Peptides/polypeptides loop conformations

The hard-sphere potential has also been used to compute the sterically allowed conformations of small polypeptides of known amino acid sequence, viz. an octapeptide loop of ribonuclease (Nemethy and Scheraga, 1965) and the cyclic decapeptide gramicidin-S (Vanderkooi et al., 1966). We shall use the calculation for gramicidin-S to illustrate the method. This decapeptide consists of two identical pentapeptides joined into a ring by peptide bonds, the amino acid sequence being... 

A very good example is the study of the extent to which residues of the loop polypeptide of lysozyme contributes to specificity. The loop peptide comprises residues 64-80 in which Cys-64 and Cys-80 form a disulfide bond, and thus this structure is highly conformational because opening the disulfide bond destroyed immunological activity. From the X-ray crystallographic study (Fig. 13), the loop peptide occurs in an exposed position. Figure 14 shows the sequence of the synthetic loop peptide and the capacity of synthetic loop peptides containing residues modified... 

This approach was recently extended to target the cleavage of RNA model compounds." A polypeptide that adopts a characteristic helix-loop-helrx conformation and accelerates the hydrolysis of the RNA model substrate 2-hydroxypropyl 4-nitrophenyl phosphate (HPNP) by about 2 orders of magnitude was used in this investigation. Two histidine and two arginine units in this peptide were believed to be responsible for catalytic activity. Analogs of... 

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