VP6 is its behavior as conducting material that allows charge transfer processes and metal electrodeposition [8]. Moreover, it is structurally polymorphic since it forms tubular particles (100 nm in diameter) at pH 5.0-9.0, spherical particles (45 nm in diameter) at pH 4.0, and sheets in pH changes from 6.0 to 4.0 [9][10].…”

Section: Introductionmentioning

confidence: 99%

Structural Variations Induced by Temperature Changes in Rotavirus VP6 Protein Immersed in an Electric Field and Their Effects on Epitopes of The Region 300-396

Pena-Negrete

Fuentes-Acosta²,

Mulia-Rodríguez

et al. 2020

J. Nucl. Phy. Mat. Sci. Rad. A.

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Rotavirus diarrhea is an infectious intestinal disease that causes about 215 thousand deaths annually in infants under five years old. This virus is formed by three layers of concentric proteins that envelop its genome, from which VP6 structural protein is the most conserved among rotavirus serotypes and an excellent vaccine candidate. Recent studies have shown that structural proteins are susceptible to losing their biological function when their conformation is modified by moderate temperature increments, and in the case of VP6, its antigen efficiency decreases. We performed an in silicoanalysis to identify the structural variations in the epitopes 301-315, 357-366, and 376-384 of the rotavirus VP6 protein -in a hydrated medium- when the temperature is increased from 310 K to 322 K. In the latter state, we applied an electric field equivalent to a low energy laser pulse and calculated the fluctuations per amino acid residue. We identified that the region 301-315 has greater flexibility and density of negative electrical charge; nevertheless, at 322 K it experiences a sudden change of secondary structure that could decrease its efficiency as an antigenic determinant. The applied electric field induces electrical neutrality in the region 357-366, whereas in 376-384 inverts the charge, implying that temperature changes in the range 310 K-322 K are a factor that promotes thermoelectric effects in the VP6 protein epitopes in the region 300-396.

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Rotavirus VP6 protein as a bio-electrochemical scaffold: Molecular dynamics and experimental electrochemistry

Cited by 9 publications

References 27 publications

Design of Bioelectrochemical Interfaces Assisted by Molecular Dynamics Simulations

Design of Bioelectrochemical Interfaces Assisted by Molecular Dynamics Simulations

Rotavirus VP6: involvement in immunogenicity, adjuvant activity, and use as a vector for heterologous peptides, drug delivery, and production of nano-biomaterials

Structural Variations Induced by Temperature Changes in Rotavirus VP6 Protein Immersed in an Electric Field and Their Effects on Epitopes of The Region 300-396

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