The Structure of the Complex of Calmodulin with KAR-2

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.

The X-ray structure of juvenile hormone diol kinase from the silkworm Bombyx mori

Insect juvenile hormones (JHs) are a family of sesquiterpenoid molecules that are secreted into the haemolymph. JHs have multiple roles in insect development, metamorphosis and sexual maturation. A number of pesticides work by chemically mimicking JHs, thus preventing insects from developing and reproducing normally. The haemolymph levels of JH are governed by the rates of its biosynthesis and degradation. One enzyme involved in JH catabolism is JH diol kinase (JHDK), which uses ATP (or GTP) to phosphorylate JH diol to JH diol phosphate, which can be excreted. The X-ray structure of JHDK from the silkworm Bombyx mori has been determined at a resolution of 2.0 Å with an R factor of 19.0% and an Rfree of 24.8%. The structure possesses three EF-hand motifs which are occupied by calcium ions. This is in contrast to the recently reported structure of the JHDK-like-2 protein from B. mori (PDB entry 6kth), which possessed only one calcium ion. Since JHDK is known to be inhibited by calcium ions, it is likely that our structure represents the calcium-inhibited form of the enzyme. The electrostatic surface of the protein suggests a binding site for the triphosphate of ATP close to the N-terminal end of the molecule in a cavity between the N- and C-terminal domains. Superposition with a number of calcium-activated photoproteins suggests that there may be parallels between the binding of JH diol to JHDK and the binding of luciferin to aequorin.

High-affinity tamoxifen analogues retain extensive positional disorder when bound to calmodulin

Using a combination of NMR and fluorescence measurements, we have investigated the structure and dynamics of the complexes formed between calcium-loaded calmodulin (CaM) and the potent breast cancer inhibitor idoxifene, a derivative of tamoxifen. High-affinity binding (K d ∼ 300  nM) saturates with a 2 : 1 idoxifene : CaM complex. The complex is an ensemble where each idoxifene molecule is predominantly in the vicinity of one of the two hydrophobic patches of CaM but, in contrast with the lower-affinity antagonists TFP, J-8, and W-7, does not substantially occupy the hydrophobic pocket. At least four idoxifene orientations per domain of CaM are necessary to satisfy the intermolecular nuclear Overhauser effect (NOE) restraints, and this requires that the idoxifene molecules switch rapidly between positions. The CaM molecule is predominantly in the form where the N and C-terminal domains are in close proximity, allowing for the idoxifene molecules to contact both domains simultaneously. Hence, the 2 : 1 idoxifene : CaM complex illustrates how high-affinity binding occurs without the loss of extensive positional dynamics.

Conformational heterogeneity of the calmodulin binding interface

Calmodulin (CaM) is a ubiquitous Ca(2+) sensor and a crucial signalling hub in many pathways aberrantly activated in disease. However, the mechanistic basis of its ability to bind diverse signalling molecules including G-protein-coupled receptors, ion channels and kinases remains poorly understood. Here we harness the high resolution of molecular dynamics simulations and the analytical power of Markov state models to dissect the molecular underpinnings of CaM binding diversity. Our computational model indicates that in the absence of Ca(2+), sub-states in the folded ensemble of CaM's C-terminal domain present chemically and sterically distinct topologies that may facilitate conformational selection. Furthermore, we find that local unfolding is off-pathway for the exchange process relevant for peptide binding, in contrast to prior hypotheses that unfolding might account for binding diversity. Finally, our model predicts a novel binding interface that is well-populated in the Ca(2+)-bound regime and, thus, a candidate for pharmacological intervention.

Calmodulin inhibitors from natural sources: an update

Calmodulin (CaM) plays a central role in regulating a myriad of cellular functions in physiological and pathophysiological processes, thus representing an important drug target. In previous reviews, our group has reported relevant information regarding natural anti-CaM compounds up to 2009. Natural sources continue to provide a diverse and unique reservoir of CaM inhibitors for drug and research tool discovery. This review provides an update of natural products with reported CaM inhibitory properties, which includes around 70 natural products and some synthetic analogues, belonging to different structural classes. Most of these natural inhibitors were isolated from fungi and plants and belong to the stilbenoid, polyketide, alkaloid, and peptide structural classes. These products were discovered mainly using a fluorescence-based method on rationally designed biosensors, which are highly specific, low-cost, and selective and have short reaction times. The effect of several antimitotic drugs on Ca(2+)-hCaM is also described.

Structural insights into the mechanism of calmodulin binding to death receptors

The death receptors Fas, p75NTRand DR6 are key components of extrinsically activated apoptosis. Characterization of how they interact with the adaptors is crucial in order to unravel the signalling mechanisms. However, the exact conformation that their intracellular death domain adopts upon binding downstream partners remains unclear. One model suggests that it adopts a typical compact fold, whilst a second model proposed an open conformation. Calmodulin (CaM), a major calcium sensor, has previously been reported to be one of the Fas adaptors that modulate apoptosis. This work reports that CaM also binds directly to the death domains of p75NTRand DR6, indicating that it serves as a common modulator of the death receptors. Two crystal structures of CaM in complexes with the corresponding binding regions of Fas and p75NTRare also reported. Interestingly, the precise CaM-binding sites were mapped to different regions: helix 1 in Fas and helix 5 in p75NTRand DR6. A novel 1–11 motif for CaM binding was observed in p75NTR. Modelling the complexes of CaM with full-length receptors reveals that the opening of the death domains would be essential in order to expose their binding sites for CaM. These results may facilitate understanding of the diverse functional repertoire of death receptors and CaM and provide further insights necessary for the design of potential therapeutic peptide agents.

Mapping the sevoflurane-binding sites of calmodulin

General anesthetics, with sevoflurane (SF) being the first choice inhalational anesthetic agent, provide reversible, broad depressor effects on the nervous system yet have a narrow margin of safety. As characterization of low-affinity binding interactions of volatile substances is exceptionally challenging with the existing methods, none of the numerous cellular targets proposed as chief protagonists in anesthesia could yet be confirmed. The recognition that most critical functions modulated by volatile anesthetics are under the control of intracellular Ca²⁺ concentration, which in turn is primarily regulated by calmodulin (CaM), motivated us for characterization of the SF–CaM interaction. Solution NMR (Nuclear Magnetic Resonance) spectroscopy was used to identify SF-binding sites using chemical shift displacement, NOESY and heteronuclear Overhauser enhancement spectroscopy (HOESY) experiments. Binding affinities were measured using ITC (isothermal titration calorimetry). SF binds to both lobes of (Ca²⁺)₄-CaM with low mmol/L affinity whereas no interaction was observed in the absence of Ca²⁺. SF does not affect the calcium binding of CaM. The structurally closely related SF and isoflurane are shown to bind to the same clefts. The SF-binding clefts overlap with the binding sites of physiologically relevant ion channels and bioactive small molecules, but the binding affinity suggests it could only interfere with very weak CaM targets.

The many faces of calmodulin in cell proliferation, programmed cell death, autophagy, and cancer

Calmodulin (CaM) is a ubiquitous Ca(2+) receptor protein mediating a large number of signaling processes in all eukaryotic cells. CaM plays a central role in regulating a myriad of cellular functions via interaction with multiple target proteins. This review focuses on the action of CaM and CaM-dependent signaling systems in the control of vertebrate cell proliferation, programmed cell death and autophagy. The significance of CaM and interconnected CaM-regulated systems for the physiology of cancer cells including tumor stem cells, and processes required for tumor progression such as growth, tumor-associated angiogenesis and metastasis are highlighted. Furthermore, the potential targeting of CaM-dependent signaling processes for therapeutic use is discussed.

Absolute configuration of acremoxanthone C, a potent calmodulin inhibitor from Purpureocillium lilacinum

Bioassay-guided fractionation of an extract prepared from the culture medium and mycelium of Purpureocillium lilacinum allowed the isolation of two calmodulin (CaM) inhibitors, namely, acremoxanthone C (1) and acremonidin A (2). The absolute configuration of 1 was established as 2R, 3R, 1'S, 11'S, and 14'R through extensive NMR spectroscopy and molecular modeling calculations at the DFT B3LYP/DGDZVP level, which included the comparison between theoretical and experimental specific rotation, ³J(C,H), and ³J(H,H) values. Compounds 1 and 2 bind to the human calmodulin (hCaM) biosensor hCaM M124C-mBBr, with dissociation constants (Kd) of 18.25 and 19.40 nM, respectively, 70-fold higher than that of chlorpromazine (Kd = 1.24 μM), used as positive control. Docking analysis using AutoDock 4.2 predicted that 1 and 2 bind to CaM at a similar site to that which KAR-2 binds, which is unusual. Furthermore, a novel, sensible, and specific fluorescent biosensor of hCaM, i.e., hCaM T110C-mBBr, was constructed; this device is labeled at a site where classical inhibitors do not interact and was successfully applied to measure the interaction of 1 with CaM. This is the first report of xanthone-anthraquinone heterodimers in species of Paecilomyces or Purpureocillium genera.

Effects of the semisynthetic bis-indole derivative KAR-2 on store-operated calcium entry in human neutrophils

We studied the effect of KAR-2 on cytosolic Ca(2+) level in human neutrophils by using a fluorescent dye (Fura-2) trapped in the cells. KAR-2 is a semisynthetic bis-indole derivative that shares vinblastine anti-microtubular properties, but does not share the vinblastine antagonistic effect on calmodulin. Therefore KAR-2 offers a convenient mean of studying the effect of microtubule destabilization, without concomitant calmodulin alterations. We found that KAR-2 induces Ca(2+) release from intracellular stores, whereby the stores are depleted. In addition KAR-2 reduces store-operated entry of extracellular Ca(2+) induced by agonists such as thapsigargin or ATP. On the other hand, in Ca(2+) refilled cells, KAR-2 promotes limited entry of extracellular Ca(2+) in the absence of agonist, but still interferes prominently with Ca(2+) entry triggered by ATP and with Ca(2+) uptake by intracellular stores. We suggest that Ca(2+) traffic through the plasma membrane is operated by two diverse pathways: the prominent pathway is interfered with by microtubule destabilization, while an alternate and minor pathway is actually favored (or uncovered) following microtubule destabilization.

Proteome-wide prediction of overlapping small molecule and protein binding sites using structure

Small molecules that modulate protein-protein interactions are of great interest for chemical biology and therapeutics. Here I present a structure-based approach to predict 'bi-functional' sites able to bind both small molecule ligands and proteins, in proteins of unknown structure. First, I develop a homology-based annotation method that transfers binding sites of known three-dimensional structure onto protein sequences, predicting residues in ligand and protein binding sites with estimated true positive rates of 98% and 88%, respectively, at 1% false positive rates. Applying this method to the human proteome predicts 8463 proteins with bi-functional residues and correctly recovers the targets of known interaction modulators. Proteins with significantly (p < 0.01) more bi-functional residues than expected were found to be enriched in regulatory and depleted in metabolism functions. Finally, I demonstrate the utility of the method by describing examples of predicted overlap and evidence of their biological and therapeutic relevance. The results suggest that combining the structures of known binding sites with established fold detection algorithms can predict regions of protein-protein interfaces that are amenable to small molecule modulation. Open-source software and the results for several complete proteomes are available at http://pibase.janelia.org/homolobind.

Calmodulin inhibitory activity of the malbrancheamides and various analogs

The preparation and biological activity of various structural analogs of the malbrancheamides are disclosed. The impact of indole chlorination, C-12a relative stereochemistry, and bicyclo[2.2.2]diazaoctane core oxidation state on the ability of these analogs to inhibit calmodulin dependent phosphodiesterase (PDE1) was studied, and a number of potent compounds were identified.

Progress in the development of early diagnosis and a drug with unique pharmacology to improve cancer therapy

Cancer continues to be one of the major health and socio-economic problems worldwide, despite considerable efforts to improve its early diagnosis and treatment. The identification of new constituents as biomarkers for early diagnosis of neoplastic cells and the discovery of new type of drugs with their mechanistic actions are crucial to improve cancer therapy. New drugs have entered the market, thanks to industrial and legislative efforts ensuring continuity of pharmaceutical development. New targets have been identified, but cancer therapy and the anti-cancer drug market still partly depend on anti-mitotic agents. The objective of this paper is to show the effects of KAR-2, a potent anti-mitotic compound, and TPPP/p25, a new unstructured protein, on the structural and functional characteristics of the microtubule system. Understanding the actions of these two potential effectors on the microtubule system could be the clue for early diagnosis and improvement of cancer therapy.

Interaction of antagonists with calmodulin: insights from molecular dynamics simulations

We report results of 12 ns, all-atom molecular dynamics simulation (MDS) and Poisson-Boltzmann free energy calculations (PBFE) on calmodulin (CaM) bound to two molecules of trifluoperazine (TFP) and of N-(3,3, diphenylpropyl)- N'-[1- R-(3,4-bis-butoxyphenyl)-ethyl]-propylenediamine (DPD). X-ray data show very similar structures for the two complexes, yet the antagonists significantly differ with respect to their CaM binding affinities, the neutral DPD is much more potent. The goal of the study was to unravel the reason why TFP is less potent although its positive charge should facilitate binding. The electrostatic energy terms in CHARMM and binding free energy terms of the PBFE approach showed TFP a better antagonist, while inspection of hydrophobic contacts supports DPD binding. Detailed inspection of the amino acid contributions of PBFE calculations unravel that steric reasons oppose the favorable binding of TFP. Structural conditions are given for a successful drug design strategy, which may benefit also from charge-charge interactions.

Structural biology in plant natural product biosynthesis--architecture of enzymes from monoterpenoid indole and tropane alkaloid biosynthesis

Several cDNAs of enzymes catalyzing biosynthetic pathways of plant-derived alkaloids have recently been heterologously expressed, and the production of appropriate enzymes from ajmaline and tropane alkaloid biosynthesis in bacteria allows their crystallization. This review describes the architecture of these enzymes with and without their ligands.

Survey of the year 2005 commercial optical biosensor literature

We identified 1113 articles (103 reviews, 1010 primary research articles) published in 2005 that describe experiments performed using commercially available optical biosensors. While this number of publications is impressive, we find that the quality of the biosensor work in these articles is often pretty poor. It is a little disappointing that there appears to be only a small set of researchers who know how to properly perform, analyze, and present biosensor data. To help focus the field, we spotlight work published by 10 research groups that exemplify the quality of data one should expect to see from a biosensor experiment. Also, in an effort to raise awareness of the common problems in the biosensor field, we provide side-by-side examples of good and bad data sets from the 2005 literature.

Can conformational change be described by only a few normal modes?

We suggest a simple method to assess how many normal modes are needed to map a conformational change. By projecting the conformational change onto a subspace of the normal-mode vectors and using root mean square deviation as a test of accuracy, we find that the first 20 modes only contribute 50% or less of the total conformational change in four test cases (myosin, calmodulin, NtrC, and hemoglobin). In some allosteric systems, like the molecular switch NtrC, the conformational change is localized to a limited number of residues. We find that many more modes are necessary to accurately map this collective displacement. In addition, the normal-mode "spectra" can provide useful information about the details of the conformational change, especially when comparing structures with different bound ligands, in this case, calmodulin. Indeed, this approach presents normal-mode analysis as a useful basis in which to capture the mechanism of conformational change, and shows that the number of normal modes needed to capture the essential collective motions of atoms should be chosen according to the required accuracy.