title: Investigation of the interaction between the large and small subunits of potato ADP-glucose pyrophosphorylase.
abstract: ADP-glucose pyrophosphorylase (AGPase), a key allosteric enzyme involved in higher plant starch biosynthesis, is composed of pairs of large (LS) and small subunits (SS). Current evidence indicates that the two subunit types play distinct roles in enzyme function. Recently the heterotetrameric structure of potato AGPase has been modeled. In the current study, we have applied the molecular mechanics generalized born surface area (MM-GBSA) method and identified critical amino acids of the potato AGPase LS and SS subunits that interact with each other during the native heterotetrameric structure formation. We have further shown the role of the LS amino acids in subunit-subunit interaction by yeast two-hybrid, bacterial complementation assay and native gel. Comparison of the computational results with the experiments has indicated that the backbone energy contribution (rather than the side chain energies) of the interface residues is more important in identifying critical residues. We have found that lateral interaction of the LS-SS is much stronger than the longitudinal one, and it is mainly mediated by hydrophobic interactions. This study will not only enhance our understanding of the interaction between the SS and the LS of AGPase, but will also enable us to engineer proteins to obtain better assembled variants of AGPase which can be used for the improvement of plant yield.
authors.affiliation: Department of Chemical and Biological Engineering, College of Engineering, Koc University, Rumeli Feneri Yolu, Istanbul, Turkey.
authors.forename: Ibrahim
authors.initials: I
authors.lastname: Baris
authors.forename: Aytug
authors.initials: A
authors.lastname: Tuncel
authors.forename: Natali
authors.initials: N
authors.lastname: Ozber
authors.forename: Ozlem
authors.initials: O
authors.lastname: Keskin
authors.forename: Ibrahim Halil
authors.initials: IH
authors.lastname: Kavakli
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D005816:Genetic Complementation Test; D051599:Glucose-1-Phosphate Adenylyltransferase / Q000235:genetics / Q000378:metabolism*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D054730:Protein Interaction Domains and Motifs / Q000235:genetics*; D055503:Protein Multimerization; D021122:Protein Subunits / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment; D011198:Solanum tuberosum / Q000235:genetics*; D013816:Thermodynamics; D020798:Two-Hybrid System Techniques; D014867:Water / Q000378:metabolism
chemical_list: D021122:Protein Subunits; D014867:Water; D051599:Glucose-1-Phosphate Adenylyltransferase