Conformational analysis of polytripeptides (Gly‐Pro‐Ala)n, (Gly‐Ala‐Hyp)n, and (Gly‐Ala‐Ala)n in connection with the problem of collagen structure

AbstractConformational analysis of triple helics of a type of collagen was performed with typical collagen tripeptide sequences based on Gly‐Pro‐Ala, Gly‐Ala‐Hyp, and Gly‐Ala‐Ala. During energy minimization, the possibility of continual deformation of the pyrrolidine cycle was taken into account in order to achieve better accuracy in the resulting structure. The (Gly‐Pro‐Ala)n structure is almost isomorphic to the (Gly‐Pro‐Hyp)n structure obtained in the previous work [Tumanyan, V. G. & Esipova, N.G. (1982) Biopolymers 21, 475–497]. For a collagen‐type structure, the optimal conformation of (Gly‐Ala‐Hyp)n tends to have a decreased unit twist (t = 15°), although the energy advantage with respect to the conformation with t = 45° is not so significant. A similar situation is observed for (Gly‐Ala‐Ala)n. In this case, the energy decrease during unwinding to t = 15° from t = 45° is quite small. The conformations of (Gly‐Ala‐Hyp)n and (Gly‐Ala‐Ala)n with t = 15° exhibit a similarity with a triple complex of polyproline II helices—a noncoiled coil such as (Gly‐Pro‐Hyp)n and (Gly‐Pro‐Ala)n. A similar structure may be postulated for subcomponent cq1 of the first component of a human complement containing substantial Gly‐X‐Pro and Gly‐X‐Y tripeptide derivatives in the primary structure (X, Y = any amino acid). The results suggest that the observed helical symmetry of collagen (t = 36°) is a consequence of superposition of diffraction patterns (for sufficiently long segments) from various helices (t varies from ∼15° for Gly‐X‐Hyp and Gly‐X‐Y to ∼56° for Gly‐Pro‐Ala). For short alternating segments, some unification of different helical structures is possible.