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.

References in corpus (2)

• Atomic Torsional Modal Analysis for high-resolution proteins
• On the Sensitivity of Protein Data Bank Normal Mode Analysis: An Application to GH10 Xylanases

Cited by in corpus (6)

• Effects of spherical confinement and backbone stiffness on flexible polymer jamming
• Slow Normal Modes of Proteins are Accurately Reproduced across Different Platforms
• A comparison of the innate flexibilities of six chains in F${}_1$-ATPase with identical secondary and tertiary folds; 3 active enzymes and 3 structural proteins
• The Symmetricity of Normal Modes in Symmetric Complexes
• Use Symmetry to Elucidate the Roles of Global Shape and Local Interactions in Protein Dynamics and Cooperativity
• Three Universal Distribution Functions for Native Proteins with Harmonic Interactions