Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide
Department of Biochemistry and Molecular Pharmacology
Peptides, Cyclic; Water; Molecular Dynamics Simulation; Molecular Conformation; Nuclear Magnetic Resonance, Biomolecular
Biochemistry, Biophysics, and Structural Biology | Pharmacology, Toxicology and Environmental Health
The influence of water binding on the conformational dynamics of the cyclic decapeptide antamanide dissolved in the model lipophilic environment chloroform is investigated by NMR relaxation measurements. The water-peptide complex has a lifetime of 35 mgrs at 250 K, which is longer than typical lifetimes of water-peptide complexes reported in aqueous solution. In addition, there is a rapid intracomplex mobility that probably involves librational motions of the bound water or water molecules hopping between different binding sites. Water binding restricts the flexibility of antamanide. The experimental findings are compared with GROMOS molecular dynamics simulations of antamanide with up to eight bound water molecules. Within the simulation time of 600 ps, no water molecule leaves the complex. Additionally, the simulations show a reduced flexibility for the complex in comparison with uncomplexed antamanide. Thus, there is a qualitative agreement between the experimental NMR results and the computer simulations.
Peng, J.W., Schiffer, C.A., Xu, P., van Gunsteren, W.F., Ernst, R.R. "Dynamics of Antamanide with Water in Chloroform." J. Biol. NMR 8:453-476 (1996).
Journal of Biomolecular NMR
Peng JW, Schiffer CA, Xu P, van Gunsteren WF, Ernst RR. (1996). Investigations of peptide hydration using NMR and molecular dynamics simulations: A study of effects of water on the conformation and dynamics of antamanide. Biochemistry and Molecular Pharmacology Publications. Retrieved from https://escholarship.umassmed.edu/bmp_pp/110