Volume 74, Issue 1, Pages 413-421 (January 1998) Comparison of Simulated and Experimentally Determined Dynamics for a Variant of the LacI DNA-Binding Domain, Nlac-P  Liskin Swint-Kruse, Kathleen Shive Matthews, Paul E. Smith, B. Montgomery Pettitt  Biophysical Journal  Volume 74, Issue 1, Pages 413-421 (January 1998) DOI: 10.1016/S0006-3495(98)77798-7 Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 1 Sequence of Nlac-P. The sequence of chimeric protein Nlac-P is listed using one-letter abbreviations for the amino acids. Sequence numbers are indicated as subscripts. The four helices are overlined, residues from LacI are in regular type, hinge residues from PurR are in bold type, and hinge residues that are conserved between the two parent proteins are underlined. The terminal GCG, designed to allow dimerization through disulfide bond formation, is in lower case. Biophysical Journal 1998 74, 413-421DOI: (10.1016/S0006-3495(98)77798-7) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 2 Structures generated by the dynamics trajectory. Starting with the structure 40ps into the trajectory, the Cα trace of Nlac-P is plotted every 100ps as thin black ribbons. The ribbons were generated with the program Quanta, version 4.1 (Molecular Simulations, Inc., San Diego, CA). (a) Alignment along the three helices of the DNA-binding domain. (b) The structures in (a) are viewed down helix II in order to compare theloop between helices II and III to the experimentally determined structures (wide, gray ribbons). The ribbon for the bound structure (Chuprina et al., 1993) is the topmost loop; the ribbon for free LacI is bottommost (Slijper et al., 1996). The ribbons for 340 and 740ps are not shown in this view. The hinge helix has been cut away in order to better view loop II-III. (c) Alignment of structures in view (a) along the hinge helix. Biophysical Journal 1998 74, 413-421DOI: (10.1016/S0006-3495(98)77798-7) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 3 Order parameters for backbone NH determined from MD simulations plotted as a function of residue number. Calculations of order parameters are described in the text (Eq. 2). Residues 3 and 49 are prolines and thus S2 cannot be determined. Black horizontal lines indicate the locations of the four helices. Light gray bars represent values determined after aligning the structures with the first three helices. Values represented with striped bars result when Nlac-P is aligned along the hinge helix. Circles (●) symbolize values of S2 estimated from 15N-NMR relaxation data (Slijper et al., 1997; Fig. 3). These data are not included after residue 48, where the sequence of Nlac-P diverges from the DNA-binding domain of LacI. Error bars represent 95% confidence limits. Biophysical Journal 1998 74, 413-421DOI: (10.1016/S0006-3495(98)77798-7) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 4 Correlation function versus simulation time. Data are shown for four residues (as indicated) which are representative of various types of plots. Thin black lines on the plots for residues 20 and 40 represent the results of fits using Eq. 3. Biophysical Journal 1998 74, 413-421DOI: (10.1016/S0006-3495(98)77798-7) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 5 Root mean square deviations of Cα during MD simulations plotted as a function of residue number. Light gray bars represent values determined after aligning the structures with the first three helices. Values represented with striped bars result when Nlac-P is aligned along the hinge helix. Biophysical Journal 1998 74, 413-421DOI: (10.1016/S0006-3495(98)77798-7) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 6 Distance of Cα in the loop between helices II and III from the DNA bound structure versus simulation time. Residue numbers for the Cα in loop II-III are in the top left-hand corners of their respective plots. Values close to zero indicate that the Cα is close to the position of the DNA bound form of the protein (Chuprina et al., 1993). Biophysical Journal 1998 74, 413-421DOI: (10.1016/S0006-3495(98)77798-7) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 7 Interatomic distances for atoms involved in hydrogen bonds of the hinge helix as a function of simulation time. Donor and acceptor atoms of the hydrogen bonds are listed in the top left-hand corners of their respective plots. The dotted lines at 2.5Å represent an average hydrogen bond length and are included to aid inspection of the data. Biophysical Journal 1998 74, 413-421DOI: (10.1016/S0006-3495(98)77798-7) Copyright © 1998 The Biophysical Society Terms and Conditions