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

Published version
Peer-reviewed

Change log

Authors

Kumar, Hemant 
Finer-Moore, Janet 
Smirnova, Irina 
Kasho, Vladimir 
Pardon, Els 

Abstract

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.

Description

Funder: research foundation-flanders

Keywords

Amino Acid Substitution, Antigen-Antibody Reactions, Binding Sites, Crystallography, X-Ray, Escherichia coli Proteins, Galactose, Glycine, Hydrogen Bonding, Kinetics, Models, Molecular, Monosaccharide Transport Proteins, Mutation, Missense, Point Mutation, Protein Binding, Protein Conformation, Protein Stability, Single-Domain Antibodies, Structure-Activity Relationship, Symporters, Thiogalactosides, Tryptophan

Journal Title

PLoS One

Conference Name

Journal ISSN

1932-6203
1932-6203

Volume Title

15

Publisher

Public Library of Science (PLoS)
Sponsorship
National Institutes of Health (GM024485)
National Institutes of Health (GM120043)
National Science Foundation (MCB1747705)
INSTRUCT-ERIC (none)
Sandler Foundation (PBBR)
University of California Office of the President (MR-15-328599)