Molecular dynamics simulation of the interaction of food proteins with small molecules

Hu, Xia; Zeng, Zhen; Zhang, Jing; Wu, Di; Li, Hui; Geng, Fang

doi:10.1016/j.foodchem.2022.134824

Cited by 108 publications

(48 citation statements)

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“…It can be used to explore conformational space, and is often the method of choice for large molecules such as proteins. Recently, due to the continuous development of MD, molecular models and docking are closer to the real response ( 46 ). Here, we recommend a method, the integration of I-TASSER and GalaxyRefine server.…”

Section: Introductionmentioning

confidence: 99%

Integration: Gospel for immune bioinformatician on epitope-based therapy

Sun

Zhang

et al. 2023

Front. Immunol.

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Section: Introductionmentioning

confidence: 99%

Integration: Gospel for immune bioinformatician on epitope-based therapy

Sun

Zhang

et al. 2023

Front. Immunol.

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“…Because protein binding to nanoparticles can be critical in determining the extent of interaction with cells and tissues, understanding how and why plasma proteins are adsorbed to these particles is essential for understanding their biological responses. [14][15][16][17] The interaction of nanoemulsions with proteins and/or other biomolecules is a complex phenomenon and involves the so-called nano-bio interface which is responsible for the biological responses in living organisms. [18] Such analysis needs the thermodynamic data, because the driving forces for chemical reactions and diffusion can be given properly in terms of thermodynamic properties.…”

Section: Introductionmentioning

confidence: 99%

PEGylation Effects on the Interaction of Sphingomyelin Nanoemulsions with Serum Albumin: A Thermodynamic Investigation

Gheorghe¹,

Díez‐Villares

Sandu³

et al. 2023

Macro Materials & Eng

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The recent focus in the development of novel nanosystems for biomedical applications lays firmly on their interactions with biomolecules. Thermodynamic parameters driving the interaction between nanoparticles and proteins provide insights into complex processes at bio/nanointerface. The present work aims to investigate the binding mechanisms and the dominant contributions that determine the adsorption processes during the interactions of a model protein, that is, bovine serum albumin, with a new type of drug delivery systems, Vitamin E/sphingomyelin nanoemulsions, plain and coated with polyethylene glycol, and d‐ɑ‐tocopheryl polyethylene glycol succinate. The binding parameters (binding constant, binding stoichiometry, enthalpy, Gibbs energy, and entropy changes of binding) are evaluated by the isothermal titration calorimetry with a MicroCaliTC200 equipment. The effect of nanoemulsions on the protein stability is examined by measuring the thermodynamic parameters for the protein's unfolding (heat capacity; enthalpy, entropy, and free energy changes) with a NanoDSC (TA Instrument) apparatus. The thermodynamic profile shows for all compositions an entropy‐driven interaction dominated by hydrophobic forces due to the rearrangements/displacement of the surrounding water molecules, while maintaining the native conformation of the protein. All the information acquired by thermodynamic approach may significantly enhance the knowledge with special focus on PEGylated nanoemulsions used for biomedical applications.

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“…Generally, the larger the R g value of the system is, the more sparse the protein structure is. 53 The system's R g value increased as a result of the HYP binding, suggesting that the addition of HYP made the structure of lipase relatively unstable, resulting in a reduction of catalytic activity at the lipase's functional location. 54 This finding corroborates the FT-IR and CD results.…”

Section: Resultsmentioning

confidence: 99%