PMFs were calculated using the umbrella sampling algorithm, which is a computational method to overcome the potential barrier and sample all possible configurations by applying harmonic restraint to the molecule of interest via a biased potential with respect to the research molecule.[ 28 ] In the RBD\antibody complex, RBD was drawn toward the bulk\water region (2.5?nm) and also pulled toward the antibody Rabbit polyclonal to EGR1 surface (0.5?nm) having a push constant of 1000?kJ mol?1 nm?2, which yields a total of 30 sample configurations (called windows) having a windowpane spacing of 0.1?nm in the distance of 3?nm. BR102375 protein of SARS\CoV\2. strong class=”kwd-title” Keywords: antibodies, binding free energy, drug finding, molecular dynamics simulations, protein\protein connection, SARS\CoV\2 Abstract Molecular dynamics simulations and free energy calculations of various antibodies bound to the receptor\binding website (RBD) of the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS\CoV\2) show the RBD\antibody binding is definitely stabilized by multivalent hydrogen bonds of polar uncharged RBD residues, suggesting the key amino acids of RBD controlling the hydrogen\relationship interactions. 1.?Intro The coronavirus disease 2019 (COVID\19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS\CoV\2), has been a serious pandemic all over the world.[ 1 ] 110 million people have been infected for last 14 weeks, leading to deaths of more than 2.5 million people as of February/2021. In fact, this pandemic today gets worse, since the winter season is coming within the northern hemisphere region. To end this disease pandemic, several vaccine candidates have been proposed and even tested on medical tests.[ 2 ] In particular, the receptor\binding website (RBD) of the spike (S) protein, which is the major surface antigen of SARS\CoV\2, is known to bind to the sponsor receptor angiotensin\transforming enzyme 2 (ACE2) that is a type I membrane protein indicated in lungs, heart, kidneys, and intestine, leading to viral illness.[ 3 , 4 BR102375 , 5 , 6 ] Consequently, RBD\focusing on antibodies have been developed to neutralize SARS\CoV\2 by inhibiting the binding between RBD and ACE2. Yan et?al. identified cryo\electron microscopy constructions of full\length human being ACE2 bound to the RBD of the S protein of SARS\CoV\2,[ 5 ] which has motivated many experimental studies on the development of SARS\CoV\2 RBD\focusing on antibodies since early this year.[ 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ] For instance, Yuan et?al. identified the crystal structure of an antibody CR3022, which is definitely isolated from an SARS patient, complexed with the RBD of SARS\CoV or SARS\CoV\2, showing a highly conserved epitope that enables mix\reactive binding between SARS\CoV and SARS\CoV\2.[ 13 ] Ju et?al. also isolated 206 antibodies from SARS\CoV\2 individuals and characterized crystal constructions of antibodies complexed with SARS\CoV\2 RBD, showing successful neutralization of those antibodies to SARS\CoV\2.[ 15 ] Rogers et?al. developed rapid platforms to evaluate plasma neutralization activity against SARS\CoV\2 and then isolated highly potent neutralizing antibodies.[ 16 ] Recently, Yuan et?al. found that immunoglobulin G weighty\chain variable 3\53 (IGHV3\53) is the most popular IGHV gene among 294 SARS\CoV\2 RBD\focusing on antibodies and identified crystal constructions of RBDs bound to IGHV3\53\neutralizing antibodies, CC12.1 and CC12.3.[ 17 ] In particular, they analyzed hydrogen\bond relationships of RBD with CC12.1 and CC12.3, which were further compared with those of RBD with ACE2 and another antibody, B38.[ 17 ] Although these experiments have provided vital information on the structure of SARS\CoV\2 RBDs and their relationships with antibodies, results from these experiments are not constantly easy to interpret at the level of specific interactions between individual amino acids of proteins under the explicit solvent condition, which is necessary to develop vaccine BR102375 or drug molecules focusing on the S protein of SARS\CoV\2. An accurate accounting of this requires simulations at nearly atomistic resolution which typically require all\atom simulations. As a further step toward understanding specific relationships controlling the binding between SARS\CoV\2 RBD and antibodies, here we statement all\atom molecular dynamics (MD) simulations of antibodies (CC12.1, CC12.3, and B38) and ACE2 BR102375 bound to SARS\CoV\2 RBD. Binding free energies are determined from umbrella sampling simulations, showing different binding advantages.
