Interfacial water molecules contribute to antibody binding to the receptor-binding domain of SARS-CoV-2 spike protein.
J Biomol Struct Dyn
; : 1-10, 2023 Apr 12.
Artigo
em Inglês
| MEDLINE | ID: covidwho-2306463
ABSTRACT
Antibodies that recognize the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially the neutralizing antibodies, carry great hope in the treatment and final elimination of COVID-19. Driven by a synchronized global effort, thousands of antibodies against the spike protein have been identified during the past two years, with the structural information available at atomistic detail for hundreds of these antibodies. We developed an improved molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method including explicitly treated interfacial water to calculate the binding free energy between representative antibodies and the receptor binding domain (RBD) domain of SARS-COV-2 spike proteins. We discovered that explicit treatment of water molecules located at the interface between RBD and antibody effectively improves the results for the WT and variants of concern (VOC) systems. Interfacial water molecules, together with surface and internal water molecules, behave drastically from bulk water and exert peculiar impacts on protein dynamics and energy, and thus warrant explicit treatment to complement implicit solvent models. Our results illustrate the importance of including interfacial water molecules to approach efficient and reliable prediction of binding free energy.Communicated by Ramaswamy H. Sarma.
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Coleções:
Bases de dados internacionais
Base de dados:
MEDLINE
Tipo de estudo:
Estudo prognóstico
Tópicos:
Variantes
Idioma:
Inglês
Revista:
J Biomol Struct Dyn
Ano de publicação:
2023
Tipo de documento:
Artigo
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