Characterization of a linear pentapeptide containing two consecutive beta-turns.
The contiguous occurrence of two beta-turns is examined using molecular mechanics calculations. A tripeptide can take up special conformations known as beta-turns resulting in the reversal of the chain. There are two major classes of beta-turns, called type I beta-turn and type II beta-turn. In the specific case described here, the third peptide unit forms a part of a second turn resulting in the formation of a two-turn motif. In the case of dihydropteridine reductase, this motif is involved in cofactor binding. This study examines the energetic and conformational preferences for chain-reversed motifs. Energy minimizations were carried out on models of pentapeptides with four different sequences for residues 2 through 5: (i) GGGG, (ii) AGGA, (iii) AGAG and (iv) AAAA. For each of the above sequences, all four possible combinations of type I and type II beta-turns were considered. Out of the four possible combinations, the (II, II) combination is the most planar one. The (I, I) combination is the least planar. For the all-Gly model and the all-Ala model, the most favored conformation energetically is a type I-type I combination. On the other hand, the sequence AGGA favors a type II-type I combination, and the sequence AGAG prefers a type II-type II combination. A computer search for double-turn motifs at the Brook-haven Protein Data Bank revealed that the (I, I) combination occurs with the highest frequency, and the (I, II) combination has the next highest frequency.(ABSTRACT TRUNCATED AT 250 WORDS)
ImmunoPharmaceutics, Inc., San Diego, CA.
K
K
Ramnarayan
V N
VN
Balaji
K I
KI
Varughese
D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D009842:Oligopeptides