<i>In silico</i>study of the binding of daunomycin and phenylalanine transfer RNA: probe molecular recognition for structure-based drug design

Wu, Gonghao; Li, Jipeng; Jiang, Yang; Xiao, Xingqing

doi:10.1039/d2me00236a

Cited by 2 publications

(1 citation statement)

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“…A single TRP molecule is solvated in a TIP3P water box and then equilibrated with the AMBER20 package in 10 ns. (Details of the atomistic simulations in the AMBER software can be found in our previous work. , ) As the mapping scheme in Figure a, three DPD particles, viz., “N”, “C”, “O”, are used to represent the three heavy groups of the mainchain, and one DPD particle “R w ” is used to describe the TRP side chain. Each TIP3P water molecule is modeled as a DPD particle “W”.…”

Section: Parametrization Of Ex-dpd Modelmentioning

confidence: 99%

Dissipative Particle Dynamics Simulation of Protein Folding in Explicit and Implicit Solvents: Coarse-Grained Model for Atomic Resolution

Zhang,

Yang,

Xiao

et al. 2024

J. Chem. Theory Comput.

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Advancements have been made to dissipative particle dynamics (DPD), a robust coarse-grained (CG) simulation method, to study the folded structures of four miniproteins (1L2Y, 1WN8, 1YRF, and 2I9M) in explicit and implicit solvents. In this endeavor, we aim to establish model parametrization and enhance computational efficiency. Unlike traditional CG models that use empirical force parameters, ex-force parameters (r 0(ex) , a, δ d , δ p ) of DPD particles constructed for specific research purposes can be obtained from atomistic molecular dynamics simulations. On the other hand, im-force parameters (r 0(im) , c, σ) can be derived from ex-DPD simulations, according to the underlying thermodynamic theory. Based on a mapping scheme proposed for the modeling of amino acids, all-atom proteins can be converted into a CG model. Both ex-/im-DPDs are then carried out to investigate the folding pathways of the four mini-proteins. Structural analysis of the RMSDs shows that the im-simulated proteins have greater structural similarity to native proteins than the ex-simulated ones. The constructed CG models achieve a resolution of Angstrom (Å), a level normally associated with atomic models. Additionally, speed tests reveal that im-DPD accelerates the simulation process and significantly improves simulation efficiency.

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Section: Parametrization Of Ex-dpd Modelmentioning

confidence: 99%

Dissipative Particle Dynamics Simulation of Protein Folding in Explicit and Implicit Solvents: Coarse-Grained Model for Atomic Resolution

Zhang,

Yang,

Xiao

et al. 2024

J. Chem. Theory Comput.

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CORAL: probing the structural requirements for α-amylase inhibition activity of 5-(3-arylallylidene)-2-(arylimino)thiazolidin-4-one derivatives based on QSAR with correlation intensity index, molecular docking, molecular dynamics, and ADMET studies

Singh,

Kumar,

Sindhu

et al. 2023

Journal of Biomolecular Structure and Dynamics

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In silicostudy of the binding of daunomycin and phenylalanine transfer RNA: probe molecular recognition for structure-based drug design

Abstract: Rational designs of pharmaceutical compounds targeting specific RNAs require a comprehensive understanding of molecular recognition mechanisms. Knowledge of binding affinity and specificity can be gained via computational modeling and simulation...

Cited by 2 publications

References 59 publications

Dissipative Particle Dynamics Simulation of Protein Folding in Explicit and Implicit Solvents: Coarse-Grained Model for Atomic Resolution

Dissipative Particle Dynamics Simulation of Protein Folding in Explicit and Implicit Solvents: Coarse-Grained Model for Atomic Resolution

CORAL: probing the structural requirements for α-amylase inhibition activity of 5-(3-arylallylidene)-2-(arylimino)thiazolidin-4-one derivatives based on QSAR with correlation intensity index, molecular docking, molecular dynamics, and ADMET studies

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