Calmodulin and STIM proteins: Two major calcium sensors in the cytoplasm and endoplasmic reticulum

An AI-informed NMR structure reveals an extraordinary LETM1 F-EF-hand domain that functions as a two-way regulator of mitochondrial calcium

AlphaFold can accurately predict static protein structures but does not account for solvent conditions. Human leucine zipper EF-hand transmembrane protein-1 (LETM1) has one sequence-identifiable EF-hand but how calcium (Ca2+) affects structure and function remains enigmatic. Here, we used highly confident AlphaFold Cα predictions to guide nuclear Overhauser effect (NOE) assignments and structure calculation of the LETM1 EF-hand in the presence of Ca2+. The resultant NMR structure exposes pairing between a partial loop-helix and full helix-loop-helix, forming an unprecedented F-EF-hand with non-canonical Ca2+ coordination but enhanced hydrophobicity for protein interactions compared to calmodulin. The structure also reveals the basis for pH sensing at the link between canonical and partial EF-hands. Functionally, mutations that augmented or weakened Ca2+ binding increased or decreased matrix Ca2+, respectively, establishing F-EF as a two-way mitochondrial Ca2+ regulator. Thus, we show how to synergize AI prediction with NMR data, elucidating a solution-specific and extraordinary LETM1 F-EF-hand.

STIM Proteins: The Gas and Brake of Calcium Entry in Neurons

Stromal interaction molecules (STIM)s are Ca2+ sensors in internal Ca2+ stores of the endoplasmic reticulum. They activate the store-operated Ca2+ channels, which are the main source of Ca2+ entry in non-excitable cells. Moreover, STIM proteins interact with other Ca2+ channel subunits and active transporters, making STIMs an important intermediate molecule in orchestrating a wide variety of Ca2+ influxes into excitable cells. Nevertheless, little is known about the role of STIM proteins in brain functioning. Being involved in many signaling pathways, STIMs replenish internal Ca2+ stores in neurons and mediate synaptic transmission and neuronal excitability. Ca2+ dyshomeostasis is a signature of many pathological conditions of the brain, including neurodegenerative diseases, injuries, stroke, and epilepsy. STIMs play a role in these disturbances not only by supporting abnormal store-operated Ca2+ entry but also by regulating Ca2+ influx through other channels. Here, we review the present knowledge of STIMs in neurons and their involvement in brain pathology.

IQCN disruption causes fertilization failure and male infertility due to manchette assembly defect

Total fertilization failure (TFF) is an important cause of infertility; however, the genetic basis of TFF caused by male factors remains to be clarified. In this study, whole-exome sequencing was firstly used to screen for genetic causes of TFF after intracytoplasmic sperm injection (ICSI), and homozygous variants in the novel gene IQ motif-containing N (IQCN) were identified in two affected individuals with abnormal acrosome structures. Then, Iqcn-knockout mice were generated by CRISPR-Cas9 technology and showed that the knockout male mice resembled the human phenotypes. Additionally, we found that IQCN regulates microtubule nucleation during manchette assembly via calmodulin and related calmodulin-binding proteins, which resulted in head deformity with aberrant oocyte activation factor PLCζ. Fortunately, ICSI with assisted oocyte activation can overcome IQCN-associate TFF and male infertility. Thus, our study firstly identified the function of IQCN, highlights the relationship between the manchette assembly and fertilization, and provides a genetic marker and a therapeutic option for male-source TFF.

Dynamics and structural changes of calmodulin upon interaction with the antagonist calmidazolium

BACKGROUND

Calmodulin (CaM) is an evolutionarily conserved eukaryotic multifunctional protein that functions as the major sensor of intracellular calcium signaling. Its calcium-modulated function regulates the activity of numerous effector proteins involved in a variety of physiological processes in diverse organs, from proliferation and apoptosis, to memory and immune responses. Due to the pleiotropic roles of CaM in normal and pathological cell functions, CaM antagonists are needed for fundamental studies as well as for potential therapeutic applications. Calmidazolium (CDZ) is a potent small molecule antagonist of CaM and one the most widely used inhibitors of CaM in cell biology. Yet, CDZ, as all other CaM antagonists described thus far, also affects additional cellular targets and its lack of selectivity hinders its application for dissecting calcium/CaM signaling. A better understanding of CaM:CDZ interaction is key to design analogs with improved selectivity. Here, we report a molecular characterization of CaM:CDZ complexes using an integrative structural biology approach combining SEC-SAXS, X-ray crystallography, HDX-MS, and NMR.

RESULTS

We provide evidence that binding of a single molecule of CDZ induces an open-to-closed conformational reorientation of the two domains of CaM and results in a strong stabilization of its structural elements associated with a reduction of protein dynamics over a large time range. These CDZ-triggered CaM changes mimic those induced by CaM-binding peptides derived from physiological protein targets, despite their distinct chemical natures. CaM residues in close contact with CDZ and involved in the stabilization of the CaM:CDZ complex have been identified.

CONCLUSION

Our results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists. Calmidazolium is a potent and widely used inhibitor of calmodulin, a major mediator of calcium-signaling in eukaryotic cells. Structural characterization of calmidazolium-binding to calmodulin reveals that it triggers open-to-closed conformational changes similar to those induced by calmodulin-binding peptides derived from enzyme targets. These results provide molecular insights into CDZ-induced dynamics and structural changes of CaM leading to its inhibition and open the way to the rational design of more selective CaM antagonists.

Cardiac K+ Channels and Channelopathies

The physiological heart function is controlled by a well-orchestrated interplay of different ion channels conducting Na⁺, Ca²⁺ and K⁺. Cardiac K⁺ channels are key players of cardiac repolarization counteracting depolarizating Na⁺ and Ca²⁺ currents. In contrast to Na⁺ and Ca²⁺, K⁺ is conducted by many different channels that differ in activation/deactivation kinetics as well as in their contribution to different phases of the action potential. Together with modulatory subunits these K⁺ channel α-subunits provide a wide range of repolarizing currents with specific characteristics. Moreover, due to expression differences, K⁺ channels strongly influence the time course of the action potentials in different heart regions. On the other hand, the variety of different K⁺ channels increase the number of possible disease-causing mutations. Up to now, a plethora of gain- as well as loss-of-function mutations in K⁺ channel forming or modulating proteins are known that cause severe congenital cardiac diseases like the long-QT-syndrome, the short-QT-syndrome, the Brugada syndrome and/or different types of atrial tachyarrhythmias. In this chapter we provide a comprehensive overview of different K⁺ channels in cardiac physiology and pathophysiology.

The protein phosphatase with EF-hand domain 1 is a calmodulin-binding protein that interacts with proteins involved in sperm capacitation, binding to the zona pellucida, and motility

Spermatozoa are highly specialized cells whose fertilizing and motility functions highly depend on intracellular Ca²⁺ -mediated events and protein posttranslational modifications like phosphorylation. Our group previously identified PPEF1, the Ser/Thr phosphatase with EF-hand domain 1, among calmodulin-affinity pulled down sperm proteins. As the mammalian ortholog of the Drosophila phosphatase rdgC that dephosphorylates rhodopsin, PPEF1 has been studied mostly in the retina. The presence and importance of this Ca²⁺ /calmodulin-binding protein phosphatase has not been studied in sperm or testicular functions despite its high expression level. In this study, we show that PPEF1 is present in testicular germ cells, and in mouse, human and bull spermatozoa where it is localized predominantly in the neck and acrosome areas. Different transcript variants encoding four predicted isoforms were detected by reverse transcription polymerase chain reaction in bull testis, spermatocytes and spermatids. Phosphatase activity of immunoprecipitated sperm PPEF1 was detected using the substrate pNPP and analysis of the coimmunoprecipitated proteins reveal an enrichment in the biological processes of sperm capacitation, binding to the zona pellucida and motility. Although this is the first demonstration of the presence of PPEF1 in sperm and testicular germ cells, its involvement in sperm fertilizing ability and motility, and the mechanisms regulating its activity remain to be further investigated.

More Than Just Simple Interaction between STIM and Orai Proteins: CRAC Channel Function Enabled by a Network of Interactions with Regulatory Proteins

The calcium-release-activated calcium (CRAC) channel, activated by the release of Ca2+ from the endoplasmic reticulum (ER), is critical for Ca2+ homeostasis and active signal transduction in a plethora of cell types. Spurred by the long-sought decryption of the molecular nature of the CRAC channel, considerable scientific effort has been devoted to gaining insights into functional and structural mechanisms underlying this signalling cascade. Key players in CRAC channel function are the Stromal interaction molecule 1 (STIM1) and Orai1. STIM1 proteins span through the membrane of the ER, are competent in sensing luminal Ca2+ concentration, and in turn, are responsible for relaying the signal of Ca2+ store-depletion to pore-forming Orai1 proteins in the plasma membrane. A direct interaction of STIM1 and Orai1 allows for the re-entry of Ca2+ from the extracellular space. Although much is already known about the structure, function, and interaction of STIM1 and Orai1, there is growing evidence that CRAC under physiological conditions is dependent on additional proteins to function properly. Several auxiliary proteins have been shown to regulate CRAC channel activity by means of direct interactions with STIM1 and/or Orai1, promoting or hindering Ca2+ influx in a mechanistically diverse manner. Various proteins have also been identified to exert a modulatory role on the CRAC signalling cascade although inherently lacking an affinity for both STIM1 and Orai1. Apart from ubiquitously expressed representatives, a subset of such regulatory mechanisms seems to allow for a cell-type-specific control of CRAC channel function, considering the rather restricted expression patterns of the specific proteins. Given the high functional and clinical relevance of both generic and cell-type-specific interacting networks, the following review shall provide a comprehensive summary of regulators of the multilayered CRAC channel signalling cascade. It also includes proteins expressed in a narrow spectrum of cells and tissues that are often disregarded in other reviews of similar topics.

Impact of arrhythmogenic calmodulin variants on small conductance Ca2+ -activated K+ (SK3) channels

Calmodulin (CaM) is a ubiquitous Ca²⁺‐sensing protein regulating many important cellular processes. Several CaM‐associated variants have been identified in a small group of patients with cardiac arrhythmias. The mechanism remains largely unknown, even though a number of ion channels, including the ryanodine receptors and the L‐type calcium channels have been shown to be functionally affected by the presence of mutant CaM. CaM is constitutively bound to the SK channel, which underlies the calcium‐gated I_SK contributing to cardiac repolarization. The CaM binding to SK channels is essential for gating, correct assembly, and membrane expression. To elucidate the effect of nine different arrhythmogenic CaM variants on SK3 channel function, HEK293 cells stably expressing SK3 were transiently co‐transfected with CaM^{WT or variant} and whole‐cell patch‐clamp recordings were performed with a calculated free Ca²⁺ concentration of 400 nmol/L. MDCK cells were transiently transfected with SK3 and/or CaM^{WT or variant} to address SK3 and CaM localization by immunocytochemistry. The LQTS‐associated variants CaM^D96V, CaM^D130G, and CaM^F142L reduced I_SK,Ca compared with CaM^WT (P < 0.01, P < 0.001, and P < 0.05, respectively). The CPVT associated variant CaM^N54I also reduced the I_SK,Ca (P < 0.05), which was linked to an accumulation of SK3/CaM^N54I channel complexes in intracellular compartments (P < 0.05). The CPVT associated variants, CaM^A103V and CaM^D132E only revealed a tendency toward reduced current, while the variants CaM^F90L and CaM^N98S, causing LQTS syndrome, did not have any impact on I_SK,Ca. In conclusion, we found that the arrhythmogenic CaM variants CaM^N54I, CaM^D96V, CaM^D130G, and CaM^F142L significantly down‐regulate the SK3 channel current, but with distinct mechanism.

Luminal STIM1 Mutants that Cause Tubular Aggregate Myopathy Promote Autophagic Processes

Stromal interaction molecule 1 (STIM1) is a ubiquitously expressed Ca2+ sensor protein that induces permeation of Orai Ca2+ channels upon endoplasmic reticulum Ca2+-store depletion. A drop in luminal Ca2+ causes partial unfolding of the N-terminal STIM1 domains and thus initial STIM1 activation. We compared the STIM1 structure upon Ca2+ depletion from our molecular dynamics (MD) simulations with a recent 2D NMR structure. Simulation- and structure-based results showed unfolding of two α-helices in the canonical and in the non-canonical EF-hand. Further, we structurally and functionally evaluated mutations in the non-canonical EF-hand that have been shown to cause tubular aggregate myopathy. We found these mutations to cause full constitutive activation of Ca2+-release-activated Ca2+ currents (ICRAC) and to promote autophagic processes. Specifically, heterologously expressed STIM1 mutations in the non-canonical EF-hand promoted translocation of the autophagy transcription factors microphthalmia-associated transcription factor (MITF) and transcription factor EB (TFEB) into the nucleus. These STIM1 mutations additionally stimulated an enhanced production of autophagosomes. In summary, mutations in STIM1 that cause structural unfolding promoted Ca2+ down-stream activation of autophagic processes.

Calcium enhances polyplex-mediated transfection efficiency of plasmid DNA in Jurkat cells

Jurkat, an immortalized cell line derived from human leukemic T lymphocytes, has been employed as an excellent surrogate model of human primary T-cells for the advancement of T-cell biology and their applications in medicine. However, presumably due to its T-cell origin, Jurkat cells are very difficult to transfect. Thus, for the genetic modification of Jurkat cells, expensive and time-consuming viral vectors are normally required. Despite many previous efforts, non-viral vectors have not yet overcome the hurdles of low transfection efficiency and/or high toxicity in transfection of Jurkat cells. Here, we report that a simple addition of calcium ions (Ca²⁺) into culture media at optimal concentrations can enhance the efficiency of the polyplex-mediated transfection using poly(ethylene imine) (PEI) by up to 12-fold when compared to the polyplex-only control. We show that calcium enhances the association between polyplex and Jurkat, which is at least partially responsible for the increase in transmembrane delivery of polyplex and consequential enhancement in expression of transgene. Other cations, Mg²⁺ or Na⁺ did not show similar enhancement. Interestingly, addition of Ca²⁺ was rather detrimental for the transfection of lipoplex on Jurkat cells. Observation of significant enhancement in the transfection of non-viral vectors with a simple and physiologically relevant reagent like Ca²⁺ in the engineering of hard-to-transfect cells such as Jurkat warrants further investigation on similar strategies.

Calmodulin disrupts plasma membrane localization of farnesylated KRAS4b by sequestering its lipid moiety

KRAS4b is a small guanosine triphosphatase (GTPase) protein that regulates several signal transduction pathways that underlie cell proliferation, differentiation, and survival. KRAS4b function requires prenylation of its C terminus and recruitment to the plasma membrane, where KRAS4b activates effector proteins including the RAF family of kinases. The Ca²⁺-sensing protein calmodulin (CaM) has been suggested to regulate the localization of KRAS4b through direct, Ca²⁺-dependent interaction, but how CaM and KRAS4b functionally interact is controversial. Here, we determined a crystal structure, which was supported by solution nuclear magnetic resonance (NMR), that revealed the sequestration of the prenyl moiety of KRAS4b in the hydrophobic pocket of the C-terminal lobe of Ca²⁺-bound CaM. Our engineered fluorescence resonance energy transfer (FRET)-based biosensor probes (CaMeRAS) showed that, upon stimulation of Ca²⁺ influx by extracellular ligands, KRAS4b reversibly translocated in a Ca²⁺-CaM-dependent manner from the plasma membrane to the cytoplasm in live HeLa and HEK293 cells. These results reveal a mechanism underlying the inhibition of KRAS4b activity by Ca²⁺ signaling pathways.

A Compartmentalized Reduction in Membrane-Proximal Calmodulin Reduces the Immune Surveillance Capabilities of CD8+ T Cells in Head and Neck Cancer

The limited ability of cytotoxic CD8+ T cells to infiltrate solid tumors and function within the tumor microenvironment presents a major roadblock to effective immunotherapy. Ion channels and Ca2+-dependent signaling events control the activity of T cells and are implicated in the failure of immune surveillance in cancer. Reduced KCa3.1 channel activity mediates the heightened inhibitory effect of adenosine on the chemotaxis of circulating T cells from head and neck squamous cell carcinoma (HNSCC) patients. Herein, we conducted experiments that elucidate the mechanisms of KCa3.1 dysfunction and impaired chemotaxis in HNSCC CD8+ T cells. The Ca2+ sensor calmodulin (CaM) controls multiple cellular functions including KCa3.1 activation. Our data showed that CaM expression is lower in HNSCC than healthy donor (HD) T cells. This reduction was due to an intrinsic decrease in the genes encoding CaM combined to the failure of HNSCC T cells to upregulate CaM upon activation. Furthermore, the reduction in CaM was confined to the plasma membrane and resulted in decreased CaM-KCa3.1 association and KCa3.1 activity (which was rescued by the delivery of CaM). IFNγ production, also Ca2+- and CaM-dependent, was instead not reduced in HNSCC T cells, which maintained intact cytoplasmic CaM and Ca2+ fluxing ability. Knockdown of CaM in HD T cells decreased KCa3.1 activity, but not IFNγ production, and reduced their chemotaxis in the presence of adenosine, thus recapitulating HNSCC T cell dysfunction. Activation of KCa3.1 with 1-EBIO restored the ability of CaM knockdown HD T cells to chemotax in the presence of adenosine. Additionally, 1-EBIO enhanced INFγ production. Our data showed a localized downregulation of membrane-proximal CaM that suppressed KCa3.1 activity in HNSCC circulating T cells and limited their ability to infiltrate adenosine-rich tumor-like microenvironments. Furthermore, they indicate that KCa3.1 activators could be used as positive CD8+ T cell modulators in cancers.

Exploiting the protein corona: coating of black phosphorus nanosheets enables macrophage polarization via calcium influx

Black phosphorus nanosheets (BPNSs) have substantially promoted biomedical nanotechnology due to their unique photothermal and chemotherapeutic properties. However, there is still a limited molecular understanding of the effects of bio-nano interfaces on BPNSs and the subsequent impacts on physiological systems. Here, it is shown that black phosphorus-corona complexes (BPCCs) could function as immune modulators to promote the polarization of macrophages. Mechanistically, BPCCs could interact with calmodulin to activate stromal interaction molecule 2 and facilitate Ca2+ influx in macrophages, which induced the activation of p38 and NF-κB and polarized M0 macrophages to the M1 phenotype. As a result, BPCC-activated macrophages show greater migration towards cancer cells, 1.3-1.9 times higher cellular cytotoxicity and effective phagocytosis of cancer cells. These findings offer insights into the development of potential and unique applications of corona on BPNSs in nanomedicine.

Sequential activation of STIM1 links Ca2+ with luminal domain unfolding

The stromal interaction molecule 1 (STIM1) has two important functions, Ca2+ sensing within the endoplasmic reticulum and activation of the store-operated Ca2+ channel Orai1, enabling plasma-membrane Ca2+ influx. We combined molecular dynamics (MD) simulations with live-cell recordings and determined the sequential Ca2+-dependent conformations of the luminal STIM1 domain upon activation. Furthermore, we identified the residues within the canonical and noncanonical EF-hand domains that can bind to multiple Ca2+ ions. In MD simulations, a single Ca2+ ion was sufficient to stabilize the luminal STIM1 complex. Ca2+ store depletion destabilized the two EF hands, triggering disassembly of the hydrophobic cleft that they form together with the stable SAM domain. Point mutations associated with tubular aggregate myopathy or cancer that targeted the canonical EF hand, and the hydrophobic cleft yielded constitutively clustered STIM1, which was associated with activation of Ca2+ entry through Orai1 channels. On the basis of our results, we present a model of STIM1 Ca2+ binding and refine the currently known initial steps of STIM1 activation on a molecular level.

Ca2+-Binding Proteins of the EF-Hand Superfamily: Diagnostic and Prognostic Biomarkers and Novel Therapeutic Targets

A multitude of Ca²⁺-sensor proteins containing the specific Ca²⁺-binding motif (helix-loop-helix, called EF-hand) are of major clinical relevance in a many human diseases. Measurements of troponin, the first intracellular Ca-sensor protein to be discovered, is nowadays the "gold standard" in the diagnosis of patients with acute coronary syndrome (ACS). Mutations have been identified in calmodulin and linked to inherited ventricular tachycardia and in patients affected by severe cardiac arrhythmias. Parvalbumin, when introduced into the diseased heart by gene therapy to increase contraction and relaxation speed, is considered to be a novel therapeutic strategy to combat heart failure. S100 proteins, the largest subgroup with the EF-hand protein family, are closely associated with cardiovascular diseases, various types of cancer, inflammation, and autoimmune pathologies. The intention of this review is to summarize the clinical importance of this protein family and their use as biomarkers and potential drug targets, which could help to improve the diagnosis of human diseases and identification of more selective therapeutic interventions.

Toward understanding calmodulin plasticity by molecular dynamics

Aim: Calmodulin interacts in many different ways with its ligands. We aim to shed light on its plasticity analyzing the changes followed by the linker region and the relative position of the lobes using conventional molecular dynamics, accelerated MD and scaled MD (sMD). Materials & methods: Three different structures of calmodulin are compared, obtaining a total of 2.5 μs of molecular dynamics, which have been analyzed using the principal component analysis and clustering methodologies. Results: sMD simulations reach conformations that conventional molecular dynamics is not able to, without compromising the stability of the protein. On the other hand, accelerated MD requires optimization of the setup parameters to be useful. Conclusion: sMD is useful to study flexible proteins, highlighting those factors that justify its promiscuity.

Excessive mechanical stress induces chondrocyte apoptosis through TRPV4 in an anterior cruciate ligament-transected rat osteoarthritis model

AIMS

Chondrocyte apoptosis is the most common pathological feature of cartilage in osteoarthritis (OA). Excessive mechanical stress can induce chondrocyte apoptosis and destroy cartilage tissue. Transient receptor potential channel vanilloid 4 (TRPV4) is a mechanosensitive ion channel that mediates chondrocyte response to mechanical stress. Here, we investigated the potential role of TRPV4 in chondrocyte apoptosis induced by excessive mechanical stress.

MAIN METHODS

Using a rat OA anterior cruciate-ligament transection (ALCT) model, we detected immunolocalization of calmodulin protein and mRNA and protein levels of TRPV4, calmodulin, and cleaved caspase-8 in articular cartilage. Primary chondrocytes were isolated and cultured in vitro, and Fluo-4AM staining was used to assess intracellular Ca²⁺ levels in order to evaluate TRPV4-mediated Ca²⁺ influx. Flow cytometry and western blot were performed to detect apoptosis and apoptosis-related protein levels in chondrocytes, respectively.

KEY FINDINGS

TRPV4 was upregulated in ALCT-induced OA articular cartilage, and we found that administration of a TRPV4 inhibitor attenuated cartilage degeneration. Additionally, TRPV4 specifically mediated extracellular Ca²⁺ influx, leading to chondrocyte apoptosis in vitro, which was inhibited by transfection of TRPV4 small-interfering RNA or administration of a TRPV4 inhibitor. Moreover, increased Ca²⁺ influx triggered apoptosis by upregulating FAS-associated protein with death domain and cleaved caspase-3, -6, -7, and -8 levels, with these effects abolished by TRPV4 knockdown or TRPV4 inhibition.

SIGNIFICANCE

These results indicated that TRPV4 was upregulated in OA articular cartilage, and that excessive mechanical stress might induce chondrocyte apoptosis via TRPV4-mediated Ca²⁺ influx, suggesting TRPV4 as a potential drug target in OA.

The Crossroad of Ion Channels and Calmodulin in Disease

Calmodulin (CaM) is the principal Ca²⁺ sensor in eukaryotic cells, orchestrating the activity of hundreds of proteins. Disease causing mutations at any of the three genes that encode identical CaM proteins lead to major cardiac dysfunction, revealing the importance in the regulation of excitability. In turn, some mutations at the CaM binding site of ion channels cause similar diseases. Here we provide a summary of the two sides of the partnership between CaM and ion channels, describing the diversity of consequences of mutations at the complementary CaM binding domains.

Expression and Purification of Calmodulin for NMR and Other Biophysical Applications

Calmodulin (CaM) is a ubiquitous calcium-sensing protein that has one of the most highly conserved sequences among eukaryotes. CaM has been a useful tool for biologists studying calcium signaling for decades. In recent years, CaM has also been implicated in numerous cancer-associated pathways, and rare CaM mutations have been identified as a cause of human cardiac arrhythmias. Here, we present a collection of our most recent and effective protocols for the expression and purification of recombinant CaM from Escherichia coli, including various isotopic labeling schemes, primarily for nuclear magnetic resonance (NMR) spectroscopy and other biophysical applications.

Calmodulinopathy: Functional Effects of CALM Mutations and Their Relationship With Clinical Phenotypes

In spite of the widespread role of calmodulin (CaM) in cellular signaling, CaM mutations lead specifically to cardiac manifestations, characterized by remarkable electrical instability and a high incidence of sudden death at young age. Penetrance of the mutations is surprisingly high, thus postulating a high degree of functional dominance. According to the clinical patterns, arrhythmogenesis in CaM mutations can be attributed, in the majority of cases, to either prolonged repolarization (as in long-QT syndrome, LQTS phenotype), or to instability of the intracellular Ca2+ store (as in catecholamine-induced tachycardias, CPVT phenotype). This review discusses how mutations affect CaM signaling function and how this may relate to the distinct arrhythmia phenotypes/mechanisms observed in patients; this involves mechanistic interpretation of negative dominance and mutation-specific CaM-target interactions. Knowledge of the mechanisms involved may allow critical approach to clinical manifestations and aid in the development of therapeutic strategies for "calmodulinopathies," a recently identified nosological entity.

STIM1 and Orai1 regulate Ca2+ microdomains for activation of transcription

Since calcium (Ca²⁺) regulates a large variety of cellular signaling processes in a cell's life, precise control of Ca²⁺ concentrations within the cell is essential. This enables the transduction of information via Ca²⁺ changes in a time-dependent and spatially defined manner. Here, we review molecular and functional aspects of how the store-operated Ca²⁺ channel Orai1 creates spatiotemporal Ca²⁺ microdomains. The architecture of this channel is unique, with a long helical pore and a six-fold symmetry. Energetic barriers within the Ca²⁺ channel pathway limit permeation to allow an extensive local Ca²⁺ increase in close proximity to the channel. The precise timing of the Orai1 channel function is controlled by direct binding to STIM proteins upon Ca²⁺ depletion in the endoplasmic reticulum. These induced Ca²⁺ microdomains are tailored to, and sufficient for, triggering long-term activation processes, such as transcription factor activation and subsequent gene regulation. We describe the principles of spatiotemporal activation of the transcription factor NFAT and compare its signaling characteristics to those of the autophagy regulating transcription factors, MITF and TFEB.

Allosteric regulators selectively prevent Ca2+-feedback of CaV and NaV channels

Calmodulin (CaM) serves as a pervasive regulatory subunit of Ca_V1, Ca_V2, and Na_V1 channels, exploiting a functionally conserved carboxy-tail element to afford dynamic Ca²⁺-feedback of cellular excitability in neurons and cardiomyocytes. Yet this modularity counters functional adaptability, as global changes in ambient CaM indiscriminately alter its targets. Here, we demonstrate that two structurally unrelated proteins, SH3 and cysteine-rich domain (stac) and fibroblast growth factor homologous factors (fhf) selectively diminish Ca²⁺/CaM-regulation of Ca_V1 and Na_V1 families, respectively. The two proteins operate on allosteric sites within upstream portions of respective channel carboxy-tails, distinct from the CaM-binding interface. Generalizing this mechanism, insertion of a short RxxK binding motif into Ca_V1.3 carboxy-tail confers synthetic switching of CaM regulation by Mona SH3 domain. Overall, our findings identify a general class of auxiliary proteins that modify Ca²⁺/CaM signaling to individual targets allowing spatial and temporal orchestration of feedback, and outline strategies for engineering Ca²⁺/CaM signaling to individual targets.

Calmodulin Enhances Cryptochrome Binding to INAD in Drosophila Photoreceptors

Light is the main environmental stimulus that synchronizes the endogenous timekeeping systems in most terrestrial organisms. Drosophila cryptochrome (dCRY) is a light-responsive flavoprotein that detects changes in light intensity and wavelength around dawn and dusk. We have previously shown that dCRY acts through Inactivation No Afterpotential D (INAD) in a light-dependent manner on the Signalplex, a multiprotein complex that includes visual-signaling molecules, suggesting a role for dCRY in fly vision. Here, we predict and demonstrate a novel Ca²⁺-dependent interaction between dCRY and calmodulin (CaM). Through yeast two hybrid, coimmunoprecipitation (Co-IP), nuclear magnetic resonance (NMR) and calorimetric analyses we were able to identify and characterize a CaM binding motif in the dCRY C-terminus. Similarly, we also detailed the CaM binding site of the scaffold protein INAD and demonstrated that CaM bridges dCRY and INAD to form a ternary complex in vivo. Our results suggest a process whereby a rapid dCRY light response stimulates an interaction with INAD, which can be further consolidated by a novel mechanism regulated by CaM.

Structural and functional diversity of EF-hand proteins: Evolutionary perspectives

We have classified 865 sequences of EF-hand proteins from five proteomes into 156 subfamilies. These subfamilies were put into six groups. Evolutionary relationships among subfamilies and groups were analyzed from the inferred ancestral sequence for each subfamily. CTER, CPV, and PEF groups arose from a common EF-lobe (pair of adjacent EF-hands). They have two or more EF-lobes; the relative positions of their EF-lobes differ from each other. Comparisons of the ancestral sequences and the inferred structures of the EF-lobes of these groups indicate that the mutual positions of EF-lobes were established soon after divergence of an EF-lobe for each group and before the duplication and fusion of EF-lobe gene(s). These ancestral sequences reveal that some subfamilies in low similarity and isolated groups did not evolve from the EF-lobe precursor, even if their conformations are similar to the canonical EF-hand. This is an example of convergent evolution.

Comparison of the protein expression of calpain-1, calpain-2, calpastatin and calmodulin between gastric cancer and normal gastric mucosa

The understanding of molecular mechanisms that are involved in the development and the progression of gastric cancer (GC) are of importance for the diagnosis and treatment. The calpain system, which contains the calpains and the endogenous inhibitor, has been suggested as an important factor in the tumorigenesis and migration of colorectal adenocarcinoma, breast and ovarian cancer, and as a prognostic marker for GC. However, the expression level of calpain system proteins in GC and normal-appearing peritumoral gastric mucosa remain unknown. The present study investigated the expression of calpain-1 (CAPN1), calpain-2 (CAPN2), calpastatin and calmodulin (CaM) in GC and uninvolved gastric mucosa tissues with immunohistochemistry. Results demonstrated that CAPN2 protein level increased in GCs compared with normal tissues, while calpastatin and CaM protein level decreased. No evident alterations were observed for CAPN1. Although the protein expression of all these four proteins was not in association with the clinical variables of GC in the present study, higher calpain enzyme activity could be a negative prognostic marker, since calpains are responsible for the generation of active forms of certain proteins that facilitate the progression of cancer. The ratio of (CAPN1 × CAPN2)/(calpastatin × CaM) may serve as a potential index for diagnosis of GC.

Cloning and Stress-Induced Expression Analysis of Calmodulin in the Antarctic Alga Chlamydomonas sp. ICE-L

Calmodulin (CaM) is a Ca²⁺-binding protein that plays a role in several Ca²⁺ signaling pathways, which dynamically regulates the activities of hundreds of proteins. The ice alga Chlamydomonas sp. ICE-L, which has the ability to adapt to extreme polar conditions, is a crucial primary producer in Antarctic ecosystem. This study hypothesized that Cam helps the ICE-L to adapt to the fluctuating conditions in the polar environment. It first verified the overall length of Cam, through RT-PCR and RACE-PCR, based on partial Cam transcriptome library of ICE-L. Then, the nucleotide and predicted amino acid sequences were, respectively, analyzed by various bioinformatics approaches to gain more insights into the computed physicochemical properties of the CaM. Potential involvements of Cam in responding to certain stimuli (i.e., UVB radiation, high salinity, and temperature) were investigated by differential expression, measuring its transcription levels by means of quantitative RT-PCR. Results showed that CaM was indeed inducible and regulated by high UVB radiation, high salinity, and nonoptimal temperature conditions. Different conditions had different expression tendencies, which provided an important basis for investigating the adaptation mechanism of Cam in ICE-L.

On the Ca2+ binding and conformational change in EF-hand domains: Experimental evidence of Ca2+-saturated intermediates of N-domain of calmodulin

Double mutation of Q41L and K75I in the N-domain of calmodulin (N-Cam) stabilizes the closed form of N-Cam such that binding of Ca²⁺ in solution no longer triggers a conformational change to the open form, and its Ca²⁺ binding affinity decreases dramatically. To further investigate the solvation effects on the structure, Ca²⁺ binding affinity and conformational dynamics of this N-Cam double mutant in the Ca²⁺ saturated state, we solved its X-ray structure. Surprisingly, the structure revealed an open conformation of the domain which contradicts its closed conformation in solution. Here we provide evidence that crystallization conditions were responsible for this Ca²⁺-saturated domain open conformation in the crystal. Importantly, we demonstrate that the presence of the crystallization co-precipitant and alcohols were able to induce a progressive opening of the closed form of this domain, in Ca²⁺ saturated state, in solution. However, in the Ca²⁺ depleted state, addition of alcohols was unable to induce any opening of this domain in solution. In addition, in the Ca²⁺ saturated state, the molecular dynamics simulations show that while N-Cam can populate the open and closed conformation, the N-Cam double mutant exclusively populates the closed conformation. Our results provide experimental evidence of intermediate conformations of Ca²⁺-saturated N-Cam in solution. We propose that conformational change of Ca²⁺ sensor EF-hand domains depends on solvation energetics, Ca²⁺ binding to promote the full open form, Ca²⁺ depleted state conformational dynamics, and the chemical properties of the molecules nearby key residues such as those at positions 41 and 75 in N-Cam.

The role of calcium concentration in the invasive capacity of Corbicula fluminea in crystalline basins

The natural variation of environmental factors in freshwater basins determines their biodiversity. Among them, calcium is a key physiological compound for freshwater invertebrates. It is required for shell formation, muscle contraction, it mediates gene expression and allows counteracting acidosis during stress periods, among other functions. Although the distribution of different freshwater species has been suggested to be linked with the environmental calcium concentration, as yet, no research studies have confirmed this. Identifying whether environmental calcium concentrations might determine the invasion success of alien species would be critical in developing and implementing effective management strategies to control them. Here, a multidisciplinary approach integrating field surveys, analytical chemistry techniques, molecular biology analyses and a lab-scale experiment was taken to decipher whether the environmental calcium concentration might hamper the establishment of Corbicula fluminea in northwestern Iberian rivers. A Principal Component Analysis on water chemistry variables from 13 water bodies identified environmental calcium concentration, among others, as one key factor that best characterized the distribution area of C. fluminea. The calcium content in animals' bodies from two representative rivers was dependent on the environmental calcium concentration of freshwater basins; the lower the concentration, the lower the body's content. The expression of stress- and calcium homeostasis-related genes was higher in C. fluminea from low calcium concentration environments than in those from calcium-rich freshwater basins. Finally, under experimental conditions, lower water calcium concentrations decreased C. fluminea growth rates. The present data suggest, for the first time, that environmental calcium concentration may act as a determinant factor on the invasion success of C. fluminea in freshwater environments. Our results provide new clues for the identification of basins with increased risk of potential invasion by C. fluminea based on environmental calcium levels.

Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis

Structural flexibility and conformational rearrangements are often related to important functions of biological macromolecules, but the experimental characterization of such transitions with high-resolution techniques is challenging. At a lower resolution, small angle X-ray scattering (SAXS) can be used to obtain information on biomolecular shapes and transitions in solution. Here, we present SREFLEX, a hybrid modeling approach that uses normal mode analysis (NMA) to explore the conformational space of high-resolution models and refine the structure guided by the agreement with the experimental SAXS data. The method starts from a given conformation of the protein (which does not agree with the SAXS data). The structure is partitioned into pseudo-domains either using structural classification databases or automatically from the protein dynamics as predicted by the NMA. The algorithm proceeds hierarchically employing NMA to first probe large rearrangements and progresses into smaller and more localized movements. At the large rearrangements stage the pseudo-domains stay as rigid bodies allowing one to avoid structural disruptions inherent to the earlier NMA-based algorithms. To validate the approach, we compiled a representative benchmark set of 88 conformational states known experimentally at high resolution. The performance of the algorithm is demonstrated in the simulated data on the benchmark set and also in a number of experimental examples. SREFLEX is included into the ATSAS program package freely available to the academic users, both for download and in the on-line mode.

From Stores to Sinks: Structural Mechanisms of Cytosolic Calcium Regulation

All eukaryotic cells have adapted the use of the calcium ion (Ca²⁺) as a universal signaling element through the evolution of a toolkit of Ca²⁺ sensor, buffer and effector proteins. Among these toolkit components, integral and peripheral proteins decorate biomembranes and coordinate the movement of Ca²⁺ between compartments, sense these concentration changes and elicit physiological signals. These changes in compartmentalized Ca²⁺ levels are not mutually exclusive as signals propagate between compartments. For example, agonist induced surface receptor stimulation can lead to transient increases in cytosolic Ca²⁺ sourced from endoplasmic reticulum (ER) stores; the decrease in ER luminal Ca²⁺ can subsequently signal the opening surface channels which permit the movement of Ca²⁺ from the extracellular space to the cytosol. Remarkably, the minuscule compartments of mitochondria can function as significant cytosolic Ca²⁺ sinks by taking up Ca²⁺ in a coordinated manner. In non-excitable cells, inositol 1,4,5 trisphosphate receptors (IP₃Rs) on the ER respond to surface receptor stimulation; stromal interaction molecules (STIMs) sense the ER luminal Ca²⁺ depletion and activate surface Orai1 channels; surface Orai1 channels selectively permit the movement of Ca²⁺ from the extracellular space to the cytosol; uptake of Ca²⁺ into the matrix through the mitochondrial Ca²⁺ uniporter (MCU) further shapes the cytosolic Ca²⁺ levels. Recent structural elucidations of these key Ca²⁺ toolkit components have improved our understanding of how they function to orchestrate precise cytosolic Ca²⁺ levels for specific physiological responses. This chapter reviews the atomic-resolution structures of IP₃R, STIM1, Orai1 and MCU elucidated by X-ray crystallography, electron microscopy and NMR and discusses the mechanisms underlying their biological functions in their respective compartments within the cell.

Solution of the structure of a calmodulin–peptide complex in a novel configuration from a variably twinned data set

Structure determination of conformationally variable proteins can prove challenging even when many possible molecular-replacement (MR) search models of high sequence similarity are available. Calmodulin (CaM) is perhaps the best-studied archetype of these flexible proteins: while there are currently ∼450 structures of significant sequence similarity available in the Protein Data Bank (PDB), novel conformations of CaM and complexes thereof continue to be reported. Here, the details of the solution of a novel peptide–CaM complex structure by MR are presented, in which only one MR solution of marginal quality was found despite the use of 120 different search models, an exclusivity enhanced by the presence of a high degree of hemihedral twinning (overall refined twin fraction = 0.43). Ambiguities in the initial MR electron-density maps were overcome by using MR-SAD: phases from the MR partial model were used to identify weak anomalous scatterers (calcium, sulfur and chloride), which were in turn used to improve the phases, automatically rebuild the structure and resolve sequence ambiguities. Retrospective analysis of consecutive wedges of the original data sets showed twin fractions ranging from 0.32 to 0.55, suggesting that the data sets were variably twinned. Despite these idiosyncrasies and obstacles, the data themselves and the final model were of high quality and indeed showed a novel, nearly right-angled conformation of the bound peptide.

Why Calcium? How Calcium Became the Best Communicator

Calcium carries messages to virtually all important functions of cells. Although it was already active in unicellular organisms, its role became universally important after the transition to multicellular life. In this Minireview, we explore how calcium ended up in this privileged position. Most likely its unique coordination chemistry was a decisive factor as it makes its binding by complex molecules particularly easy even in the presence of large excesses of other cations, e.g. magnesium. Its free concentration within cells can thus be maintained at the very low levels demanded by the signaling function. A large cadre of proteins has evolved to bind or transport calcium. They all contribute to buffer it within cells, but a number of them also decode its message for the benefit of the target. The most important of these "calcium sensors" are the EF-hand proteins. Calcium is an ambivalent messenger. Although essential to the correct functioning of cell processes, if not carefully controlled spatially and temporally within cells, it generates variously severe cell dysfunctions, and even cell death.

Molecular modulators of store-operated calcium entry

Three decades ago, store-operated Ca(2+) entry (SOCE) was identified as a unique mechanism for Ca(2+) entry through plasma membrane (PM) Ca(2+)-permeable channels modulated by the intracellular Ca(2+) stores, mainly the endoplasmic reticulum (ER). Extensive analysis of the communication between the ER and the PM leads to the identification of the protein STIM1 as the ER-Ca(2+) sensor that gates the Ca(2+) channels in the PM. Further analysis on the biophysical, electrophysiological and biochemical properties of STIM1-dependent Ca(2+) channels has revealed the presence of a highly Ca(2+)-selective channel termed Ca(2+) release-activated Ca(2+) channel (CRAC), consisting of Orai1 subunits, and non-selective cation channels named store-operated channels (SOC), including both Orai1 and TRPC channel subunits. Since the identification of the key elements of CRAC and SOC channels a number of intracellular modulators have been reported to play essential roles in the stabilization of STIM-Orai interactions, collaboration with STIM1 conformational changes or mediating slow Ca(2+)-dependent inactivation. Here, we review our current understanding of some of the key modulators of STIM1-Orai1 interaction, including the proteins CRACR2A, STIMATE, SARAF, septins, golli and ORMDL3.