Efficient and Robust Analysis of Biomacromolecular Flexibility Using Ensembles of Network Topologies Based on Fuzzy Noncovalent Constraints Christopher.

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Efficient and Robust Analysis of Biomacromolecular Flexibility Using Ensembles of Network Topologies Based on Fuzzy Noncovalent Constraints Christopher Pfleger, Holger Gohlke Structure Volume 21, Issue 10, Pages 1725-1734 (October 2013) DOI: 10.1016/j.str.2013.07.012 Copyright © 2013 Elsevier Ltd Terms and Conditions

Structure 2013 21, 1725-1734DOI: (10.1016/j.str.2013.07.012) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 1 Work Flow of the ENTFNC Approach The ENTFNC approach has been integrated into the CNA software package. RAND(0,1) draws a random number with equal probability from the range [0,1]. See Theory for further details. Structure 2013 21, 1725-1734DOI: (10.1016/j.str.2013.07.012) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 2 Local Stability Characteristics of HEWL (A) Rigid cluster decompositions using the FIRST program (Jacobs et al., 2001) obtained with a cutoff of the hydrogen bond energy EHB = −1.0 kcal/mol and a hydrophobic tether distance cutoff Dcut = 0.25 Å. Rigid clusters are depicted as uniformly colored bodies with the largest rigid cluster in blue. (B) Rigidity index ri for the SNT analyses of the ten HEWL structures (red), ri curves for the ten ENTMD analyses of HEWL (gray), and the average over all ENTMD analyses (black). The histogram below shows the standard deviation of the ris across the crystal structures and the MD ensembles, respectively. (C) Rigidity index ri for the ENTFNC analyses of the ten HEWL structures (green). The histogram below shows the standard deviation of the ris. For comparison, the results from the ENTMD analyses are depicted again. (D–F) The mean ri values and standard deviations from the SNT analyses (D), ENTMD analyses (E), and ENTFNC analyses (F) are mapped onto a HEWL structure. The colors show the ri values and the diameter of the putty plot the standard deviation at each residue position. The diameter is scaled with respect to the maximum SD of all three analyses. See also Table S2 and Figures S1 and S4. Structure 2013 21, 1725-1734DOI: (10.1016/j.str.2013.07.012) Copyright © 2013 Elsevier Ltd Terms and Conditions

Figure 3 Correlations between Predicted Tp and Optimal Growth Temperatures Tog (A–D) Correlations between predicted Tp and optimal growth temperatures Tog from SNT (A), ENTMD (B), SNTmin (C), and ENTFNC (D) analyses of five different CS structures. Error bars in (B) and (D) show the SEM. Least squares fit lines have been added. See also Table S4. Structure 2013 21, 1725-1734DOI: (10.1016/j.str.2013.07.012) Copyright © 2013 Elsevier Ltd Terms and Conditions