Volume 94, Issue 9, Pages (May 2008)

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Volume 94, Issue 9, Pages 3590-3600 (May 2008) Predicting Thymine Dimerization Yields from Molecular Dynamics Simulations Yu Kay Law, Javad Azadi, Carlos E. Crespo-Hernández, Eric Olmon, Bern Kohler Biophysical Journal Volume 94, Issue 9, Pages 3590-3600 (May 2008) DOI: 10.1529/biophysj.107.118612 Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 1 The most abundant stereoisomers of the thymine photodimer. Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 2 (A) Two-parameter model for identification of dimerizable conformations in dTpdT. At each time step during the molecular dynamics simulation, the separation between the midpoints of the C5-C6 double bonds, d, and the improper torsion angle between the same bonds, η, are calculated. (B) A conformer is assumed to dimerize when photoexcited if these parameters satisfy the inequalities 0<d≤d1 and 0≤|η|≤η1, corresponding to the shaded area in the graph. Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 3 Probability density of the C5-C6 bond separation (d) for all conformers of dTpdT in water (solid line), 40% (v/v) ethanol (short-dashed line), 60% (v/v) ethanol (long-dashed line), and 50% (v/v) dioxane (dotted line). Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 4 Distribution of conformers at different values of d and |η| for (A) dTpdT in water and (B) dTpdT in 50% (v/v) dioxane. The axes on the graphs are scaled the same for comparison. Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 5 Loci of points d1, η1 (defined in Fig. 2) such that the fraction of dimerizable conformers is equal to the experimental thymine dimer quantum yield (Table 1) in each solvent. The errors in the d values are ±0.03Å. Line styles are the same as in Fig. 3. Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 6 Distribution of the angle between the normal vectors of the two bases of dTpdT in water. The black line is for all conformers, and the red line represents the subset of dimerizable conformers. Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 7 Distribution of the glycosidic torsion angle (χ) of the (A) 5′ base and (B) 3′ base of dTpdT for various conformer sets in water. Black line, all conformers; solid red line, cis-syn dimerizable conformers; dashed red line, trans-syn dimerizable conformers; blue line, nondimerizable conformations with d<3.66Å. Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 8 Probability distribution for the δ dihedral angle of the 5′ base of dTpdT in water for different conformer populations. Line styles are the same as in Fig. 7. Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 9 Distribution of the dihedral angle β of the 3′ base of dTpdT in water. Line styles are the same as in Fig. 7. Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 10 cis-syn mean dimerizable structure (magenta) compared with the canonical B-form dTpdT structure (black). Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions

Figure 11 cis-syn mean dimerizable structure (magenta) compared with the actual cis-syn dimer structure (green) from McAteer et al. (53). Biophysical Journal 2008 94, 3590-3600DOI: (10.1529/biophysj.107.118612) Copyright © 2008 The Biophysical Society Terms and Conditions