In silico insights into protein-protein interactions and folding dynamics of the saposin-like domain of Solanum tuberosum aspartic protease

• Published in: PloS one Vol. 9; no. 9; p. e104315
• Main Authors: De Moura, Dref C, Bryksa, Brian C, Yada, Rickey Y
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 04-09-2014; Public Library of Science (PLoS)
• Subjects: Acidification; Analysis; Antimicrobial agents; Aspartic Acid Proteases - chemistry; Aspartic endopeptidase; Barley; Bioinformatics; Biology and Life Sciences; Biophysics; Computer Simulation; Crystal structure; Crystals; Dissociation; Energy of dissociation; Enzyme Stability; Food science; Free energy; Hydrogen ions; Hydrogen-Ion Concentration; Ligands; Models, Molecular; Molecular Dynamics Simulation; Oligomerization; pH effects; Plant Proteins - chemistry; Potatoes; Principal components analysis; Protease; Proteases; Protein Conformation; Protein Folding; Protein interaction; Protein Interaction Domains and Motifs; Protein Multimerization; Protein structure; Protein Structure, Quaternary; Protein-protein interactions; Proteins; Quaternary; Research and Analysis Methods; Saposins - chemistry; Solanum tuberosum; Solanum tuberosum - enzymology; Structure; Substrates; Tertiary structure; Canada; Guelph Ontario Canada
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0104315

The plant-specific insert is an approximately 100-residue domain found exclusively within the C-terminal lobe of some plant aspartic proteases. Structurally, this domain is a member of the saposin-like protein family, and is involved in plant pathogen defense as well as vacuolar targeting of the parent protease molecule. Similar to other members of the saposin-like protein family, most notably saposins A and C, the recently resolved crystal structure of potato (Solanum tuberosum) plant-specific insert has been shown to exist in a substrate-bound open conformation in which the plant-specific insert oligomerizes to form homodimers. In addition to the open structure, a closed conformation also exists having the classic saposin fold of the saposin-like protein family as observed in the crystal structure of barley (Hordeum vulgare L.) plant-specific insert. In the present study, the mechanisms of tertiary and quaternary conformation changes of potato plant-specific insert were investigated in silico as a function of pH. Umbrella sampling and determination of the free energy change of dissociation of the plant-specific insert homodimer revealed that increasing the pH of the system to near physiological levels reduced the free energy barrier to dissociation. Furthermore, principal component analysis was used to characterize conformational changes at both acidic and neutral pH. The results indicated that the plant-specific insert may adopt a tertiary structure similar to the characteristic saposin fold and suggest a potential new structural motif among saposin-like proteins. To our knowledge, this acidified PSI structure presents the first example of an alternative saposin-fold motif for any member of the large and diverse SAPLIP family.