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J Biomol Struct Dyn. 2017 May;35(6):1331-1338. doi: 10.1080/07391102.2016.1182948. Epub 2016 May 20.

Evidence for the residual tertiary structure in the urea-unfolded form of bacteriophage T5 endolysin.

Author information

1
a Institute of Theoretical and Experimental Biophysics , Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia.
2
b Branch of Shemyakin & Ovchinnikov's Institute of Bioorganic Chemistry , Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia.
3
c Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine, University of South Florida , Tampa , FL , USA.
4
d Laboratory of Structural Dynamics, Stability and Folding of Proteins , Institute of Cytology, Russian Academy of Sciences , Tikhoretsky Ave. 4, St. Petersburg 194064 , Russia.

Abstract

Using high-resolution NMR spectroscopy, we studied peculiarities of the unfolding process of the bacteriophage T5 endolysin (EndoT5) by strong denaturants. It was shown that in the absence of zinc ions this protein is mostly unfolded in the solution of 8 M urea or 6 M guanidine hydrochloride. However, in the presence of zinc ions EndoT5 unfolding can be achieved only in acidic solutions (at pH < 4.0), whereas at pH > 4.0 NMR spectra of the metal-bound protein (Zn2+-Ca2+-EndoT5 or Zn2+-EndoT5 complexes) exhibit a few chemical shifts characteristic of the native or native-like proteins. Our data, including the pH-titration curve with the pK of ~5, suggested involvement of the zinc-binding histidines in the stabilization of this protein. Up-field signals that appear in the NMR spectra of apo-EndoT5 in the presence of high concentrations of strong denaturants are probably derived from the amino acid residues included in the formation of structured hydrophobic cluster, which likely corresponds to the 81-93 region of EndoT5 and contains some residual tertiary structure. It is possible also that this hydrophobic fragment serves as a foundation for the formation of structured cluster in the unfolded state.

KEYWORDS:

high-resolution NMR spectroscopy; hydrophobic cluster; protein folding; residual structure; unfolded protein

PMID:
27109308
DOI:
10.1080/07391102.2016.1182948
[Indexed for MEDLINE]

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