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)
Ramnarayan
K
K
ImmunoPharmaceutics, Inc., San Diego, CA.
Balaji
V N
VN
Varughese
K I
KI
D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary
D009842:Oligopeptides