title: Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin.
abstract: CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the β-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable "tense" state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin.
authors.affiliation: Research and Development Centre, Bharathiar University, Coimbatore, India; Polyclone Bioservices, Bangalore, India.
authors.forename: R Pravin
authors.initials: RP
authors.lastname: Kumar
authors.affiliation: Research and Development Centre, Bharathiar University, Coimbatore, India.
authors.forename: L
authors.initials: L
authors.lastname: Roopa
authors.affiliation: Department of Molecular Reproduction Development and Genetics, Indian Institute of Science, Bangalore, India. Electronic address: upendra@mrdg.iisc.ernet.in.
authors.forename: Upendra
authors.initials: U
authors.lastname: Nongthomba
authors.affiliation: Department of Botany, Government Arts College, Coimbatore, India. Electronic address: mmsudheer@rediffmail.com.
authors.forename: M M
authors.initials: MM
authors.lastname: Sudheer Mohammed
authors.affiliation: Polyclone Bioservices, Bangalore, India.
authors.forename: Naveen
authors.initials: N
authors.lastname: Kulkarni
mesh_terms: D000199:Actins / Q000037:antagonists & inhibitors / Q000737:chemistry*; D000244:Adenosine Diphosphate / Q000737:chemistry*; D001665:Binding Sites; D028464:Cucurbita / Q000737:chemistry; D006801:Humans; D007700:Kinetics; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D014315:Triterpenes / Q000737:chemistry*
chemical_list: D000199:Actins; D014315:Triterpenes; D000244:Adenosine Diphosphate; C102326:cucurbitacin E
keywords: Actin depolymerization; Cucurbitacin; DFT simulation; Motional correlation; Quantum mechanics