Assessing the Current State of Amber Force Field Modifications for DNA ,2023 Edition

0574520 - BFÚ 2024 RIV US eng J - Journal Article
Love, O. - Galindo-Murillo, R. - Zgarbová, M. - Šponer, Jiří - Jurečka, P. - Cheatham III, T. E.
Assessing the Current State of Amber Force Field Modifications for DNA ,2023 Edition.
Journal of Chemical Theory and Computation. Roč. 19, č. 13 (2023), s. 4299-4307. ISSN 1549-9618. E-ISSN 1549-9626
R&D Projects: GA ČR(CZ) GA21-23718S
Institutional support: RVO:68081707
Keywords : MOLECULAR-DYNAMICS SIMULATIONS * PARTICLE MESH EWALD * NUCLEIC-ACIDS
OECD category: Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)
Impact factor: 5.5, year: 2022
Method of publishing: Open access
https://pubs.acs.org/doi/10.1021/acs.jctc.3c00233

Advances in moleculardynamics (MD) software alongside enhancedcomputational power and hardware have allowed for MD simulations tosignificantly expand our knowledge of biomolecular structure, dynamics,and interactions. Furthermore, it has allowed for the extension ofconformational sampling times from nanoseconds to the microsecondlevel and beyond. This has not only made convergence of conformationalensembles through comprehensive sampling possible but consequentlyexposed deficiencies and allowed the community to overcome limitationsin the available force fields. The reproducibility and accuracy ofthe force fields are imperative in order to produce biologically relevantdata. The Amber nucleic acid force fields have been used widely sincethe mid-1980s, and improvement of these force fields has been a communityeffort with several artifacts revealed, corrected, and reevaluatedby various research groups. Here, we focus on the Amber force fieldsfor use with double-stranded DNA and present the assessment of tworecently developed force field parameter sets (OL21 and Tumuc1). ExtensiveMD simulations were performed with six test systems and two differentwater models. We observe the improvement of OL21 and Tumuc1 comparedto previous generations of the Amber DNA force. We did not detectany significant improvement in the performance of Tumuc1 comparedto OL21 despite the reparameterization of bonded force field termsin the former, however, we did note discrepancies in Tumuc1 when modelingZ-DNA sequences.
Permanent Link: https://hdl.handle.net/11104/0350087