title: Mechanical unfolding of ribose binding protein and its comparison with other periplasmic binding proteins.
abstract: Folding and unfolding studies on large, multidomain proteins are still rare despite their high abundance in genomes of prokaryotes and eukaryotes. Here, we investigate the unfolding properties of a 271 residue, two-domain ribose binding protein (RBP) from the bacterial periplasm using single-molecule force spectroscopy. We observe that RBP predominately unfolds via a two-state pathway with an unfolding force of ∼80 pN and an unfolding contour length of ∼95 nm. Only a small population (∼15%) of RBP follows three-state pathways. The ligand binding neither increases the mechanical stability nor influences the unfolding flux of RBP through different pathways. The kinetic partitioning between two-state and three-state pathways, which has been reported earlier for other periplasmic proteins, is also observed in RBP, albeit to a lesser extent. These results provide important insights into the mechanical stability and unfolding processes of large two-domain proteins and highlight the contrasting features upon ligand binding. Protein structural topology diagrams are used to explain the differences in the mechanical unfolding behavior of RBP with other periplasmic binding proteins.
authors.affiliation: Department of Chemical Sciences, Tata Institute of Fundamental Research , Homi Bhabha Road, Colaba, Mumbai 400005, India.
authors.forename: Hema Chandra
authors.initials: HC
authors.lastname: Kotamarthi
authors.forename: Satya
authors.initials: S
authors.lastname: Narayan
authors.forename: Sri Rama Koti
authors.initials: SR
authors.lastname: Ainavarapu
mesh_terms: D004926:Escherichia coli / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D018625:Microscopy, Atomic Force; D033902:Periplasmic Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D011489:Protein Denaturation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
chemical_list: D029968:Escherichia coli Proteins; D033902:Periplasmic Binding Proteins; C028003:RbsB protein, E coli