Literature DB >> 17125398

Collective dynamics of lysozyme in water: terahertz absorption spectroscopy and comparison with theory.

Jing Xu1, Kevin W Plaxco, S James Allen.   

Abstract

To directly measure the low-frequency vibrational modes of proteins in biologically relevant water environment rather than previously explored dry or slightly hydrated phase, we have developed a broadband terahertz spectrometer suitable for strongly attenuating protein solutions. Radiation is provided by harmonic multipliers (up to 0.21 THz), a Gunn oscillator (at 0.139 THz), and the UCSB free-electron lasers (up to 4.8 THz). Our spectrometer combines these intense sources with a sensitive cryogenic detector and a variable path length sample cell to detect radiation after it is attenuated by more than 7 orders of magnitudes by the aqueous sample. Using this spectrometer, we have measured the molar extinction of solvated lysozyme between 0.075 and 3.72 THz (2.5-124 cm(-1)), and we made direct comparison to several published theoretical models based on molecular dynamics simulations and normal-mode analysis. We confirm the existence of dense, overlapping normal modes in the terahertz frequency range. Our observed spectrum, while in rough qualitative agreement with these models, differs in detail. Further, we observe a low-frequency cutoff in terahertz dynamics between 0.2 and 0.3 THz, and we see no evidence of a predicted normal mode at approximately 0.09 THz for the protein.

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Year:  2006        PMID: 17125398     DOI: 10.1021/jp064830w

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  6 in total

1.  Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin.

Authors:  Saravana Prakash Thirumuruganandham; Herbert M Urbassek
Journal:  J Mol Model       Date:  2009-02-03       Impact factor: 1.810

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

Authors:  K N Woods
Journal:  J Biol Phys       Date:  2014-03-30       Impact factor: 1.365

3.  Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach.

Authors:  Lei Zhou; Steven A Siegelbaum
Journal:  Biophys J       Date:  2008-01-22       Impact factor: 4.033

4.  Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics.

Authors:  Lei Zhou; Qinglian Liu
Journal:  J Phys Chem B       Date:  2014-04-08       Impact factor: 2.991

5.  Kinetic coherence underlies the dynamics of disordered proteins.

Authors:  Alexander Tenenbaum
Journal:  RSC Adv       Date:  2021-11-10       Impact factor: 3.361

6.  Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes.

Authors:  Kristina N Woods; Juergen Pfeffer
Journal:  Mol Biol Evol       Date:  2015-09-03       Impact factor: 16.240

  6 in total

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