A comprehensive library of blocked dipeptides reveals intrinsic backbone conformational propensities of unfolded proteins.
Despite prolonged scientific efforts to elucidate the intrinsic peptide backbone preferences of amino-acids based on understanding of intermolecular forces, many open questions remain, particularly concerning neighboring peptide interaction effects on the backbone conformational distribution of short peptides and unfolded proteins. Here, we show that spectroscopic studies of a complete library of 400 dipeptides reveal that, irrespective of side-chain properties, the backbone conformation distribution is narrow and they adopt polyproline II and β-strand, indicating the importance of backbone peptide solvation and electronic effects. By directly comparing the dipeptide circular dichroism and NMR results with those of unfolded proteins, the comprehensive dipeptides form a complete set of structural motifs of unfolded proteins. We thus anticipate that the present dipeptide library with spectroscopic data can serve as a useful database for understanding the nature of unfolded protein structures and for further refinements of molecular mechanical parameters.
Department of Chemistry, Korea University, Seoul 136-701, Korea.
Kwang-Im
KI
Oh
Kyung-Koo
KK
Lee
Eun-Kyung
EK
Park
Youngae
Y
Jung
Geum-Sook
GS
Hwang
Minhaeng
M
Cho
D000596:Amino Acids / Q000737:chemistry; D002942:Circular Dichroism; D004151:Dipeptides / Q000138:chemical synthesis / Q000737:chemistry*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D019151:Peptide Library; D011487:Protein Conformation; D055550:Protein Stability; D058767:Protein Unfolding; D012997:Solvents / Q000737:chemistry; D055672:Static Electricity; D014867:Water / Q000737:chemistry
D000596:Amino Acids; D004151:Dipeptides; D019151:Peptide Library; D012997:Solvents; D014867:Water