Structural fluctuation of proteins revealed by terahertz time-domain spectroscopy

Kambara, Ohki; Tominaga, Keisuke

doi:10.1155/2010/391586

Cited by 5 publications

(4 citation statements)

References 7 publications

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“…16 A well-defined dynamical transition related to biomolecule functioning above specific hydration levels (27% w/w), or temperatures (above 200 K), is detectable in THz spectrum. [16][17][18][19][20] Another study reveals the existence of structural collective modes for cytochrome c protein. 15 Solvated proteins (lysozyme and bovine serum albumin (BSA)), along with alcohols, have been also studied at different concentrations by micro-fluidic systems 4,21 over 50-110 GHz.…”

Section: Introductionmentioning

confidence: 99%

Sub-terahertz spectroscopy reveals that proteins influence the properties of water at greater distances than previously detected

Sushko¹,

Dubrovka²,

Donnan³

2015

The Journal of Chemical Physics

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Erratum: "Sub-terahertz spectroscopy reveals that proteins influence the properties of water at greater distances than previously detected" [J. Chem. Phys. 142, 055101 (2015) The initial purpose of the study is to systematically investigate the solvation properties of different proteins in water solution by terahertz (THz) radiation absorption. Transmission measurements of protein water solutions have been performed using a vector network analyser-driven quasi-optical bench covering the WR-3 waveguide band (0.220-0.325 THz). The following proteins, ranging from low to high molecular weight, were chosen for this study: lysozyme, myoglobin, and bovine serum albumin (BSA). Absorption properties of solutions were studied at different concentrations of proteins ranging from 2 to 100 mg/ml. The concentration-dependent absorption of protein molecules was determined by treating the solution as a two-component model first; then, based on protein absorptivity, the extent of the hydration shell is estimated. Protein molecules are shown to possess a concentration-dependent absorptivity in water solutions. Absorption curves of all three proteins sharply peak towards a dilution-limit that is attributed to the enhanced flexibility of protein and amino acid side chains. An alternative approach to the determination of hydration shell thickness is thereby suggested, based on protein absorptivity. The proposed approach is independent of the absorption of the hydration shell. The derived estimate of hydration shell thickness for each protein supports previous findings that protein-water interaction dynamics extends beyond 2-3 water solvation-layers as predicted by molecular dynamics simulations and other techniques such as NMR, X-ray scattering, and neutron scattering. According to our estimations, the radius of the dynamic hydration shell is 16, 19, and 25 Å, respectively, for lysozyme, myoglobin, and BSA proteins and correlates with the dipole moment of the protein. It is also seen that THz radiation can serve as an initial estimate of the protein hydrophobicity. C 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License. [http://dx

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Section: Introductionmentioning

confidence: 99%

Sub-terahertz spectroscopy reveals that proteins influence the properties of water at greater distances than previously detected

Sushko¹,

Dubrovka²,

Donnan³

2015

The Journal of Chemical Physics

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“…Water plays a key role in structural organization of biomolecules and is a driving force that stimulates proteins to obtain their folded, functional state . Over the past decade, studies of water solutions of different molecules in the tetrahertz (THz) and sub-THz domain have attracted growing interest by many. − They are stimulated by the fact that any molecule dissolved in water alters the dynamics of the surrounding water molecules to adopt quasi-coherent or organized character. This happens primarily via a reorganized, loose hydrogen-bond network.…”

Section: Introductionmentioning

confidence: 99%

Terahertz Spectral Domain Computational Analysis of Hydration Shell of Proteins with Increasingly Complex Tertiary Structure

2013

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Solvation dynamics of biomolecules and water in a hydration shell have been studied by different methods; however, a clear picture of this process is not yet established. Terahertz (THz) studies of molecular behavior in binary solutions present unique information on the picosecond motions of molecules. A complete mechanical interpretation of THz absorption spectra associated with solvated biomolecules remains a challenging task. The Gromacs molecular dynamics (MD) simulation package is used here to examine the spectral characteristics of water molecules in close proximity to biomolecules using vibrational density of states (VDOS). Systematic simulation of solvation dynamics of proteins of different size and tertiary structure are presented. The following have been selected for analysis. They range from less to more complex tertiary structure (corresponding to an increased number of secondary structure elements): TRP-cage13-20 peptide, TRP-cage, BPTI, and lysozyme. The initial study predicts that the depth of the hydration shell, determined by VDOS of water, extends to approximately 10 Å and does not depend on protein size. Furthermore the integral perturbation coefficient of the whole solvation layer is found to be increased for larger proteins due to a higher retardation rate of water molecules in their shells. Differences in solvation dynamics among the proteins considered originate primarily from the water molecules buried in the interior of the protein and not from the on-surface molecules.

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“…However, recent studies on the dynamical transition of proteins such as lysozyme and bacteriorhodopsin by THz spectroscopy have shown that the present experimental results are quite similar to those obtained by EINS where the motions of atoms constituting the protein are monitored. 21,39 Therefore, we conclude that the major contribution is from the atomic motions of the polypeptide itself. We will further discuss the microscopic origin of the dynamical transition of polyE in Section 5.3.…”

Section: Microscopic Origin Of the Dynamical Transitionmentioning

confidence: 72%

Temperature and hydration dependence of low-frequency spectra of poly-l-glutamic acid with different secondary structures studied by terahertz time-domain spectroscopy

et al. 2012

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Structural fluctuation of proteins revealed by terahertz time-domain spectroscopy

Cited by 5 publications

References 7 publications

Sub-terahertz spectroscopy reveals that proteins influence the properties of water at greater distances than previously detected

Sub-terahertz spectroscopy reveals that proteins influence the properties of water at greater distances than previously detected

Terahertz Spectral Domain Computational Analysis of Hydration Shell of Proteins with Increasingly Complex Tertiary Structure

Temperature and hydration dependence of low-frequency spectra of poly-l-glutamic acid with different secondary structures studied by terahertz time-domain spectroscopy

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