Candice S. Klug

Methods and Applications of Site-Directed Spin Labeling EPR Spectroscopy

Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy has emerged as a well-established method that can provide specific information on the location and environment of an individual residue within large and complex protein structures. The SDSL technique involves introducing a cysteine residue at the site of interest and then covalently labeling with a sulfhydryl-specific spin label containing a stable free radical, which is used as the EPR-detectable probe. SDSL directly probes the local environment, structure, and proximity of individual residues, and is often greatly advantageous over techniques that give global information on protein structure and changes. SDSL can detect and follow changes in local structure due to intramolecular conformational changes or dynamic interactions with other proteins, peptides, or substrates. In addition, this technique can detect changes in distances between two sites and provide information on the depth of spin labels located within a membrane bilayer. EPR is neither limited by the size of the protein or peptide nor limited by the optical properties of the sample and has the unique ability to address and answer structure and dynamics questions that are not solvable solely by genetic or crystal structure analysis, making it highly complementary to other structural methods. In this chapter, we introduce the basic methods for using SDSL EPR spectroscopy in the study of the structure and dynamics of proteins and peptides and illustrate the practical applications of this method through specific examples in the literature.

Both maltose-binding protein and ATP are required for nucleotide-binding domain closure in the intact maltose ABC transporter

The maltose transporter MalFGK2 of Escherichia coli is a member of the ATP-binding cassette superfamily. A periplasmic maltose-binding protein (MBP) delivers maltose to MalFGK2 and stimulates its ATPase activity. Site-directed spin labeling EPR spectroscopy was used to study the opening and closing of the nucleotide-binding interface of MalFGK2 during the catalytic cycle. In the intact transporter, closure of the interface coincides not just with the binding of ATP, as seen with isolated nucleotide-binding domains, but requires both MBP and ATP, implying that MBP stimulates ATPase activity by promoting the closure of the nucleotide-binding interface. After ATP hydrolysis, with MgADP and MBP bound, the nucleotide-binding interface resides in a semi-open configuration distinct from the fully open configuration seen in the absence of any ligand. We propose that Pi release coincides with the reorientation of transmembrane helices to an inward-facing conformation and the final step of maltose translocation into the cell.

Structure and function of the visual arrestin oligomer

A distinguishing feature of rod arrestin is its ability to form oligomers at physiological concentrations. Using visible light scattering, we show that rod arrestin forms tetramers in a cooperative manner in solution. To investigate the structure of the tetramer, a nitroxide side chain (R1) was introduced at 18 different positions. The effects of R1 on oligomer formation, EPR spectra, and inter‐spin distance measurements all show that the structures of the solution and crystal tetramers are different. Inter‐subunit distance measurements revealed that only arrestin monomer binds to light‐activated phosphorhodopsin, whereas both monomer and tetramer bind microtubules, which may serve as a default arrestin partner in dark‐adapted photoreceptors. Thus, the tetramer likely serves as a ‘storage’ form of arrestin, increasing the arrestin‐binding capacity of microtubules while readily dissociating to supply active monomer when it is needed to quench rhodopsin signaling.

Few Residues within an Extensive Binding Interface Drive Receptor Interaction and Determine the Specificity of Arrestin Proteins

Arrestins bind active phosphorylated forms of G protein-coupled receptors, terminating G protein activation, orchestrating receptor trafficking, and redirecting signaling to alternative pathways. Visual arrestin-1 preferentially binds rhodopsin, whereas the two non-visual arrestins interact with hundreds of G protein-coupled receptor subtypes. Here we show that an extensive surface on the concave side of both arrestin-2 domains is involved in receptor binding. We also identified a small number of residues on the receptor binding surface of the N- and C-domains that largely determine the receptor specificity of arrestins. We show that alanine substitution of these residues blocks the binding of arrestin-1 to rhodopsin in vitro and of arrestin-2 and -3 to β2-adrenergic, M2 muscarinic cholinergic, and D2 dopamine receptors in intact cells, suggesting that these elements critically contribute to the energy of the interaction. Thus, in contrast to arrestin-1, where direct phosphate binding is crucial, the interaction of non-visual arrestins with their cognate receptors depends to a lesser extent on phosphate binding and more on the binding to non-phosphorylated receptor elements.

Visual Arrestin Binding to Microtubules Involves a Distinct Conformational Change

Recently we found that visual arrestin binds microtubules and that this interaction plays an important role in arrestin localization in photoreceptor cells. Here we use site-directed mutagenesis and spin labeling to explore the molecular mechanism of this novel regulatory interaction. The microtubule binding site maps to the concave sides of the two arrestin domains, overlapping with the rhodopsin binding site, which makes arrestin interactions with rhodopsin and microtubules mutually exclusive. Arrestin interaction with microtubules is enhanced by several “activating mutations” and involves multiple positive charges and hydrophobic elements. The comparable affinity of visual arrestin for microtubules and unpolymerized tubulin (KD > 40 μm and >65 μm, respectively) suggests that the arrestin binding site is largely localized on the individual αβ-dimer. The changes in the spin-spin interaction of a double-labeled arrestin indicate that the conformation of microtubule-bound arrestin differs from that of free arrestin in solution. In sharp contrast to rhodopsin, where tight binding requires an extended interdomain hinge, arrestin binding to microtubules is enhanced by deletions in this region, suggesting that in the process of microtubule binding the domains may move in the opposite direction. Thus, microtubule and rhodopsin binding induce different conformational changes in arrestin, suggesting that arrestin assumes three distinct conformations in the cell, likely with different functional properties.

Maltose-binding Protein Is Open in the Catalytic Transition State for ATP Hydrolysis during Maltose Transport

The maltose transport complex of Escherichia coli, a member of the ATP-binding cassette superfamily, mediates the high affinity uptake of maltose at the expense of ATP. The membrane-associated transporter consists of two transmembrane subunits, MalF and MalG, and two copies of the cytoplasmic ATP-binding cassette subunit, MalK. Maltose-binding protein (MBP), a soluble periplasmic protein, delivers maltose to the MalFGK2 transporter and stimulates hydrolysis by the transporter. Site-directed spin labeling electron paramagnetic resonance spectroscopy is used to monitor binding of MBP to MalFGK2 and conformational changes in MBP as it interacts with MalFGK2. Cysteine residues and spin labels have been introduced into the two lobes of MBP so that spin-spin interaction will report on ligand-induced closure of the protein (Hall, J. A., Thorgeirsson, T. E., Liu, J., Shin, Y. K., and Nikaido, H. (1997) J. Biol. Chem. 272, 17610–17614). At least two different modes of interaction between MBP and MalFGK2 were detected. Binding of MBP to MalFGK2 in the absence of ATP resulted in a decrease in motion of spin label at position 41 in the C-terminal domain of MBP. In a vanadate-trapped transition state intermediate, all free MBP became tightly bound to MalFGK2, spin label in both lobes became completely immobilized, and spin-spin interactions were lost, suggesting that MBP was in an open conformation. Binding of non-hydrolyzable MgATP analogs or ATP in the absence of Mg is sufficient to stabilize a complex of open MBP and MalFGK2. Taken together, these data suggest that closure of the MalK dimer interface coincides with opening of MBP and maltose release to the transporter.

A Model for the Solution Structure of the Rod Arrestin Tetramer

Visual rod arrestin has the ability to self-associate at physiological concentrations. We previously demonstrated that only monomeric arrestin can bind the receptor and that the arrestin tetramer in solution differs from that in the crystal. We employed the Rosetta docking software to generate molecular models of the physiologically relevant solution tetramer based on the monomeric arrestin crystal structure. The resulting models were filtered using the Rosetta energy function, experimental intersubunit distances measured with DEER spectroscopy, and intersubunit contact sites identified by mutagenesis and site-directed spin labeling. This resulted in a unique model for subsequent evaluation. The validity of the model is strongly supported by model-directed crosslinking and targeted mutagenesis that yields arrestin variants deficient in self-association. The structure of the solution tetramer explains its inability to bind rhodopsin and paves the way for experimental studies of the physiological role of rod arrestin self-association.

The Role of Arrestin α-Helix I in Receptor Binding

Arrestins rapidly bind phosphorylated activated forms of their cognate G protein-coupled receptors, thereby preventing G protein coupling and often switching signaling to other pathways. Amphipathic alpha-helix I (residues 100-111) has been implicated in receptor binding, but the mechanism of its action has not been determined yet. Here we show that several mutations in the helix itself and in adjacent hydrophobic residues in the body of the N-domain reduce arrestin1 binding to light-activated phosphorylated rhodopsin (P-Rh*). On the background of phosphorylation-independent mutants that bind with high affinity to both P-Rh* and light-activated unphosphorylated rhodopsin, these mutations reduce the stability of the arrestin complex with P-Rh*, but not with light-activated unphosphorylated rhodopsin. Using site-directed spin labeling, we found that the local structure around alpha-helix I changes upon binding to rhodopsin. However, the intramolecular distances between alpha-helix I and adjacent beta-strand I (or the rest of the N-domain), measured using double electron-electron resonance, do not change, ruling out relocation of the helix due to receptor binding. Collectively, these data demonstrate that alpha-helix I plays an indirect role in receptor binding, likely keeping beta-strand I, which carries several phosphate-binding residues, in a position favorable for its interaction with receptor-attached phosphates.

Site-Directed Spin Labeling of Membrane Proteins and Peptide-Membrane Interactions

In summary, SDSL is rapidly becoming a mature technique with which to approach questions related to structure-function relationships in proteins. This ESR method is uniquely suited to membrane proteins, and it can provide information on systems that are not amenable to modern NMR and crystallographic methods. SDSL methods are adept at defining local secondary structure (e.g., α-helix and β-strand) through nitroxide-scanning experiments and the sensitivity of the ESR spin label spectrum to molecular motion can give insights into both local and global conformational changes that accompany such events as ligand binding and denaturation. Continued improvements in methods for making distance measurements for both nitroxide: nitroxide and metal: nitroxide pairs will enhance the future application of the site-directed spin-labeling approach even further.

Site-Directed Spin Labeling Reveals Pentameric Ligand-Gated Ion Channel Gating Motions

Pentameric ligand-gated ion channels (pLGICs) are neurotransmitter-activated receptors that mediate fast synaptic transmission. In pLGICs, binding of agonist to the extracellular domain triggers a structural rearrangement that leads to the opening of an ion-conducting pore in the transmembrane domain and, in the continued presence of neurotransmitter, the channels desensitize (close). The flexible loops in each subunit that connect the extracellular binding domain (loops 2, 7, and 9) to the transmembrane channel domain (M2–M3 loop) are essential for coupling ligand binding to channel gating. Comparing the crystal structures of two bacterial pLGIC homologues, ELIC and the proton-activated GLIC, suggests channel gating is associated with rearrangements in these loops, but whether these motions accurately predict the motions in functional lipid-embedded pLGICs is unknown. Here, using site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy and functional GLIC channels reconstituted into liposomes, we examined if, and how far, the loops at the ECD/TMD gating interface move during proton-dependent gating transitions from the resting to desensitized state. Loop 9 moves ∼9 Å inward toward the channel lumen in response to proton-induced desensitization. Loop 9 motions were not observed when GLIC was in detergent micelles, suggesting detergent solubilization traps the protein in a nonactivatable state and lipids are required for functional gating transitions. Proton-induced desensitization immobilizes loop 2 with little change in position. Proton-induced motion of the M2–M3 loop was not observed, suggesting its conformation is nearly identical in closed and desensitized states. Our experimentally derived distance measurements of spin-labeled GLIC suggest ELIC is not a good model for the functional resting state of GLIC, and that the crystal structure of GLIC does not correspond to a desensitized state. These findings advance our understanding of the molecular mechanisms underlying pLGIC gating.