Peptides tertiary structure prediction

A Caflisch, M Karplus. Molecular dynamics studies of protein and peptide folding and unfolding. In K Merz Jr, S Le Grand, eds. The Protein Eoldmg Problem and Tertiary Structure Prediction. Boston Birkhauser, 1994, pp 193-230. 

In a first step towards the design of / -peptides tyligomers (oligomers that fold into predictable tertiary structures [8]), carefully controlled interhelical hydrophobic interactions have been utilized to stabilize a / -peptide two-helix bundle (92) [179] (Fig. 2.17). 

The biological function of peptides and proteins depends on their native conformation. The side-chain functionalities of the a-amino acids that comprise peptides and proteins have profound effects on their properties. These functionalities reside in the 20 naturally occurring a-amino acids, which have different propensities for formation of the three major secondary structural conformations. 1 In addition to these naturally occurring a-amino acids whose primary structure enables the polypeptide to fold into a predictable secondary and tertiary structure, the incorporation of unnatural amino acids has opened important areas of research. 

Since aromatic amino acids and cysteine are absent, there is no protein absorption above 270 nm. Metallothioneins exhibit a broad absorption peak, with the maximum at 190 mn. Absorptions due to the metal-thiolate complexes show as shoulders at 250 nm (Cd), 220 nm (Zn) and 270 nm (Cu).1458,1459 Theoretical predictions based on the amino acid sequence of the peptide chain indicate that the or-helical conformation is forbidden, and /3-structure is almost impossible to attain. CD and NMR studies on both the metal-containing and metal-free protein confirmed the predictions.1459 1460 However, metallothioneins are stable to tryptic digestion and the slow exchange of many peptide hydrogens of metallothionein with those of the solvent suggest that the protein has a compact and well-defined tertiary structure. 

H. Kawai, T. Kikuchi, and Y. Okamoto, Protein Engin., 3, 85 (1989). A Prediction of Tertiary Structures of Peptide by the Monte Carlo Simulated Annealing Method. 

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