Computational study on transfer of L-ascorbic acid by UlaA through Escherichia coli membrane.
In this study, the transfer of L-ascorbic acid by UlaA through Escherichia coli (E. coli) membrane was evaluated using density functional theory (DFT), molecular docking, and molecular dynamics (MD) simulation methods. DFT calculations at the B3lyp/6[Formula: see text]311[Formula: see text]G(p,d) level were performed to investigate the interaction properties and molecular descriptors. The physical properties, such as chemical potential, chemical hardness, and chemical electrophilicity of all studied molecules, were investigated. Natural population analysis was employed to describe the state of charge transfer between interactions using the natural bond orbital (NBO). The atoms in molecules (AIM) theory was used to examine the properties of the bond critical points such as their electron densities and Laplacians. Molecular docking studies showed that L-ascorbic acid was bounded to the internal cavity of UlaA. It was found that there were some hydrogen bond interactions between L-ascorbic acid and active sites of UlaA. The results of the MD simulation showed that the root mean square deviation (RMSD) of UlaA and L-ascorbic acid bound-UlaA reached equilibrium after 3.7[Formula: see text]ns. An evaluation of the radius of gyration ([Formula: see text]) revealed that UlaA and L-ascorbic acid bound-UlaA were stabilized around 10,000[Formula: see text]ns. Finally, analysis of the RMS fluctuations suggested that the structure of the L-ascorbic acid binding site remained approximately rigid during simulation. All obtained results shed light on the special manner of L-ascorbic acid transfer through E. coli membrane, and confirmed the results of previous studies on this issue.
* Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.|† Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman 76175493, Iran.
Ehsan
E
Faghih-Mirzaee
‡ Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, 76169-13,3 Iran.
Maryam
M
Dehestani
‡ Department of Chemistry, Shahid Bahonar University of Kerman, Kerman, 76169-13,3 Iran.
Leila
L
Zeidabadinejad
D001205:Ascorbic Acid / Q000378:metabolism*; D020134:Catalytic Domain; D002462:Cell Membrane / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000378:metabolism*; D006639:Histidine / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D026901:Membrane Transport Proteins / Q000378:metabolism*; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D010710:Phosphates / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D055672:Static Electricity; D013816:Thermodynamics
D029968:Escherichia coli Proteins; D026901:Membrane Transport Proteins; D010710:Phosphates; C473320:SgaT protein, E coli; D006639:Histidine; D001205:Ascorbic Acid
L-ascorbic acid; density functional theory; molecular docking; quantum theory of atoms in molecules