Fundamentals - Ubiquitin

Ubiquitin Conformational Transitions

Protein Conformations Emerging from Solution into the Gas Phase

Ubiquitin [M+8H]⁸⁺ Ions (Native) Simulated at 470 K

Parameters

For the purposes of these ubiquitin conformational dynamics simulations, GROMACS (v 4.5.5) was used with the OPLS-AA force field. The native state structure was obtained from the Protein Data Bank (1UBQ). Additional conformations (A state and helix) were constructed using INSIGHT II.

Charge Site Assignment

Ubiquitin has a large number of charge-carrying sites within the amino acid sequence. For the purposes of these calculations and simulations, the following charge-site configurations were employed.

Steps

1. Energy Minimization (Steepest descent minimization)
2. Simulated at 300 K for 50 ps
3. Production Simulation:
   1. Temperature coupling (V-rescale)
   2. No pressure coupling
   3. No cutoff for electrostatics and van der Waals interactions

Selected References

1. Berendsen, H. J. C., van der Spoel, D., and van Drunen, R. GROMACS: A Message-Passing Parallel Molecular Dynamics Implementation. Comput. Phys. Commun. 1995, 91, 43–56.
2. Lindahl, E., Hess, B. A., and van der Spoel, D. GROMACS 3.0: A Package for Molecular Simulations and Trajectory Analysis, J. Mol. Model. 2001, 7, 306–317.
3. van der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., and Berendsen, H. J. C. GROMACS: Fast, Flexible and Free, J. Comput. Chem. 2005, 26, 1701–1718.
4. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E.; GROMACS 4: Algorithms for Highly Efficient, Loaded-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 2008, 4, 435–447.
5. Miteva, M.; Demirev, P. A.; Karshikoff, A. D. Multiply-Protonated Protein Ions in the Gas-Phase: Calculation of the Electrostatic Interactions between Charged Sites. J. Phys. Chem. B 1997, 101, 9645–9650.
6. Breuker, K. Oh, H.; Horn, D. M.; Cerda, B. A.; McLafferty, F. W. Detailed Unfolding and Folding of Gaseous Ubiquitin Ions Characterized by Electron Capture Dissociation. J. Am. Chem. Soc. 2002, 124, 6407–6420.