A novel beta-turn location in an LHRH antagonist: a combined conformational search and molecular dynamics study.
A 50 pico-second molecular dynamics simulation on a cyclic LHRH antagonist analogue Ac-D-Phe1-D-Phe2-D-Trp3-Ser4-Glu5-D-Arg6-Leu7-Lys8+ ++-Pro9-D-Ala10-NH2 (where the cyclisation is via an amide linkage between the Glu5 and Lys8 side chains), reveals some hitherto unseen conformational features. The LHRH analogue is found to adopt a near beta-sheet type of conformation with the reversal in the chain being brought about by a D-Trp3-Ser4-Glu5-D-Arg6 beta turn. The N- and C-terminal ends of the peptide come close together and interact through a network of hydrogen bonds. Additional hydrogen bonds expected of a sheet type of conformation stabilise the lowest energy minima. A conformational search of all possible cyclic structures of a model system c(Glu-D-Ala-Ala-Lys) which was used to determine the starting structure for the simulation studies of the cyclic LHRH antagonist analogue is also highlighted. The influence of the cyclic part on the conformation of this LHRH analogue is discussed.
Paul
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PK
Molecular Graphics Unit, School of Chemistry, University of Bath, U.K.
Dauber-Osguthorpe
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Campbell
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Osguthorpe
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DJ
D000595:Amino Acid Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003500:Cyclization; D007987:Gonadotropin-Releasing Hormone / Q000031:analogs & derivatives / Q000037:antagonists & inhibitors*; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011487:Protein Conformation
D007987:Gonadotropin-Releasing Hormone