Table 1.
Structure calculation for human GliPR, using an input of conformational constraints obtained with the NMR- and homology-based approach described in the text and comparison with the NMR structure of P14a (7)
| GliPR | P14a | |
|---|---|---|
| Conformational constraints | ||
| Total number of constraints | 1,216 | 2,021 |
| Upper distance limits | 932 | 1,692 |
| Disulfide bond constraints* | 18 | 18 |
| β-Sheet hydrogen bond constraints* | 32 | — |
| ψ,φ-dihedral angle constraints | 202 | 228 |
| χ1-dihedral angle constraints | 32 | 83 |
| 20 diana conformers used to represent the structure, after energy minimization (average value ± SD) | ||
| diana target function, Å2† | 6.5 ± 0.7 | 3.1 ± 0.7 |
| NOE constraint violations, Å: Sum | 7.86 ± 0.49 | 9.20 ± 0.64 |
| Max | 0.11 ± 0.14 | 0.10 ± 0.01 |
| Dihedral angle violations, °: Sum | 25.6 ± 4.3 | 45.0 ± 5.1 |
| Max | 2.4 ± 0.3 | 2.3 ± 0.2 |
| amber energies, kcal⋅mol−1: Van der Waals | −358 ± 21 | −570 ± 12 |
| Electrostatic | −4,203 ± 182 | −4,576 ± 74 |
| Average rms deviations for different atom selections (average value ± SD) | ||
| Backbone N, Cα, C′ of constrained segments‡ | 1.66 ± 0.26 | 0.88 ± 0.08 |
| All heavy atoms of constrained segments‡ | 2.37 ± 0.24 | 1.30 ± 0.09 |
| Backbone of the regular secondary structures§ | 0.98 ± 0.19 | 0.45 ± 0.08 |
| Backbone of constrained segments‡ + core side chains¶ | 1.60 ± 0.21 | 0.91 ± 0.07 |
In GliPR, the disulfide bonds between C65–C146, C121–C125, and C141–C163, and the hydrogen bonds W91⋅⋅⋅F161, A142⋅⋅⋅I162, Q144⋅⋅⋅H160, H160⋅⋅⋅Q144, F161⋅⋅⋅W91, I162⋅⋅⋅A142, C163⋅⋅⋅N89, and N164⋅⋅⋅G140 in the β-sheet were constrained following ref. 8.
Before energy minimization.
“Constrained segments” of GliPR are those parts of the polypeptide chain for which conformational constraints were available from the NMR measurements with P14a, which includes the residues 21–38, 44–72, 87–146, 148–151, and 159–176 (see also Fig. 1).
The secondary structure elements in GliPR are as follows: α-helix I, residues 24–37; α-II, 52–64; α-III, 100–111; α-IV, 127–132; β-strand A, 49–50; β-B, 87–92; β-C, 138–145; β-D, 159–166 (see Fig. 1).
The “molecular core” of GliPR includes the residues 27, 28, 30, 31, 34, 35, 38, 45, 48, 50, 54, 55, 58, 61, 62, 65, 67, 89–91, 98, 103, 104, 106–108, 114, 116, 121, 125, 128–131, 133, 136, 139–142, 144, 146, 160, 161, 163–165, 170, 175, 176, which are indicated with “1” or “2” in Fig. 1. The displacements calculated for all these residues except C65, F67, C121, and C146, after superimposing the backbone heavy atoms N, Cα, and C′ of the “constrained segments” and the side chain heavy atoms of the core residues for minimal rms deviation, are smaller than 2.3 Å. The corresponding displacements in the NMR solution structure of P14a (7) were all smaller than 1.9 Å.