Low-Frequency Modes of Peptides and Globular Proteins in Solution Observed by Ultrafast OHD-RIKES Spectroscopy

Giraud, G.; Karolin, Jan; Wynne, Klaas

doi:10.1016/s0006-3495(03)74618-9

Cited by 124 publications

(173 citation statements)

References 48 publications

(67 reference statements)

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“…Although uncovered computationally, this mode was not expected to contribute significantly to the experimental IR absorption spectrum of liquid water under normal conditions, but was conjectured to be enhanced through solute-induced modifications within the liquid water solvation shell. Additionally an 80 cm −1 mode has been reported in Raman-induced Kerr-effect spectroscopy measurements on globular proteins [39]. In this case, the 80 cm −1 mode has been attributed to fluctuations taking place within the protein secondary structure.…”

Section: Protein Interactions and Potential Energy Barrier Transitionsmentioning

confidence: 83%

“…Correspondingly, it is possible that the increase in intensity at ∼20 cm −1 in the protein-ligand sample also reflects localized protein, intramolecular interactions that accompany ligand binding. The 20 cm −1 experimental mode may be associated with delocalized side-chain fluctuations and has been uncovered in numerous protein investigations [37][38][39].…”

Section: Hinge-bending Mode and Protein Intramolecular Interactionsmentioning

confidence: 92%

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THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions

Woods

2014

J Biol Phys

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Predicting the conformational changes in proteins that are relevant for substrate binding is an ongoing challenge in the aim of elucidating the functional states of proteins. The motions that are induced by protein-ligand interactions are governed by the protein global modes. Our measurements indicate that the detected changes in the global backbone motion of the enzyme upon binding reflect a shift from the large-scale collective dominant mode in the unbound state towards a functional twisting deformation that assists in closing the binding cleft. Correlated motion in lysozyme has been implicated in enzyme function in previous studies, but detailed characterization of the internal fluctuations that enable the protein to explore the ensemble of conformations that ultimately foster largescale conformational change is yet unknown. For this reason, we use THz spectroscopy to investigate the picosecond time scale binding modes and collective structural rearrangements that take place in hen egg white lysozyme (HEWL) when bound by the inhibitor (NAG) 3 . These protein thermal motions correspond to fluctuations that have a role in both selecting and sampling from the available protein intrinsic conformations that communicate function. Hence, investigation of these fast, collective modes may provide knowledge about the mechanism leading to the preferred binding process in HEWL-(NAG) 3 . Specifically, in this work we find that the picosecond time scale hydrogen-bonding rearrangements taking place in the protein hydration shell with binding modify the packing density within the hydrophobic core on a local level. These localized, intramolecular contact variations within the protein core appear to facilitate the large cooperative movements within the interfacial region separating the α-and β-domain that mediate binding. The THz time-scale fluctuations identified in the protein-ligand system may also reveal a molecular mechanism for substrate recognition.

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Section: Protein Interactions and Potential Energy Barrier Transitionsmentioning

confidence: 83%

Section: Hinge-bending Mode and Protein Intramolecular Interactionsmentioning

confidence: 92%

THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions

Woods

2014

J Biol Phys

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“…The experimental setup for the OKE measurements has been described previously [16,[69][70][71][72] and uses 800-nm 24-fs (FWHM) sech 2 pulses with 8 nJ per pulse at a repetition rate of 76 MHz. The beam is split into pump and probe beams (9:1), which are co-focused by a 10-cm focal length achromat into the sample contained in a 2-mm-pathlength quartz cuvette.…”

Section: Methodsmentioning

confidence: 99%

Rattling the cage: Micro- to mesoscopic structure in liquids as simple as argon and as complicated as water

Turton

Hunger

Stoppa

et al. 2011

Journal of Molecular Liquids

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ÔØ Å ÒÙ× Ö ÔØThis is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Abstract. The water molecule has the convenient property that its molecular polarizability tensor is nearly isotropic while its dipole moment is large. As a result, the low-frequency anisotropic Raman spectrum of liquid water is mostly collision induced and therefore reports primarily translational motions while the far-infrared (terahertz) and dielectric spectrum is dominated by rotational modes. A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPTAtomic and globular-molecular liquids have a zero dipole moment as well as an isotropic polarizability tensor. These spectrum-simplifying properties were exploited in a study of a number of liquids and solutions using ultrafast optical Kerr-effect (OKE) spectroscopy combined with dielectric relaxation spectroscopy (DRS), terahertz time-domain spectroscopy (THz-TDS), and terahertz field-induced second-harmonic generation (TFISH) spectroscopy. For room-temperature ionic liquids (RTILs), liquid water, aqueous salt solutions, noble gas liquids, and globular molecular liquids it was found that, in each case, surprising structure and/or inhomogeneity is observed, ranging from mesoscopic clustering in RTILs to stretched exponential dynamics in the noble gas liquids. For aqueous electrolyte solutions it is shown that the viscosity, normally described by the Jones-Dole expression, can be explained in terms of a jamming transition, a concept borrowed from soft condensed matter studies of glass transitions in colloidal suspensions.

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“…Generally it is found that these modes can be satisfactorily fit by the Brownian (dampedharmonic) oscillator function [16,23] …”

Section: Interpretation Of the Intermolecular Spectrummentioning

confidence: 98%

“…The full DR spectrum is reconstructed by patching using the Kramers-Kronig transform. OKE measures the <α xy α xy (t)> correlation function of the anisotropic part of the polarisability tensor directly in the time domain [17,[21][22][23][24]. In our set-up using a laser producing 20-fs pulses, delays from 10 fs to 4 ns can be achieved corresponding to the effective frequency range 250 MHz to ~50 THz.…”

Section: Introductionmentioning

confidence: 99%

Terahertz dynamics of ionic liquids from a combined dielectric relaxation, terahertz, and optical Kerr effect study: evidence for mesoscopic aggregation

et al. 2010

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To exploit the great potential of room-temperature ionic liquids (RTILs) as solvents that offer both low environmental impact and product selectivity, an understanding of the liquid structure, the microscopic dynamics, and the way in which the pertinent macroscopic properties, such as viscosity, thermal conductivity, ionic diffusion, and solvation dynamics depend on these properties, is essential. We have measured the intermolecular dynamics of the 1,3-dialkylimidazolium- and [bmim][DCA], at 25 °C from below 1 GHz to 10 THz by ultrafast optical Kerr effect (OKE) spectroscopy and dielectric relaxation spectroscopy (DRS) augmented by time-domain terahertz and far-infrared FTIR spectroscopy. This concerted approach allows a more detailed analysis to be made of the relatively featureless terahertz region, where the higher frequency diffusional modes are strongly overlapped with librations and intermolecular vibrations. In the terahertz region, the signal-to-noise ratio of the OKE spectra is particularly high and the data show that there is a greater number of librational and intermolecular vibrational modes than previously detected. Of greatest interest though, is an intense low frequency (sub-alpha) relaxation that we show is in strong accordance with recent simulations that observe mesoscopic structure arising from aggregates or clusters; structure that explains the anomalous and inconveniently-high viscosities of these liquids.Terahertz spectroscopy, dielectric relaxation spectroscopy, Kerr spectroscopy, room-temperature ionic liquids

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Low-Frequency Modes of Peptides and Globular Proteins in Solution Observed by Ultrafast OHD-RIKES Spectroscopy

Cited by 124 publications

References 48 publications

THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions

THz time scale structural rearrangements and binding modes in lysozyme-ligand interactions

Rattling the cage: Micro- to mesoscopic structure in liquids as simple as argon and as complicated as water

Terahertz dynamics of ionic liquids from a combined dielectric relaxation, terahertz, and optical Kerr effect study: evidence for mesoscopic aggregation

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