Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides

• Published in: Journal of biomolecular NMR 2012-05, Vol.53 (1), p.25-41
• Main Authors: Oh, Kwang-Im, Jung, Young-Sang, Hwang, Geum-Sook, Cho, Minhaeng
• Format: Article
• Language: English
• Subjects: Bacterial Outer Membrane Proteins - chemistry; Bacterial Outer Membrane Proteins - metabolism; Biochemistry; Biological and Medical Physics; Biophysics; Dipeptides - chemistry; Dipeptides - metabolism; E coli; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - metabolism; Humans; Hydrolases - chemistry; Hydrolases - metabolism; Models, Molecular; Nuclear Magnetic Resonance, Biomolecular; Physics; Physics and Astronomy; Protein Conformation; Protein Denaturation; Protein Unfolding; Proteins; Proteins - chemistry; Proteins - metabolism; Spectroscopy/Spectrometry; Viral Proteins - chemistry; Viral Proteins - metabolism
• ISSN: 0925-2738; 1573-5001
• DOI: 10.1007/s10858-012-9618-5

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 1 H 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 amino-acids (Ac–X–NHMe), oligopeptides (Ac–GGXGG–NH 2 ), 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.