Table 1

Parameters derived from retrostructural analysis of natural proteins

Protein namerms deviation (Å)Atoms superimposedSymmetryα, degreesβ, degreesγ, degreesXtrans, ÅYtrans, ÅZtrans, Å
Zif268a0.6622N/A−35.8−18.7−3.1−1.88.85.2
Rubredoxinb0.7820C221.5−13.812.20.8−5.4N/A
Bacterioferritinc1.0348D28.513.6−4.14.55.67.5
Rubrerythrind0.8948D210.311.2−3.74.26.07.3
H Ferritine1.3748D26.78.5−4.14.36.38.0
Ribonucleotide reductase (R2)f1.1148D23.918.3−1.44.65.76.9
Methane monooxygenaseg0.9636D20.119.92.24.15.46.5
Δ9 ACP desaturaseh1.2936D2−11.914.8−2.24.55.79.1
Myohemerythrini1.2374D24.810.04.55.35.27.3
Hemerythrinj1.4574D20.29.63.75.25.27.2
Hemocyanink2.0942D25.514.4−17.16.96.111.2
  • Retrostructural parameterization of metal sites. Models of proteins based on idealized secondary structure motifs were generated and fit to experimental structures of metalloproteins. The best-fit Cα rms deviation and the parameters used to generate the tertiary structure fold are shown above. To create the model helical bundles, an ideal helix (φ = −65.0, ψ = −40.0) was first placed in a Cartesian coordinate system with its axis directed along Z. Structures containing β-hairpins (Zif268 and rubredoxin) similarly used an idealized hairpin oriented with its β sheet along Z. The sheet was additionally aligned onto X-Z by minimizing the deviations between the Cα coordinates and the X-Z plane. The idealized hairpin was generated by averaging the φ and ψ angles of the hairpins in Ziff268 and rubredoxin. To create the bundles, the helix (or sheet) was then translated along X, Y, and Z (Xtrans, Ytrans, Ztrans) and rotated about its own axis by the angle α. The value of α is given relative to an “ideal” value expected if a vector originating at the center of the helix and bisecting the Cα atoms of the central “a” and “d” positions were directed precisely towards the bundle axis (in a projection onto the X-Y plane). Additionally, the secondary structure was then tilted (through the angle β) by rotating about an axis defined by the bundle origin and the intersection of the helix axis with the X-Y plane. Further, the inclination of the helix (γ) was produced by rotation about an axis in the X-Y plane orthogonal to that used to produce the β-tilt angle. Finally, the bundles were created by using the symmetry operation shown. Optimal values of the fitting parameters were obtained by using a genetic algorithm to optimize the superposition of the D2 symmetric model onto each crystal structure. The optimal superposition and associated rms deviation were calculated by using the Cα coordinates. Calculations were run on an SGI Indigo2 workstation using code written in Fortran 77. The PDB codes are as follows:  

  • a Zif268, 1ZAA (61), residues 35–44, 47–59;  

  • b 1BRF (84), residues 3–12, 36–45;  

  • c 1BCF (67), residues 47–58, 14–25, 90–101, 123–134;  

  • d 1RYT (68), residues 16–27, 49–60, 90–98, 100–102, 124–135;  

  • e 2FHA (85), residues 23–34, 58–69, 103–114, 137–148;  

  • f 1RIB (86), residues 80–91, 111–122, 234–245, 200–204, 206–212;  

  • g 1MTY (72), residues 110–121, 140–151, 239–250;  

  • h 1AFR (71), residues 139–150, 192–203, 222–233;  

  • i 2MHR (64) residues 21–37, 40–65, 70–87, 94–106;  

  • j 1HMO (87) residues 21–37, 40–65, 70–87, 89–101;  

  • k 1OXY (88), residues 170–180, 198–207, 321–331, 358–367.