Molecular dynamics simulation ubiquitin

Alonso D. O. V. and Daggett V. Molecular dynamics simulations of protein unfolding and limited refolding characterization of partially unfolded states of ubiquitin in 60 % methanol and in water. J. Mol. Biol. (1995) 247 501-520. 

As the last example we mention the study of Takemura and Kitao. They studied different models for molecular-mechanics simulations on water. To this end, they studied the dynamics of a ubiquitin molecule solvated in water. They performed molecular-dynamics simulations for a system with periodic boundary conditions. At first they considered pure water without the solute and studied boxes with 360, 720, 1080, and 2160 water molecules. It turned out that even for these fairly large systems, finite-size effects could be recognized. Thus, the translational diffusion constant was found to depend linearly on where V is the volume of the repeated unit. 

Alonso DOV and Daggett B. Molecular Dynamics Simulations of Protein Unfolding and Limited Refolding Characterization of Partially Unfolded States of Ubiquitin in 60% Methanol and in Waiter. J Mol Biol 1995 247 501-520. 

Segev, E. Wyttenhach, T. Bowers, M. T. Gerber, R. B. Conformational evolution of ubiquitin ions in electrospray mass spectrometry Molecular dynamics simulations at gradually increasing temperatures. Phys. Chem. Chem. Phys. 2008,10, 3077-3082. 

A. Das and C. Mukhopadhyay, Proteins Struct., Funct., Bioinf, 75, 1024 (2009). Mechanical Unfolding Pathway and Origin of Mechanical Stability of Proteins of Ubiquitin Family An Investigation by Steered Molecular Dynamics Simulation. 

In the work of Zachmann et al. new approaches to the quantification of surface flexibility have been suggested. The basis data for these approaches are supplied by molecular dynamics (MD) simulations. The methods have been applied to two proteins (PTI and ubiquitin). The calculation and visualization of the local flexibility of molecular surfaces is based on the notion of the solvent accessible surface (SAS), which was introduced by Connolly. For every point on this surface a probability distribution p(r) is calculated in the direction of the surface normal, i.e., the rigid surface is replaced by a soft surface. These probability distributions are well suited for the interactive treatment of molecular entities because the former can be visualized as color coded on the molecular surface although they cannot be directly used for quantitative shape comparisons. In Section IV we show that the p values can form the basis for a fuzzy definition of vaguely defined surfaces and their quantitative comparison. 

Recently, Lindorff-Larsen el al.uo included the order parameter (S 2) in the target function, and refined an ubiquitin X-ray structure by restrained molecular dynamics (Section 6.4) to obtain an NMR structure ensemble (Section 6.5) from the trajectories. They simulated the values of RDCs (Section 9.1) and side chain scalar coupling from the calculated ensemble to confirm that the method can determine the protein three-dimensional structure and dynamic structure simultaneously. The simulated values were in good agreement with the corresponding measurement data. The simulation accuracy was improved from the preliminary calculated structure without the order parameters. The approach is typically important, because they tried to link the ensemble with a dynamic structure directly. 

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