Ana M. Rossi

Analysis of protein-ligand interactions by fluorescence polarization

Quantification of the associations between biomolecules is required both to predict and understand the interactions that underpin all biological activity. Fluorescence polarization (FP) provides a nondisruptive means of measuring the association of a fluorescent ligand with a larger molecule. We describe an FP assay in which binding of fluorescein-labeled inositol 1,4,5-trisphosphate (IP3) to N-terminal fragments of IP3 receptors can be characterized at different temperatures and in competition with other ligands. The assay allows the standard Gibbs free energy (ΔG°), enthalpy (ΔH°) and entropy (ΔS°) changes of ligand binding to be determined. The method is applicable to any purified ligand-binding site for which an appropriate fluorescent ligand is available. FP can be used to measure low-affinity interactions in real time without the use of radioactive materials, it is nondestructive and, with appropriate care, it can resolve ΔH° and ΔS°. The first part of the protocol, protein preparation, may take several weeks, whereas the FP measurements, once they have been optimized, would normally take 1–6 h.

Structural and functional conservation of key domains in InsP3 and ryanodine receptors.

Inositol-1,4,5-trisphosphate receptors (InsP3Rs) and ryanodine receptors (RyRs) are tetrameric intracellular Ca2+ channels. In each of these receptor families, the pore, which is formed by carboxy-terminal transmembrane domains, is regulated by signals that are detected by large cytosolic structures. InsP3R gating is initiated by InsP3 binding to the InsP3-binding core (IBC, residues 224–604 of InsP3R1) and it requires the suppressor domain (SD, residues 1–223 of InsP3R1). Here we present structures of the amino-terminal region (NT, residues 1–604) of rat InsP3R1 with (3.6 Å) and without (3.0 Å) InsP3 bound. The arrangement of the three NT domains, SD, IBC-β and IBC-α, identifies two discrete interfaces (α and β) between the IBC and SD. Similar interfaces occur between equivalent domains (A, B and C) in RyR1 (ref. 9). The orientations of the three domains when docked into a tetrameric structure of InsP3R and of the ABC domains docked into RyR are remarkably similar. The importance of the α-interface for activation of InsP3R and RyR is confirmed by mutagenesis and, for RyR, by disease-causing mutations. Binding of InsP3 causes partial closure of the clam-like IBC, disrupting the β-interface and pulling the SD towards the IBC. This reorients an exposed SD loop (‘hotspot’ (HS) loop) that is essential for InsP3R activation. The loop is conserved in RyR and includes mutations that are associated with malignant hyperthermia and central core disease. The HS loop interacts with an adjacent NT, suggesting that activation re-arranges inter-subunit interactions. The A domain of RyR functionally replaced the SD in full-length InsP3R, and an InsP3R in which its C-terminal transmembrane region was replaced by that from RyR1 was gated by InsP3 and blocked by ryanodine. Activation mechanisms are conserved between InsP3R and RyR. Allosteric modulation of two similar domain interfaces within an N-terminal subunit reorients the first domain (SD or A domain), allowing it, through interactions of the second domain of an adjacent subunit (IBC-β or B domain), to gate the pore.

Synthetic partial agonists reveal key steps in IP3 receptor activation.

Inositol 1,4,5-trisphosphate receptors (IP3R) are ubiquitous intracellular Ca2+ channels. IP3binding to the IP3-binding core (IBC) near the N-terminal initiates conformational changes that lead to opening of a pore. The mechanisms are unresolved. We synthesized 2-O-modified IP3 analogues that are partial agonists of IP3R. These are like IP3 in their interactions with the IBC, but they are less effective than IP3 in rearranging the relationship between the IBC and N-terminal suppressor domain (SD), and they open the channel at slower rates. IP3R with a mutation in the SD occupying a position similar to the 2-O-substituent of the partial agonists has a reduced open probability that is similar for full and partial agonists. Bulky or charged substituents from either the ligand or SD therefore block obligatory coupling of the IBC and SD. Analysis of ΔG for ligand binding shows that IP3 is recognised by the IBC and conformational changes then propagate entirely via the SD to the pore.

Counting Functional Inositol 1,4,5-Trisphosphate Receptors into the Plasma Membrane

Inositol 1,4,5-trisphosphate receptors (IP3R) within the endoplasmic reticulum mediate release of Ca2+ from intracellular stores. Different channels usually mediate Ca2+ entry across the plasma membrane. In B lymphocytes and a cell line derived from them (DT40 cells), very few functional IP3R(∼2/cell) are invariably expressed in the plasma membrane, where they mediate about half the Ca2+ entry evoked by activation of the B-cell receptor. We show that cells reliably count ∼2 functional IP3R into the plasma membrane even when their conductance and ability to bind IP3 are massively attenuated. We conclude that very small numbers of functional IP3R can be reliably counted into a specific membrane compartment in the absence of feedback signals from the active protein.

CaBP1, a neuronal Ca2+ sensor protein, inhibits inositol trisphosphate receptors by clamping intersubunit interactions

Calcium-binding protein 1 (CaBP1) is a neuron-specific member of the calmodulin superfamily that regulates several Ca2+ channels, including inositol 1,4,5-trisphosphate receptors (InsP3Rs). CaBP1 alone does not affect InsP3R activity, but it inhibits InsP3-evoked Ca2+ release by slowing the rate of InsP3R opening. The inhibition is enhanced by Ca2+ binding to both the InsP3R and CaBP1. CaBP1 binds via its C lobe to the cytosolic N-terminal region (NT; residues 1–604) of InsP3R1. NMR paramagnetic relaxation enhancement analysis demonstrates that a cluster of hydrophobic residues (V101, L104, and V162) within the C lobe of CaBP1 that are exposed after Ca2+ binding interact with a complementary cluster of hydrophobic residues (L302, I364, and L393) in the β-domain of the InsP3-binding core. These residues are essential for CaBP1 binding to the NT and for inhibition of InsP3R activity by CaBP1. Docking analyses and paramagnetic relaxation enhancement structural restraints suggest that CaBP1 forms an extended tetrameric turret attached by the tetrameric NT to the cytosolic vestibule of the InsP3R pore. InsP3 activates InsP3Rs by initiating conformational changes that lead to disruption of an intersubunit interaction between a “hot-spot” loop in the suppressor domain (residues 1–223) and the InsP3-binding core β-domain. Targeted cross-linking of residues that contribute to this interface show that InsP3 attenuates cross-linking, whereas CaBP1 promotes it. We conclude that CaBP1 inhibits InsP3R activity by restricting the intersubunit movements that initiate gating.

Activation of IP3 receptors by synthetic bisphosphate ligands

Ca(2+) release by d-myo-inositol 1,4,5-trisphosphate receptors (IP(3)Rs) is widely considered to require the vicinal 4,5-bisphosphate motif of IP(3), with P-5 and P-4 engaging the alpha and beta domains of the binding site; using synthesis and mutagenesis we show that the adenine of synthetic glyconucleotides, through an interaction with Arg504, can replace the interaction of either P-1 or P-5 with the alpha-domain producing, respectively, the most potent bisphosphate agonist yet synthesised and the first agonist of IP(3)R without a vicinal bisphosphate motif; this will stimulate new approaches to IP(3)R ligand design.

Binding of Inositol 1,4,5-trisphosphate (IP3) and Adenophostin A to the N-Terminal region of the IP3 Receptor: Thermodynamic Analysis Using Fluorescence Polarization with a Novel IP3 Receptor Ligand

Inositol 1,4,5-trisphosphate (IP3) receptors (IP3R) are intracellular Ca2+ channels. Their opening is initiated by binding of IP3 to the IP3-binding core (IBC; residues 224–604 of IP3R1) and transmitted to the pore via the suppressor domain (SD; residues 1–223). The major conformational changes leading to IP3R activation occur within the N terminus (NT; residues 1–604). We therefore developed a high-throughput fluorescence polarization (FP) assay using a newly synthesized analog of IP3, fluorescein isothiocyanate (FITC)-IP3, to examine the thermodynamics of IP3 and adenophostin A binding to the NT and IBC. Using both single-channel recording and the FP assay, we demonstrate that FITC-IP3 is a high-affinity partial agonist of the IP3R. Conventional [3H]IP3 and FP assays provide similar estimates of the KD for both IP3 and adenophostin A in cytosol-like medium at 4°C. They further establish that the isolated IBC retains the ability of full-length IP3R to bind adenophostin A with ∼10-fold greater affinity than IP3. By examining the reversible effects of temperature on ligand binding, we established that favorable entropy changes (TΔS) account for the greater affinities of both ligands for the IBC relative to the NT and for the greater affinity of adenophostin A relative to IP3. The two agonists differ more substantially in the relative contribution of ΔH and TΔS to binding to the IBC relative to the NT. This suggests that different initial binding events drive the IP3R on convergent pathways toward a similar open state.

Selective determinants of inositol 1,4,5-trisphosphate and adenophostin A interactions with type 1 inositol 1,4,5-trisphosphate receptors

BACKGROUND AND PURPOSE Adenophostin A (AdA) is a potent agonist of inositol 1,4,5‐trisphosphate receptors (IP3R). AdA shares with IP3 the essential features of all IP3R agonists, namely structures equivalent to the 4,5‐bisphosphate and 6‐hydroxyl of IP3, but the basis of its increased affinity is unclear. Hitherto, the 2′‐phosphate of AdA has been thought to provide a supra‐optimal mimic of the 1‐phosphate of IP3.

Adenophostins:high-affinity agonists of IP3 receptors

Publisher Summary Adenophostins are naturally occurring high-affinity agonists of inositol 1,4,5-trisphosphate receptors (IP3R). The three components of adenophostin—bisphosphorylated glucose, phosphorylated ribose, and adenine—are connected by potentially flexible linkages, and the central five-membered ribose ring is also intrinsically more flexible than a six-membered ring such as inositol or glucose. Many different conformations of adenophostin are therefore possible and the receptor-bound conformation is difficult to predict. Molecular modeling suggests that adenophostin can adopt extended conformations in which the adenosine holds the 20-phosphate close to the glucose ring in a position similar to that occupied by the 1-phosphate of IP3. Activation of an IP3R begins with IP3 binding to the IP3-binding core (IBC). The two domains of the IBC—α and β—form a clam-like structure, the inside of which includes many basic residues that coordinate the phosphate groups of IP3. Extensive analyses suggest that IP3R behave similarly whether activated by IP3 or adenophostin; however the latter typically binds with ∼10-fold greater affinity to all IP3R subtypes.

Subtype-selective regulation of IP3 receptors by thimerosal via cysteine residues within the IP3-binding core and suppressor domain

IP3R (IP3 [inositol 1,4,5-trisphosphate] receptors) and ryanodine receptors are the most widely expressed intracellular Ca2+ channels and both are regulated by thiol reagents. In DT40 cells stably expressing single subtypes of mammalian IP3R, low concentrations of thimerosal (also known as thiomersal), which oxidizes thiols to form a thiomercurylethyl complex, increased the sensitivity of IP3-evoked Ca2+ release via IP3R1 and IP3R2, but inhibited IP3R3. Activation of IP3R is initiated by IP3 binding to the IBC (IP3-binding core; residues 224–604) and proceeds via re-arrangement of an interface between the IBC and SD (suppressor domain; residues 1–223). Thimerosal (100 μM) stimulated IP3 binding to the isolated NT (N-terminal; residues 1–604) of IP3R1 and IP3R2, but not to that of IP3R3. Binding of a competitive antagonist (heparin) or partial agonist (dimeric-IP3) to NT1 was unaffected by thiomersal, suggesting that the effect of thimerosal is specifically related to IP3R activation. IP3 binding to NT1 in which all cysteine residues were replaced by alanine was insensitive to thimerosal, so too were NT1 in which cysteine residues were replaced in either the SD or IBC. This demonstrates that thimerosal interacts directly with cysteine in both the SD and IBC. Chimaeric proteins in which the SD of the IP3R was replaced by the structurally related A domain of a ryanodine receptor were functional, but thimerosal inhibited both IP3 binding to the chimaeric NT and IP3-evoked Ca2+ release from the chimaeric IP3R. This is the first systematic analysis of the effects of a thiol reagent on each IP3R subtype. We conclude that thimerosal selectively sensitizes IP3R1 and IP3R2 to IP3 by modifying cysteine residues within both the SD and IBC and thereby stabilizing an active conformation of the receptor.