Microscopic Mechanism of Antibiotics Translocation through a Porin

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Microscopic Mechanism of Antibiotics Translocation through a Porin Matteo Ceccarelli, Christophe Danelon, Alessandro Laio, Michele Parrinello Biophysical Journal Volume 87, Issue 1, Pages 58-64 (July 2004) DOI: 10.1529/biophysj.103.037283 Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 1 (A) View of the constriction zone along the z direction. The important residues are in stick, the Asp and Glu in red, the Arg and Lys in blue, the Tyr in yellow. The loop L3 is in red. (B) Schematic view of OmpF along y with the charged residues. (C) Ampicillin molecule in an all-atom representation with atom labels. Biophysical Journal 2004 87, 58-64DOI: (10.1529/biophysj.103.037283) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 2 Snapshots of the simulated system on the z (A) and y (B) planes. Biophysical Journal 2004 87, 58-64DOI: (10.1529/biophysj.103.037283) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 3 Contour plot of the free energy surface (each color is 0.5kcal/mol) obtained with two standard MD simulations of 4.5ns each. Crosses label the initial configurations. Biophysical Journal 2004 87, 58-64DOI: (10.1529/biophysj.103.037283) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 4 Contour plot of the free energy surfaces, each color is 1 kcal/mol of difference. The calculation does not give the relative probability of the minima because we did not observe a recrossing. Only the free energy barriers along the arrows are meaningful. (A) Process Ext-to-Int and (B) Int-to-Ext. Biophysical Journal 2004 87, 58-64DOI: (10.1529/biophysj.103.037283) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 5 All-atom representation viewed along z of the most characteristic conformations sampled during the process Ext-to-Int (see Fig. 4 for the position on the free energy surface). Contacts: I, COO-Arg132, NH3- Glu117; II, COO-Arg82, O2-Arg82, O1-Arg42, NH3- Glu117; and III, O2-Lys16, O1-Arg42, NH3- Glu117. Biophysical Journal 2004 87, 58-64DOI: (10.1529/biophysj.103.037283) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 6 All-atom representation viewed along z of the most characteristic conformations sampled during the process Int-to-Ext (see Fig. 4 for the position on the free energy surface). Contacts (in orange): VI, COO-Arg82, NH3-Asp113; VII, O2-Arg82, O1-Arg82, NH3-Asp113; and VIII, COO- Arg168. Biophysical Journal 2004 87, 58-64DOI: (10.1529/biophysj.103.037283) Copyright © 2004 The Biophysical Society Terms and Conditions

Figure 7 Values of the ω1 (solid line) and ω2 (dotted line) torsional angles of Amp during the metadynamics simulations. (A) Process Ext-to-Int; (B) process Int-to-Ext; and (C) process Ext-to-Int with ω1 restrained at −80°. Biophysical Journal 2004 87, 58-64DOI: (10.1529/biophysj.103.037283) Copyright © 2004 The Biophysical Society Terms and Conditions