Molecular dynamics (MD) simulation The structures of the Class IV antibody and SARS-CoV-2 WT spike RBD (residues 334–527) were obtained from the Protein Data Bank (PDB: 7YCN, 6ZER) [27,49]. Omicron variants were generated by introducing mutations into the RBD region with the coordinates...
Human Coronavirus 2019 (HCoV-19/SARS-CoV-2)Coronavirus Disease 2019 (COVID-19)Receptor Binding Domain (RBD)Molecular Dynamics (MD) SimulationMolecular mechanics/Poisson-Boltzmann surface area (MM/PBSA)Computational Alanine scanning (CAS)Aims & Objective: Coronavirus Disease 2019 (COVID-19) caused ...
6b). Analysis of the MD trajectories of the RBD/Fab complex (see below) revealed a significantly lower RMSD value in this region between the MD frames and our structure (1.15 ± 0.27 Å, mean ± SD, minimal value ~0.57 Å) than with the 6XDG structure (1.44 ...
From computational scanning mutageneses and MD simulations, we found the single mutation H:V106R and the double mutations H:V106R/H:P107Y of P2B-2F6 resulted in higher binding affinities with the RBD domain of SARS-CoV-2 than others. To reveal changes in interactions between the antibody ...
The final frame of the simulation is the current model of the structure of the MAb362:SARS-CoV-2-RBD complex (Fig. 2c). The interface of the complex is predicted to form an extensive interface (Fig. 2d and Supplementary Fig. 3) with the CDRs of both the heavy and light chains ...
(GUIDE)—combines high-performance computing, simulation and machine learning to co-optimize binding affinity to multiple antigen targets, such as RBDs from several SARS-CoV-2 strains, along with other critical attributes such as thermostability. The computational platform operates in a ‘zero-shot’...
For RBD bound with ACE2, three hydrogen bonds in crystal structure could not form stable network during 200 ns simulation. Due to the high flexibility, the hydrogen bonds formed between G476 and Q24, N487 and Y83 maintain only 31.14% and 35.09% of the whole simulation. A475 and Q24 ...
The binding of the CR3022 to the epitope on RBD of SARS-CoV-2 spike was recently studied using structural Molecular Dynamics (MD) simulations [28]. On the other hand, S309 monoclonal antibody was recently identified as a therapeutic agent that potently neutralizes SARS-CoV-2 by recognizing ...
Yellow rectangles indicate the substitution cluster and their effect on the weight of RBD-ACE2 interaction. First, in order to provide insight into how the substitutions affect ACE2 binding, all-atom MD simulation in explicit water was set up (Methods) and checked for important biological events...
MD simulations and Markov state models systematically characterized conformational landscapes of XBB.1, XBB.1.5 Omicron variants and their complexes, showing that convergent mutation sites could control evolution allosteric pockets through modulation of conformational flexibility of functional RBD regions [62]...