title: Effect of Inactivating Mutations on Peptide Conformational Ensembles: The Plant Polypeptide Hormone Systemin.
abstract: As part of their basal immune mechanism against insect/herbivore attacks, plants have evolved systemic response mechanisms. Such a systemic wound response in tomato was found to involve an 18 amino acid polypeptide called systemin, the first polypeptide hormone to be discovered in plants. Systematic alanine scanning and deletion studies showed differential modulation in its activity, particularly a major loss of function due to alanine substitution at positions 13 and 17 and less extentive loss of function due to substitution at position 12. We have studied the conformational ensembles of wild-type systemin along with its 17 variants by carrying out a total of 5.76 μs of replica-exchange molecular dynamics simulation in an implicit solvent environment. In our simulations, wild-type systemin showed a lack of α-helical and β-sheet structures, in conformity with earlier circular dichroism and NMR data. On the other hand, two regions containing diproline segments showed a tendency to adopt polyproline II structures. Examination of conformational ensembles of the 17 variants revealed a change in the population distributions, suggesting a less flexible structure for alanine substitutions at positions 12 and 13 but not for position 17. Combined with the experimental observations that positions 1-14 of systemin are important for the formation of the peptide-receptor complex, this leads to the hypothesis that loss of conformational flexibility may play a role in the loss of activity of systemin due to the P12A and P13A substitutions, while T17A deactivation probably occurs for a different reason, most likely the loss of the threonine phosphorylation site. We also indicate possible structural reasons why the substitution of the prolines at positions 12 and 13 leads to a loss of conformational freedom in the peptide.
authors.affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta , 92 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India.
authors.forename: Saikat Dutta
authors.initials: SD
authors.lastname: Chowdhury
authors.affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta , 92 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India.
authors.forename: Aditya K
authors.initials: AK
authors.lastname: Sarkar
authors.affiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta , 92 Acharya Prafulla Chandra Road, Kolkata 700009, West Bengal, India.
authors.forename: Ansuman
authors.initials: A
authors.lastname: Lahiri
mesh_terms: D000595:Amino Acid Sequence; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009154:Mutation; D036361:Peptide Hormones / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D010455:Peptides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D010937:Plant Growth Regulators / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017433:Protein Structure, Secondary; D012399:Rotation; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D036361:Peptide Hormones; D010455:Peptides; D010937:Plant Growth Regulators; D012997:Solvents; C073704:systemin