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Computer simulations of a tumor surface octapeptide epitope

✍ Scribed by Robert H. Reid; Charles A. Hooper; Bernard R. Brooks

Publisher
Wiley (John Wiley & Sons)
Year
1989
Tongue
English
Weight
446 KB
Volume
28
Category
Article
ISSN
0006-3525

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✦ Synopsis

Molecular dynamics using CHARMM and GEMM programs with the Star Technologies ST 100 array processor functioning at the speed of super computers was used as a searching algorithm for conformational exploration of the octapeptide Gly-Am-Thr-Ile-Val-Ala-Glu. This poorly soluble odapeptide is the N-terminal epitope of an 11 KD glycoprotein antigen residing on human ductal carcinoma (breast) cells. Very long (nanoseconds) simulations were required. Both an a-helix and the N-acetyl-N'-methylamide derived minimized starting structures gave the same lowest potential energy conformation with simulation^ at 600 K. The same conformation was found only when using the latter starting conformation with simulations at 300 K. The lowest potential energy conformation was stabilized by 4 hydrophobic contacts and 13 H bonds completing one turn of a left-handed helix.

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