Agustí Emperador, Oliver Carrillo, Manuel Rueda, Modesto Orozco

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Presentation transcript:

Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics Agustí Emperador, Oliver Carrillo, Manuel Rueda, Modesto Orozco Biophysical Journal Volume 95, Issue 5, Pages 2127-2138 (September 2008) DOI: 10.1529/biophysj.107.119115 Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 1 Total variances (in Å2) computed for the set of proteins using MD (dark gray), BD (gray), and DMD (light gray). Biophysical Journal 2008 95, 2127-2138DOI: (10.1529/biophysj.107.119115) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 2 Entropies (in cal/molK) associated with the samplings obtained using MD (dark gray), BD (gray), and DMD (light gray). Biophysical Journal 2008 95, 2127-2138DOI: (10.1529/biophysj.107.119115) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 3 Harmonic force constants (kcal/mol Å2) associated with the deformation along eigenvectors derived from MD (blue), BD (red), and DMD (green) for representative proteins. The inset corresponds to values obtained for the first 10 eigenvectors. Biophysical Journal 2008 95, 2127-2138DOI: (10.1529/biophysj.107.119115) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 4 Dimensionality (top) and number (bottom) of essential modes required to explain 90% of the variance for the set of proteins using MD (dark gray), BD (gray), and DMD (light gray). Biophysical Journal 2008 95, 2127-2138DOI: (10.1529/biophysj.107.119115) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 5 Rank distance between the DMD (light gray) or BD (gray) eigenvectors (x axis) and the MD eigenvectors showing the best overlap for representative proteins. Biophysical Journal 2008 95, 2127-2138DOI: (10.1529/biophysj.107.119115) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 6 Normalized spread (Eq. 21) of DMD (light gray) and BD (gray) eigenvectors in MD essential space. Biophysical Journal 2008 95, 2127-2138DOI: (10.1529/biophysj.107.119115) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 7 Similarity index (γ; Eq. 19) between MD and coarse-grained important spaces in DMD (light gray) and BD (gray) simulations for the set of proteins. The important space is defined for each protein as (top) the minimum number of eigenvectors required to explain 90% of variance, and (bottom) the first 50 eigenvectors were selected for all proteins. Biophysical Journal 2008 95, 2127-2138DOI: (10.1529/biophysj.107.119115) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 8 Z-scores (Eq. 20) associated with similarity indices (Eq. 19 and Fig. 7) between MD and coarse-grained models with DMD (light gray) and BD (gray). The important space is defined for each protein as (top) the minimum number of eigenvectors required to explain 90% of variance and (bottom) the first 50 eigenvectors. Biophysical Journal 2008 95, 2127-2138DOI: (10.1529/biophysj.107.119115) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 9 α-Carbons B-factors (in Å2) computed from MD (blue), DMD (green), and BD (red) simulations for representative proteins. Biophysical Journal 2008 95, 2127-2138DOI: (10.1529/biophysj.107.119115) Copyright © 2008 The Biophysical Society Terms and Conditions