Rigidity, secondary structure, and the universality of the boson peak in proteins

Stefania Perticaroli; Jonathan D. Nickels; Georg Ehlers; Alexei P. Sokolov

doi:10.1016/j.bpj.2014.05.009

Rigidity, secondary structure, and the universality of the boson peak in proteins

Stefania Perticaroli, Jonathan D. Nickels, Georg Ehlers, Alexei P. Sokolov

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65 Scopus citations

Abstract

Complementary neutron- and light-scattering results on nine proteins and amino acids reveal the role of rigidity and secondary structure in determining the time- and lengthscales of low-frequency collective vibrational dynamics in proteins. These dynamics manifest in a spectral feature, known as the boson peak (BP), which is common to all disordered materials. We demonstrate that BP position scales systematically with structural motifs, reflecting local rigidity: disordered proteins appear softer than α-helical proteins; which are softer than β-sheet proteins. Our analysis also reveals a universal spectral shape of the BP in proteins and amino acid mixtures; superimposable on the shape observed in typical glasses. Uniformity in the underlying physical mechanism, independent of the specific chemical composition, connects the BP vibrations to nanometer-scale heterogeneities, providing an experimental benchmark for coarse-grained simulations, structure/rigidity relationships, and engineering of proteins for novel applications.

Original language	English
Pages (from-to)	2667-2674
Number of pages	8
Journal	Biophysical Journal
Volume	106
Issue number	12
DOIs	https://doi.org/10.1016/j.bpj.2014.05.009
State	Published - Jun 17 2014

Funding

The authors acknowledge Department of Energy support through the EPSCoR program (grant DE-FG02–08ER46528) and the Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy. Oak Ridge National Laboratory facilities are sponsored by UT-Battelle, LLC, for the U.S. Department of Energy under contract No. DEAC05–00OR22725.

Funders	Funder number
EPSCoR program	DE-FG02–08ER46528
Scientific User Facilities Division
U.S. Department of Energy
Basic Energy Sciences
UT-Battelle	DEAC05–00OR22725

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10.1016/j.bpj.2014.05.009

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abstract = "Complementary neutron- and light-scattering results on nine proteins and amino acids reveal the role of rigidity and secondary structure in determining the time- and lengthscales of low-frequency collective vibrational dynamics in proteins. These dynamics manifest in a spectral feature, known as the boson peak (BP), which is common to all disordered materials. We demonstrate that BP position scales systematically with structural motifs, reflecting local rigidity: disordered proteins appear softer than α-helical proteins; which are softer than β-sheet proteins. Our analysis also reveals a universal spectral shape of the BP in proteins and amino acid mixtures; superimposable on the shape observed in typical glasses. Uniformity in the underlying physical mechanism, independent of the specific chemical composition, connects the BP vibrations to nanometer-scale heterogeneities, providing an experimental benchmark for coarse-grained simulations, structure/rigidity relationships, and engineering of proteins for novel applications.",

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Rigidity, secondary structure, and the universality of the boson peak in proteins

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