Molecular dynamics study of structural properties of   γ-aminobutyric acid (GABA)

Khanal, Shyam P.; Koirala, R. P.; Mishra, Esha; Adhikari, Narayan Prasad

doi:10.3126/bibechana.v18i1.29442

Cited by 3 publications

(3 citation statements)

References 20 publications

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“…Then evaluation was carried out on the effect of each parameter variation on atomic density or probability at a certain radius using the radial distribution factor (RDF) (Fig. 3 and 4), which will illustrate the distribution of a molecule around another molecule giving the possibility of finding atomic pairs located at a distance of "r" [40][41][42]. The RDF value from 14-Deoxy-11,12-didehydroandrographolide-1XVP (6.27 g(r)) and Andrographolide-1XVP (6.23 g(r)) not much different with native ligand CITCO (6.26 g(r)).…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Molecular interactions of <i>Andrographis paniculata</i> Burm. f. Active Compound with Nuclear Receptor (CAR and PXR): An In Silico Assessment Approach

et al. 2022

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The study aims to analyze the potential Herb-Drug Interactions (HDIs) of the chemical compound in Andrographis paniculate Burm. f. against Constitutive Androstane Receptor (CAR) and Pregnane X Receptor (PXR). The 1XVP and 1SKX obtained from the Protein Data Bank (PDB) were used as the targeted protein. The molecular docking analysis was done using the Molecular Operating Environment (MOE) and molecular dynamics simulation using Gromacs. The results of the docking analysis showed that 14-Deoxy-11,12-didehydroandrographolide had the strongest binding energy (1XVP-21.0998 Å) with the Arene-H binding type on Tyr326 and Andrographidine A had the strongest binding energy (1SKX-24.7363 Å) with the Arene-H binding type on Trp299. While Andrographolide is the major component, it also has a high affinity for the two PDB IDs (1XVP-17.4044 Å and 1SKX-21.8881 Å). Based on the RMSD value, the radius of gyration (Rg), and MM/PBSA on molecular dynamic simulations, it shows that the ligand and protein complex as a whole can bind strongly to amino acid residues at the active site. The complex also has sufficient stability and good affinity. Therefore, this study can predict the mechanism in HDIs, especially in CYP 450 expression through the activation pathways of CAR and PXR receptors.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Molecular interactions of <i>Andrographis paniculata</i> Burm. f. Active Compound with Nuclear Receptor (CAR and PXR): An In Silico Assessment Approach

et al. 2022

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“…The Particle Mesh Edward (PME) was used to treat the long-range interactions with a 12.0 Å nonbonded cutoff. To remove the steric hindrance and undesired position of atoms, the prepared system was executed for energy minimization run for 10,000 steps [24][25][26][27]. The output structure of the molecular system was then used as the input of equilibration run.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Flipping Back of Extrahelical Guanine after Methyl Repair

Koirala¹,

Adhikari²

2022

BIBECHANA

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Methylation at O6 atom of guanine is a type of DNA damage which can cause a cancer. This damage at O6 atom of guanine in a DNA can be transferred to SG atom of cysteine in O6-alkylguanine-DNA alkyltransferase (AGT). Flipping out of methylated guanine from its base stack is essential to give off the methyl adduct (CH3) to AGT. AGT receives the methyl adduct at cysteine leaving guanine demethylated, but still in flipped out orientation. The repair mechanism of DNA would be completed only when the extrahelically flipped guanine returns back into the base stack, which is considered as the final step of the DNA repair mechanism. Here, the intrahelical flipping mechanism of repaired guanine has been studied. The work is further extended to examine the stability of hydrogen bonds between guanine and its pair partner cytosine. The overall result shows that intrahelical rotation of repaired guanine is possible and the base pairing is stable as the ordinary hydrogen bonding. BIBECHANA 19 (2022) 201-207

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“…As the radial distribution function (RDF) of hard spheres is a measure of the probability of finding a particle at a certain distance from another particle, given that the particles are hard spheres and cannot overlap so that is commonly used in statistical mechanics to study the properties of liquids and other condensed matter systems. The RDF can be helpful to determine the thermodynamic properties and the structure of the system, such as pressure and density [18]. Additionally, it can be used to determine the pair distribution function, which can provide details about the short-range order in the system.…”

Section: Introductionmentioning

confidence: 99%

Radial Distribution Function of Hard Spheres at Different Densities

Khanal,

Gyawali,

Khati

et al. 2023

J. Nep. Phys. Soc.

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The model of hard sphere system has important part in modern theories of liquids. Hard sphere fluid is considered as the most intensively studied system among all model fluids. The thermodynamic and structural properties of real fluids can be studied with the help of hard spheres fluid. The exact solution of Ornstein-Zernike (OZ) equation with Percus-Yevick (PY) along with the equation of state provides an approximate analytical expression for radial distribution function (RDF). This work intends to study the radial distribution function of Hard sphere (HS) using the PY approximation for different densities ranging from low to high to find out their structural properties, packing behavior, phase transitions, and thermodynamics. We use FORTRAN program for this purpose. At low densities, the RDF has a single peak at a distance corresponding to the hard sphere diameter, indicating that the particles are well- separated and not interacting with each other like gaseous. As density increases, the peak becomes broader and shifts to smaller distances, indicating that the particles are coming into closer contact and interacting more strongly with each other. The height of the peak also increases, indicating that there is a greater probability of finding a particle at a certain distance from another particle.

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Molecular dynamics study of structural properties of γ-aminobutyric acid (GABA)

Cited by 3 publications

References 20 publications

Molecular interactions of <i>Andrographis paniculata</i> Burm. f. Active Compound with Nuclear Receptor (CAR and PXR): An In Silico Assessment Approach

Molecular interactions of <i>Andrographis paniculata</i> Burm. f. Active Compound with Nuclear Receptor (CAR and PXR): An In Silico Assessment Approach

Flipping Back of Extrahelical Guanine after Methyl Repair

Radial Distribution Function of Hard Spheres at Different Densities

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