For example, for residue i of a target protein, a peak for N-HSQC at position (Ni, HNi) and a peak for HNCO at positions (Ni, HNi, Ci−1) are generated, where Ni, HNi and Ci−1 are experimentally assigned chemical shift values of backbone N and HN atoms for residues i, and a chemical shift value of the backbone C atom for residue i − 1, respectively.
The root mean square deviation (RMSd) values of the backbone atoms in the initial models assess the convergence of the protein system.
The overall root-mean-square (rms) values of the backbone atoms relative to original crystallographic coordinates are 1.9 and 2.6 Å for WT and S193E, respectively.
The random coil shift values of the backbone NH protons in AST3-88 and AMW3-130, especially in the His, DPhe, Arg, and Trp region, have negative random coil shift values between 0.2 and 0.3 ppm.
The kinetic model in this example produced near state-of-the-art folded structure with RMSD values for the backbone atoms of test proteins while using less than a minute of desktop computer CPU time.
We measured the φ values for the backbone amides of PKA-C in three different forms: apo, ADP-bound (binary complex), and ADP/PKI peptide-bound (ternary complex).
The calculated rmsd values for the backbone atom positions of active site residues were 1.4 and 1.4 Å, and 1.2 and 1.3 Å, respectively.
Structural similarity or divergence was evaluated by a pairwise root mean square deviation (RMSD) value upon superposition of the backbone Cα trace from the two groups of structurally equivalent atoms in MHC class I α1 and α2 domains.
This clearly indicated the RMSD values of the protein backbone atoms and ligand atoms were always kept around 1.5 Å and 0.4 Å respectively, which showed that the MD-simulated binding models were stable.
To explore the dynamic stability of the two AChE/inhibitor complexes and to ensure the rationality of the sampling strategy, the time-dependent RMSD values of the complex backbone atoms were calculated from the X-ray crystal structure of AChE during MD trajectories of 10 ns.
Among the first three original models, which were quite similar with respect to violations and energy values, the model possessing the least root mean square deviation (RMSD) value with the backbone atoms of 1zgl (0.23 Å for VB1VB and 0.26 Å for VB1OE), was selected for further study.
