Long‐scale molecular‐dynamics simulations of cyclic peptide hormones vasopressin, urotensin and analogues
Student thesis: Doctoral Thesis
This thesis describes unrestrained microsecond‐scale molecular‐dynamics (MD) simulations of the structurally related peptide hormones Arg8‐vasopressin (AVP), urotensin II (UII), urotensin‐related peptide (URP), Leu8‐oxytocin (OT) and analogous. All are agonistic ligands of G‐protein coupled receptors that regulate a multitude of physiological functions. They are thus, connected with many pathophysiological processes, making them a major target for drug design.
The common structural feature of these intrinsically flexible peptides is a cyclic 6‐residue moiety closed by a disulphide bridge. The conformational space was explored and systematically clustered with the analysis method DASH. The main conformations were classified: They all show two main classes of ring conformations independently of their primary sequence. One comprises unfolded ring conformations (denoted as open) with no significant transannular hydrogen bonds and the other folded, ring conformations with multiple turns stabilised by highly populated hydrogen bonds. The conformations of the latter type are often considered as the bioactive structure within the binding pocket of the receptor. C‐ or N‐terminal tails either adopt extended or folded conformations that generally interconvert more frequently than the ring. An interdependence of ring and tail conformations is possible; however, it is most appropriate to base the conformational classification primarily on the ring conformation. Structure coordinates of the main conformations may serve as input for 3D drug design, receptor/ligand modelling or further simulations.
Fast conformational equilibria in solution are difficult to access with experimental methods. A new technique is introduced that is able to decipher nuclear magnetic resonance (NMR) data of these equilibria with a combination of MD simulations and NMR calculations without classical analysis of Nuclear‐Overhauser effect (NOE) distances and coupling constants. The technique was tested successfully for AVP, a “known system”, and subsequently applied to UII/URP, a “less well known system”. Based on these results, current single‐conformation descriptions of AVP and UII/URP need to be replaced by a description as fast equilibria of open and folded conformations with characteristic open:folded ratios (AVP 30:70, UII 72:28, URP 86:14). Insights into the pre‐allosteric dynamics may contribute to the understanding of factors that influence bioactivity.
The NMR data from experiments performed within this research supplement experimental data from the literature (e.g. assignment of cis‐Pro3‐UII; 15N chemical shifts for AVP and UII/URP).
The main results of this thesis have been published in peer reviewed journals.
|Award date||Jun 2017|
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