A novel ligand swing-mediated active site coordination change of human apurinic/apyrimidinic endonuclease 1: A potential cytotoxic mechanism of nickel ion in the base excision repair

Wu, Zhixiang; Duan, Huaichuan; Cheng, Yan; Du, Guotong; Peng, Lianxin; Hu, Yichen; Hu, Jianping; Luo, Ting

doi:10.1016/j.chemphys.2022.111456

Cited by 3 publications

(2 citation statements)

References 72 publications

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“…Principal component analysis (PCA) is a standard method for finding global, correlated motions from MD trajectories through dimensionality reduction. PCA has been successfully applied to some functional motion studies in many biological systems ( Wu et al., 2020 , 2022 ). The PCA is mainly based on the construction and diagonalization of the covariance matrix, whose element

is given by:

where

is the coordinate of the

th/

th atom of the systems, and

denotes an ensemble average.…”

Section: Methodsmentioning

confidence: 99%

Insight into the nucleoside transport and inhibition of human ENT1

Han

Zhou

et al. 2022

Current Research in Structural Biology

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is given by:

where

is the coordinate of the

th/

th atom of the systems, and

denotes an ensemble average.…”

Section: Methodsmentioning

confidence: 99%

Insight into the nucleoside transport and inhibition of human ENT1

Han

Zhou

et al. 2022

Current Research in Structural Biology

Self Cite

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“…A particularly interesting nuclease is human apurinic/apyrimidinic endonuclease (APE1) due to its significant roles in human health, 8,9 including inflammatory responses, diabetic neuropathy, inflammatory bowel disease, macular edema and degeneration, atherosclerosis, and liver, lung, bladder and pancreatic cancers. [10][11][12][13][14][15] Indeed, cells genetically engineered to be deficient in APE1 are not viable, 16 overexpression of APE1 has been directly connected to disease, 12 and APE1 has shown promise as a therapeutic target.…”

Section: Introductionmentioning

confidence: 99%

The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme

Kaur

Aboelnga

Nikkel

et al. 2022

Phys. Chem. Chem. Phys.

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Molecular Dynamics Simulation of Lipid Nanoparticles Encapsulating mRNA

Zhang,

Cheng,

Luo

et al. 2024

Molecules

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mRNA vaccines have shown great potential in responding to emerging infectious diseases, with their efficacy and stability largely dependent on the delivery vehicles—lipid nanoparticles (LNPs). This study aims to explore the mechanisms by which LNPs encapsulate mRNA, as well as the effects of different N/P ratios and acid types in nucleic acid solutions on the structure and properties of LNPs, using the ethanol solvent injection method as the encapsulation technique. Six systems were designed, based on the composition and proportions of the existing mRNA vaccine mRNA-1273, and molecular dynamics (MD) simulations were employed to investigate the self-assembly process of LNPs. Ethanol was used as a solvent instead of pure water to better mimic experimental conditions. The results indicate that lipid components self-assemble into nanoparticles under neutral conditions, with the ionizable lipid SM-102 predominantly concentrating in the core of the particles. Upon mixing with nucleic acids in acidic conditions, LNPs undergo disassembly, during which protonated SM-102 encapsulates mRNA through electrostatic interactions, forming stable hydrogen bonds. Cluster structure analysis revealed that the four lipid components of LNPs are distributed sequentially from the outside inwards as DMG-PEG 2000, DSPC, cholesterol, and protonated SM-102. Moreover, LNPs constructed under low pH or low N/P ratios using citric acid exhibited larger volumes and more uniform distribution. These findings provide a scientific basis for further designing and optimizing LNP components to enhance the efficacy of mRNA vaccine encapsulation.

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A novel ligand swing-mediated active site coordination change of human apurinic/apyrimidinic endonuclease 1: A potential cytotoxic mechanism of nickel ion in the base excision repair

Cited by 3 publications

References 72 publications

Insight into the nucleoside transport and inhibition of human ENT1

Insight into the nucleoside transport and inhibition of human ENT1

The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme

Molecular Dynamics Simulation of Lipid Nanoparticles Encapsulating mRNA

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