title: In silico understanding of the cyclodextrin-phenanthrene hybrid assemblies in both aqueous medium and bacterial membranes.
abstract: The explicit-solvent molecular dynamic (MD) simulation and adaptive biased forces (ABF) methods were employed to systemically study the structural and thermodynamic nature of the β-cyclodextrin (βCD) monomer, phenanthrene (Phe) monomer, and their inclusion complexes in both the aqueous and membrane environments, aiming at clarifying the atomic-level mechanisms underlying in the CD-enhanced degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria. Simulations showed that βCD and Phe monomers could associate together to construct two distinctive assemblies, i.e, βCD1-Phe1 and βCD2-Phe1, respectively. The membrane-involved equilibrium simulations and the data of potential of mean forces (PMFs) further confirmed that Phe monomer was capable of penetrating through the membranes without confronting any large energy barrier, whereas, the single βCD and βCD-involved assemblies were unable to pass across the membranes. These observations clearly suggested that βCD only served as the carrier to enhance the bioavailability of Phe rather than the co-substrate in the Phe biodegradation process. The Phe-separation PMF profiles indicated that the maximum of the Phe uptake by bacteria would be achieved by the "optimal" βCD:Phe molar ratio, which facilitated the maximal formation of βCD1-Phe1 inclusion and the minimal construction of βCD2-Phe1 complex.
authors.affiliation: College of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
authors.forename: Baiping
authors.initials: B
authors.lastname: Ren
authors.affiliation: College of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China.
authors.forename: Huipeng
authors.initials: H
authors.lastname: Gao
authors.affiliation: College of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China.
authors.forename: Yafeng
authors.initials: Y
authors.lastname: Cao
authors.affiliation: College of Life Science and Biotechnology, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China. Electronic address: lyj81@dlut.edu.cn.
authors.forename: Lingyun
authors.initials: L
authors.lastname: Jia
mesh_terms: D001419:Bacteria / Q000378:metabolism; D001673:Biodegradation, Environmental; D002462:Cell Membrane / Q000378:metabolism; D008051:Lipid Bilayers / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D010616:Phenanthrenes / Q000737:chemistry* / Q000378:metabolism; D012989:Soil Pollutants / Q000737:chemistry* / Q000378:metabolism; D014867:Water / Q000737:chemistry; D047392:beta-Cyclodextrins / Q000737:chemistry*
chemical_list: D008051:Lipid Bilayers; D010616:Phenanthrenes; D012989:Soil Pollutants; D047392:beta-Cyclodextrins; D014867:Water; C031181:phenanthrene; C031215:betadex
keywords: Adaptive biased force; Bacterial membrane; Cyclodextrin extraction; Molecular dynamics simulation; Phenanthrene; Polycyclic aromatic hydrocarbon degradation