Calmodulin binding to recombinant myosin-1c and myosin-1c IQ peptides
© Gillespie and Cyr; licensee BioMed Central Ltd. 2002
Received: 22 August 2002
Accepted: 26 November 2002
Published: 26 November 2002
Bullfrog myosin-1c contains three previously recognized calmodulin-binding IQ domains (IQ1, IQ2, and IQ3) in its neck region; we identified a fourth IQ domain (IQ4), located immediately adjacent to IQ3. How calmodulin binds to these IQ domains is the subject of this report.
In the presence of EGTA, calmodulin bound to synthetic peptides corresponding to IQ1, IQ2, and IQ3 with Kd values of 2–4 μM at normal ionic strength; the interaction with an IQ4 peptide was much weaker. Ca2+ substantially weakened the calmodulin-peptide affinity for all of the IQ peptides except IQ3. To reveal how calmodulin bound to the linearly arranged IQ domains of the myosin-1c neck, we used hydrodynamic measurements to determine the stoichiometry of complexes of calmodulin and myosin-1c. Purified myosin-1c and T701-Myo1c (a myosin-1c fragment with all four IQ domains and the C-terminal tail) each bound 2–3 calmodulin molecules. At a physiologically relevant temperature (25°C) and under low-Ca2+ conditions, T701-Myo1c bound two calmodulins in the absence and three calmodulins in the presence of 5 μM free calmodulin. Ca2+ dissociated nearly all calmodulins from T701-Myo1c at 25°C; one calmodulin was retained if 5 μM free calmodulin was present.
We inferred from these data that at 25°C and normal cellular concentrations of calmodulin, calmodulin is bound to IQ1, IQ2, and IQ3 of myosin-1c when Ca2+ is low. The calmodulin bound to one of these IQ domains, probably IQ2, is only weakly associated. Upon Ca2+ elevation, all calmodulin except that bound to IQ3 should dissociate.
Unconventional myosins contain from one to several IQ domains, which are calmodulin-binding motifs that adhere to the general consensus sequence IQX3RGX3R . Calmodulin, which can bind up to four Ca2+ ions, generally binds IQ domains in the Ca2+-free conformation; interaction of Ca2+-bound calmodulin to other proteins occurs through alternative binding motifs .
Myo1c contains three readily recognized IQ motifs of 23 amino acids each (Fig. 1C; refs. [10, 15–18]). Purified Myo1c apparently includes 2–3 calmodulins per Myo1c heavy chain [19–21]; calmodulin supplementation can increase the stoichiometry to as many as 4 calmodulins per Myo1c . Unfortunately, the lack of appropriate quantitation standards for the Myo1c heavy chain in those experiments limits the reliability of these values.
How Ca2+ and calmodulin regulate Myo1c or indeed any myosin-I is unclear. Although Ca2+ increases ATPase activity of most myosin-I isozymes, in vitro motility is usually blocked under identical conditions . Ca2+ dissociates one or more calmodulins from the myosin-calmodulin complex, which apparently elevates ATPase activity and inhibits motility . In conventional myosin, light chains related to calmodulin appear to be essential for stabilization of the myosin lever arm , a domain that is vital for efficient conversion of chemical energy into mechanical work . Calmodulin probably plays a similar lever-arm stabilizing role for Myo1c; Ca2+-induced calmodulin release would reverse the stabilization and inhibit motility.
To better understand the regulation of Myo1c activity by calmodulin, we sought to more accurately determine how calmodulin binds to Myo1c by measuring the Ca2+-dependence of calmodulin binding to individual Myo1c IQ peptides. In addition, to examine the consequences of calmodulin binding to adjacent IQ domains, we measured hydrodynamic properties of recombinant Myo1c-calmodulin complexes, under differing conditions of Ca2+, calmodulin, and temperature. These measurements allowed us to determine the molecular mass and hence stoichiometry of the Myo1c complex. Our results indicate that IQ1, IQ2, and IQ3 have calmodulin bound when the concentration of Ca2+ is low, and that increased Ca2+ induces release of calmodulin from IQ1 and IQ2.
Sequence analysis of IQ domains
Examination of the primary sequence of the bullfrog Myo1c neck region reveals an exact repeat of five amino acids located both in the IQ3 region (YRNQP; residues 761–765) and at residues 786–790. Alignment of the residues surrounding the repeat revealed reasonable homology with the three known IQ domains, with particular similarity to IQ3, suggesting that this region may be a fourth IQ domain (Fig. 1C). Although the pair of amino acids (LM; residues 782 and 783) that align with the RG of the IQ consensus motif are not conserved, the first pair of amino acids (IR; residues 777 and 778) that align with the consensus IQ adhere to the consensus better than those of IQ3. Because of the sequence similarity to IQ3 and because this peptide binds calmodulin (albeit weakly; see below), we refer to this domain as IQ4.
IQ – Alexa-calmodulin interaction on plastic plates
Substantial amounts of Alexa-calmodulin bound to wells derivatized with IQ1, IQ2, and IQ3; by contrast, relatively little bound to IQ4-coated wells under these conditions (Fig. 2A). As has been noted for the neuromodulin IQ domain , increasing the KCl concentration reduced binding to each IQ peptide. Although the data shown in Fig. 2A were obtained at room temperature, we saw a similar rank order of binding – albeit with lower total Alexa-calmodulin bound – at 4°C (data not shown).
To confirm the approximate binding strength reported by this assay, we used free IQ peptides to prevent Alexa-calmodulin binding to an IQ3-derivatized plate. Because the IQ peptides strongly quenched Alexa-calmodulin fluorescence when bound, we corrected fluorescence measurements using an identical assay in an underivatized plate. Although this quenching correction introduced substantial scatter into the data, we found that the apparent affinities for binding of peptides to Alexa-calmodulin followed the order IQ3 > IQ1 ≈ IQ2 > IQ4 (Fig. 2B).
IQ – calmodulin interaction by quenching of Alexa-calmodulin fluorescence
Interaction of Myo1c IQ peptides with Alexa-calmodulin
7.3 ± 1.2 μM
0.14 ± 0.02
9.2 ± 1.0 μM
0.39 ± 0.07
9.3 ± 1.4 μM
0.21 ± 0.05
6.4 ± 1.4 μM
0.50 ± 0.05
2.0 ± 0.4 μM
0.23 ± 0.03
1.3 ± 0.4 μM
0.47 ± 0.03
45 ± 5 μM
0.36 ± 0.10
37 ± 19 μM
0.71 ± 0.02
IQ – calmodulin interaction under stoichiometric-titration conditions
To determine the affinities of the Myo1c IQ peptides for unlabeled calmodulin, we used Alexa-calmodulin as a reporter (Alexa-calmodulin : unlabeled calmodulin ratio of 1:100) in our binding studies. This approach assumes that Alexa-calmodulin is functionally equivalent to unlabeled calmodulin.
These experimental conditions resembled a stoichiometric titration, where the total concentration of calmodulin was higher than the Kd values for IQ1, IQ2, and IQ3. Under true stoichiometric-titration conditions (fixed concentration of receptor at 100-fold or more than the Kd, varying the ligand concentration up to and beyond the receptor concentration), almost all of the added IQ peptide would bind tightly to calmodulin and linearly decrease the fluorescence; at the point where the IQ-peptide concentration exceeds the calmodulin concentration multiplied by the peptide:calmodulin stoichiometry (m), a plateau in the fluorescence intensity would be reached. Because the relatively weak affinities observed here make such true stoichiometric titration impractical, we used an intermediate concentration of calmodulin (50 μM, ~10-fold larger than Kd) and used equation (7) to describe the equilibrium precisely. This approach allowed us to determine both m and Kd in the same experiment.
Interaction of Myo1c IQ peptides with unlabeled calmodulin
4.0 ± 0.8 μM
56 ± 13 μM
4.2 ± 2.0 μM
70 ± 15 μM
1.7 ± 0.7 μM
3.2 ± 1.1 μM
In the presence of Ca2+, IQ3 also bound to calmodulin with a stoichiometry of 1:1 (Fig. 5). The fits to m = 1 and 2 were equally good for IQ1 and IQ2 in the presence of Ca2+, signifying the inability for this analysis to determine precise binding stoichiometry of IQ1 and IQ2 under these conditions. In addition, these data indicate that the apparent affinities of IQ1 and IQ2 for unlabeled calmodulin were substantially weakened by Ca2+ (Table 2), unlike results with Alexa-calmodulin alone (Table 1). Because the assumption that affinities of Alexa-calmodulin and unlabeled calmodulin for IQ peptides are identical was violated for IQ1 and IQ2, the actual affinities of these IQ peptides for unlabeled calmodulin may be even weaker than those reported in Table 2. By contrast, Ca2+ had only a very modest effect on IQ3 affinity for unlabeled calmodulin.
Binding of IQ4 to unlabeled calmodulin was distinct from that of the other IQ peptides. The data with IQ4 were best fit with a Hill equation (equation 4), with a Hill coefficient of greater than 2 (Fig. 5, thick solid lines), suggesting that binding of two peptides per calmodulin may be required for the fluorescence change. The apparent affinities (~100 μM) were similar to the concentration of calmodulin (50 μM), however, indicating that the apparent affinities did not accurately reflect Kd values. These results with a mixture of unlabeled and Alexa-calmodulin were different from those with Alexa-calmodulin alone, where IQ4 Hill coefficients were close to 1 (data not shown). Nevertheless, these data show that unlabeled calmodulin can bind to IQ4, albeit with weak affinity and uncertain stoichiometry.
Hydrodynamic analysis of full-length Myo1c
Hydrodynamic analysis of full-length Myo1c
100 μM EGTA
25 μM CaCl2
6.70 ± 0.07 S (n = 5)
6.90 ± 0.08 S (n = 4)
6.28 ± 0.21 S (n = 8)
6.06 ± 0.08 nm (n = 7)
6.07 ± 0.05 nm (n = 4)
5.78 ± 0.11 nm (n = 5)
168 ± 4 kD
4°C: 173 ± 3 kD
150 ± 7 kD
1.7 ± 0.1
1.7 ± 0.1
1.7 ± 0.1
Calmodulins per molecule
2.5 ± 0.2
2.9 ± 0.2
1.5 ± 0.4
To calculate the molecular mass of Myo1c-calmodulin complexes, we applied the modified Svedberg equation, which relates mass to the diffusion constant (calculated here from Stokes radius) and the sedimentation coefficient . The partial specific volume of each protein complex was determined using the amino-acid composition of the constituent proteins (Table 3; ref. ). Although the uncertainty in calmodulin stoichiometry leads to ambiguity in this calculation, the calculated partial specific volumes were so close (e.g., 0.734 for one and 0.731 for three calmodulins per Myo1c complex) that the precise value did not significantly affect the final molecular-mass value.
Full-length Myo1c bound ~3 calmodulins per Myo1c at 4°C in the presence of EGTA or CaCl2 (Table 3). One of the bound calmodulins was only weakly associated, as elevation of the temperature to 25°C induced the release of 1 mole of calmodulin in the presence of EGTA. When Ca2+ was elevated to 25 μM at 25°C, however, we could not detect substantial full-length Myo1c in solution after sucrose-gradient centrifugation or gel filtration, suggesting that the protein had aggregated.
Hydrodynamic analysis of T701-Myo1c
Because the size of full-length Myo1c (125 kD, including purification and detection tags) is much larger than calmodulin (16.7 kD), we improved our ability to determine stoichiometry from molecular mass by examining a smaller (45 kD) neck-tail recombinant fragment of Myo1c. This construct, T701-Myo1c, contained amino acids 701–1028 of bullfrog Myo1c, including all four IQ domains, the entire C-terminal tail, and N-terminal purification and epitope tags (Fig. 1A,1B).
Hydrodynamic analysis of T701-Myo1c.
100 μM EGTA
25 μM CaCl2
4.64 ± 0.11 S (n = 4)
4.27 ± 0.21 S (n = 3)
3.83 ± 0.06 S (n = 11)
3.13 ± 0.30 S (n = 7)
4.52 ± 0.06 nm (n = 4)
4.19 ± 0.11 nm (n = 6)
4.74 ± 0.13 nm (n = 6)
3.78 ± 0.07 nm (n = 6)
87 ± 5 kD
74 ± 6 kD
75 ± 3 kD
49 ± 5 kD
1.5 ± 0.1
1.5 ± 0.1
1.7 ± 0.1
1.6 ± 0.2
Calmodulins per molecule
2.5 ± 0.1
1.8 ± 0.2
1.8 ± 0.2
0.3 ± 0.3
We could not prevent the release of calmodulin at 25°C by saturating T701-Myo1c with excess calmodulin immediately prior to centrifugation (preloading). In EGTA, the sedimentation coefficient of calmodulin-preloaded T701-Myo1c measured at 25°C (3.85 ± 0.07 S; n = 2) was nearly identical to that measured without preloading (3.83 S; Table 4). Likewise, the sedimentation coefficient of calmodulin-preloaded T701-Myo1c measured at 25°C and in 25 μM CaCl2 (2.80 ± 0.42 S; n = 2) was similar to that measured without preloading (3.13 S; Table 4).
Hydrodynamic analysis of T701-Myo1c in the presence of 5 μM calmodulin
100 μM EGTA
25 μM CaCl2
4.68 ± 0.11 S (n = 2)
3.95 ± 0.33 S (n = 4)
92 ± 4 kD
62 ± 12 kD
Calmodulins per molecule
2.8 ± 0.2
1.0 ± 0.7
Myo1c-calmodulin stoichiometry by gel scanning
Calmodulin interaction with individual Myo1c IQ domains
To examine how calmodulin binds to the Myo1c IQ sites, we developed two binding assays using a commercially available fluorescent calmodulin and individual IQ peptides. In one assay, we covalently attached peptides to plastic plates, then measured the amount of fluorescent calmodulin that remained unbound after incubation with the peptide-derivatized plate. This assay was simple and fast, and allowed us to measure binding under a wide variety of conditions. In our second assay, we exploited the empirical observation that the Alexa-calmodulin fluorescence intensity is quenched by binding of IQ peptides. As in other assays with fluorescently labeled calmodulins (e.g., ref. ), binding of the peptides to Alexa-calmodulin did not perfectly mimic binding to unlabeled calmodulin. For example, Alexa-calmodulin bound IQ peptides more strongly in the presence of Ca2+ than did unlabeled calmodulin. Moreover, excess unlabeled calmodulin could not fully reverse the quenching of Alexa-calmodulin fluorescence induced by IQ peptides, suggesting that IQ peptides could bind to Alexa-calmodulin at two sites, including one where unlabeled calmodulin could not bind. Indeed, binding of IQ peptides to both sites on a single fluorescent calmodulin could account for Hill coefficients of >1 seen in some experiments (e.g., Figs. 3B and 4). Nevertheless, these discrepancies should not prevent use of Alexa-calmodulin for measuring interaction with calmodulin's targets, particularly if the interaction with unlabeled calmodulin is compared to the interaction with Alexa-calmodulin.
Calmodulin bound to peptides corresponding to each of the four Myo1c IQ domains, although with differing affinity and Ca2+ sensitivity. Affinities for calmodulin binding to IQ1 and IQ2 were relatively modest (Kd values of ~5 μM). As with other IQ domains , Ca2+ weakened the affinity of calmodulin for IQ1 and IQ2 by more than 10-fold.
By contrast, calmodulin binding to IQ3 was slightly stronger and was affected much less by Ca2+. Because calmodulin binds strongly to classic IQ domains only in the absence of Ca2+ [14, 32], its strong binding to IQ3 in the presence of Ca2+ suggests the participation of an additional Ca2+-requiring binding motif. Two common calmodulin-binding motifs, called 1-8-14 and 1-5-10 for the pattern of hydrophobic amino-acid residues, require Ca2+ for calmodulin binding . IQ3 has two nearly perfect 1-5-10 domains that are at +2 net charge instead of the minimum +3 in the consensus . In addition, IQ3 has a 1-8-14 motif with a proline residue at position 14 instead of phenylalanine, isoleucine, leucine, valine, or tryptophan. Because most proteins that bind calmodulin through the 1-8-14 and 1-5-10 motifs do so strongly, the relatively modest affinity of IQ3 for calmodulin in the presence of Ca2+ suggests that calmodulin binds through one of these imperfect motifs located within this IQ domain. To interact with an alternate set of residues, Ca2+-calmodulin must adopt a new conformation. A similar Ca2+-dependent rearrangement was predicted for the complex of calmodulin and the first IQ domain of myosin-1a (brush-border myosin I) .
In support of this view, we observed evidence for Ca2+-dependent conformational changes in calmodulin while bound to IQ peptides. When Alexa-calmodulin was bound to Myo1c IQ peptides, its fluorescence was higher in the presence of Ca2+ than in its absence, suggesting that that Ca2+-bound Alexa-calmodulin binds to the IQ peptides in a different conformation than does Ca2+-free Alexa-calmodulin. For example, in the absence of Ca2+, Alexa-calmodulin may bind to IQ peptides in a more compact conformation, quenching fluorescence by burying dye moieties in a less polar environment. Although the Ca2+-induced conformational change could be a property of Alexa-calmodulin rather than calmodulin itself, the Ca2+-dependent changes in affinity of calmodulin for IQ1 and IQ2 (Table 2) and calmodulin's likely shift to a new binding site on IQ3 suggests that the conformational change is probably also a property of authentic calmodulin.
Calmodulin also bound to a newly identified domain, IQ4. Because the affinity of calmodulin for IQ4 is very weak, calmodulin should only occupy IQ4 in subcellular locations with a low Ca2+ concentration and a high level of free calmodulin. For example, a small population of Myo1c molecules with calmodulin bound to IQ4 should be present in the stereocilia of inner-ear hair cells, which contain ~35 μM free calmodulin . Although most tissues contain less free calmodulin , concentrations in other individual organelles can reach the millimolar range . On the other hand, the weak affinity of this IQ domain for calmodulin suggests that IQ4 may play another role, such as interacting with another protein.
Calmodulin interaction with Myo1c
The binding affinities of calmodulin for the individual IQ peptides do not reflect exactly the affinities of calmodulin for the IQ domains within Myo1c. For example, despite micromolar Kd values for calmodulin-IQ peptide interactions, calmodulin remains bound to Myo1c during long gel-filtration or centrifugation experiments, even at nanomolar Myo1c concentrations (Fig. 6). This result suggests that calmodulin binds to some of Myo1c's four tandem IQ domains substantially more strongly than to the individual peptides. For example, other regions of Myo1c could constrain the IQ domains in conformations that are substantially more (or less) favorable for calmodulin binding than the population of conformations adopted by a soluble IQ peptide. Moreover, calmodulin binding to Myo1c could be influenced by interactions with adjacent calmodulin molecules or to the Myo1c head or tail domains.
To examine calmodulin binding to IQ domains in Myo1c, we determined the molecular mass (and hence calmodulin:Myo1c stoichiometry) and shape of Myo1c under the appropriate conditions of temperature and Ca2+. Although analytical ultracentrifugation is more commonly used to measure molecular size of protein-protein complexes , we instead used classic hydrodynamic methods of velocity sedimentation on sucrose gradients to obtain sedimentation coefficients and gel filtration to obtain Stokes' radius. One advantage of this approach was that by detecting Myo1c using a sensitive ELISA method, we were able to use very low concentrations of Myo1c. Furthermore, we were able to carry out sedimentation in the presence of a high concentration of calmodulin, a manipulation that prevents Myo1c detection in a standard analytical ultracentrifugation experiment. A disadvantage of this approach was the need for high concentrations of sucrose, which in rare conditions can substantially affect the hydrodynamic properties of a protein ; nevertheless, changes in Myo1c size were observed both in velocity sedimentation (in the presence of sucrose) and in gel filtration (in its absence). Another disadvantage of our classic approach to molecular-mass determination was that the gel filtration and velocity sedimentations were done on different time scales (~1 hour vs. 15–18 hours). If calmodulin slowly dissociated during the analysis (which in both assays diluted Myo1c well below 1 μM), the degree of dissociation would be larger in the velocity sedimentation experiments than in the gel filtration experiments. Nevertheless, our approach was validated by the demonstration that the number of calmodulins per T701-Myo1c was identical in hydrodynamic and gel-scanning experiments, at least in EGTA at 4°C.
Because T701-Myo1c mimicked properties of the full-length protein (except under low-temperature, high-Ca2+ conditions), we exploited the neck-tail construct for a more detailed analysis of calmodulin binding. As expected from the large Ca2+-dependent weakening of calmodulin affinity for IQ1 and IQ2 (Fig. 5; Table 2), Ca2+ decreased the number of calmodulins bound to T701-Myo1c at high ionic strength. When Ca2+ was low at 25°C, each T701-Myo1c had about two bound calmodulins, with a third bound if the calmodulin concentration reached 5 μM. At this calmodulin concentration, IQ domains 1, 2, and 3 are likely occupied by calmodulin. When Ca2+ is high at 25°C, all but one calmodulin dissociated from T701-Myo1c in the presence of 5 μM free calmodulin. The strong affinity of IQ3 for Ca2+-calmodulin suggests that the remaining calmodulin was bound to this IQ domain.
How many calmodulins are bound to Myo1c in the cell at increased Ca2+ concentrations? The elevated ionic strength used for the hydrodynamic analysis probably weakened the affinity of the calmodulin for IQ3 (Fig. 2A), requiring 5 μM free calmodulin to maintain occupancy of that site. We therefore infer that at a physiologically significant temperature and at a cellular ionic strength, Ca2+ triggers release of calmodulins from IQ1 and IQ2 from T701-Myo1c, leaving only IQ3 occupied. Although these results contrast with those reported for mammalian Myo1c, where only one of three calmodulins is released by Ca2+ [19, 38], our T701 construct lacks Myo1c's motor domain. It is entirely plausible that even in the presence of Ca2+, calmodulin remains bound to IQ1, albeit in a different conformation and dependent on interactions with the myosin head. Our results therefore suggest that Ca2+ either induces the release of calmodulin from IQ1 or causes it to change its interaction with Myo1c substantially.
Of the three calmodulins bound to Myo1c, one of these binds relatively weakly at 25°C, even in EGTA. To which IQ domain does this weakly bound light chain bind? Although calmodulin binds to IQs 1–3 with approximately the same strength in the presence of EGTA, we suggest that the readily released calmodulin is likely to be that bound to IQ2. To bind three calmodulins, IQs 1–3, each of which are only 23 amino acids long, must be arranged without kinks ; this arrangement may produce unfavorable strain on each of the calmodulin molecules. Release of calmodulin from IQ2 would relieve all of that strain; release from IQs 1 or 3 would not. Strain relief also may accelerate calmodulin release in the presence of Ca2+; because Ca2+ apparently rearranges the three-dimensional interaction of calmodulin with IQ3, binding of an adjacent calmodulin – on IQ2 – might be destabilized even more .
Despite the loss of calmodulin from T701-Myo1c induced by elevation of the temperature from 4°C to 25°C, the frictional ratio (a measure of the protein's asymmetry) increased (Table 4). The neck-tail region of Myo1c thus appears to adopt a compact structure at 4°C, becoming more extended at 25°C. Less calmodulin may be released at lower temperatures because the Myo1c tail may bind to and stabilize calmodulin's interaction with the Myo1c neck.
Implications for Myo1c activity
The Ca2+-dependent change in interaction of calmodulin with IQ1, the IQ domain closest to the motor domain, has important implications for Myo1c mechanochemical function. Although Ca2+ increases Myo1c ATPase activity, the ion completely halts in vitro motility . Ca2+-dependent changes in conformation may prevent amplification of a small converter-domain movement into a large motor step. In the presence of an external force, as is seen by Myo1c during an excitatory mechanical stimulus in a hair cell , Ca2+ (which enters the cell through open transduction channels), should permit Myo1c to go through its ATPase cycle, binding and unbinding from actin, but the altered interaction of calmodulin and IQ1 may prevent force production by the motor. We predict that Ca2+ will decrease the stiffness of a Myo1c-actin interaction, preventing coupling of the energy released by ATP hydrolysis to the swing of the neck . This behavior will assist Myo1c in its role of adaptation in hair cells, where the motor reduces force applied to the hair cell's transduction channel.
A limitation of our experiments is the restriction of Myo1c binding to a single type of light chain, calmodulin. Other light chains can interact with IQ domains, including essential light chain isoforms  and calmodulin-like protein . Although purified bovine adrenal Myo1c does not appear to have alternative associated light chains , we can not rule out the possibility that other light chains bind in a cellular context. Nevertheless, purified recombinant full-length Myo1c associated with calmodulin light chains exhibited actin-activated ATPase activity and motility in vitro , indicating that calmodulin can function as a Myo1c light chain.
That Myo1c does not bind calmodulin tightly is, at first glance, surprising. Weak calmodulin binding may, however, permit access of IQ domains to intracellular Myo1c receptors. Accordingly, we have found that a Myo1c fragment containing only IQs 1–3, partially complexed with calmodulin, binds avidly to hair-cell receptors; excess calmodulin blocks this interaction, probably by binding to an unoccupied IQ site on the Myo1c fragment . IQ2 is highly conserved between species, leading us to propose that hair-cell receptors interact through this region . Because Myo1c-interacting proteins in hair cells and elsewhere may interact through IQ domains, regulation of calmodulin binding to Myo1c – for example, by Ca2+ – likely affects coupling of the motor protein to its cargo.
Under low Ca2+ conditions and normal ionic strength, calmodulin binds moderately tightly to three Myo1c IQ domains, IQ1, IQ2, and IQ3. IQ4 will only be occupied when the calmodulin concentration is very high. When linearly arranged in the Myo1c molecule, at least one calmodulin (most likely that bound to IQ2) is bound less tightly, probably due to steric constraints. Upon binding Ca2+, calmodulin bound to IQ2 dissociates; that bound to IQ1 either dissociates or changes its conformation sufficiently that chemomechanical coupling cannot ensue.
Peptide – calmodulin interaction on plates
Bullfrog Myo1c IQ peptides were synthesized (Genemed Synthesis, South San Francisco, CA) with N-terminal cysteine residues: IQ1 (residues 698–720), CRKHSIATFLQARWRGYHQRQKFL; IQ2 (721–743), CHMKHSAVEIQSWWRGTIGRRKAA; IQ3 (744–766), CKRKWAVDVVRRFIKGFIYRNQPR; and IQ4 (767–791; native cysteine at residue 767), CTENEYFLDYIRYSFLMTLYRNQPK. Peptide concentrations were measured by determining optical density at 280 nm, using calculated molar extinction coefficients of 7090 (IQ1), 11500 (IQ2), 7090 (IQ3), and 5240 M-1 cm -1 (IQ4). We also synthesized a negative-control peptide ("PVP") corresponding to amino acids 792–816 of frog Myo1c (SVLDKSWPVPPPSLREASELLREMC; native C816) and a positive control IQ-peptide ("NM") corresponding to amino acids 29–52 of bovine neuromodulin with an added C-terminal cysteine (KAHKAATKIQASFRGHITRKKLKC) .
For measuring interaction of calmodulin with peptides conjugated to plastic plates, we incubated 10 μM peptide in phosphate-buffered saline (PBS; 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO4, 1.4 mM KH2PO4, pH 7.4) overnight at room temperature in a maleimide-derivatized 96-well plate (Pierce, Rockford, IL). Peptide was present in large excess over free binding sites (25–50 pmol) on the plates. To remove unconjugated peptides, plates were washed with PBS; unreacted sites were saturated by incubating with 10 μg/ml cysteine for 1 hour. We then incubated the peptide-conjugated plates with 50 nM Alexa Fluor 488 calmodulin (Alexa-calmodulin; Molecular Probes, Eugene, OR) in 100 μl of a solution that contained 150 or 400 mM KCl, 1 mM MgCl2, 100 μM ethylene glycol-bis(β-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA) or 25 μM CaCl2, and 15 mM 2-[4-(2-hydroxyethyl)-1-piperazinyl] ethanesulfonic acid (HEPES) at pH 7.5. According to the manufacturer, Alexa-calmodulin had two dye moieties per calmodulin molecule; the modified residues were likely Lys-75 and Lys-94, the most reactive of calmodulin's lysine residues . After incubation for 2 hours at room temperature, we transferred 50 μl of the solution to another 96-well plate and measured fluorescence (excitation 485 nm; emission, 520 nm) using a BMG Labtechnologies Fluorostar 403 microplate fluorometer (Durham, NC). Under the assay conditions, the inner-filter effect (absorption of excitation or emission photons by the sample) was negligible. From this measurement, we calculated the amount of calmodulin bound to the conjugated peptides. In some experiments, we also included 0.1–100 μM unconjugated IQ peptide; in that case, we carried out duplicate control reactions in underivatized 96-well plates to correct for fluorescence quenching exerted by IQ peptides.
Peptide – calmodulin interaction by fluorescence quench
We used empirically observed changes in the fluorescence intensity of Alexa-calmodulin, large in magnitude, to measure binding of IQ peptides to calmodulin. Peptides and 50–500 nM Alexa-calmodulin were mixed in 96- or 384-well microtiter plates with 150 mM KCl, 1 mM MgCl2, 100 μM EGTA or 25 μM CaCl2, 0.5 mg/ml bovine serum albumin, and 15 mM HEPES at pH 7.5; in some experiments we added 50–75 μM bovine-brain calmodulin. Total volume varied from 10 μl (384-well plates) to 100 μl (96-well plates). After 1–2 hours at room temperature, fluorescence was read directly.
When IQ peptides bound to Alexa-calmodulin, the fluorescence intensity was reduced as the quantum yield decreased (fluorescence quenching). We assumed that two fluorescent species were present, Alexa-calmodulin and IQ peptide-bound Alexa-calmodulin, and that the fluorescence intensity (I) was a linear combination of the fluorescence of the two species:
I = fCaM ICaM +fCaM-IQ ICaM-IQ (1)
where fCaM and fCaM-IQ are the mole fractions of the two components and ICaM and ICaM-IQ are their fluorescence intensities. Because the quantum yield of Alexa-calmodulin is reduced when IQ peptides bind, ICaM-IQ <ICaM. The fraction of peptide bound is:
To calculate Kd, we fit the data with a bimolecular-binding isotherm:
where [IQ] was the free IQ-peptide concentration added. Because we used concentrations of Alexa-calmodulin in our experiments that were much less than the Kd, we approximated [IQ] using the total IQ peptide concentration.
In other cases, however, the binding data were fit better with a modified Hill equation:
where h is the Hill coefficient. A value for h greater than one suggests the fluorescence change arose from a more complex equilibrium than just one peptide binding per calmodulin.
To carry out stoichiometric-titration experiments (calmodulin concentration greater than the Kd), we used a low concentration of Alexa-calmodulin as a reporter and added an excess of unlabeled calmodulin. For simplicity in analysis, we assumed that Alexa-calmodulin behaved identically to calmodulin, and thus this calmodulin mixture was equivalent to a decrease in specific activity (fluorescence quench) of calmodulin. We then solved the bimolecular-binding isotherm to enable us to plot the total ligand concentration (T) added versus fluorescence intensity (I). The concentration of peptide bound (B) was:
B = m [CaM] fCaM-IQ (5)
where m is the number of binding sites per calmodulin and [CaM] is the fixed concentration of calmodulin. The free concentration of IQ peptide (F) was T – B. We substituted the expression for B in equations (2) and (5) into:
Note that n [CaM] is the maximum amount of IQ peptide that can bind (Bmax). We then solved equation (6) for fluorescence intensity using Mathematica 4.0 (Wolfram Research, Champaign, IL):
For m = 1, the only free parameters were Kd and ICaM-IQ. We were forced to include ICaM-IQ as one of the fit parameters; the limited solubility of IQ peptides in the assay solution prevented us from using very high peptide concentrations that would independently establish its value by producing a plateau in the T vs. I plot. We then used the value of ICaM-IQ determined from the m = 1 fit and refit the data for m = 2, using Kd as the only free parameter. To judge the stoichiometry, we compared by eye the effectiveness of the fit under the two conditions.
Using methods described previously for rat Myo1c , we cloned full-length bullfrog Myo1c into the baculovirus transfer vector pBlueBacHis2B (Invitrogen, Carlsbad, CA), introducing an N-terminal hexahistidine tag for purification and a DLYDDDDK epitope tag for antibody detection. Baculoviruses were generated, purified, and characterized using standard techniques [43, 45].
Protein expression and purification
Bullfrog Myo1c or its neck-tail fragment (Fig. 1A,1B) were co-expressed with Xenopus calmodulin in Sf9 cells using methods described previously . Xenopus calmodulin is identical to all other sequenced vertebrate calmodulins, including bovine calmodulin ; we presume that bullfrog calmodulin is also identical. Recombinant proteins were partially purified by centrifugation of an Sf9-cell extract and Ni2+-nitrilotriacetic acid chromatography ; further purification was achieved using gel filtration at 4°C on a 25-ml Superdex 200 HR 10/30 column run at 0.5 ml/min in 400 mM KCl, 1 mM MgCl2, 100 μM EGTA, 15 mM HEPES pH 7.5 with an AKTA-FPLC system (Amersham Pharmacia Biotech, Piscataway, NJ). The concentration of each purified recombinant protein was calculated by measuring absorption at 280 nm and using extinction coefficients calculated from the appropriate aminoacid sequence using the ExPASy ProtParam tool http://www.expasy.ch/tools/protparam.html, assuming 2.5 calmodulins per full-length Myo1c (53,619 M-1cm-1) or T701 fragment (65,565 M-1cm-1). We typically obtained 100–300 μg of recombinant protein from ~109 Sf9 cells. Full-length Myo1c had NH4Cl-activated ATPase activity  of 1.8 ± 0.7 s-1, with a Km for ATP of 0.3 ± 0.1 mM. Actin activated basal Mg2+-ATPase activity ~15-fold. Calmodulin was purified from bovine brain (Pel-Freez, Rogers, AR) by isoelectric precipitation and phenyl-agarose (Sigma, St. Louis, MO) chromatography ; its concentration was measured assuming a molar extinction coefficient of 3030 M-1 cm -1 at 276 nm .
Stokes radii of Myo1c and T701-Myo1c were measured using gel filtration on a 25-ml Superdex 200 HR 10/30 column at either 4°C or room temperature (23–25°C). Columns were run at 0.5 ml/min in 400 mM KCl, 1 mM MgCl2, 15 mM HEPES pH 7.5, and either 100 μM EGTA or 25 μM CaCl2; 5–20 μg of recombinant protein was applied to the column. Columns were calibrated using 20–200 μg each of globular proteins of known Stokes radii (thyroglobulin, 8.50 nm; ferritin, 6.10 nm; catalase, 5.22 nm; aldolase, 4.81 nm; bovine serum albumin, 3.55 nm; ovalbumin, 3.05 nm; chymotrypsinogen, 2.09 nm; and RNase A, 1.64 nm; all obtained from Amersham Pharmacia Biotech). Proteins were detected by absorption at 280 nm.
Velocity sedimentation on sucrose gradients
Sedimentation coefficients of full-length and T701-Myo1c were measured using linear 5–20% sucrose gradients in 11.5 ml of 400 mM KCl, 1 mM MgCl2, 15 mM HEPES pH 7.5, 0.2 mM phenylmethylsulfonyl fluoride, 10 μM leupeptin, 10 μM pepstatin, and either 100 μM EGTA or 25 μM CaCl2. Gradients were calibrated with 2–20 μg internal standards of known sedimentation coefficients (catalase, 11.3 S; bovine serum albumin, 4.31 S; lysozyme, 1.91 S; all obtained from Sigma-Aldrich). After centrifugation at 33,000–40,000 rpm in an SW 41 rotor for 15–18 hours at 4°C or 25°C, gradients were fractionated from the bottom into ~30 fractions. Calibration proteins were located using a Bradford protein assay ; Myo1c-containing fractions were located by ELISA  using an antibody against the Myo1c tail (mT2/M2; ref. ) or against the DLYDDDDK epitope tag (anti-Xpress; Invitrogen). To determine the location of protein peaks, plots of fraction number versus the levels of Myo1c or calibration proteins were fit with either one, two, or three Gaussian curves.
For calmodulin preloading of T701-Myo1c, 10 μM purified calmodulin was incubated with 1 μM Myo1c in a solution containing either 100 μM EGTA or 25 μM CaCl2 for 60 min at room temperature prior to centrifugation.
Determination of molecular mass
We used the modified Svedberg equation for molecular-mass determination:
where M = molecular mass, η = viscosity of the medium, N = Avogadro's number, a = Stokes radius, s = sedimentation coefficient, = partial specific volume, and ρ = density of the medium. Partial specific volume was calculated from the composition of Myo1c or T701-Myo1c, along with the appropriate number of calmodulins, by summing the partial specific volumes of each amino acid . We used η = 1.002 × 10-2 g cm-1 s-1 and ρ = 0.998 g cm-3.
Errors in molecular mass were propagated from standard deviations for Stokes radius and sedimentation coefficient measurements. To calculate error in calmodulin stoichiometry, we used the conservative assumption that all error in the molecular-mass measurement was due to variability in the number of calmodulins.
The frictional ratio was determined from:
where f is the frictional coefficient of the Myo1c-calmodulin complex and f0 is the frictional coefficient of a sphere of equal volume. Accordingly, the frictional ratio of a globular protein will be 1; that of an elongated protein will be >1.
Stoichiometry determination by gel scanning
T701-Myo1c and bovine-brain calmodulin were separated by sodium dodecyl sulfate gel electrophoresis (SDS-PAGE) and stained with Coomassie blue R250. Gels were scanned with a flatbed scanner; calmodulin was quantified using analysis of the resulting images with NIH Image version 1.62. The concentration of the T701-Myo1c heavy chain was determined by measuring absorbance at 280 nm, although the analysis was complicated by the uncertain calmodulin stoichiometry (p). To circumvent this problem, we solved several simultaneous equations for p. The molar extinction coefficient of the T701-Myo1c/calmodulin complex (εT701-CaM) is given by:
εT701-CaM = εT701 + p·εCaM (10)
where εT701 is the extinction coefficient of the T701-Myo1c heavy chain alone (57,990 M-1 cm-1), εCaM is the extinction coefficient of calmodulin (2560 M-1cm-1), and p is the calmodulin:T701 stoichiometry. The concentration of T701-Myo1c heavy chain is given by:
where A280 is the absorbance of the complex at 280 nm for a 1 cm pathlength. Finally,
p·[T701HC] = [CaM] (12)
where [CaM] is the calmodulin concentration determined by gel scanning. Solving for p:
We measured the free Ca2+ concentrations in our solutions using spectrofluorometry with Calcium Green-2 (Molecular Probes). SDS-PAGE was carried out with 18% acrylamide Criterion gels (Bio-Rad Laboratories; Hercules, CA); gels were stained with Coomassie blue R250.
We thank Dr. Serge Jean for producing the original full-length bullfrog Myo1c baculovirus construct. Weiyi Zhao provided excellent technical support; Drs. Susan Gillespie and Kevin Nusser provided additional support and advice. Research was supported by NIH grant DC02368.
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