Induced Fit and the Entropy of Structural Adaptation in the Complexation of CAP and λ- Repressor with Cognate DNA Sequences Surjit B. Dixit, David Q.

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Presentation transcript:

Induced Fit and the Entropy of Structural Adaptation in the Complexation of CAP and λ- Repressor with Cognate DNA Sequences Surjit B. Dixit, David Q. Andrews, D.L. Beveridge Biophysical Journal Volume 88, Issue 5, Pages 3147-3157 (May 2005) DOI: 10.1529/biophysj.104.053843 Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 1 AMBER parm94-compatible atom types and the partial atomic charges derived using the RESP procedure for the cyclic AMP molecule. Biophysical Journal 2005 88, 3147-3157DOI: (10.1529/biophysj.104.053843) Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 2 Convergence profile of the estimated configurational entropy based on the quasiharmonic analysis of molecular dynamics trajectories. The data for the CAP-DNA (5ns) and λ-repressor-operator system (4ns) is marked with plus and cross symbols, respectively. The plot presents the convergence of the configurational entropy of the complex, the protein, and DNA in the trajectory of the complex and the configurational entropy of unbound forms of the constituent protein and DNA. Biophysical Journal 2005 88, 3147-3157DOI: (10.1529/biophysj.104.053843) Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 3 Overlay of superimposed structures from the MD simulation of the unbound form of the CAP binding site (left), CAP (middle), and the CAP-DNA complex (right), respectively. Figures prepared using MOLMOL (Koradi et al., 1996). Biophysical Journal 2005 88, 3147-3157DOI: (10.1529/biophysj.104.053843) Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 4 Overlay of superimposed structures from the MD simulation of the unbound OL1 operator DNA (left), λ-repressor protein (middle), and the λ-repressor-operator complex (right), respectively. Biophysical Journal 2005 88, 3147-3157DOI: (10.1529/biophysj.104.053843) Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 5 Direction of DNA axis curvature as observed in the MD simulation of DNA bound to CAP (red) and the free form of DNA (blue). The image presents four different views of the same set of structures. Biophysical Journal 2005 88, 3147-3157DOI: (10.1529/biophysj.104.053843) Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 6 The original crystallographic structure of the CAP-DNA complex (1CGP) with the helix axis shown with a dark solid line. The ∼35° out-of-plane bend in the helical axis is presented by the dihedral angle between the sections A,B,C and B,C,D of the DNA. Biophysical Journal 2005 88, 3147-3157DOI: (10.1529/biophysj.104.053843) Copyright © 2005 The Biophysical Society Terms and Conditions

Figure 7 Time series of the out-of-plane bend in the DNA helical axis in the 5-ns MD simulation of DNA bound to CAP (dotted line) and the unbound form (solid line). The running average of the out-of-plane bend dihedral angle is shown for the two cases as thick lines. Biophysical Journal 2005 88, 3147-3157DOI: (10.1529/biophysj.104.053843) Copyright © 2005 The Biophysical Society Terms and Conditions

Scheme 1 . Biophysical Journal 2005 88, 3147-3157DOI: (10.1529/biophysj.104.053843) Copyright © 2005 The Biophysical Society Terms and Conditions