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Frequency Response of a Protein to Local Conformational Perturbations

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  • Dilek Eren
  • Burak Alakent

Abstract

Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions. In the current study, signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B (PTP1B) was investigated using frequency response techniques. Using restrained Targeted Molecular Dynamics (TMD) potential on WPD and R loops, PTP1B was driven between its crystal structure conformations at different frequencies. Propagation of the local perturbation signal was manifested via peaks at the fundamental frequency and upper harmonics of 1/f distributed spectral density of atomic variables, such as Cα atoms, dihedral angles, or polar interaction distances. Frequency of perturbation was adjusted high enough (simulation length >∼10×period of a perturbation cycle) not to be clouded by random diffusional fluctuations, and low enough (

Suggested Citation

  • Dilek Eren & Burak Alakent, 2013. "Frequency Response of a Protein to Local Conformational Perturbations," PLOS Computational Biology, Public Library of Science, vol. 9(9), pages 1-15, September.
    • Handle: RePEc:plo:pcbi00:1003238
    DOI: 10.1371/journal.pcbi.1003238
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    References listed on IDEAS

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    1. Rob L. M. van Montfort & Miles Congreve & Dominic Tisi & Robin Carr & Harren Jhoti, 2003. "Oxidation state of the active-site cysteine in protein tyrosine phosphatase 1B," Nature, Nature, vol. 423(6941), pages 773-777, June.
    2. Katherine A. Henzler-Wildman & Vu Thai & Ming Lei & Maria Ott & Magnus Wolf-Watz & Tim Fenn & Ed Pozharski & Mark A. Wilson & Gregory A. Petsko & Martin Karplus & Christian G. Hübner & Dorothee Kern, 2007. "Intrinsic motions along an enzymatic reaction trajectory," Nature, Nature, vol. 450(7171), pages 838-844, December.
    3. Hsiao-Mei Lu & Jie Liang, 2009. "Perturbation-based Markovian Transmission Model for Probing Allosteric Dynamics of Large Macromolecular Assembling: A Study of GroEL-GroES," PLOS Computational Biology, Public Library of Science, vol. 5(10), pages 1-13, October.
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