NMR characterization of the near native and unfolded states of the PTB domain of Dok1 : alternate conformations and residual clusters

Background: Phosphotyrosine binding (PTB) domains are critically involved in cellular signaling and diseases. PTB domains are categorized into three distinct structural classes namely IRS-like, Shc-like and Dab-like. All PTB domains consist of a core pleckstrin homology (PH) domain with additional...

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Main Authors: Gupta, Sebanti, Bhattacharjya, Surajit
Other Authors: Driscoll, Paul C.
Format: Article
Language:English
Published: 2014
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Online Access:https://hdl.handle.net/10356/102910
http://hdl.handle.net/10220/19074
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Institution: Nanyang Technological University
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spelling sg-ntu-dr.10356-1029102023-02-28T17:01:25Z NMR characterization of the near native and unfolded states of the PTB domain of Dok1 : alternate conformations and residual clusters Gupta, Sebanti Bhattacharjya, Surajit Driscoll, Paul C. School of Biological Sciences DRNTU::Science::Biological sciences::Biochemistry Background: Phosphotyrosine binding (PTB) domains are critically involved in cellular signaling and diseases. PTB domains are categorized into three distinct structural classes namely IRS-like, Shc-like and Dab-like. All PTB domains consist of a core pleckstrin homology (PH) domain with additional structural elements in Shc and Dab groups. The core PH fold of the PTB domain contains a seven stranded b-sheet and a long C-terminal helix. Principal Findings: In this work, the PTB domain of Dok1 protein has been characterized, by use of NMR spectroscopy, in solutions containing sub-denaturing and denaturing concentrations of urea. We find that the Dok1 PTB domain displays, at sub-denaturing concentrations of urea, alternate conformational states for residues located in the C-terminal helix and in the b5 strand of the b-sheet region. The b5 strand of PTB domain has been found to be experiencing significant chemical shift perturbations in the presence of urea. Notably, many of these residues in the helix and in the b5 strand are also involved in ligand binding. Structural and dynamical analyses at 7 M urea showed that the PTB domain is unfolded with islands of motionally restricted regions in the polypeptide chain. Further, the C-terminal helix appears to be persisted in the unfolded state of the PTB domain. By contrast, residues encompassing b-sheets, loops, and the short N-terminal helix lack any preferred secondary structures. Moreover, these residues demonstrated an intimate contact with the denaturant. Significance: This study implicates existence of alternate conformational states around the ligand binding pocket of the PTB domain either in the native or in the near native conditions. Further, the current study demonstrates that the C-terminal helical region of PTB domain may be considered as a potential site for the initiation of folding. Published version 2014-04-02T01:26:49Z 2019-12-06T21:02:09Z 2014-04-02T01:26:49Z 2019-12-06T21:02:09Z 2014 2014 Journal Article Gupta, S., & Bhattacharjya, S. (2014). NMR Characterization of the Near Native and Unfolded States of the PTB Domain of Dok1: Alternate Conformations and Residual Clusters. PLoS ONE, 9(2), e90557-. 1932-6203 https://hdl.handle.net/10356/102910 http://hdl.handle.net/10220/19074 10.1371/journal.pone.0090557 24587391 en PLoS ONE © 2014 Gupta, Bhattacharjya. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. application/pdf
institution Nanyang Technological University
building NTU Library
continent Asia
country Singapore
Singapore
content_provider NTU Library
collection DR-NTU
language English
topic DRNTU::Science::Biological sciences::Biochemistry
spellingShingle DRNTU::Science::Biological sciences::Biochemistry
Gupta, Sebanti
Bhattacharjya, Surajit
NMR characterization of the near native and unfolded states of the PTB domain of Dok1 : alternate conformations and residual clusters
description Background: Phosphotyrosine binding (PTB) domains are critically involved in cellular signaling and diseases. PTB domains are categorized into three distinct structural classes namely IRS-like, Shc-like and Dab-like. All PTB domains consist of a core pleckstrin homology (PH) domain with additional structural elements in Shc and Dab groups. The core PH fold of the PTB domain contains a seven stranded b-sheet and a long C-terminal helix. Principal Findings: In this work, the PTB domain of Dok1 protein has been characterized, by use of NMR spectroscopy, in solutions containing sub-denaturing and denaturing concentrations of urea. We find that the Dok1 PTB domain displays, at sub-denaturing concentrations of urea, alternate conformational states for residues located in the C-terminal helix and in the b5 strand of the b-sheet region. The b5 strand of PTB domain has been found to be experiencing significant chemical shift perturbations in the presence of urea. Notably, many of these residues in the helix and in the b5 strand are also involved in ligand binding. Structural and dynamical analyses at 7 M urea showed that the PTB domain is unfolded with islands of motionally restricted regions in the polypeptide chain. Further, the C-terminal helix appears to be persisted in the unfolded state of the PTB domain. By contrast, residues encompassing b-sheets, loops, and the short N-terminal helix lack any preferred secondary structures. Moreover, these residues demonstrated an intimate contact with the denaturant. Significance: This study implicates existence of alternate conformational states around the ligand binding pocket of the PTB domain either in the native or in the near native conditions. Further, the current study demonstrates that the C-terminal helical region of PTB domain may be considered as a potential site for the initiation of folding.
author2 Driscoll, Paul C.
author_facet Driscoll, Paul C.
Gupta, Sebanti
Bhattacharjya, Surajit
format Article
author Gupta, Sebanti
Bhattacharjya, Surajit
author_sort Gupta, Sebanti
title NMR characterization of the near native and unfolded states of the PTB domain of Dok1 : alternate conformations and residual clusters
title_short NMR characterization of the near native and unfolded states of the PTB domain of Dok1 : alternate conformations and residual clusters
title_full NMR characterization of the near native and unfolded states of the PTB domain of Dok1 : alternate conformations and residual clusters
title_fullStr NMR characterization of the near native and unfolded states of the PTB domain of Dok1 : alternate conformations and residual clusters
title_full_unstemmed NMR characterization of the near native and unfolded states of the PTB domain of Dok1 : alternate conformations and residual clusters
title_sort nmr characterization of the near native and unfolded states of the ptb domain of dok1 : alternate conformations and residual clusters
publishDate 2014
url https://hdl.handle.net/10356/102910
http://hdl.handle.net/10220/19074
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