| energy minimization | The protein contains paramagnetic copper(II), whose electronic relaxation times are quite unfavorable for NMR solution studies. The structure has been solved on the basis of 1041 meaningful NOESY cross peaks, 18 1D NOEs, 26 T1 values, 96 dihedral angle constraints and 18 H-bonds. The detection of broad hyperfine shifted signals and their full assignment allowed the identification of the copper(II) ligands and the determination of the Cu-S-C-H dihedral angle for the coordinated cysteine. The global root mean square deviation from the mean structure for the solution structure family is 0.72 and 1.16 for backbone and heavy atoms, respectively. The mean structure from the DYANA family was calculated using MOLMOL and subjected to restrained energy minimization (REM) using the SANDER module of the AMBER 5.0 program package. The force field parameters for all residues, excluded those for the copper-coordinated ligands, were the standard AMBER "all-atoms" parameters. The calculations were performed in vacuo with the distance-dependent dielectric constant option. The non-bonded interactions were evaluated with a cut-off of 10 A. The mixed linear-harmonic flat-bottomed potential implemented in SANDER was applied to all structural constraints. This potential involves a null force constant for structural constraints within the allowed limits, a non-zero harmonic force constant in a small interval outside the allowed limits, and a linearly dependent potential beyond that limit. NOE-derived distance constraints were restricted below the upper distance limit (ri), using a force constant of 32 kcal mol-1 A-2 for the interval ri+0.5 A. Distance constraints involving the same H-bonds used for DYANA calculations were included in the REM calculation, restricting the NH...O and N...O distances to the same upper (ri) values used in DYANA, with a force constant of 32 kcal mol-1 A-2 for the range ri + 0.5 A. The Cu-H distances derived from the analysis of the non-selective longitudinal relaxation rates were also restrained to the same upper (ri) limits used in DYANA, with a force constant of 32 kcal mol-1 A-2 for ri + 0.5 A. The Cu-NHis and Cu-SCys distances were constrained at 2.1+/-0.1 A and 2.2+/-0.1 A, respectively, using a linear-harmonic flat-bottomed potential with force constants of 50 kcal mol-1 A-2 in the 0.3-A distance ranges below and above these limits. The Cu-SMet distance was analogously constrained within the 2.75+/-0.05 A range, using a force constant of 40 kcal mol-1 A-2. The Cu-N(His)-Cg, Cu-N(His)-Ce, Cu-S(Cys)-Cb, Cu-S(Met)-Cg, and Cu-S(Met)-Ce angles were restrained around 127+/-0, 127+/-0, 105+/-5, 130+/-10, 110+/-10, respectively, using a linear-harmonic flat-bottomed potential with force constants of 50 kcal mol-1 deg-2 in the 50 ranges below and above the given values. Analogously, the (His)N-Cu-N(His), (His)N-Cu-S(Cys), (His)N-Cu-S(Met), and (Met)S-Cu-S(Cys) angles were restrained in the 110+/-10, 125+/-15, 95+/-15, and 100+/-10 range with a force constant of 20 kcal mol-1 deg-2 in the 50 angle ranges below and above these limits. | XwinNMR |
