Ubiquitin Volume

The reader should consult earlier reviews [70, 94, 95] and other chapters in this volume for a detailed discussion of UbL biology and biochemistry. There are two important points for the current discussion. First, the conjugation cascades of UbLs differ from that of ubiquitin chiefly in terms of complexity - there is one conjugating enzyme per UbL, and many fewer E3s. Second, because modifier proteins (including ubiquitin) do not interact strongly with their dedicated E2s (Section 5.6.1), it is believed that El enzymes play the major role in matching E2s with the correct modifier protein (see Ref [96]). 

M 35] [protocol see [119]] A protein conformation kinetic study of the small protein ubiquitin was performed both in the continuous and in a stopped-flow mode at low reactant consumption [119], The bifurcation mixer was used prior to an IR flow cell for data monitoring. The change of conformation from native to the A-state was followed when adding methanol under low pH conditions to the protein solution. In the continuous mode, long data acquisition could be made and the reaction time was determined by the flow rate and the volume interconnecting zone between the mixer and IR flow cell, which was small, but not negligible. In the stopped-flow mode, the reaction time resolved was dependent on the time resolution of the FTIR instrument. 

Fig. 10.8. Changes in the structure and in the volume components associated with the pressure-induced structural transition of ubiquitin. Solid ribbon representation of low-pressure (3 MPa) and high-pressure (300 MPa) structures. The data shown are the total change in the partial molar volume (V) and the changes in the van der Waals (Vw), void (W), thermal (VT), and interaction (Vi) volumes...

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. 

Subsequently, they studied a periodically repeated volume containing the ubiquitin molecule as well as 4908, 9133, 13 200, or 29 182 water molecules. Again, the linear dependence of the translational diffusion constant of the protein on was... 

A more challenging example was demonstrated by Stanek and Kozmihski [85], who applied their algorithm to 3D N- and C-labeled NOESY spectra of ubiquitin without suppression of diagonal peaks. The efficiency of artifact suppression was investigated by comparison of the reconstruction with the conventionally acquired reference spectrum. Less than 2% of peaks were missing, and about 1.5% false peaks were reported. The correlation coefficient between peak volumes of... 

Volume 54 Conjugation and Deconjugation of Ubiquitin Family Modifiers... 

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