Mutagenesis of the fourth calcium-binding domain of yeast calmodulin

Roles of the C-terminal residues of calmodulin in structure and function

Electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy, flow dialysis, and bioactivity measurements were employed to investigate the roles of the C-terminal residues of calmodulin (CaM). In the present study, we prepared a series of truncated mutants of chicken CaM that lack four (CCMΔ4) to eight (CCMΔ8) residues at the C-terminal end. It was found that CCMΔ4, lacking the last four residues (M145 to K148), binds four Ca²⁺ ions. Further deletion gradually decreased the ability to bind the fourth Ca²⁺ ion, and CCMΔ8 completely lost the ability. Interestingly, both lobes of Ca²⁺-sturated CCMΔ5 showed instability in the conformation, although limited part in the C-lobe of Ca²⁺-saturated CCMΔ4 was instable. Moreover, unlike CCMΔ4, structure of the C-lobe in CCMΔ5 bound to the target displayed dissimilarity to that of CaM, suggesting that deletion of M144 changes the binding manner. Deletion of the last five residues (M144 to K148) and further truncation of the C-terminal region decreased apparent capacity for target activation. Little contribution of the last four residues including M145 was observed for structural stability, Ca²⁺-binding, and target activation. Although both M144 and M145 have been recognized as key residues for the function, the present data suggest that M144 is a more important residue to attain Ca²⁺ induced conformational change and to form a proper Ca²⁺-saturated conformation.

Protein grabs a ligand by extending anchor residues: molecular simulation for Ca2+ binding to calmodulin loop

The structural difference in proteins between unbound and bound forms directly suggests the importance of the conformational plasticity of proteins. However, pathways that connect two-end structures and how they are coupled to the binding reaction are not well understood at atomic resolution. Here, we analyzed the free-energy landscape, explicitly taking into account coupling between binding and conformational change by performing atomistic molecular dynamics simulations for Ca2+ binding to a calmodulin loop. Using the AMBER force field with explicit water solvent, we conducted umbrella sampling for the free-energy surface and steered molecular dynamics for the pathway search. We found that, at an early stage of binding, some key residue side chains extend their "arms" to catch Ca2+ and, after catching, they carry the Ca2+ to the center of the binding pocket. This grabbing motion resulted in smooth and stepwise exchange in coordination partners of Ca2+ from water oxygen to atoms in the calmodulin loop. The key residue that first caught the ion was one of the two acidic residues, which are highly conserved. In the pathway simulations, different pathways were observed between binding and dissociation reactions: The former was more diverse than the latter.

Structural investigation into the differential target enzyme regulation displayed by plant calmodulin isoforms

The conserved calmodulin (CaM) isoform SCaM-1 and the divergent SCaM-4 from soybean bind to many of the same target enzymes, but differentially activate or competitively inhibit them. Class 1 target enzymes are activated by both calcium (Ca(2+))-bound SCaM-1 (Ca(2+)-SCaM-1) and Ca(2+)-bound SCaM-4 (Ca(2+)-SCaM-4), while class 2 enzymes are activated by Ca(2+)-SCaM-1 but competitively inhibited by Ca(2+)-SCaM-4, and class 3 enzymes are activated by Ca(2+)-SCaM-4 but competitively inhibited by Ca(2+)-SCaM-1. To determine whether these differences can be attributed to unique interactions with the CaM-binding domains (CaMBD) of these enzymes, we have studied the binding of each protein to peptides derived from the CaMBD of a representative target enzyme from each of these three classes. Using a combination of NMR spectroscopy and isothermal titration calorimetry, we demonstrate that the N- and C-domains of either Ca(2+)-SCaM bind to each peptide to form structurally compact complexes driven by the burial of hydrophobic surfaces. Interestingly, the interactions with the CaMBD peptides from classes 1 and 2 are similar for the two proteins; however, binding to the peptide from class 3 is structurally and thermodynamically distinct for Ca(2+)-SCaM-1 and -4. We also demonstrate that both calcium-free SCaM-1 (apo-SCaM-1) and calcium-free SCaM-4 (apo-SCaM-4) bind to the CaMBD from cyclic nucleotide phosphodiesterase, and that the interactions are similar to each other and to the interactions with apo-mammalian CaM. Therefore, the apo-SCaMs are also capable of binding to the same target enzymes, which could provide an additional mechanism for CaM-dependent signaling in plants.

Ligand-linked stability of mutants of the C-domain of calmodulin

There is a necessary energetic linkage between ligand binding and stability in biological molecules. The critical glutamate in Site 4 was mutated to create two mutants of the C-domain of calmodulin yielding E140D and E140Q. These proteins were stably folded in the absence of calcium, but had dramatically impaired binding of calcium. We determined the stability of the mutant proteins in the absence and presence of calcium using urea-induced unfolding monitored by circular dichroism (CD) spectroscopy. These calcium-dependent unfolding curves were fit to models that allowed for linkage of stability to binding of a single calcium ion to the native and unfolded states. Simultaneous analysis of the unfolding profiles for each mutant yielded estimates for calcium-binding constants that were consistent with results from direct titrations monitored by fluorescence. Binding to the unfolded state was not an important energetic contributor to the ligand-linked stability of these mutants.

The calmodulin-binding domain of the catalytic gamma subunit of phosphorylase kinase interacts with its inhibitory alpha subunit: evidence for a Ca2+ sensitive network of quaternary interactions

Chemical cross-linking as a probe of conformation has consistently shown that activators, including Ca(2+) ions, of the (alphabetagammadelta)(4) phosphorylase kinase holoenzyme (PhK) alter the interactions between its regulatory alpha and catalytic gamma subunits. The gamma subunit is also known to interact with the delta subunit, an endogenous molecule of calmodulin that mediates the activation of PhK by Ca(2+) ions. In this study, we have used two-hybrid screening and chemical cross-linking to dissect the regulatory quaternary interactions involving these subunits. The yeast two-hybrid system indicated that regions near the C termini of the gamma (residues 343-386) and alpha (residues 1060-1237) subunits interact. The association of this region of alpha with gamma was corroborated by the isolation of a cross-linked fragment of alpha containing residues 1015-1237 from an alpha-gamma dimer that had been formed within the PhK holoenzyme by formaldehyde, a nearly zero-length cross-linker. Because the region of gamma that we found to interact with alpha has previously been shown to contain a high affinity binding site for calmodulin (Dasgupta, M., Honeycutt, T., and Blumenthal, D. K. (1989) J. Biol. Chem. 264, 17156-17163), we tested the influence of Ca(2+) on the conformation of the alpha subunit and found that the region of alpha that interacts with gamma was, in fact, perturbed by Ca(2+). The results herein support the existence of a Ca(2+)-sensitive communication network among the delta, gamma, and alpha subunits, with the regulatory domain of gamma being the primary mediator. The similarity of such a Ca(2+)-dependent network to the interactions among troponin C, troponin I, and actin is discussed in light of the known structural and functional similarities between troponin I and the gamma subunit of PhK.

Genetic analysis of calmodulin and its targets in Saccharomyces cerevisiae

Calmodulin, a small, ubiquitous Ca2+-binding protein, regulates a wide variety of proteins and processes in all eukaryotes. CMD1, the single gene encoding calmodulin in S. cerevisiae, is essential, and this review discusses studies that identified many of calmodulin's physiological targets and their functions in yeast cells. Calmodulin performs essential roles in mitosis, through its regulation of Nuf1p/Spc110p, a component of the spindle pole body, and in bud growth, by binding Myo2p, an unconventional class V myosin required for polarized secretion. Surprisingly, mutant calmodulins that fail to bind Ca2+ can perform these essential functions. Calmodulin is also required for endocytosis in yeast and participates in Ca2+-dependent, stress-activated signaling pathways through its regulation of a protein phosphatase, calcineurin, and the protein kinases, Cmk1p and Cmk2p. Thus, calmodulin performs important physiological functions in yeast cells in both its Ca2+-bound and Ca2+-free form.

Solution structures of the N-terminal domain of yeast calmodulin: Ca2+-dependent conformational change and its functional implication

We have determined solution structures of the N-terminal half domain (N-domain) of yeast calmodulin (YCM0-N, residues 1-77) in the apo and Ca(2+)-saturated forms by NMR spectroscopy. The Ca(2+)-binding sites of YCM0-N consist of a pair of helix-loop-helix motifs (EF-hands), in which the loops are linked by a short beta-sheet. The binding of two Ca(2+) causes large rearrangement of the four alpha-helices and exposes the hydrophobic surface as observed for vertebrate calmodulin (CaM). Within the observed overall conformational similarity in the peptide backbone, several significant conformational differences were observed between the two proteins, which originated from the 38% disagreement in amino acid sequences. The beta-sheet in apo YCM0-N is strongly twisted compared with that in the N-domain of CaM, while it turns to the normal more stable conformation on Ca(2+) binding. YCM0-N shows higher cooperativity in Ca(2+) binding than the N-domain of CaM, and the observed conformational change of the beta-sheet is a possible cause of the highly cooperative Ca(2+) binding. The hydrophobic surface on Ca(2+)-saturated YCM0-N appears less flexible due to the replacements of Met51, Met71, and Val55 in the hydrophobic surface of CaM with Leu51, Leu71, and Ile55, which is thought to be one of reasons for the poor activation of target enzymes by yeast CaM.

The whole is not the simple sum of its parts in calmodulin from S. cerevisiae

Calmodulin is an essential Ca(2+)-binding protein involved in a multitude of cellular processes. The calmodulin sequence is highly conserved among all eukaryotic species; calmodulin from the yeast S. cerevisiae (yCaM) is the most divergent form, while still sharing 60% sequence identity with vertebrate calmodulin (vCaM). Although yCaM can be functionally substituted by vCaM in vivo, the two calmodulin proteins possess significantly different Ca(2+)-binding properties as well as abilities to activate vertebrate target enzymes in vitro. In addition, it has been observed that certain properties of the N-terminal and C-terminal domains of Ca(2+)-yCaM differ depending on whether they are in the context of the whole protein or isolated as half-molecule fragments. To investigate the structural basis for these differing properties, we have undertaken nuclear magnetic resonance (NMR) studies on yCaM and the two half-molecule fragments representing its two individual domains, yTr1(residues 1-76) and yTr2 (residues 75-146). We present direct evidence that the two domains of Ca(2+)-yCaM interact via their exposed hydrophobic surfaces. Thus, the Ca(2+)-bound form of yCaM exists in a novel compact structure in direct contrast to the well-established structure of Ca(2+)-vCaM comprised of two independent globular domains.

Calcium binding induces interaction between the N- and C-terminal domains of yeast calmodulin and modulates its overall conformation

Calmodulin from the yeast Saccharomyces cerevisiae binds 3 mol of Ca2+ cooperatively. We report here lines of evidence supporting the intramolecular interaction between the N- and C-terminal domains which modulates the Ca2+ binding properties of yeast calmodulin. First, the sum of the Ca2+ binding curves of the N-terminal and the C-terminal half-molecule did not yield the Ca2+ binding curve of yeast calmodulin. Second, the mean residue CD of yeast calmodulin at 222 nm (-Delta epsilon222) decreased with increases in the concentration of Ca2+, whereas those of each half-molecule increased. Finally, the C2 proton of His107 in the C-terminal domain of yeast calmodulin showed three resonance peaks with increases in the concentration of Ca2+, each corresponding to the apo, the intermediate, and the Ca2+-saturated state. The intermediate peak could not be observed in the C-terminal half-molecule of yeast calmodulin. Computer simulation considering the macroscopic Ca2+ binding constants assigned this intermediate to a species consisting of the apo C-terminal domain and the N-terminal domain with at least one of the two sites occupied by Ca2+. Peptide segments spanning the defective fourth Ca2+ binding site may be involved in the interdomain interaction and the yeast-specific function of calmodulin.

Solution X-ray scattering data show structural differences between yeast and vertebrate calmodulin: implications for structure/function

We present here the first evidence, obtained by the use of solution X-ray scattering, of the solution structure of yeast calmodulin, a poor activator of vertebrate enzymes. The radius of gyration of yeast calmodulin decreased from 21.1 to 19.9 angstroms when excess Ca2+ ions were added. The profiles of the pair-distribution function suggested that yeast calmodulin without Ca2+ has a dumbbell-like shape which changes toward a rather asymmetric globular shape, from its dumbbell shape, by the binding of Ca2+. In the presence of a calmodulin binding peptide such as MLCK-22 (a synthetic peptide corresponding to residues 577-598 of skeletal myosin light chain kinase), the radius of gyration of yeast calmodulin decreased by 1.6 angstroms, and the molecular shape of it estimated from the profile of the pair-distribution function was globular but less compact than that of vertebrate calmodulin. These results for the structure of yeast calmodulin complexed with Ca2+ and with Ca(2+)-peptides are quite different from those of vertebrate calmodulin. Thus, the functional differences between yeast and vertebrate calmodulin which we reported previously [Matsuura, I., et al. (1993) J. Biol. Chem. 268, 13267-13273] have been interpreted on the basis of the structural differences between them. Moreover, the structural studies on chimeric proteins of chicken and yeast calmodulin suggest that Ca2+ binding at site IV is essential to form the full active dumbbell structure, which is characteristic of vertebrate-type calmodulin.

Gain of function mutations for yeast calmodulin and calcium dependent regulation of protein kinase activity

Yeast calmodulin binds only three calcium ions in the presence of millimolar concentrations of magnesium due to a defective calcium-binding sequence in its carboxyl terminal domain. Yeast calmodulin's diminished calcium-binding activity can be restored to that of other calmodulins by the use of site-directed mutagenesis to substitute its fourth calcium-binding domain with that of a vertebrate calmodulin sequence. However, the repair of yeast calmodulin's calcium-binding activity is not sufficient to repair quantitatively yeast calmodulin's defective protein kinase activator activity. Yeast calmodulin's activator activity with smooth muscle and skeletal muscle myosin light chain kinases and brain calmodulin-dependent protein kinase II can be progressively repaired by additional substitutions of vertebrate calmodulin sequences, provided that the four calcium-binding sites remain intact. An unexpected result obtained during the course of these studies was the observation that myosin light chain kinases from smooth and skeletal muscle tissues can respond differently to mutations in calmodulin. These and previous results indicate that the binding of four calcium ions by calmodulin is necessary but not sufficient to bring about quantitative activation of protein kinases, and are consistent with the conformational selection/restriction model of the dynamic equilibrium among calcium, calmodulin and each calmodulin regulated enzyme.

Inactivation of individual Ca(2+)-binding sites in the paired EF-hand sites of parvalbumin reveals asymmetrical metal-binding properties

Previously a rat parvalbumin mutant protein PVF102W was constructed with a reporter Trp at position 102 in the middle of the hydrophobic center [Pauls, T. L., et al. (1993) J. Biol. Chem. 268, 20897-20903]. In the present study three new parvalbumin mutant proteins, derived from PVF102W and containing alterations at positions essential for Ca2+ binding in either one of the two Ca(2+)-binding sites (PV-CD and PV-EF) or in both (PV-CD/-EF), were expressed and purified. With the flow dialysis method it was established that both PV-CD and PV-EF bind 1 Ca2+ with affinity constants KCa of 1.1 x 10(7) and 3.2 x 10(6) M-1, respectively. Mg2+ binding, monitored by equilibrium gel filtration in the absence of Ca2+, showed that both mutants bind 1 Mg2+ with KMg = 8 10(4) for PV-CD and 3 x 10(3) M-1 for PV-EF. Compared to the parameters of the parent mutant PVF102W (two sites with equal affinities of 2.7 x 10(7) and 3 x 10(4) M-1 for Ca2+ and Mg2+, respectively), these data indicate that inactivation of the EF site, much more than of the CD site, impairs divalent cation binding. The binding of Ca2+ and Mg2+ is mutually exclusive, indicative of a Ca2+/Mg2+ mixed site. However, as for PVF102W, the KMg values obtained from the competition equation are approximately 40-fold lower than the affinities measured by direct binding. PV-CD/-EF binds neither Ca2+ nor Mg2+. Trp fluorimetry revealed that in the three mutant PVs the residue Trp-102 is deeply buried in the hydrophobic core.(ABSTRACT TRUNCATED AT 250 WORDS)