title: Positive Selection or Free to Vary? Assessing the Functional Significance of Sequence Change Using Molecular Dynamics.
abstract: Evolutionary arms races between pathogens and their hosts may be manifested as selection for rapid evolutionary change of key genes, and are sometimes detectable through sequence-level analyses. In the case of protein-coding genes, such analyses frequently predict that specific codons are under positive selection. However, detecting positive selection can be non-trivial, and false positive predictions are a common concern in such analyses. It is therefore helpful to place such predictions within a structural and functional context. Here, we focus on the p19 protein from tombusviruses. P19 is a homodimer that sequesters siRNAs, thereby preventing the host RNAi machinery from shutting down viral infection. Sequence analysis of the p19 gene is complicated by the fact that it is constrained at the sequence level by overprinting of a viral movement protein gene. Using homology modeling, in silico mutation and molecular dynamics simulations, we assess how non-synonymous changes to two residues involved in forming the dimer interface-one invariant, and one predicted to be under positive selection-impact molecular function. Interestingly, we find that both observed variation and potential variation (where a non-synonymous change to p19 would be synonymous for the overprinted movement protein) does not significantly impact protein structure or RNA binding. Consequently, while several methods identify residues at the dimer interface as being under positive selection, MD results suggest they are functionally indistinguishable from a site that is free to vary. Our analyses serve as a caveat to using sequence-level analyses in isolation to detect and assess positive selection, and emphasize the importance of also accounting for how non-synonymous changes impact structure and function.
authors.affiliation: Centre for Theoretical Chemistry and Physics & Institute of Natural and Mathematical Sciences, Massey University Albany, Auckland, New Zealand.|Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.|Maurice Wilkins Centre for Molecular Biodiscovery, Massey University Albany, Auckland, New Zealand.
authors.forename: Jane R
authors.initials: JR
authors.lastname: Allison
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
authors.forename: Marcus
authors.initials: M
authors.lastname: Lechner
authors.affiliation: Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology, Kiel, Germany.
authors.forename: Marc P
authors.initials: MP
authors.lastname: Hoeppner
authors.affiliation: Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.|School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
authors.forename: Anthony M
authors.initials: AM
authors.lastname: Poole
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D015870:Gene Expression; D057131:Immune Evasion / Q000235:genetics; D018551:Solanum lycopersicum / Q000276:immunology / Q000821:virology; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D010935:Plant Diseases / Q000276:immunology / Q000821:virology; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D017433:Protein Structure, Secondary; D012313:RNA / Q000737:chemistry*; D012641:Selection, Genetic; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D017864:Tombusvirus / Q000145:classification / Q000235:genetics* / Q000276:immunology; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: C493885:P19 protein, tomato bushy stunt virus; D014764:Viral Proteins; D012313:RNA