It is shown that the density of modes of the vibrational spectrum of globularproteins is universal, i.e., regardless of the protein in question it closelyfollows one universal curve. The present study, including 135 proteins analyzedwith a full atomic empirical potential (CHARMM22) and using the full complementof all atoms Cartesian degrees of freedom, goes far beyond previous claims ofuniversality, confirming that universality holds even in the high-frequencyrange (300- 4000 1/cm), where peaks and turns in the density of states arefaithfully reproduced from one protein to the next. We also characterizefluctuations of the spectral density from the average, paving the way to ameaningful discussion of rare, unusual spectra and the structural reasons forthe deviations in such "outlier" proteins. Since the method used for thederivation of the vibrational modes (potential energy formulation, set ofdegrees of freedom employed, etc.) has a dramatic effect on the spectraldensity, another significant implication of our findings is that theuniversality can provide an exquisite tool for assessing and improving thequality of various models used for NMA computations. Finally, we show that theinput configuration too affects the density of modes, thus emphasizing theimportance of simplified potential energy formulations that are minimized atthe outset.
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