Ionization States of Residues in OmpF and Mutants: Effects of Dielectric Constant and Interactions between Residues Sameer Varma, Eric Jakobsson Biophysical.

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Presentation transcript:

Ionization States of Residues in OmpF and Mutants: Effects of Dielectric Constant and Interactions between Residues Sameer Varma, Eric Jakobsson Biophysical Journal Volume 86, Issue 2, Pages 690-704 (February 2004) DOI: 10.1016/S0006-3495(04)74148-X Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 1 Partial view of the x-ray structure of OmpF-trimer highlighting titratable residues in the constriction zone. Several loops have been truncated for clarity. Our calculations described in text predict residues colored in red to be positively charged at neutral pH and residues colored in green to be negatively charged at neutral pH. E296 colored in orange is expected to be protonated. Charge assignment of D127 was found to be sensitive to the value of dielectric constant assumed for the protein. Other assignments are not sensitive to assumption of dielectric constant. This figure was created with RasMol Version 2.6. Biophysical Journal 2004 86, 690-704DOI: (10.1016/S0006-3495(04)74148-X) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 2 Thermodynamic cycle for ionizing a titratable residue in the presence and absence of protein system. Subscript (s) denotes water and subscript (p) denotes protein system (protein in solvent). Biophysical Journal 2004 86, 690-704DOI: (10.1016/S0006-3495(04)74148-X) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 3 Dielectric model of OmpF used in pKa calculations is shown embedded in a low dielectric slab (width, 24Å) composed of neutral nonpolar spheres (radii, 2 A). The position of the slab was postulated to lie between Tyr-180 and Trp-214. Biophysical Journal 2004 86, 690-704DOI: (10.1016/S0006-3495(04)74148-X) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 4 Network-1 is shown in Fig. 4 a whereas Network-2 is shown in Fig. 4 b. Fig. 4 c shows the H-bond configuration resulting upon accounting for the most probable ionization states of all residues belonging to the loop 3 cluster predicted using Network-2. These figures were created with RasMol Version 2.6. Biophysical Journal 2004 86, 690-704DOI: (10.1016/S0006-3495(04)74148-X) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 5 The H-bond network used in calculations involving Arg-82. R132 is truncated and R42 is not shown to clearly depict the H-bond network. This figure was created with RasMol Version 2.6. Biophysical Journal 2004 86, 690-704DOI: (10.1016/S0006-3495(04)74148-X) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 6 Truncated view of OmpF mutant R42C showing the side chains of residues C42, R82, and R132 located at the constriction zone of the channel. Biophysical Journal 2004 86, 690-704DOI: (10.1016/S0006-3495(04)74148-X) Copyright © 2004 The Biophysical Society Terms and Conditions