Conformations of a model cyclic hexapeptide, CYIQNC: (1)H-NMR and molecular dynamics studies.
Solution conformation of the cyclic hexapeptide sequence, [cyclo-S-Cys-Tyr-Ile-Gln-Asn-Cys-S] (CYIQNC) - a disulfide-linked fragment of a neurohypophyseal peptide hormone oxytocin (OT) - has been investigated by high-field one-dimensional (1D) and two-dimensional (2D) NMR spectroscopic methods and compared with the results obtained from computer simulation studies. (1)H-NMR results based on temperature dependence of amide proton chemical shifts and nuclear Overhauser effect indicate that peptide in solution populates different conformations, characterized by two fused β-turns. The segment Ile(3)-Gln(4)-Asn(5)-Cys(6) yields a preferred type-III β-turn at residues 4, 5 (HB, 3HN → 6CO), while the segment Cys(6), Cys(1)-Tyr(2)-Ile(3) exhibits inherently weaker, flexible β-turn either of type I/II'/III/half-turn at residues 1, 2 (HB, 6HN → 3CO). The computer simulation studies using a mixed protocol of distance geometry-simulated annealing followed by constrained minimization, restrained molecular dynamics, and energy minimization showed the possibility of existence of additional conformations with the hydrogen bonds, (a) 5HN → 3CO and (b) 2HN → 6CO. These results, therefore, indicate that the additional conformations obtained from both NMR and simulation studies can also be possible to the peptide. These additional conformations might have very small population in the solution and did not show their signatures in these conditions. These findings will be helpful in designing more analogs with modifications in the cyclic moiety of OT.
a Department of Physiology , MediCiti Institute of Medical Sciences , Ghanpur, Medchal Mandal, R. R. Dist., Hyderabad 501401 , India.
Ashok Kumar
AK
Kulkarni
Rajendra Prasad
RP
Ojha
D000595:Amino Acid Sequence; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D010456:Peptides, Cyclic / Q000737:chemistry*; D011487:Protein Conformation; D011522:Protons; D012996:Solutions / Q000737:chemistry*; D013696:Temperature
D010456:Peptides, Cyclic; D011522:Protons; D012996:Solutions
1H-NMR; distance geometry; inverse γ-turn; oxytocin; restrained molecular dynamics; β-turn