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• W2120273997 abstract "Abstract The standard (absolute) binding free energy of the antibiotic sparsomycin with the 50S bacteria ribosomal subunit is calculated using molecular dynamics (MD) free energy perturbation (FEP) simulations with restraining potentials developed by Wang et al. [Biophys. J. 91:2798–2814 (2006)]. In the simulation protocol, restraining potentials are activated for the orientational and translational movements of the ligand relative to the binding site when it is decoupled from the binding pocket, and then released once the ligand fully interacts with the rest of the system. A reduced system is simulated to decrease the computational cost of the FEP/MD calculations and the effects of the surrounding atoms are incorporated using the generalized solvent boundary potential (GSBP) method. The loss of conformational freedom of the ligand upon binding is characterized using the potential of mean force (PMF) as a function of the root‐mean‐square deviation (RMSD) relative to the bound conformation. The number of water molecules in the binding pocket is allowed to fluctuate dynamically in response to the ligand during the calculations by combining FEP/MD with grand canonical Monte Carlo (GCMC) simulations. The calculated binding free energy is about −6 kcal/mol, which is in reasonable agreement with the experimental value. The information gleaned from this study provides new insight on the recognition of ribosome by sparsomycin and highlights the challenges in calculations of absolute binding free energies in these systems. Copyright © 2010 John Wiley & Sons, Ltd." @default.
• W2120273997 created "2016-06-24" @default.
• W2120273997 creator A5011596226 @default.
• W2120273997 creator A5029040247 @default.
• W2120273997 date "2010-02-11" @default.
• W2120273997 modified "2023-10-06" @default.
• W2120273997 title "Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials" @default.
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• W2120273997 doi "https://doi.org/10.1002/jmr.996" @default.
• W2120273997 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/20151411" @default.
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