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Article

Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein

1
Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
2
Department of Theoretical Physics, Jožef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
3
Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
4
Department of Chemistry, The College of New Jersey, 2000 Pennington Road, Ewing, NJ 08628, USA
*
Author to whom correspondence should be addressed.
Materials 2020, 13(23), 5362; https://doi.org/10.3390/ma13235362
Received: 31 October 2020 / Revised: 23 November 2020 / Accepted: 24 November 2020 / Published: 26 November 2020
(This article belongs to the Section Advanced Materials Characterization)
The novel coronavirus disease 2019 (COVID-19) pandemic has disrupted modern societies and their economies. The resurgence in COVID-19 cases as part of the second wave is observed across Europe and the Americas. The scientific response has enabled a complete structural characterization of the Severe Acute Respiratory Syndrome—novel Coronavirus 2 (SARS-CoV-2). Among the most relevant proteins required by the novel coronavirus to facilitate the cell entry mechanism is the spike protein. This protein possesses a receptor-binding domain (RBD) that binds the cellular angiotensin-converting enzyme 2 (ACE2) and then triggers the fusion of viral and host cell membranes. In this regard, a comprehensive characterization of the structural stability of the spike protein is a crucial step to find new therapeutics to interrupt the process of recognition. On the other hand, it has been suggested that the participation of more than one RBD is a possible mechanism to enhance cell entry. Here, we discuss the protein structural stability based on the computational determination of the dynamic contact map and the energetic difference of the spike protein conformations via the mapping of the hydration free energy by the Poisson–Boltzmann method. We expect our result to foster the discussion of the number of RBD involved during recognition and the repurposing of new drugs to disable the recognition by discovering new hotspots for drug targets apart from the flexible loop in the RBD that binds the ACE2. View Full-Text
Keywords: SARS-CoV-2; spike protein; RBD; conformational space; structural stability; solvation energy; native contacts SARS-CoV-2; spike protein; RBD; conformational space; structural stability; solvation energy; native contacts
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MDPI and ACS Style

Moreira, R.A.; Guzman, H.V.; Boopathi, S.; Baker, J.L.; Poma, A.B. Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein. Materials 2020, 13, 5362. https://doi.org/10.3390/ma13235362

AMA Style

Moreira RA, Guzman HV, Boopathi S, Baker JL, Poma AB. Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein. Materials. 2020; 13(23):5362. https://doi.org/10.3390/ma13235362

Chicago/Turabian Style

Moreira, Rodrigo A., Horacio V. Guzman, Subramanian Boopathi, Joseph L. Baker, and Adolfo B. Poma. 2020. "Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein" Materials 13, no. 23: 5362. https://doi.org/10.3390/ma13235362

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