Modeling conformational changes in cyclosporin A

Abstract

NMR and X-ray structures for the immunosuppressant cyclosporin A (CsA) reveal a remarkable difference between the unbound (free) conformation in organic solvents and the conformation bound to cyclophilin. We have performed computer simulations of the molecular dynamics of CsA under a variety of conditions and confirmed the stability of these two conformations at room temperature in water and in vacuum. However, when the free conformation was modeled in vacuum a t 600 K, a transition pathway leading to the bound conformation was observed. This involved a change in the cis MeLeu-9 peptide bond to a trans conformation and the movement of the side chains forming the dominant hydrophobic cluster (residues MeBmt-1, MeLeu-4, MeLeu-6, and MeLeu-10) to the opposite side of the plane formed by the backbone atoms in the molecular ring. The final conformation had a backbone RMS deviation from the bound conformation of 0.53 A and was as stable in dynamics simulations as the bound conformation. Our calculations allowed us to make a detailed analysis of a transition pathway between the free and the bound conformations of CsA and to identify two distinct regions of coordinated movement in CsA, both of which underwent transitions independently.

Thermodynamics of lipid–peptide interactions

“…2. Two conformations have been reported for CyA: one for pure CyA, the other bound to immunophilin or calcineurin [7]. In addition, CyA in solution also appears to adopt two different conformations [8].…”

Solution conformations of cyclosporins and magnesium‐cyclosporin complexes determined by vibrational circular dichroism

“…In the unbound state, the hydrophobic region is on the outside, allowing CsA to assume a compact shape that would aid in transport across the cell membrane. 19 Once in the cell, where Mg 2ϩ is abundant, 20 Mg 2ϩ can bind to CsA, inducing a conformational change that facilitates formation of the CsA:CypA complex.…”

PEPCAT?A new tool for conformational analysis of peptides

“…CsA can be divided into two regions (Leu10-Abu2, and Gly3-Leu9) roughly comprising the two halves of the molecular ring with flexible hinge regions at Gly3 and Leu9. 38 The intermediate state 29 (see Fig. 9) has one region Leu10-Abu2 that has flipped into a backbone conformation similar to that of the bound conformation, while the two remaining monitored hydrophobic residues Leu10 and Bmt1 have remained in the configuration found in the free conformation (see Fig.…”

“…The high population in Figure 9 is an indication of the stability of this state, as identified earlier. 38 Interestingly, no pathway could be observed where one side chain alone flipped to the other ring plane to initiate the transition from the free to the bound CsA conformation. A cooperative change of at least two side chains seems to be required.…”

“…The coordinates for the bound conformation were obtained from the X-ray structure of the CsA-Cp complex 35,36 (Brookhaven Protein Databank 37 access code: 1CWA). The molecular dynamics trajectory that is used as the basis for the PEPCAT analysis described here was reported by O'Donohue et al 38 for an investigation of conformational changes in CsA. The trajectory monitors the transition from a free CsA conformation in vacuo at 600 K through a number of conformational changes to a structure nearly identical to the bound conformation (backbone RMS deviation of 0.53 Å).…”