Conformational flexibility of pyruvate dehydrogenase complexes: A computational analysis by quantized elastic deformational model

Yifei Kong, Dengming Ming, Yinghao Wu, James K. Stoops, Z. Hong Zhou, Jianpeng Ma

Research output: Contribution to journalArticle

27 Scopus citations

Abstract

Pyruvate dehydrogenase complex (PDC) is one of the largest multienzyme complexes known and consists of a dodecahedral E2 core to which other components are attached. We report the results of applying a new computational method, quantized elastic deformational model, to simulating the conformational fluctuations of the truncated E2 core, using low-resolution electron cryomicroscopy density maps. The motional features are well reproduced; especially, the symmetric breathing mode revealed in simulation is nearly identical with what was observed experimentally. Structural details of the motions of the trimeric building blocks, which are critical to facilitating the global expansion and contraction of the complex, were revealed. Using the low-resolution maps from electron cryomicroscopy reconstructions, the simulations showed a picture of the motional mechanism of the PDC core, which is an example without precedent of thermally activated global dynamics. Moreover, the current results support an earlier suggestion that, at low resolution and without the use of amino acid sequence and atomic coordinates, it is possible for computer simulations to provide an accurate description of protein dynamics.

Original languageEnglish (US)
Pages (from-to)129-135
Number of pages7
JournalJournal of Molecular Biology
Volume330
Issue number1
DOIs
StatePublished - Jun 27 2003

Keywords

  • Conformational flexibility
  • Elastic deformation
  • Elastic network
  • Large conformational change
  • Normal mode analysis

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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