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Title: Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K

Abstract

An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about 2-2.5 meV, originates from 102 collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.

Authors:
 [1];  [2]
  1. University of Heidelberg
  2. ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
932176
DOE Contract Number:
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of the American Chemical Society; Journal Volume: 128; Journal Issue: 7
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; BOSONS; FUNCTIONALS; GLASS; HARMONICS; MYOGLOBIN; PROTEINS; SIMULATION; STRUCTURE FACTORS; TRAJECTORIES

Citation Formats

Kurkal-Siebert, V, and Smith, Jeremy C. Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K. United States: N. p., 2006. Web. doi:10.1021/ja055962q.
Kurkal-Siebert, V, & Smith, Jeremy C. Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K. United States. doi:10.1021/ja055962q.
Kurkal-Siebert, V, and Smith, Jeremy C. Wed . "Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K". United States. doi:10.1021/ja055962q.
@article{osti_932176,
title = {Low-Temperature Protein Dynamics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K},
author = {Kurkal-Siebert, V and Smith, Jeremy C},
abstractNote = {An understanding of low-frequency, collective protein dynamics at low temperatures can furnish valuable information on functional protein energy landscapes, on the origins of the protein glass transition and on protein-protein interactions. Here, molecular dynamics (MD) simulations and normal-mode analyses are performed on various models of crystalline myoglobin in order to characterize intra- and interprotein vibrations at 150 K. Principal component analysis of the MD trajectories indicates that the Boson peak, a broad peak in the dynamic structure factor centered at about 2-2.5 meV, originates from 102 collective, harmonic vibrations. An accurate description of the environment is found to be essential in reproducing the experimental Boson peak form and position. At lower energies other strong peaks are found in the calculated dynamic structure factor. Characterization of these peaks shows that they arise from harmonic vibrations of proteins relative to each other. These vibrations are likely to furnish valuable information on the physical nature of protein-protein interactions.},
doi = {10.1021/ja055962q},
journal = {Journal of the American Chemical Society},
number = 7,
volume = 128,
place = {United States},
year = {Wed Feb 01 00:00:00 EST 2006},
month = {Wed Feb 01 00:00:00 EST 2006}
}
  • Low-temperature (2 K{<=}T{<=}350 K) heat capacity and room-temperature shear modulus measurements ({nu}=1.4 MHz) have been performed on bulk Pd{sub 41.25}Cu{sub 41.25}P{sub 17.5} in the initial glassy, relaxed glassy, and crystallized states. It has been found that the height of the low-temperature Boson heat capacity peak strongly correlates with the changes in the shear modulus upon high-temperature annealing. It is this behavior that was earlier predicted by the interstitialcy theory, according to which dumbbell interstitialcy defects are responsible for a number of thermodynamic and kinetic properties of crystalline, (supercooled) liquid, and solid glassy states.
  • We report the pronounced low-temperature specific-heat C{sub p} anomalies associated with the boson peak in the new CuZr-based bulk metallic glasses. The origin of the C{sub p} anomalies in the atomic glasses is interpreted with the harmonic localized mode based on the dense-packed atomic clusters structural model of metallic glass. The results might have important implications for understanding the origin of the boson peak and the structural features of metallic glasses.
  • The low-frequency dynamics in glasses is compared with that in icosahedral quasicrystals. For both arrangements of matter, the existence of nanometric heterogeneities, implying the existence of a nanometric inhomogeneous elastic network, is expected to play a crucial role. Thanks to this comparison, mostly based on inelastic x-ray (neutron) scattering data, it is proposed that the excess of vibrational density of states observed in both materials is due to the hybridization of longitudinal and transverse acoustic modes with modes localized around the heterogeneities.
  • We recently proposed the method of time-structure based independent component analysis (tICA) to examine the slow dynamics involved in conformational fluctuations of a protein as estimated by molecular dynamics (MD) simulation [Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011)]. Our previous study focused on domain motions of the protein and examined its dynamics by using rigid-body domain analysis and tICA. However, the protein changes its conformation not only through domain motions but also by various types of motions involving its backbone and side chains. Some of these motions might occur on a slow time scale: we hypothesizemore » that if so, we could effectively detect and characterize them using tICA. In the present study, we investigated slow dynamics of the protein backbone using MD simulation and tICA. The selected target protein was lysine-, arginine-, ornithine-binding protein (LAO), which comprises two domains and undergoes large domain motions. MD simulation of LAO in explicit water was performed for 1 μs, and the obtained trajectory of C{sub α} atoms in the backbone was analyzed by tICA. This analysis successfully provided us with slow modes for LAO that represented either domain motions or local movements of the backbone. Further analysis elucidated the atomic details of the suggested local motions and confirmed that these motions truly occurred on the expected slow time scale.« less
  • An enduring challenge in the understanding of internal protein motions is the effective separation and characterization of diffusive and vibrational dynamical components. To address this problem, here nanosecond molecular dynamics trajectories of myoglobin in aqueous solution, performed over a range of temperatures between 120 and 300 K, are subjected to principal component analysis, and the coordinate autocorrelation functions of the resulting principal modes are interpreted using a model combining damped Langevin vibration within potential wells and barrier-crossing diffusion between them. Both the vibrational frequency and the fraction of the mean-square fluctuation arising from vibrational motion undergo transitions with temperature atmore » about 180 K. In contrast, the vibrational friction remains linear with temperature. The diffusional component of the mean-square fluctuation increases dramatically at the dynamical transition. The heights of the energy barriers between the potential wells are estimated, and the associated diffusion constants are calculated using Kramers' rate theory. Model functions of the frequency dependence of the frictional and diffusional quantities are obtained. The dynamic structure factor from the full molecular dynamics trajectory is well reproduced by the model. Overall, the results indicate that a global description of nanosecond temperature-dependent diffusion and vibrational internal protein dynamics can be obtained by applying the results of the present diffusion-vibration model to the vibrational motions obtained from a normal-mode analysis.« less