High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32

TY - JOUR

T1 - High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32

AU - Zachariae, Ulrich

AU - Klühspies, Thomas

AU - De, Sharmila

AU - Engelhardt, Harald

AU - Zeth, Kornelius

N1 - The on-line version of this article (available at http://www.jbc.org) contains supplemental data

PY - 2006/3/17

Y1 - 2006/3/17

N2 - The porin Omp32 is the major outer membrane protein of the bacterium Delftia acidovorans. The crystal structures of the strongly anion-selective porin alone and in complex with the substrate malate were solved at 1.5 and 1.45 Å resolution, respectively, and revealed a malate-binding motif adjacent to the channel constriction zone. Binding is mediated by interaction with a cluster of two arginine residues and two threonines. This binding site is specific for Omp32 and reflects the physiological adaptation of the organism to organic acids. Structural studies are combined with a 7-ns unbiased molecular dynamics simulation of the trimeric channel in a model membrane. Molecular dynamics trajectories show how malate ions are efficiently captured from the surrounding bulk solution by the electrostatic potential of the channel, translocated to the binding site region, and immobilized in the constriction zone. In accordance with these results, conductance measurements with Omp32 inserted in planar lipid membranes revealed binding of malate. The anion-selective channel Omp32 is the first reported example of a porin with a 16-stranded β-barrel and proven substrate specificity. This finding suggests a new view on the correlation of porin structure with substrate binding in specific channels.

AB - The porin Omp32 is the major outer membrane protein of the bacterium Delftia acidovorans. The crystal structures of the strongly anion-selective porin alone and in complex with the substrate malate were solved at 1.5 and 1.45 Å resolution, respectively, and revealed a malate-binding motif adjacent to the channel constriction zone. Binding is mediated by interaction with a cluster of two arginine residues and two threonines. This binding site is specific for Omp32 and reflects the physiological adaptation of the organism to organic acids. Structural studies are combined with a 7-ns unbiased molecular dynamics simulation of the trimeric channel in a model membrane. Molecular dynamics trajectories show how malate ions are efficiently captured from the surrounding bulk solution by the electrostatic potential of the channel, translocated to the binding site region, and immobilized in the constriction zone. In accordance with these results, conductance measurements with Omp32 inserted in planar lipid membranes revealed binding of malate. The anion-selective channel Omp32 is the first reported example of a porin with a 16-stranded β-barrel and proven substrate specificity. This finding suggests a new view on the correlation of porin structure with substrate binding in specific channels.

UR - https://www.scopus.com/pages/publications/33646354636

U2 - 10.1074/jbc.M510939200

DO - 10.1074/jbc.M510939200

M3 - Article

C2 - 16434398

AN - SCOPUS:33646354636

SN - 0021-9258

VL - 281

SP - 7413

EP - 7420

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

IS - 11

ER -