title: Recognition mechanism of siRNA by viral p19 suppressor of RNA silencing: a molecular dynamics study.
abstract: The p19 protein (p19) encoded from Tombusvirus is involved in various activities such as pathogenicity and virus transport. Recent studies have found that p19 is a plant suppressor of RNA silencing, which binds to short interfering RNAs (siRNAs) with high affinity. We use molecular dynamics (MD) simulations of the wild-type and mutant p19 protein (W39 and W42G) binding with a 21-nt siRNA duplex to study the p19-siRNA recognition mechanism and mutation effects. Our simulations with standard MD and steered molecular dynamics have shown that the double mutant structure is indeed much less stable than the wild-type, consistent with the recent experimental findings. Comprehensive structural analysis also shows that the W39/42G mutations first induce the loss of stacking interactions between p19 and siRNA, Trp(42)-Cyt1 (Cyt1 from the 5' to 3' strand) and Trp(39)-Gua'19 (Gua19 from the 3' to 5' strand), and then breaks the hydrophobic core formed by W39-W42 with nucleotide basepairs in the wild-type. The steered molecular dynamics simulations also show that the mutant p19 complex is "decompounded" very fast under a constant separation force, whereas the wild-type remains largely intact under the same steering force. Moreover, we have used the free energy perturbation to predict a binding affinity loss of 6.98 +/- 0.95 kcal/mol for the single mutation W39G, and 12.8 +/- 1.0 kcal/mol loss for the double mutation W39/42G, with the van der Waals interactions dominating the contribution ( approximately 90%). These results indicate that the W39/42G mutations essentially destroy the important p19-siRNA recognition by breaking the strong stacking interaction between Cyt1 and Gua'19 with end-capping tryptophans. These large scale simulations might provide new insights to the interactions and co-evolution relationship between RNA virus proteins and their hosts.
authors.affiliation: Institute of Bioinformatics, Zhejang University, Hangzhou 310027, People's Republic of China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Xia
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Zhu
authors.forename: Jun
authors.initials: J
authors.lastname: Zhu
authors.forename: Ruhong
authors.initials: R
authors.lastname: Zhou
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D055503:Protein Multimerization; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D017864:Tombusvirus; D014758:Viral Core Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D050505:Mutant Proteins; D034741:RNA, Small Interfering; D014758:Viral Core Proteins