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Deprecated: Implicit conversion from float 284.79999999999995 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Adv+Theory+Simul 2021 ; 4 (5): 2100012 Nephropedia Template TP
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All-Atom Simulations and Free-Energy Calculations of Antibodies Bound to the Spike Protein of SARS-CoV-2: The Binding Strength and Multivalent Hydrogen-Bond Interactions #MMPMID34230907
Lee H
Adv Theory Simul 2021[May]; 4 (5): 2100012 PMID34230907show ga
All-atom simulations of various antibodies bound to the receptor-binding domain (RBD) of the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are performed. Binding free energies calculated from umbrella sampling simulations show the strong binding between SARS-CoV-2 RBDs and antibodies, in agreement with recent experiments. Binding strengths of antibodies slightly differ, as further confirmed by calculating solvent accessible surface areas. Polar uncharged residues of RBD more predominantly bind to antibodies than do charged or hydrophobic residues of RBD. In particular, the binding between RBD and antibody is more significantly stabilized by multivalent hydrogen bonds of RBD residues ( approximately 406th-505th) than by locally formed hydrogen bonds of only a few RBD residues ( approximately 417th-487th or approximately 487th-505th). Hydrogen-bond analyses reveal key residues of RBD for strong hydrogen-bond interactions between RBDs and antibodies, which help in the rational design of vaccine and drug molecules targeting the S protein of SARS-CoV-2.