Journal
BIOPOLYMERS
Volume 68, Issue 1, Pages 16-34Publisher
WILEY
DOI: 10.1002/bip.10270
Keywords
molecular mechanics Poisson-Boltzmann surface area (MM-PBSA); RNA aptamer; theophylline; theophylline analogs
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Funding
- NATIONAL CENTER FOR RESEARCH RESOURCES [P41RR001081, P41RR012255] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM029072] Funding Source: NIH RePORTER
- NCRR NIH HHS [P41-RR01081, RR12255] Funding Source: Medline
- NIGMS NIH HHS [GM29072] Funding Source: Medline
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We have applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method (J. Srinivasan, T. E. Cheatham, P. Cieplak, P. A. Kollman, and D. A. Case, Journal of the American Chemical Society, 1998, Vol. 120, pp. 9401-9409) to study the interaction of an RNA aptamer with theophylline and its analogs. The MM-PBSA free energy analysis provides a reasonable absolute binding free energy for the RNA aptamer-theophylline complex formation. Energetic analysis reveals that the van der Waals interaction and the nonpolar contribution to solvation provide the basis for the favorable absolute free energy of complex. This trend is similar to other protein-ligand interactions studied previously. The MM-PBSA method also ranks the relative binding energies of five theophylline analogs approximately correctly, but not as well as the more conventional thermodynamic integration calculations, which were carried out to convert theophylline into its analogs. The comparison of MM-PBSA with TI suggests that the MM-PBSA method has some difficulties with the first-solvation-shell energetics. (C) 2002 Wiley Periodicals, Inc.
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