Proteins fluctuations

Nadler and Schulten, 1984] Nadler, W., and Schulten, K. Theory of Mossbauer spectra of proteins fluctuating between conformational substates. Proc. Natl. Acad. Sci. USA. 81 (1984) 5719-5723... 

Since Ca is transferred from one side of the membrane to the other side in association with the Ca -ATPase, thermal fluctuation of critical regions of the Ca -ATPase influenced in specific ways through the phosphorylation of the enzyme by ATP may play a role in Ca translocation. Similar ideas have been proposed some time ago by Huxley [419] in relationship to crossbridge movements during muscle contraction and by Welch and others on the role of protein fluctuations in enzyme action [420-430]. 

Li TP, Hassanali AAP, Kao YT, Zhong DP, Singer SJ (2007) Hydration dynamics and time scales of coupled water-protein fluctuations. J Am Chem Soc 129(11) 3376-3382... 

Nienhaus, K., Ostermann, A., Nienhaus, U., Parak, R, and Schmidt M. 2005. Ligand migration and protein fluctuations in myoglobin mutant L29W. Biochemistry 44 5095-5105. 

Srajer, V., Reinisch, L., and Champion, P. M. 1988. Protein fluctuations, distributed coupling, and the binding of ligands to heme-proteins. J. Am. Chem. Soc. 110 6656-70. 

HYDRATION DYNAMICS AND COUPLED WATER-PROTEIN FLUCTUATIONS PROBED BY INTRINSIC TRYPTOPHAN... 

V. Global Mapping of Surface Hydration and Protein Fluctuations... 

B. Time Scales, Correlations, and Water-Protein Fluctuations... 

V. GLOBAL MAPPING OF SURFACE HYDRATION AND PROTEIN FLUCTUATIONS... 

MD simulations with either protein or water constrained at the instant of photoexcitation were performed for both isomer 1 and isomer 2. For isomer 1, because surface water relaxation dominates the slow component of the total Stokes shift, in Fig. 44a we show the result of simulations of isomer 1 with an ensemble of frozen protein configurations to examine the role of protein fluctuations. Clearly the long component of indole-water interactions disappears when the protein is constrained. This result shows that without protein fluctuations, indole-water relaxation over tens of picoseconds does not occur. Thus, although surface hydrating water molecules seem to drive the global solvation and, from the dynamics of the protein and water contributions, are apparently responsible for the slowest component of the solvation Stokes shift for isomer 1 (Fig. 42), local protein fluctuations are still required to facilitate this rearrangement process. When the protein is frozen, the ultrafast... 

Figure 44. Solvation dynamics from constrained MD simulations, (a) Comparison of indole-water relaxation with and without frozen protein structure for isomer 1. The slow component of the water response nearly disappears, which indicates that slow water relaxation needs protein fluctuations, (b) Comparison of indole—protein relaxation with and without frozen water for isomer 2. Similarly, the slow component of the indole—protein disappears, which indicates that the protein relaxation also requires water fluctuations.

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