Concerted motions in allosteric model proteins at terahertz frequencies

Authors

  • Valeria Conti Nibali Ruhr Universität
  • Giulia Morra Istituto di Chimica del Riconoscimento Molecolare del CNR
  • Martina Havenith Ruhr Universität
  • Giovanna D'Angelo Università degli Studi di Messina
  • Giorgio Colombo Istituto di Chimica del Riconoscimento Molecolare del CNR

DOI:

https://doi.org/10.1478/AAPP.961A6

Keywords:

MD simulation, Protein dynamics, Dynamic allostery

Abstract

PDZ3 is an allosteric protein that represents an ideal test system to analyze the molecular determinants at the basis of the allosteric mechanism. Recent computational studies of the terahertz (THz) fluctuations of this protein have highlighted a response nucleus for binding modulated by the ligand that is visible only at THz frequencies and that overlaps with the known allosterically responding residues (Conti et al. 2017). With the aim of further characterizing the changes in the terahertz dynamics of this allosteric protein following the binding event, we have carried out an analysis of the correlation motions of pairs of PDZ3 residues from molecular dynamic simulations. We identify concerted and non-random THz fluctuations in the main secondary structure elements of the PDZ3. Importantly, we highlight a concerted motion of some residues belonging to the allosteric response nucleus for binding.

Author Biographies

  • Valeria Conti Nibali, Ruhr Universität
    Lehrstuhl für Physikalische Chemie II, 44801 Bochum
  • Giulia Morra, Istituto di Chimica del Riconoscimento Molecolare del CNR
    Via Mario Bianco 9, 20131 Milano
  • Martina Havenith, Ruhr Universität
    Lehrstuhl für Physikalische Chemie II, 44801 Bochum
  • Giovanna D'Angelo, Università degli Studi di Messina
    Dipartimento di Scienze Matematiche ed Informatiche, Scienze Fisiche e Scienze della Terra
  • Giorgio Colombo, Istituto di Chimica del Riconoscimento Molecolare del CNR
    Via Mario Bianco 9, 20131 Milano

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Published

2018-06-13

Issue

Vol. 96 No. 1 (2018)

Section

Articles

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