Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding

PLoS Comput Biol. 2015 Sep 22;11(9):e1004496. doi: 10.1371/journal.pcbi.1004496. eCollection 2015.

Abstract

Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central "hubs". Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Hydrophobic and Hydrophilic Interactions
  • Molecular Chaperones / chemistry*
  • Molecular Chaperones / metabolism*
  • Molecular Dynamics Simulation
  • Protein Binding*
  • Protein Conformation
  • Protein Folding*

Substances

  • Molecular Chaperones

Grant support

LT is funded by INSPIRE Faculty Fellowship from Department of Science and Technology. KM is funded by IYBA fellowship from Department of Biotechnology. SN and ST’s financial support is from CSIR network projects BSC0123 and BSC0124, respectively. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.