Diversity in kinetics correlated with structure in nano body-stabilized LacY

• Published in: PloS one 2020-05, Vol.15 (5), p.e0232846
• Main Authors: Kumar, Hemant, Finer-Moore, Janet, Smirnova, Irina, Kasho, Vladimir, Pardon, Els, Steyaert, Jan, Kaback, H Ronald, Stroud, Robert M
• Format: Article
• Language: English
• Subjects: Binding sites; Biochemistry; Biology and Life Sciences; Biophysics; Bonds (Securities); Complementarity-determining region 3; Crystallization; Escherichia coli; Galactosides; Glycine; Hydrogen; Hydrogen bonding; Hydrogen bonds; Interfaces; Kinetics; Lactose; Lactose permease; Membrane proteins; Molecular biology; Mutants; Nanobodies; Nanoparticles; Permease; Physical Sciences; Physiological aspects; Physiology; Protein binding; Protein conformation; Protein research; Proteins; Structure; Structure (Literature); Substrates; Transport proteins
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0232846

The structure of lactose permease, stabilized in a periplasmic open conformation by two Gly to Trp replacements (LacYww) and complexed with a nanobody directed against this conformation, provides the highest resolution structure of the symporter. The nanobody binds in a different manner than two other nanobodies made against the same mutant, which also bind to the same general region on the periplasmic side. This region of the protein may represent an immune hotspot. The CDR3 loop of the nanobody is held by hydrogen bonds in a conformation that partially blocks access to the substrate-binding site. As a result, kon and koff for galactoside binding to either LacY or the double mutant complexed with the nanobody are lower than for the other two LacY/nanobody complexes though the Kd values are similar, reflecting the fact that the nanobodies rigidify structures along the pathway. While the wild-type LacY/nanobody complex clearly stabilizes a similar 'extracellular open' conformation in solution, judged by binding kinetics, the complex with wild-type LacY did not yet crystallize, suggesting the nanobody does not bind strongly enough to shift the equilibrium to stabilize a periplasmic side-open conformation suitable for crystallization. However, the similarity of the galactoside binding kinetics for the nanobody-bound complexes with wild type LacY and with LacYWW indicates that they have similar structures, showing that the reported co-structures reliably show nanobody interactions with LacY.