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

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

Author information

1
CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.
2
CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
3
CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh, India.

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.

PMID:
26394388
PMCID:
PMC4578939
DOI:
10.1371/journal.pcbi.1004496
[Indexed for MEDLINE]
Free PMC Article

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