title: Exploring the interactions between isoprenoid chain and labdenediol diphosphate synthase based on molecular docking and quartz crystal microbalance.
abstract: Many natural products and biosynthetic intermediates contain isoprenoid chains. Isoprenoid chains are believed to interact with some proteins in the biological systems, but such interactions remain poorly understood. Here labdenediol diphosphate synthase (LPPS) was used as a model to explore the molecular interactions involving isoprenoid chains. Both homology modeling and docking simulation results indicated that binding form between isoprenoid chain and LPPS is dominated by hydrophobic forces in one binding site. The interactions were also examined via quartz crystal microbalance (QCM) technology using synthetic isoprenoid chain-contained probes. The binding constant (1.51 μM(-1)), binding site number (n = 1) and key amino acid residues (Y196, F262, W266, F301, F308, W398, W439, and Y445) were obtained. Both computational and QCM results suggested that LPPS interacts strongly with farnesyl and geranylgeranyl groups. These interactions are primarily caused by hydrophobic and π-π interaction nature. Together, this study provided insightful information to understand molecular interactions between isoprenoid chains and proteins.
authors.affiliation: Division of Biotechnology and Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, People's Republic of China, wujunliu@dicp.ac.cn.
authors.forename: Wujun
authors.initials: W
authors.lastname: Liu
authors.forename: Wei
authors.initials: W
authors.lastname: Yang
authors.forename: Yixin
authors.initials: Y
authors.lastname: Zhang
authors.forename: Zongbao Kent
authors.initials: ZK
authors.lastname: Zhao
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D002384:Catalysis; D004798:Enzymes / Q000737:chemistry* / Q000378:metabolism; D057927:Hydrophobic and Hydrophilic Interactions; D062105:Molecular Docking Simulation; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011106:Polyisoprenyl Phosphates / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D058525:Quartz Crystal Microbalance Techniques; D012717:Sesquiterpenes / Q000737:chemistry; D013729:Terpenes / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004798:Enzymes; D011106:Polyisoprenyl Phosphates; D012717:Sesquiterpenes; D013729:Terpenes; C004808:farnesyl pyrophosphate; C002963:geranylgeranyl pyrophosphate