title: Molecular dynamics simulation of carboxy and deoxy human cytoglobin in solution.
abstract: Cytoglobin (Cgb), the fourth member of the vertebrate heme globin family, is widely expressed in mammalian tissues, and reversibly binds to CO, O(2) and other small ligands. The diverse functions of Cgb may include ligand transport, redox reactions and enzymatic catalysis. Recent studies indicate that Cgb is a potential gene medicine for fibrosis and cancer therapy. In the present work, molecular dynamics (MD) simulations were performed to investigate the functionally related structural properties and dynamic characteristics in carboxy and deoxy human Cgb. The simulation results showed that the loop regions and internal cavities were significantly affected through the binding of an exogenous ligand. The AB, GH and EF loops were found to undergo significant rearrangement and this led to distinct cavity adjustments in Xe2, Xe4 and the distal pocket. In addition, solvent accessibility and torsion angle analyses revealed an interactive distal network comprised of His(81)(E7), Leu(46)(B10) and Arg(84)(E10). The MD study of carboxy and deoxy human Cgb revealed that CO-ligated Cgb modulates the protein conformation primarily by loop and cavity rearrangements rather than the heme sliding mechanism found in neuroglobin (Ngb). The significant differences between Cgb and Ngb in the loop and cavity properties are presumably linked to their various biological functions.
authors.affiliation: Department of Chemistry, Renmin University of China, Beijing, China.
authors.forename: Bingbing
authors.initials: B
authors.lastname: Zhang
authors.forename: Jia
authors.initials: J
authors.lastname: Xu
authors.forename: Yiming
authors.initials: Y
authors.lastname: Li
authors.forename: Weihong
authors.initials: W
authors.lastname: Du
authors.forename: Weihai
authors.initials: W
authors.lastname: Fang
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D002248:Carbon Monoxide / Q000737:chemistry*; D000078842:Cytoglobin; D005914:Globins / Q000737:chemistry*; D006418:Heme / Q000737:chemistry; D006801:Humans; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D013499:Surface Properties
chemical_list: C000627265:CYGB protein, human; D000078842:Cytoglobin; D006418:Heme; D002248:Carbon Monoxide; D005914:Globins