Effects of Membrane and Biological Target on the Structural and Allosteric Properties of Recoverin: A Computational Approach

Abstract

Recoverin (Rec) is a prototypical calcium sensor protein primarily expressed in the vertebrate retina. The binding of two Ca2+ ions to the functional EF-hand motifs induces the extrusion of a myristoyl group that increases the affinity of Rec for the membrane and leads to the formation of a complex with rhodopsin kinase (GRK1). Here, unbiased all-atom molecular dynamics simulations were performed to monitor the spontaneous insertion of the myristoyl group into a model multicomponent biological membrane for both isolated Rec and for its complex with a peptide from the GRK1 target. It was found that the functional membrane anchoring of the myristoyl group is triggered by persistent electrostatic protein-membrane interactions. In particular, salt bridges between Arg43, Arg46 and polar heads of phosphatidylserine lipids are necessary to enhance the myristoyl hydrophobic packing in the Rec-GRK1 assembly. The long-distance communication between Ca2+-binding EF-hands and residues at the interface with GRK1 is significantly influenced by the presence of the membrane, which leads to dramatic changes in the connectivity of amino acids mediating the highest number of persistent interactions (hubs). In conclusion, specific membrane composition and allosteric interactions are both necessary for the correct assembly and dynamics of functional Rec-GRK1 complex.

Affinity of rhodopsin to raft enables the aligned oligomer formation from dimers: Coarse-grained molecular dynamics simulation of disk membranes

“…It should be noted that our simulation strongly suggested that lipid raft formation was essential for the formation of the row of Rh dimers, but did not suggest much about the molecular mechanism of lipid raft formation. In order to reveal the detailed mechanism of lipid raft domain formations, we need to consider various other physicochemical properties of lipids, such as the electrostatic properties of the polar head [44,45], as well as, the effects of cholesterols by the considering molecular models with microscopic details; this is one of our future challenges. On the other hand, we expect to obtain results that are similar to Coarse-grained molecular dynamics simulation of rhodopsin aligned oligomer formation the ones presented, if such physicochemical properties of lipids play weak or positive roles in raft formation.…”

New Approach for Untangling the Role of Uncommon Calcium-Binding Proteins in the Central Nervous System

“…This group can, therefore, be considered as important retinal calcium-binding proteins. This observation is consistent with the literature: CaBP4 is localised in photoreceptor synaptic terminals and is essential for neurotransmission between photoreceptors and bipolar cells as part of the Cav1.4 channel complex in the retina [ 35 ]; CaBP5 in mice is expressed in type 5 ON-cone bipolar cells, and in type 3 OFF-cone bipolar cells as well as in rod bipolar cells [ 36 , 37 , 38 ]; Guca1b is important for rod cell recovery after light exposure, by stimulation of guanylate cyclases in these photoreceptors [ 39 ]; Secretagogin plays an essential role in synapse maturation and in mouse, rat, and rabbit retina it is expressed in subtypes of cone bipolar cells, but cannot be detected in the rod bipolar cells [ 40 ]; Recoverin is thought to be a calcium sensor in retinal rod cells that can control the lifetime of photoexcited rhodopsin by inhibiting rhodopsin kinase [ 41 , 42 ]; and last but not least Plch1 has been shown to be expressed in mouse and human retina as well [ 43 ].…”

Bringing the Ca 2+ sensitivity of myristoylated recoverin into the physiological range

“…On the other hand, prompt sequestration of the myristoyl group in the protein milieu at low [Ca 2+ ] is essential to permit GRK1 function. While both experimental studies [ 21 , 23 ] and molecular dynamics simulations [ 24 , 25 ] are consistent with the notion that Ca 2+ -bound mRec stabilizes the R state and allows the spontaneous insertion of the myristic moiety into the ROS disc membrane, the low apparent affinity ( K D app = 17–18 µM) for Ca 2+ binding of mRec in aqueous solution raised concerns as to the actual role of Rec in vivo [ 26 – 28 ], where [Ca 2+ ] varies in a narrow sub-micromolar range (20–250 nM in mouse rods [ 29 ], but see ref. [ 30 ] for higher values in other vertebrates).…”