All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution

MacKerell, Alexander D.; Banavali, Nilesh K.

doi:10.1002/(sici)1096-987x(20000130)21:2<105::aid-jcc3>3.0.co;2-p

Cited by 714 publications

(728 citation statements)

References 92 publications

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“…Figures were prepared with PyMOL (http://www.pymol.org). MD simulations were performed with CHARMM (54) and NAMD (55) using the CHARMM additive force field (56)(57)(58). Additional details are in SI Materials and Methods.…”

Section: Methodsmentioning

confidence: 99%

Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

Maiti

Noon

MacKerell

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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168

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DNA base excision repair is essential for maintaining genomic integrity and for active DNA demethylation, a central element of epigenetic regulation. A key player is thymine DNA glycosylase (TDG), which excises thymine from mutagenic G·T mispairs that arise by deamination of 5-methylcytosine (mC). TDG also removes 5-formylcytosine and 5-carboxylcytosine, oxidized forms of mC produced by Tet enzymes. Recent studies show that the glycosylase activity of TDG is essential for active DNA demethylation and for embryonic development. Our understanding of how repair enzymes excise modified bases without acting on undamaged DNA remains incomplete, particularly for mismatch glycosylases such as TDG. We solved a crystal structure of TDG (catalytic domain) bound to a substrate analog and characterized active-site residues by mutagenesis, kinetics, and molecular dynamics simulations. The studies reveal how TDG binds and positions the nucleophile (water) and uncover a previously unrecognized catalytic residue (Thr197). Remarkably, mutation of two active-site residues (Ala145 and His151) causes a dramatic enhancement in G·T glycosylase activity but confers even greater increases in the aberrant removal of thymine from normal A·T base pairs. The strict conservation of these residues may reflect a mechanism used to strike a tolerable balance between the requirement for efficient repair of G·T lesions and the need to minimize aberrant action on undamaged DNA, which can be mutagenic and cytotoxic. Such a compromise in G·T activity can account in part for the relatively weak G·T activity of TDG, a trait that could potentially contribute to the hypermutability of CpG sites in cancer and genetic disease. D NA base excision repair (BER) plays an established role in maintaining genomic integrity, and recent studies indicate that BER is also essential for active DNA demethylation, a key element of epigenetic gene regulation (1-3). A central player in both processes is thymine DNA glycosylase (TDG), which initiates BER by excising damaged or modified forms of 5-methylcytosine (mC) that arise at 5′-CpG-3′ sites. TDG was discovered for its ability to selectively remove T from G·T mispairs, mutagenic lesions that can arise from deamination of mC to T (4, 5). TDG also excises 5-formylcytosine (fC) and 5-carboxylcytosine (caC), oxidized forms of mC that are generated by Tet enzymes (6, 7). In addition, TDG was shown to be essential for active DNA demethylation and for embryonic development (8, 9), a role that likely involves excision of deaminated or oxidized forms of mC generated by a deaminase or Tet enzyme (7,(10)(11)(12). Thus, the ability of TDG to remove deaminated and oxidized forms of mC is important for genetic and epigenetic integrity.The question of how DNA glycosylases remove modified bases without acting upon the huge excess of undamaged DNA remains largely unresolved, particularly for mismatch glycosylases such as TDG and MBD4 (methyl binding domain IV) (13-15). These enzymes face the formidable task of removing a normal base, t...

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Section: Methodsmentioning

confidence: 99%

Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

Maiti

Noon

MacKerell

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

168

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“…The molecules were represented by the CHARMM all-hydrogen force field (33)(34)(35)(36); parameters for the mGua base were generated in a consistent fashion (see SI Methods, SI Fig. 9, and SI Tables 2 and 3).…”

Section: Methodsmentioning

confidence: 99%

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT

Dinner

2008

Proc. Natl. Acad. Sci. U.S.A.

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O 6 -alkylguanine-DNA alkyltransferase (AGT) repairs damage to the human genome by flipping guanine and thymine bases into its active site for irreversible transfer of alkyl lesions to Cys-145, but how the protein identifies its targets has remained unknown. Understanding molecular recognition in this system, which can serve as a paradigm for the many nucleotide-flipping proteins that regulate genes and repair DNA in all kingdoms of life, is particularly important given that inhibitors are in clinical trials as anticancer therapeutics. Computational approaches introduced recently for harvesting and statistically characterizing trajectories of molecularly rare events now enable us to elucidate a pathway for nucleotide flipping by AGT and the forces that promote it. In contrast to previously proposed flipping mechanisms, we observe a two-step process that promotes a kinetic, rather than a thermodynamic, gate-keeping strategy for lesion discrimination. Connection is made to recent single-molecule studies of DNA-repair proteins sliding on DNA to understand how they sense subtle chemical differences between bases efficiently. commitment probabilities ͉ DNA repair ͉ reaction coordinates ͉ transition path sampling

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“…Parameterization of the CHARMM27 force field was based on ab initio and experimental data for small molecules, 42 as well as macromolecular simulation data of DNA and RNA 46 in order to more accurately capture experimental condensed phase properties. This was an important improvement to the CHARMM22 force field 47 that was parameterized more heavily on the basis of small molecule target data alone.…”

Section: Methodsmentioning

confidence: 99%

“…Current non-bonded parameters exist for Mg 2+ in the CHARMM27 force field 46 and OH − parameters are available from Lee et al 71 However, these parameters are not optimal for the specific problems that involve di-metal bridges or RNA phosphate binding. Hence, the parameters for OH − and Mg 2+ have been re-optimized specifically for these types of systems.…”

Section: Magnesium Complexesmentioning

confidence: 99%

CHARMM force field parameters for simulation of reactive intermediates in native and thio‐substituted ribozymes

et al. 2006

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Force field parameters specifically optimized for residues important in the study of RNA catalysis are derived from density-functional calculations in a fashion consistent with the CHARMM27 allatom empirical force field. Parameters are presented for residues that model reactive RNA intermediates and transition state analogs, thio-substituted phosphates and phosphoranes, and bound Mg 2+ and di-metal bridge complexes. Target data was generated via density-functional calculations at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p) level. Partial atomic charges were initially derived from the CHelpG electrostatic potential fitting and subsequently adjusted to be consistent with the CHARMM27 charges and Lennard-Jones parameters were determined to reproduce interaction energies with water molecules. Bond, angle and torsion parameters were derived from the density-functional calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters for standard residues. The extension of the CHARMM27 force field parameters for the non-standard biological residues presented here will have considerable use in simulations of ribozymes, including the study of freeze-trapped catalytic intermediates, metal ion binding and occupation, and thio effects.

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All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution

Cited by 714 publications

References 92 publications

Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT

CHARMM force field parameters for simulation of reactive intermediates in native and thio‐substituted ribozymes

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