The Loop Opening/Closing Motion of the Enzyme Triosephosphate Isomerase  Philippe Derreumaux, Tamar Schlick  Biophysical Journal  Volume 74, Issue 1, Pages 72-81 (January 1998) DOI: 10.1016/S0006-3495(98)77768-9 Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 1 Schematic ribbon diagrams of the open (top) and closed (bottom) x-ray structures of subunit 1, created with MOLSCRIPT (Kraulis, 1991). The surface of loop residues is in yellow, that of residues 208–212 in green, and those of the others in blue. Residues Gly173, Ala176, Tyr208, and Ser211 are identified, as well as the hydrogen bonds (in red) between Ser211 and Gly173, and between Tyr208 and Ala176 in the closed form. Biophysical Journal 1998 74, 72-81DOI: (10.1016/S0006-3495(98)77768-9) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 2 Three-dimensional adiabatic potential energy surface for the TIM/solvent model (in kcal/mol) in the space of the two hydrogen bonds: hb1, formed between Ser211 and Gly173; and hb2, formed between Tyr208 and Ala176. The closed, open, and “transition state” forms are characterized by the following triplets of values (hb1 in Å, hb2 in Å, E in kcal/mol): (3.6, 3.0, −565), (8.1, 5.1, −557), and (7.5, 3.9, −550), respectively. They are identified by C, O, and T. Biophysical Journal 1998 74, 72-81DOI: (10.1016/S0006-3495(98)77768-9) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 3 The stereo open (A) and closed (B) minimized forms of subunit 1 in solvent model, drawn with MOLSCRIPT (Kraulis, 1991). These structures are obtained from the adiabatic potential energy surface (Fig. 2). The surface of loop 164–177 residues is in yellow, that of residues 208–212 in green, and the water molecules are in red and white. Residues Tyr164, Thr172, Gly173, Leu174, Ala176, Tyr208, and Ser211 are identified. The two hydrogen bonds hb1 and hb2 of the closed form (Fig. 3 B) are shown dashed in red; the three specific solvent-solute hydrogen bonds that compensate for the loss of the two hb1 and hb2 interactions of the closed form are shown dashed in red (Fig. 3 A), and the other solute-solvent hydrogen bonds in both forms are shown dashed in blue. Biophysical Journal 1998 74, 72-81DOI: (10.1016/S0006-3495(98)77768-9) Copyright © 1998 The Biophysical Society Terms and Conditions

Figure 4 Plots of the α-carbon pseudodihedral loop angles. The angle i corresponds to rotation about atoms i, i+1. (A) The rms fluctuations of angles from the average LD and DA forms generated with set 1 of flexible residues in solvent simulations. (B) The open LD structure (see LD|| in Table 2) minus the open crystal structure, and the DA open structure (see DA¶¶ in Table 2) minus the open crystal structure. (C) The rms fluctuations of angles from the average 300K MD form in solvent simulation with harmonic constraints of 2 kcal/(mol Å2) on hb1 and hb2. Biophysical Journal 1998 74, 72-81DOI: (10.1016/S0006-3495(98)77768-9) Copyright © 1998 The Biophysical Society Terms and Conditions