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A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations
Ming Huang1, Thakshila Dissanayake1, Erich Kuechler1
1Center for Integrative Proteomics Research, Laboratory for Biomolecular Simulation Research and Department of Chemistry and Chemical Biology, Rutgers University , 174 Frelinghuysen Road, Piscataway, New Jersey 08854, United States.
Journal of Chemical Theory and Computation
|August 3, 2017
Summary
This study introduces a B-spline correction map (BMAP) to accurately model sugar ring puckers in nucleic acid systems. The BMAP correction improves computational models for RNA and DNA, enhancing predictions of biological reactions.
Area of Science:
- Computational Chemistry
- Biochemistry
- Molecular Modeling
Background:
- Approximate quantum mechanical methods enable reaction profile construction but struggle with nucleic acid sugar puckers.
- Neglect of Diatomic Differential Overlap (NDDO) models exhibit limitations in accurately describing deoxyribose and ribose ring conformations.
- Existing models limit the predictive accuracy for RNA and DNA systems.
Purpose of the Study:
- To develop and implement a B-spline correction map (BMAP) for improved sugar pucker description in nucleic acid systems.
- To enhance the accuracy of semiempirical quantum mechanical methods for modeling biological phosphoryl transfer reactions.
- To evaluate the BMAP correction's performance in molecular dynamics simulations.
Main Methods:
- Development and implementation of a multidimensional B-spline correction map (BMAP).
- Application of the BMAP correction within the AM1/d-PhoT semiempirical Hamiltonian.
- Utilizing molecular dynamics simulations for gas-phase and condensed-phase reaction studies.
- Employing Quantum Mechanics/Molecular Mechanics (QM/MM) for free energy surface calculations.
Main Results:
- The BMAP correction significantly improved adiabatic potential energy surface profiles for DNA and RNA sugar rings.
- Simulations using the AM1/d-PhoT Hamiltonian with BMAP correction showed stable and efficient performance.
- BMAP correction enhanced both potential energy and free energy profiles for transesterification reactions compared to ab initio and experimental data.
- Treating the full CpA dinucleotide quantum mechanically with BMAP correction yielded the best agreement with experimental reaction barriers.
Conclusions:
- The BMAP correction is a stable and efficient method for improving the description of sugar puckering in nucleic acid systems.
- This approach enhances the accuracy of computational models for studying RNA and DNA systems and their reactions.
- The BMAP correction offers a valuable tool for advancing research in biological phosphoryl transfer and nucleic acid chemistry.
