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Decoding the components of dynamics in three-domain proteins.

Mateusz Maciejewski1, Paul N Barlow, Nico Tjandra

  • 1Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, 250 Massachusetts Ave., Cambridge, Massachusetts, 02139.

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|December 11, 2013
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Summary

We studied motional correlations in linear three-domain proteins. Strong repulsive potentials between domains can cause correlated motions of terminal domains, impacting protein dynamics.

Keywords:
interdomain dynamicsnuclear magnetic resonanceprotein dynamicsprotein functionprotein structure

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Area of Science:

  • Biophysics
  • Computational Biology
  • Protein Dynamics

Background:

  • Linear three-domain proteins exhibit complex motional behaviors.
  • Understanding interdomain motion is crucial for protein function.

Purpose of the Study:

  • To assess the feasibility of describing motional behavior in linearly connected three-domain proteins.
  • To investigate correlations in motion between protein domains.
  • To explore the limitations in experimentally determining interdomain motional correlations.

Main Methods:

  • Utilized dynamics simulations to investigate motional correlations.
  • Applied model-free (MF) and extended MF formalisms (Lipari and Szabo).
  • Examined two limiting cases: weak and strong interdomain repulsive potentials.

Main Results:

  • Identified and quantified interdomain motional correlations.
  • Found that terminal domain motions become correlated under strong repulsive potentials (domain angle > 60°).
  • Separated protein motion into concerted overall and independent domain components when timescales are distinct and domain angles are between 60° and 160°.

Conclusions:

  • Motional behavior in three-domain proteins can be characterized by overall and independent domain motions.
  • Interdomain repulsive potentials significantly influence motional correlations.
  • Dynamics simulations are essential for understanding interdomain motion, particularly for terminal domains.