Universality of Vibrational Spectra of Globular Proteins

Abstract

It is shown that the density of modes of the vibrational spectrum of globular proteins is universal, i.e., regardless of the protein in question it closely follows one universal curve. The present study, including 135 proteins analyzed with a full atomic empirical potential (CHARMM22) and using the full complement of all atoms Cartesian degrees of freedom, goes far beyond previous claims of universality, confirming that universality holds even in the high-frequency range (300- 4000 1/cm), where peaks and turns in the density of states are faithfully reproduced from one protein to the next. We also characterize fluctuations of the spectral density from the average, paving the way to a meaningful discussion of rare, unusual spectra and the structural reasons for the deviations in such "outlier" proteins. Since the method used for the derivation of the vibrational modes (potential energy formulation, set of degrees of freedom employed, etc.) has a dramatic effect on the spectral density, another significant implication of our findings is that the universality can provide an exquisite tool for assessing and improving the quality of various models used for NMA computations. Finally, we show that the input configuration too affects the density of modes, thus emphasizing the importance of simplified potential energy formulations that are minimized at the outset

Predicting the functional motions of p97 using symmetric normal modes

“…First, it does not require energy minimization and thus can be applied to experimental structures directly . Second, it is superior to other simplified models such as ANM in that it is highly accurate and closely resembles CNMA: sbNMA gives a high correlation with CNMA in mean square fluctuations (close to 0.9 on average, while ANM's average correlation with CNMA was 0.46 for the dataset used) and is able to reproduce vibrational spectra given by CNMA with high accuracy …”

On the sensitivity of protein data bank normal mode analysis: an application to GH10 xylanases

“…In order to reestablish the overall energy scale of the computed eigenspectra one adjustable parameter, C, was necessary to analyze each PDB entry. Just as proteins across all classes and sizes obtain predictable mass per unit volume measures (density), proteins also obtain universal eigenfrequency spectra with predictable distributions, especially of slow modes [28]. We see, for example, both experimentally as well as within the NMA predictions, a distinct peak at 25 cm −1 that seems to be due to the inter-packing constraints of secondary elements [10].…”

Investigating the effects of different force fields on spring-based normal mode analysis

“…Similarly, red and gray area contain 90% and 100% densities at a frequency bin respectively. As a result, the university of density spectrum of vibrational modes is appear to be as universal as it was with CHARMM (Na 2016). Other than the different unique spectrum profile, the distribution at each bin is little bit wider than The faithful reproduction of spectrum profile throughout the whole frequency range with both CHARMM and AMBER must imply a connection to certain physical characteristics as Na and Song (2016) claimed.…”

“…The density is properly normalized to see the universal spectrum (ben-Avraham 1993 and Tirion 1993). The figure design is directly adopted from the previous study in order to compare the spectrum of AMBER with that of CHARMM easily (Na 2016). The Hessian matrices for NMA, sbNMA and ssNMA were obtained in section 3.1.…”

“…One significant advantage of their model over NMA is that it does not require a computationintensive minimization step that NMA has to go through. In addition, Na and Song (2016) presented method that can potentially be used to tune parameters in empirical potentials.…”