title: Investigation of α-conotoxin unbinding using umbrella sampling.
abstract: α-Conotoxins, a class of short and disulfide rich peptide toxins, specifically and potently block nicotinic acetylcholine receptors (nAChRs). In this study umbrella sampling was performed to study the unbinding pathways and potential of mean force (PMF) of α-conotoxin ImI and PNIA(A10L,D14K). Our results suggest that (i) the unbinding pathways of ImI and PNIA(A10L,D14K) are similar despite of their different disulfide framework and structure, and (ii) α-conotoxin unbinding requires large conformation perturbation of the C-loop and the backbone flexibility of the C-loop can affect the binding or unbinding kinetics of the α-conotoxins. In addition, (iii) umbrella sampling gave correct ranking of the binding affinities of ImI and PNIA(A10L,D14K) indicating its efficacy on prediction of the binding affinities of α-conotoxins and implicating its potential application in design of more potent α-conotoxin analogs.
authors.affiliation: Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China. Electronic address: ryu@ouc.edu.cn.
authors.forename: Rilei
authors.initials: R
authors.lastname: Yu
authors.affiliation: Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
authors.forename: Nargis
authors.initials: N
authors.lastname: Tabassum
authors.affiliation: Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China. Electronic address: jiangtao@mail.ouc.edu.cn.
authors.forename: Tao
authors.initials: T
authors.lastname: Jiang
mesh_terms: D001665:Binding Sites; D020916:Conotoxins / Q000737:chemistry* / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011978:Receptors, Nicotinic / Q000737:chemistry / Q000378:metabolism
chemical_list: D020916:Conotoxins; D011978:Receptors, Nicotinic; C087686:alpha-conotoxin ImI
keywords: Nicotinic acetylcholine receptor; Potential of mean force; Umbrella sampling; α-Conotoxin