Development of ABEEMσπ polarizable force field for oxidized adenine base pairs: investigation of the interaction and mutagenic mechanism

Liu, Cui; Wang, Yan; Zhao, Dong‐Xia; Gong, Liutang; Yang, Zhong-Zhi

doi:10.1007/s00214-014-1469-6

Cited by 6 publications

(3 citation statements)

References 45 publications

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“…The range of model molecules is very extensive, including amino acid residues, normal bases, base pairs, etc. For all the parameters of ABEEM σπ PFF, the partial charge of each site q was calculated in terms of valence state electronegativity ( χ* ), valence state hardness ( η* ), and k HB whose value was designed through a regression and least-squares optimization procedure not only to reproduce the charges of HF/STO-3G calculation but also to obtain a good dipole moment compared with those from the M06-2X/6-311++G** calculation. The labels of atomic types defined in the ABEEM σπ model are shown in Figure S1 of the Supporting Information.…”

Section: Model Molecules and Methodsmentioning

confidence: 99%

Development of the ABEEMσπ Polarization Force Field for Base Pairs with Amino Acid Residue Complexes

Liu

Han

et al. 2017

J. Chem. Theory Comput.

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DNA damage caused by oxidized bases can lead to aging and cancer in living beings. Luckily, a repair enzyme is able to repair the oxidized bases. The key step is to accurately recognize the oxidized bases, which mainly rely on complex hydrogen bond interactions. We have calibrated the charge parameters and torsional parameters of the ABEEMσπ polarization force field (ABEEMσπ PFF) to accurately describe the intermolecular and intramolecular interactions. Taking the experiment and quantum chemical method as the benchmark, a series of properties of base pair-amino acid residue systems, DNA and DNA-protein interaction systems were calculated and compared with those of other force fields. We have done a tremendous amount of tasks in testing, calibrations, and analyses. The ABEEMσπ PFF not only explicitly gives the position and the partial charge of lone-pair electrons but also introduces a function k to fit special electrostatic interactions in hydrogen bond interaction regions. Therefore, it can accurately simulate the polarization effect and charge transfer of hydrogen bond interactions, especially for charged systems and sulfur-containing systems, such as the binding energy between amino acid and base pairs (24-28 kcal/mol), which is induced by charge transfer. The RMSD of ABEEMσπ PFF is 1.18 kcal/mol, whereas the RMSD of Amber OL15 is 8.21 kcal/mol. The relative positions of the amino acid residue have significantly changed, and the hydrogen bonds were broken when simulated by fixed charge force fields. In addition, owing to refitting the reasonable torsional parameters, the geometric structures optimized by ABEEMσπ PFF were well consistent with those of the M06-2X/6-311++G** method, but the simulations by fixed force fields have a large rotation of methyl and distortion of the plane of the base pair. After extensive MD simulation with four test DNAs and a DNA-protein system, we conclude that ABEEMσπ PFF shows better agreement when compared to experimental structures, which illustrates the reliability of our model and the transferability of the parameters.

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Section: Model Molecules and Methodsmentioning

confidence: 99%

Development of the ABEEMσπ Polarization Force Field for Base Pairs with Amino Acid Residue Complexes

Liu

Han

et al. 2017

J. Chem. Theory Comput.

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“…It can directly represent the anisotropy of the charge distribution around an atom, the electrostatic polarization effect, and the charge transfer effect. At present, this force field can quickly calculate the total energy and charge distribution for organic and biological macromolecular systems and has successfully been applied to simulate water clusters and pure aqueous solutions, aqueous ion systems, peptides and proteins, and nucleic acids. − …”

Section: Introductionmentioning

confidence: 99%

Water-Mediated Oxidation of Guanine by a Repair Enzyme: Simulation Using the ABEEM Polarizable Force Field

Cui

Yao

et al. 2021

J. Chem. Theory Comput.

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The recognition mechanism of oxidative damage in organisms has long been a research hotspot. Water is an important medium in the recognition process, but its specific role remains unknown. There is a need to develop a suitable force field that can adequately describe the electrostatic, hydrogen bond, and other interactions among the molecules in the complex system of the repair enzyme and oxidized base. The developing ABEEM polarizable force field (PFF) has been used to simulate the repaired enzyme hOGG1 and oxidized DNA (PDB ID: 1EBM) in a biological environment, and the corresponding results are better than those of the fixed-charge force fields OPLS/AA and AMBER OL15. 8-Oxo-G is recognized by Gln315 of hOGG1 mainly through hydrogen bonds mediated by continuous exchange of 2 water molecules. Phe319 and Cys253 are stacked on both sides of the π planes of bases to form sandwich structures. The charge polarization effect gives an important signal to drive the exchange of water molecules and maintains the recognition of oxidation bases by enzymes. The mediated main water molecule A and mediated auxiliary water molecule B together pull Gln315 to recognize 8-oxo-G by hydrogen bond interactions. Then, the charge polarization signal of solvent water molecule C with a large absolute charge causes the absolute charge of O atoms in water molecule A or B to increase by approximately 0.2 e, and water molecule A or B leaves Gln315 and 8-oxo-G. The other water molecule and water molecule C synergistically recognize 8-oxo-G with Gln315. Even though the water molecules between Gln315 and 8-oxo-G are removed, the MD simulation results show that water molecules appear between Gln315 and 8-oxo-G in a very short time (<2 ps). The dwell time of each water molecule is approximately 60 ps. The radial distribution function and dwell time support the correctness of the above mechanism. These polarization effects and hydrogen bonding interactions cannot be simulated by a fixed-charge force field.

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“…Therefore, how to deal with a double bond in the model is very important. In view of this, Yang and co-workers proposed and developed the atombond electronegativity equalization method plus σπ (ABEEM-σπ) model [22][23][24][25][26][27][28][29] based on the DFT. [30,31] One of the significant characteristics of the ABEEMσπ method is that the double bond is explicitly partitioned, and a molecule is decomposed into atomic regions, chemical bond regions, that is, σ and π bond regions, and lone-pair regions.…”

Section: Introductionmentioning

confidence: 99%

Insight into generalized local softness based on ABEEM‐σπ method: Electrophilic additions to alkenes

Ding

Sun

Guo

et al. 2021

J Chinese Chemical Soc

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According to the local hard-soft acidbase (HSAB) principle, the generalized local softness has been investigated based on the electrophilic reactions of H 2 O, HF, HCl and HBr to alkenes, and the effect of the softness on the chemical reactivity was studied in terms of the ab initio and atom-bond electronegativity equalization method plus σπ (ABEEM-σπ) method. Studies show that the finite difference approximation with ab initio method cannot always be used to predict the regioselectivity of the investigated reactions in terms of the local HSAB principle. But ABEEM-σπ model could well describe chemical reactivity according to the local HSAB principle. A significant characteristic of the ABEEM-σπ method is that the double bond is explicitly considered and partitioned. The square sums of differences of the local softness of the reaction center atoms, that is, Δs, or ΔS G with the generalized local softness and Δs χ with the electronegativity, have been studied on the considered electrophilic additions. Studies indicate that ΔS G can be utilized not only to predict regioselectivity rules but also to rationalize the chemical reactivity of these addition reactions, and the generalized local softness is more suitable for the investigation of chemical reactivity between two chemical species.

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Development of ABEEMσπ polarizable force field for oxidized adenine base pairs: investigation of the interaction and mutagenic mechanism

Cited by 6 publications

References 45 publications

Development of the ABEEMσπ Polarization Force Field for Base Pairs with Amino Acid Residue Complexes

Development of the ABEEMσπ Polarization Force Field for Base Pairs with Amino Acid Residue Complexes

Water-Mediated Oxidation of Guanine by a Repair Enzyme: Simulation Using the ABEEM Polarizable Force Field

Insight into generalized local softness based on ABEEM‐σπ method: Electrophilic additions to alkenes

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