Interfacial water molecules contribute to antibody binding to the receptor-binding domain of SARS-CoV-2 spike protein

Zhang, Xin1; Wu, Ruiping1,2; Liu, Qinglian3; Zhou, Lei1

2023-04-01

10.1080/07391102.2023.2199336

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS   影响因子和分区

0739-1102

1538-0254

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.

SARS-CoV-2 Binding free energy MM/PBSA interfacial water explicit water

SCI

英语

其他

National Natural Science Foundation of China[32171150] ; Shenzhen Bay Laboratory[S211101001-3]

Biochemistry & Molecular Biology ; Biophysics

Biochemistry & Molecular Biology ; Biophysics

WOS:000970439500001

TAYLOR & FRANCIS INC

BIOLOGY & BIOCHEMISTRY

Web of Science

1.Inst Mol Physiol, Shenzhen Bay Lab, Shenzhen, Guangdong, Peoples R China
2.Southern Univ Sci & Technol, Dept Chem, Shenzhen, Guangdong, Peoples R China
3.Virginia Commonwealth Univ, Sch Med, Dept Physiol & Biophys, Richmond, VA USA

Zhang, Xin,Wu, Ruiping,Liu, Qinglian,et al. Interfacial water molecules contribute to antibody binding to the receptor-binding domain of SARS-CoV-2 spike protein[J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS,2023.

Zhang, Xin,Wu, Ruiping,Liu, Qinglian,&Zhou, Lei.(2023).Interfacial water molecules contribute to antibody binding to the receptor-binding domain of SARS-CoV-2 spike protein.JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS.

Zhang, Xin,et al."Interfacial water molecules contribute to antibody binding to the receptor-binding domain of SARS-CoV-2 spike protein".JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2023).