International Tables for Crystallography (2006). Vol. F, ch. 20.1, pp. 481-488   | 1 | 2 |
doi: 10.1107/97809553602060000705

Chapter 20.1. Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin

Contents

  • 20.1. Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin  (pp. 481-488) | html | pdf | chapter contents |
    • 20.1.1. Introduction  (p. 481) | html | pdf |
    • 20.1.2. Methods  (pp. 481-482) | html | pdf |
    • 20.1.3. Results  (pp. 482-488) | html | pdf |
      • 20.1.3.1. Energetic properties  (p. 482) | html | pdf |
      • 20.1.3.2. Structural properties  (pp. 482-483) | html | pdf |
      • 20.1.3.3. Effect of the translational and rotational fitting procedure  (pp. 483-486) | html | pdf |
      • 20.1.3.4. Effect of the averaging period  (pp. 486-487) | html | pdf |
      • 20.1.3.5. Internal motions of the proteins  (p. 487) | html | pdf |
      • 20.1.3.6. Dihedral-angle fluctuations and transitions  (pp. 487-488) | html | pdf |
      • 20.1.3.7. Water diffusion  (p. 488) | html | pdf |
    • 20.1.4. Conclusions  (p. 488) | html | pdf |
    • References | html | pdf |
    • Figures
      • Fig. 20.1.3.1. Non-bonded energies (in kJ mol −1 ) of the simulated system as a function of time  (p. 482) | html | pdf |
      • Fig. 20.1.3.2. Root-mean-square atom-positional deviations (RMSD) in nm from the X-ray structure of the four different protein molecules in the unit cell as a function of time  (p. 482) | html | pdf |
      • Fig. 20.1.3.3. Root-mean-square Cα-atom-position deviation (RMSD) in nm from a reference structure as a function of the residue number using the final 1.6 ns of the simulation  (p. 483) | html | pdf |
      • Fig. 20.1.3.4. Root-mean-square Cα-atom-position fluctuations (RMSFs) in nm are shown for molecule 4 as a function of residue number  (p. 486) | html | pdf |
      • Fig. 20.1.3.5. Root-mean-square Cα-atom-position fluctuations (RMSFs) in nm are shown using the same fitting protocols as in Fig. 20.1.3.4, but averaged over all four protein molecules in the unit cell  (p. 486) | html | pdf |
      • Fig. 20.1.3.6. Root-mean-square Cα-atom-position fluctuations (RMSFs) in nm are shown for molecule 4, with full translational and rotational fitting over the Cα atoms of residues 1–72  (p. 486) | html | pdf |
      • Fig. 20.1.3.7. Root-mean-square Cα-atom-position fluctuations (RMSFs) in nm are shown using the same averaging periods as in Fig. 20.1.3.6, but averaged over all four protein molecules in the unit cell  (p. 487) | html | pdf |
      • Fig. 20.1.3.8. Root-mean-square Cα-atom-position fluctuations (RMSFs) in nm for the four protein molecules in the unit cell as a function of the residue number  (p. 487) | html | pdf |
      • Fig. 20.1.3.9. The number of water molecules with a given root-mean-square oxygen-position fluctuation (RMSF) in nm are shown for different averaging periods: 400–800 ps (solid line), 400–1200 ps (short-dashed line), 400–2000 ps (long-dashed line)  (p. 488) | html | pdf |
    • Tables
      • Table 20.1.3.1. Occurrence of intramolecular hydrogen bonds (%) during the final 1.6 ns of the simulation  (pp. 484-485) | html | pdf |
      • Table 20.1.3.2. Occurrence of intermolecular hydrogen bonds (%) during the final 1.6 ns of the simulation  (p. 485) | html | pdf |
      • Table 20.1.3.3. Root-mean-square fluctuations of polypeptide backbone and ψ dihedral angles (°) for the different molecules using different time-averaging periods  (p. 488) | html | pdf |
      • Table 20.1.3.4. Number of protein-backbone dihedral-angle transitions per 100 ps for the different molecules using different time periods  (p. 488) | html | pdf |