Electrostatic properties of the anion selective porin Omp32 from Delftia acidovorans and of the arginine cluster of bacterial porins

Abstract

The functional properties of the anion-selective porin Omp32 from the bacterium Delftia acidovorans, formerly Comamonas acidovorans, are determined by the particularly narrow channel constriction and the electrostatic field inside and outside the pore. A cluster of arginines (Arg 38, Arg 75, and Arg 133) determines the electrostatic field close to the constriction zone. Stacked amino acids carrying charges are prone to drastic pK a shifts. However, optimized calculations of the titration behavior of charged groups, based on the finite-difference Poisson-Boltzmann technique, suggest that all the arginines are charged at physiological pH. Protonation of the clustered arginines is stabilized by one buried glutamate residue (Glu 58), which is strongly interacting with Arg 75 and Arg 38. This functional arrangement of three charged amino acid residues is of general significance because it is found in the constriction zones of all known 16-stranded porins from the ␣-, ␤-, and ␥-proteobacteria.

Using Multiconformation Continuum Electrostatics to Compare Chloride Binding Motifs in α-Amylase, Human Serum Albumin, and Omp32

“…Compared to HSA where many surface ionizable residues change ionization states at neutral pH with ion binding, most of the residues in the transmembrane region of Omp32 are basic with high pK a s. In addition, these residues are sufficiently far apart that their pK a s do not significantly perturb each other. The lack of pH dependence is consistent with earlier calculations 56 and with the experimental observation that the channel conductance is pH independent. 93 The Boltzmann-averaged energies of the chlorides occupied in Monte Carlo sampling versus the coordinates along the channel axis (z-axis) are shown in Fig.…”

“…94 The positive potential that repels cations continues into this narrow region. 56 Interactions with the protein backbone dipoles are small, while interactions with side chains favor anions in the channel and repel cations. It should be noted that the interaction profiles of bound anions and cations are not a simple mirror of each other because anions are favored by positive surface potential and cations by negative potential, leading to different Boltzmann-weighted distributions.…”

“…19,[51][52][53] Methods incorporating continuum electrostatics have been used to study the electrostatic basis of ion selectivity 18,54 and the side-chain ionization states in channels. 55,56 Other techniques including grand canonical Monte Carlo 48 and free-energy perturbation and umbrella sampling 57,58 have been integrated into these studies.…”

Topology of the Porin MspA in the Outer Membrane of Mycobacterium smegmatis

“…(iii) Large pK a shifts have been observed in several instances both for aspartates and for arginines within proteins or in model peptides when compared with the free amino acids (45,46). Thus, some of the arginines, aspartates, and glutamates in membrane facing loops of MspA may not be charged in their native environment.…”

Molecular Basis of Bacterial Outer Membrane Permeability Revisited

“…At the constriction zone, three arginine residues are clustered, yet apparently all of them remain positively charged. A large factor here is the presence of a glutamate residue, whose side chain does not protrude into the channel yet stabilizes the positive charges of the two arginine residues protruding into the channel (770). Inspection of three-dimensional structures as well as the primary sequences of many porins from ␤-and ␥-proteobacteria suggests that this arrangement is rather common in the trimeric, classical porins (770).…”