Intra- and interdomain effects due to mutation of calcium-binding sites in calmodulin

Unveiling the applications of membrane proteins from oil bodies: leading the way in artificial oil body technology and other biotechnological advancements

Oil bodies (OBs) function as organelles that store lipids in plant seeds. An oil body (OB) is encased by a membrane composed of proteins (e.g., oleosins, caleosins, and steroleosins) and a phospholipid monolayer. The distinctive protein-phospholipid membrane architecture of OBs imparts exceptional stability even in extreme environments, thereby sparking increasing interest in their structure and properties. However, a comprehensive understanding of the structure-activity relationships determining the stability and properties of oil bodies requires a more profound exploration of the associated membrane proteins, an aspect that remains relatively unexplored. In this review, we aim to summarize and discuss the structural attributes, biological functions, and properties of OB membrane proteins. From a commercial perspective, an in-depth understanding of the structural and functional properties of OBs is important for the expansion of their applications by producing artificial oil bodies (AOB). Besides exploring their structural intricacies, we describe various methods that are used for purifying and isolating OB membrane proteins. These insights may provide a foundational framework for the practical utilization of OB membrane proteins in diverse applications within the realm of AOB technology, including biological and probiotic delivery, protein purification, enzyme immobilization, astringency detection, and antibody production.

Role of water-bridged interactions in metal ion coupled protein allostery

Allosteric communication between distant parts of proteins controls many cellular functions, in which metal ions are widely utilized as effectors to trigger the allosteric cascade. Due to the involvement of strong coordination interactions, the energy landscape dictating the metal ion binding is intrinsically rugged. How metal ions achieve fast binding by overcoming the landscape ruggedness and thereby efficiently mediate protein allostery is elusive. By performing molecular dynamics simulations for the Ca²⁺ binding mediated allostery of the calmodulin (CaM) domains, each containing two Ca²⁺ binding helix-loop-helix motifs (EF-hands), we revealed the key role of water-bridged interactions in Ca²⁺ binding and protein allostery. The bridging water molecules between Ca²⁺ and binding residue reduces the ruggedness of ligand exchange landscape by acting as a lubricant, facilitating the Ca²⁺ coupled protein allostery. Calcium-induced rotation of the helices in the EF-hands, with the hydrophobic core serving as the pivot, leads to exposure of hydrophobic sites for target binding. Intriguingly, despite being structurally similar, the response of the two symmetrically arranged EF-hands upon Ca²⁺ binding is asymmetric. Breakage of symmetry is needed for efficient allosteric communication between the EF-hands. The key roles that water molecules play in driving allosteric transitions are likely to be general in other metal ion mediated protein allostery.

Natural proteins often utilize allostery in executing a variety of functions. Metal ions are typical cofactors to trigger the allosteric cascade. In this work, using the Ca²⁺ sensor protein calmodulin as the model system, we revealed crucial roles of water-bridged interactions in the metal ion coupled protein allostery. The coordination of the Ca²⁺ to the binding site involves an intermediate in which the water molecule bridges the Ca²⁺ and the liganding residue. The bridging water reduces the free energy barrier height of ligand exchange, therefore facilitating the ligand exchange and allosteric coupling by acting as a lubricant. We also showed that the response of the two symmetrically arranged EF-hand motifs of CaM domains upon Ca²⁺ binding is asymmetric, which is directly attributed to the differing dehydration process of the Ca²⁺ ions and is needed for efficient allosteric communication.

EF-hand protein, EfhP, specifically binds Ca2+ and mediates Ca2+ regulation of virulence in a human pathogen Pseudomonas aeruginosa

Calcium (Ca2+) is well known as a second messenger in eukaryotes, where Ca2+ signaling controls life-sustaining cellular processes. Although bacteria produce the components required for Ca2+ signaling, little is known about the mechanisms of bacterial Ca2+ signaling. Previously, we have identified a putative Ca2+-binding protein EfhP (PA4107) with two canonical EF-hand motifs and reported that EfhP mediates Ca2+ regulation of virulence factors production and infectivity in Pseudomonas aeruginosa, a human pathogen causing life-threatening infections. Here, we show that EfhP selectively binds Ca2+ with 13.7 µM affinity, and that mutations at the +X and -Z positions within each or both EF-hand motifs abolished Ca2+ binding. We also show that the hydrophobicity of EfhP increased in a Ca2+-dependent manner, however no such response was detected in the mutated proteins. 15 N-NMR showed Ca2+-dependent chemical shifts in EfhP confirming Ca2+-binding triggered structural rearrangements in the protein. Deletion of efhP impaired P. aeruginosa survival in macrophages and virulence in vivo. Disabling EfhP Ca2+ binding abolished Ca2+ induction of pyocyanin production in vitro. These data confirm that EfhP selectively binds Ca2+, which triggers its structural changes required for the Ca2+ regulation of P. aeruginosa virulence, thus establishing the role of EfhP as a Ca2+ sensor.

The stress induced caleosin, RD20/CLO3, acts as a negative regulator of GPA1 in Arabidopsis

KEY MESSAGE

A stress induced calcium-binding protein, RD20/CLO3 interacts with the alpha subunit of the heterotrimeric G-protein complex in Arabidopsis and affects etiolation and leaf morphology. Heterotrimeric G proteins and calcium signaling have both been shown to play a role in the response to environmental abiotic stress in plants; however, the interaction between calcium-binding proteins and G-protein signaling molecules remains elusive. We investigated the interaction between the alpha subunit of the heterotrimeric G-protein complex, GPA1, of Arabidopsis thaliana with the calcium-binding protein, the caleosin RD20/CLO3, a gene strongly induced by drought, salt and abscisic acid. The proteins were found to interact in vivo by bimolecular fluorescent complementation (BiFC); the interaction was localized to the endoplasmic reticulum and to oil bodies within the cell. The constitutively GTP-bound GPA1 (GPA1QL) also interacts with RD20/CLO3 as well as its EF-hand mutant variations and these interactions are localized to the plasma membrane. The N-terminal portion of RD20/CLO3 was found to be responsible for the interaction with GPA1 and GPA1QL using both BiFC and yeast two-hybrid assays. RD20/CLO3 contains a single calcium-binding EF-hand in the N-terminal portion of the protein; disruption of the calcium-binding capacity of the protein obliterates interaction with GPA1 in in vivo assays and decreases the interaction between the caleosin and the constitutively active GPA1QL. Analysis of rd20/clo3 mutants shows that RD20/CLO3 plays a key role in the signaling pathway controlling hypocotyl length in dark grown seedlings and in leaf morphology. Our findings indicate a novel role for RD20/CLO3 as a negative regulator of GPA1.

Influence of Subcellular Localization and Functional State on Protein Turnover

Protein homeostasis is an equilibrium of paramount importance that maintains cellular performance by preserving an efficient proteome. This equilibrium avoids the accumulation of potentially toxic proteins, which could lead to cellular stress and death. While the regulators of proteostasis are the machineries controlling protein production, folding and degradation, several other factors can influence this process. Here, we have considered two factors influencing protein turnover: the subcellular localization of a protein and its functional state. For this purpose, we used an imaging approach based on the pulse-labeling of 17 representative SNAP-tag constructs for measuring protein lifetimes. With this approach, we obtained precise measurements of protein turnover rates in several subcellular compartments. We also tested a selection of mutants modulating the function of three extensively studied proteins, the Ca²⁺ sensor calmodulin, the small GTPase Rab5a and the brain creatine kinase (CKB). Finally, we followed up on the increased lifetime observed for the constitutively active Rab5a (Q79L), and we found that its stabilization correlates with enlarged endosomes and increased interaction with membranes. Overall, our data reveal that both changes in protein localization and functional state are key modulators of protein turnover, and protein lifetime fluctuations can be considered to infer changes in cellular behavior.

Non-Additive Effects of Binding Site Mutations in Calmodulin

Despite decades of research on ion-sensing proteins, gaps persist in the understanding of ion binding affinity and selectivity even in well-studied proteins such as calmodulin. Site-directed mutagenesis is a powerful and popular tool for addressing outstanding questions about biological ion binding and is employed to selectively deactivate binding sites and insert chromophores at advantageous positions within ion binding structures. However, even apparently nonperturbative mutations can distort the binding dynamics they are employed to measure. We use Fourier transform infrared (FTIR) and ultrafast two-dimensional infrared (2D IR) spectroscopy of the carboxylate asymmetric stretching mode in calmodulin as a mutation- and label-independent probe of the conformational perturbations induced in calmodulin's binding sites by two classes of mutation, tryptophan insertion and carboxylate side-chain deletion, commonly used to study ion binding in proteins. Our results show that these mutations not only affect ion binding but also induce changes in calmodulin's conformational landscape along coordinates not probed by vibrational spectroscopy, remaining invisible without additional perturbation of binding site structure. Comparison of FTIR line shapes with 2D IR diagonal slices provides a clear example of how nonlinear spectroscopy produces well-resolved line shapes, refining otherwise featureless spectral envelopes into more informative vibrational spectra of proteins.

The Nkd EF-hand domain modulates divergent wnt signaling outputs in zebrafish

Wnt proteins regulate diverse biological responses by initiating two general outcomes: β-catenin-dependent transcription and β-catenin-independent activation of signaling cascades, the latter including modulation of calcium and regulation of cytoskeletal dynamics (Planar Cell Polarity, PCP). It has been difficult to elucidate the mechanisms by which Wnt signals are directed to effect one or the other outcome due to shared signaling proteins between the β-catenin-dependent and -independent pathways, such as the Dishevelled binding protein Naked. While all Naked paralogs contain a putative calcium-binding domain, the EF-Hand, Drosophila Naked does not bind calcium. Here we find a lineage-specific evolutionary change within the Drosophila Naked EF-hand that is not shared with other insects or vertebrates. We demonstrate the necessary role of the EF-hand for Nkd localization changes in calcium fluxing cells and using in vivo assays, we identify a role for the zebrafish Naked EF-hand in PCP but not in β-catenin antagonism. In contrast, Drosophila-like Nkd does not function in PCP, but is a robust antagonist of Wnt/β-catenin signaling. This work reveals that the zebrafish Nkd1 EF-hand is essential to balance Wnt signaling inputs and modulate the appropriate outputs, while the Drosophila-like EF-Hand primarily functions in β-catenin signaling.

Allostery in Orai1 binding to calmodulin revealed from conformational thermodynamics

Here, we study microscopic mechanism of complex formation between Ca²⁺-bound calmodulin (holoCaM) and Orai1 that regulates Ca²⁺-dependent inactivation process in eukaryotic cells. We compute conformational thermodynamic changes in holoCaM with respect to complex of Orai1 bound to C-terminal domain of holoCaM using histograms of dihedral angles of the proteins over trajectories from molecular dynamics simulations. Our analysis shows that the N-terminal domain residues L4, T5, Q41, N42, T44 and E67 of holoCaM get destabilized and disordered due to Orai1 binding to C-terminal domain of calmodulin affect the N-terminal domain residues. Among these residues, polar T44, having maximum destabilization and disorder via backbone fluctuations, shows the largest change in solvent exposure. This suggests that N-terminal domain is allosterically regulated via T44 by the binding of Orai1 to the C-terminal domain.

Structural Consequences of Calmodulin EF Hand Mutations

Calmodulin (CaM) is a cytosolic Ca²⁺-binding protein that serves as a control element for many enzymes. It consists of two globular domains, each containing two EF hand pairs capable of binding Ca²⁺, joined by a flexible central linker region. CaM is able to bind and activate its target proteins in the Ca²⁺-replete and Ca²⁺-deplete forms. To study the Ca²⁺-dependent/independent properties of binding and activation of target proteins by CaM, CaM constructs with Ca²⁺-binding disrupting mutations of Asp to Ala at position one of each EF hand have been used. These CaM mutant proteins are deficient in binding Ca²⁺ in either the N-lobe EF hands (CaM₁₂), C-lobe EF hands (CaM₃₄), or all four EF hands (CaM₁₂₃₄). To investigate potential structural changes these mutations may cause, we performed detailed NMR studies of CaM₁₂, CaM₃₄, and CaM₁₂₃₄ including determining the solution structure of CaM₁₂₃₄. We then investigated if these CaM mutants affected the interaction of CaM with a target protein known to interact with apoCaM by determining the solution structure of CaM₃₄ bound to the iNOS CaM binding domain peptide. The structures provide direct structural evidence of changes that are present in these Ca²⁺-deficient CaM mutants and show these mutations increase the hydrophobic exposed surface and decrease the electronegative surface potential throughout each lobe of CaM. These Ca²⁺-deficient CaM mutants may not be a true representation of apoCaM and may not allow for native-like interactions of apoCaM with its target proteins.

Relative Cosolute Size Influences the Kinetics of Protein-Protein Interactions

Protein signaling occurs in crowded intracellular environments, and while high concentrations of macromolecules are postulated to modulate protein-protein interactions, analysis of their impact at each step of the reaction pathway has not been systematically addressed. Potential cosolute-induced alterations in target association are particularly important for a signaling molecule like calmodulin (CaM), where competition among >300 targets governs which pathways are selectively activated. To explore how high concentrations of cosolutes influence CaM-target affinity and kinetics, we methodically investigated each step of the CaM-target binding mechanism under crowded or osmolyte-rich environments mimicked by ficoll-70, dextran-10, and sucrose. All cosolutes stabilized compact conformers of CaM and modulated association kinetics by affecting diffusion and rates of conformational change; however, the results showed that differently sized molecules had variable effects to enhance or impede unique steps of the association pathway. On- and off-rates were modulated by all cosolutes in a compensatory fashion, producing little change in steady-state affinity. From this work insights were gained on how high concentrations of inert crowding agents and osmolytes fit into a kinetic framework to describe protein-protein interactions relevant for cellular signaling.

Chemical shift assignments of calmodulin constructs with EF hand mutations

Calmodulin (CaM) is a ubiquitous cytosolic Ca(2+)-binding protein able to bind and regulate hundreds of different proteins. It consists of two globular domains joined by a flexible central linker region. Each one of these domains contains two EF hand pairs capable of binding to Ca(2+). Upon Ca(2+) binding CaM undergoes a conformational change exposing hydrophobic patches that interact with its intracellular target proteins. CaM is able to bind to target proteins in the Ca(2+)-replete and Ca(2+)-deplete forms. To study the Ca(2+)-dependent/independent properties of binding and activation of target proteins by CaM, CaM constructs with Ca(2+) binding disrupting mutations of Asp to Ala at position one of each EF hand have been used. One target protein of CaM is nitric oxide synthase, which catalyzes the production of nitric oxide. At elevated Ca(2+) concentrations, CaM binds to neuronal NOS and endothelial NOS, making them the Ca(2+)-dependent NOS enzymes. In contrast, inducible NOS is transcriptionally regulated in vivo and binds to CaM at basal levels of Ca(2+). Here we report the NMR backbone and sidechain resonance assignments of C-lobe Ca(2+)-replete and deplete CaM12, N-lobe Ca(2+)-replete and deplete CaM34, CaM1234 in the absence of Ca(2+) and N-lobe Ca(2+)-replete CaM34 with the iNOS CaM-binding domain peptide.

PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory

The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity.

Two helices in the third intracellular loop determine anoctamin 1 (TMEM16A) activation by calcium

Anoctamin 1 (ANO1)/TMEM16A is a Cl⁻ channel activated by intracellular Ca²⁺ mediating numerous physiological functions. However, little is known of the ANO1 activation mechanism by Ca²⁺. Here, we demonstrate that two helices, “reference” and “Ca²⁺ sensor” helices in the third intracellular loop face each other with opposite charges. The two helices interact directly in a Ca²⁺-dependent manner. Positively and negatively charged residues in the two helices are essential for Ca²⁺-dependent activation because neutralization of these charges change the Ca²⁺ sensitivity. We now predict that the Ca²⁺ sensor helix attaches to the reference helix in the resting state, and as intracellular Ca²⁺ rises, Ca²⁺ acts on the sensor helix, which repels it from the reference helix. This Ca²⁺-dependent push-pull conformational change would be a key electromechanical movement for gating the ANO1 channel. Because chemical activation of ANO1 is viewed as an alternative means of rescuing cystic fibrosis, understanding its gating mechanism would be useful in developing novel treatments for cystic fibrosis.

Neurogranin alters the structure and calcium binding properties of calmodulin

Neurogranin (Ng) is a member of the IQ motif class of calmodulin (CaM)-binding proteins, and interactions with CaM are its only known biological function. In this report we demonstrate that the binding affinity of Ng for CaM is weakened by Ca(2+) but to a lesser extent (2-3-fold) than that previously suggested from qualitative observations. We also show that Ng induced a >10-fold decrease in the affinity of Ca(2+) binding to the C-terminal domain of CaM with an associated increase in the Ca(2+) dissociation rate. We also discovered a modest, but potentially important, increase in the cooperativity in Ca(2+) binding to the C-lobe of CaM in the presence of Ng, thus sharpening the threshold for the C-domain to become Ca(2+)-saturated. Domain mapping using synthetic peptides indicated that the IQ motif of Ng is a poor mimetic of the intact protein and that the acidic sequence just N-terminal to the IQ motif plays an important role in reproducing Ng-mediated decreases in the Ca(2+) binding affinity of CaM. Using NMR, full-length Ng was shown to make contacts largely with residues in the C-domain of CaM, although contacts were also detected in residues in the N-terminal domain. Together, our results can be consolidated into a model where Ng contacts residues in the N- and C-lobes of both apo- and Ca(2+)-bound CaM and that although Ca(2+) binding weakens Ng interactions with CaM, the most dramatic biochemical effect is the impact of Ng on Ca(2+) binding to the C-terminal lobe of CaM.

Surface dynamics in allosteric regulation of protein-protein interactions: modulation of calmodulin functions by Ca2+

Knowledge of the structural basis of protein-protein interactions (PPI) is of fundamental importance for understanding the organization and functioning of biological networks and advancing the design of therapeutics which target PPI. Allosteric modulators play an important role in regulating such interactions by binding at site(s) orthogonal to the complex interface and altering the protein's propensity for complex formation. In this work, we apply an approach recently developed by us for analyzing protein surfaces based on steered molecular dynamics simulation (SMD) to the study of the dynamic properties of functionally distinct conformations of a model protein, calmodulin (CaM), whose ability to interact with target proteins is regulated by the presence of the allosteric modulator Ca(2+). Calmodulin is a regulatory protein that acts as an intracellular Ca(2+) sensor to control a wide variety of cellular processes. We demonstrate that SMD analysis is capable of pinpointing CaM surfaces implicated in the recognition of both the allosteric modulator Ca(2+) and target proteins. Our analysis of changes in the dynamic properties of the CaM backbone elicited by Ca(2+) binding yielded new insights into the molecular mechanism of allosteric regulation of CaM-target interactions.

The calmodulin regulator protein, PEP-19, sensitizes ATP-induced Ca2+ release

PEP-19 is a small, intrinsically disordered protein that binds to the C-domain of calmodulin (CaM) via an IQ motif and tunes its Ca(2+) binding properties via an acidic sequence. We show here that the acidic sequence of PEP-19 has intrinsic Ca(2+) binding activity, which may modulate Ca(2+) binding to CaM by stabilizing an initial Ca(2+)-CaM complex or by electrostatically steering Ca(2+) to and from CaM. Because PEP-19 is expressed in cells that exhibit highly active Ca(2+) dynamics, we tested the hypothesis that it influences ligand-dependent Ca(2+) release. We show that PEP-19 increases the sensitivity of HeLa cells to ATP-induced Ca(2+) release to greatly increase the percentage of cells responding to sub-saturating doses of ATP and increases the frequency of Ca(2+) oscillations. Mutations in the acidic sequence of PEP-19 that inhibit or prevent it from modulating Ca(2+) binding to CaM greatly inhibit its effect on ATP-induced Ca(2+) release. Thus, this cellular effect of PEP-19 does not depend simply on binding to CaM via the IQ motif but requires its acidic metal binding domain. Tuning the activities of Ca(2+) mobilization pathways places PEP-19 at the top of CaM signaling cascades, with great potential to exert broad effects on downstream CaM targets, thus expanding the biological significance of this small regulator of CaM signaling.

Differential contribution of EF-hands to the Ca²⁺-dependent activation in the plant two-pore channel TPC1

Two-pore channels (TPC) have been established as components of calcium signalling networks in plants and animals. In plants, TPC1 in the vacuolar membrane is gated open upon binding of calcium in a voltage-dependent manner. Here, we analyzed the molecular mechanism of the Ca²⁺-dependent activity of TPC1 from Arabidopsis thaliana, using site-directed mutagenesis of its two canonical EF-hands. Wild-type TPC1 and TPC1-D335A with a mutated first Ca²⁺ ligand in EF-hand 1 produced channels that retained their voltage- and Ca²⁺-dependent gating characteristics, but were less sensitive at Ca²⁺ concentrations < 200 μm. Additional mutation of the first Ca²⁺ ligand in EF-hand 2 resulted in silent TPC1-D335A/D376A channels. Similarly, the single mutant TPC1-D376A could not be activated up to 1 mm Ca²⁺, indicating that the second EF-hand is essential for the Ca²⁺-dependent channel gating. Molecular modeling suggests that EF-hand 1 displays a low-affinity Ca²⁺/Mg²⁺-binding site, while EF-hand 2 represents a high-affinity Ca²⁺-binding site. Together, our data prove that EF-hand 2 is responsible for the Ca²⁺-receptor characteristics of TPC1, while EF-hand 1 is a structural site required to enable channel responses at physiological changes in Ca²⁺ concentration.

The effect of macromolecular crowding, ionic strength and calcium binding on calmodulin dynamics

The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells.

Proteins are workhorses for driving biological functions inside cells. Calmodulin (CaM) is a protein that can carry cellular signals by triggered conformational changes due to calcium binding that alters target binding. Interestingly, CaM is able to bind over 300 targets. One of the challenges in characterizing CaM's ability to bind multiple targets lies in that CaM is a flexible protein and its structure is easily modulated by the physicochemical changes in its surroundings, particularly inside a complex cellular milieu. In order to determine structure-function relationships of CaM, we employed a combined approach of experiments, computer simulations and statistical physics in the investigation of the effect of calcium-binding, salt concentration, and macromolecular crowding on CaM. The results revealed unique folding energy landscapes of CaM in the absence and presence of calcium ions and the structural implications of CaM are interpreted under cell-like conditions. Further, a large conformational change in CaM in response to environmental impacts, dictates the packing of local helices that may be critical to its function of target binding and recognition among vast target selections.

Intrinsically disordered PEP-19 confers unique dynamic properties to apo and calcium calmodulin

PEP-19 (Purkinje cell protein 4) is an intrinsically disordered protein with an IQ calmodulin (CaM) binding motif. Expression of PEP-19 was recently shown to protect cells from apoptosis and cell death due to Ca(2+) overload. Our initial studies showed that PEP-19 causes novel and dramatic increases in the rates of association of Ca(2+) with and dissociation of Ca(2+) from the C-domain of CaM. The goal of this work was to study interactions between the C-domain of CaM (C-CaM) and PEP-19 by solution nuclear magnetic resonance (NMR) to identify mechanisms by which PEP-19 regulates binding of Ca(2+) to CaM. Our results show that PEP-19 causes a greater structural change in apo C-CaM than in Ca(2+)-C-CaM, and that the first Ca(2+) binds preferentially to site IV in the presence of PEP-19 with exchange characteristics that are consistent with a decrease in Ca(2+) binding cooperativity. Relatively weak binding of PEP-19 has distinct effects on chemical and conformational exchange on the microsecond to millisecond time scale. In apo C-CaM, PEP-19 binding causes a redistribution of residues that experience conformational exchange, leading to an increase in the number of residues around Ca(2+) binding site IV that undergo conformational exchange on the microsecond to millisecond time scale. This appears to be caused by an allosteric effect because these residues are not localized to the PEP-19 binding site. In contrast, PEP-19 increases the number of residues that exhibit conformational exchange in Ca(2+)-C-CaM. These residues are primarily localized to the PEP-19 binding site but also include Asp93 in site III. These results provide working models for the role of protein dynamics in the regulation of binding of Ca(2+) to CaM by PEP-19.

Global dynamic conformational changes in the suppressor domain of IP3 receptor by stepwise binding of the two lobes of calmodulin

The roles of calmodulin (CaM) have been key points of controversy in the regulation of inositol-1,4,5-trisphosphate receptor (IP(3)R). To address the issue, we studied the interaction between CaM and the suppressor domain of IP(3)R, a key allosteric regulatory domain. First, by means of a pulldown and a fluorescence titration experiment, we confirmed the interaction. Through subsequent NMR binding experiments, we observed dramatic peak disappearances of the suppressor domain on interaction with apo-CaM. The data indicated that apo-CaM induces large-scale dynamic conformational changes in the suppressor domain, involving partial unfolding and subdomain rearrangement. Analysis of the NMR data of CaM surprisingly revealed that its C lobe alone can cause such changes. Further binding experiments showed that calcium allows the free N lobe to bind to the suppressor domain, which induces extra conformational changes in both of the proteins. These results were also confirmed with CaM deletion mutants with either the N or C lobe. On the basis of this novel binding mechanism, we propose a model in which the partial unfolding of the suppressor domain by apo-CaM and the stepwise binding of the N lobe of CaM to the suppressor domain are important elements of calcium/CaM inhibition of IP(3)R. We believe that our working model encompasses previous regulation mechanisms of IP(3)R by calcium/CaM and provides new insights into the CaM-target interaction.