TY - JOUR
T1 - Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides
AU - Oh, Kwang Im
AU - Jung, Young Sang
AU - Hwang, Geum Sook
AU - Cho, Minhaeng
N1 - Funding Information:
Acknowledgments This work was supported by the National Research Foundation of Korea (NRF) grants funded by the Korea government (MEST) (No. 20090078897 and 20110020033) to MC. Also, we thank the financial supports from the Korea Basic Science Institute (T31401) grant to GH and MC. KIO thanks the financial support by Korea University.
PY - 2012/5
Y1 - 2012/5
N2 - Understanding intrinsic conformational preferences of amino-acids in unfolded proteins is important for elucidating the underlying principles of their stability and re-folding on biological timescales. Here, to investigate the neighbor interaction effects on the conformational propensities of amino-acids, we carried out 1H NMR experiments for a comprehensive set of blocked dipeptides and measured the scalar coupling constants between alpha protons and amide protons as well as their chemical shifts. Detailed inspection of these NMR properties shows that, irrespective of amino-acid side-chain properties, the distributions of the measured coupling constants and chemical shifts of the dipeptides are comparatively narrow, indicating small variances of their conformation distributions. They are further compared with those of blocked aminoacids (Ac-X-NHMe), oligopeptides (Ac-GGXGG-NH2), and native (lysozyme), denatured (lysozyme and outer membrane protein X from Escherichia coli), unstructured (Domain 2 of the protein 5A of Hepatitis C virus), and intrinsically disordered (hNlg3cyt: intracellular domain of human NL3) proteins. These comparative investigations suggest that the conformational preferences and local solvation environments of the blocked dipeptides are quite similar to not only those of other short oligopeptides but also those of denatured and natively unfolded proteins.
AB - Understanding intrinsic conformational preferences of amino-acids in unfolded proteins is important for elucidating the underlying principles of their stability and re-folding on biological timescales. Here, to investigate the neighbor interaction effects on the conformational propensities of amino-acids, we carried out 1H NMR experiments for a comprehensive set of blocked dipeptides and measured the scalar coupling constants between alpha protons and amide protons as well as their chemical shifts. Detailed inspection of these NMR properties shows that, irrespective of amino-acid side-chain properties, the distributions of the measured coupling constants and chemical shifts of the dipeptides are comparatively narrow, indicating small variances of their conformation distributions. They are further compared with those of blocked aminoacids (Ac-X-NHMe), oligopeptides (Ac-GGXGG-NH2), and native (lysozyme), denatured (lysozyme and outer membrane protein X from Escherichia coli), unstructured (Domain 2 of the protein 5A of Hepatitis C virus), and intrinsically disordered (hNlg3cyt: intracellular domain of human NL3) proteins. These comparative investigations suggest that the conformational preferences and local solvation environments of the blocked dipeptides are quite similar to not only those of other short oligopeptides but also those of denatured and natively unfolded proteins.
KW - Blocked dipeptide
KW - NMR scalar coupling
KW - Peptide backbone conformation
KW - Unfolded protein
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U2 - 10.1007/s10858-012-9618-5
DO - 10.1007/s10858-012-9618-5
M3 - Article
C2 - 22426785
AN - SCOPUS:84863091846
SN - 0925-2738
VL - 53
SP - 25
EP - 41
JO - Journal of Biomolecular NMR
JF - Journal of Biomolecular NMR
IS - 1
ER -
