Universality of vibrational spectra of globular proteins. 2016

Hyuntae Na, and Guang Song, and Daniel ben-Avraham
Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, Iowa 50011, USA.

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 frequency range that is well above 100 cm(-1) (300-4000 cm(-1)), 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 potential functions and the quality of various models used for NMA computations. Finally, we show that the input configuration also affects the density of modes, thus emphasizing the importance of simplified potential energy formulations that are minimized at the outset. In summary, our findings call for a serious two-way dialogue between theory and experiment: experimental spectra of proteins could now guide the fine tuning of theoretical empirical potentials, and the various features and peaks observed in theoretical studies--being universal, and hence now rising in importance--would hopefully spur experimental confirmation.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D014732 Vibration A continuing periodic change in displacement with respect to a fixed reference. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Vibrations
D017510 Protein Folding Processes involved in the formation of TERTIARY PROTEIN STRUCTURE. Protein Folding, Globular,Folding, Globular Protein,Folding, Protein,Foldings, Globular Protein,Foldings, Protein,Globular Protein Folding,Globular Protein Foldings,Protein Foldings,Protein Foldings, Globular

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