Electrostatic strain and concerted motions in the transient complex between plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum

Abstract

Many fleeting macromolecular interactions, like those being involved in electron transport, are essential in biology. However, little is known about the behaviour of the partners and their dynamics within their short-lived complex. To tackle such issue, we have performed molecular dynamics simulations on an electron transfer complex formed by plastocyanin and cytochrome f from the cyanobacterium Phormidium laminosum. Besides simulations of the isolated partners, two independent trajectories of the complex were calculated, starting from the two different conformations in the NMR ensemble. The first one leads to a more stable ensemble with a shorter distance between the metal sites of the two partners. The second experiences a significant drift of the complex conformation. Analyses of the distinct calculations show that the conformation of cytochrome f is strained upon binding of its partner, and relaxes upon its release. Interestingly, the principal component analysis of the trajectories indicates that plastocyanin displays a concerted motion with the small domain of cytochrome f that can be attributed to electrostatic interactions between the two proteins.

Dimerization model of the C‐terminal RNA Recognition Motif of HuR

“…Then, for each computation, success was defined as the occurrence of a given number of pair‐wise distance cut‐off. Two pairs were considered independent if the distance between them was larger of 6 Å. Translational and rotational diffusion constants for BD were calculated using the tcl script ARO (former main axis; [27]) on the tcl console of VMD [28]. 45 000 trajectories were calculated for every kinetic or docking simulation.…”

The cytochrome f–plastocyanin complex as a model to study transient interactions between redox proteins

“…This results in the attraction of the copper site towards C f and repulsion of site 2. The resulting net coulombic term between the two proteins is repulsive, but is mostly compensated by solvent polarization phenomena to yield a small ionic strength effect [28]. The Phormidium complex shows a highly dynamic nature that could explain the lower precision of the solved structure – with an RMSD of 3.7 Å – compared with other C f –Pc models.…”

“…Altogether, the major contribution to in higher plants and Nostoc cyanobacterium is electrostatics, which leads to the encounter between proteins and to the formation of a well‐defined functional complex. The opposite is valid for the thermophilic Phormidium cyanobacterium, in which non‐polar interactions play the main role because of the small net contribution of electrostatics [23,26,28]. Nevertheless, the hydrophobic interactions are essential for ET in all complexes, since the reorganization of water molecules at the interface should impair the charge transfer process.…”

“…Despite all the kinetic, structural and theoretical studies performed on the Phormidium C f –Pc complex, there is certain controversy regarding NMR and functional data. Hence, MD simulations combined to continuum electrostatic calculations on this particular interaction [28] try to harmonize the two sets of data. The MD trajectories reveal that Pc tilts towards the small domain of C f approaching site 2 to the heme protein (Fig.…”

“…(A) Drift of Pc around C f along the MD trajectory in Ref. [28]. The dihedral first angle projections of the trajectories of iron from C f (brown dots), copper (blue dots) and center of mass of Pc (grey dots) are represented with respect to the main axes and mass center of the large domain of C f .…”