Filip Van Petegem


Research Classification

Research Interests

Biological and Biochemical Mechanisms
Genetic Diseases
Calcium signaling
Cardiac arrhythmia
electrical signaling
Ion channels
Structural Biology

Relevant Thesis-Based Degree Programs

Affiliations to Research Centres, Institutes & Clusters


Research Methodology

Electron Microscopy
X-ray crystallography
Protein expression and purification
Isothermal titration calorimetry


Master's students
Doctoral students
Postdoctoral Fellows
Any time / year round

1) Muscle excitation-contraction coupling: How does an electrical signal in a muscle cell get transmitted into contraction? We investigate the membrane proteins involved in this process (L-type calcium channels, Ryanodine Receptors), as well as the various proteins that modulate these channels. Projects include solving crystal and cryo-EM structures of these channels in complex with the additional proteins. Functional experiments (e.g. electrophysiology) are used to test the hypotheses originating from these structures. 2) Channelopathies Ion channels are responsible for electrical signals in excitable cells. Mutations in the ion channel genes can lead to severe and often fatal disorders, including cardiac arrhythmias, epilepsy, ataxias, chronic pain and much more. We investigate the primary disease mechanisms by mapping disease mutations on the 3D structures, comparing structures of wild-type and disease mutant proteins, and functional experiments. Together these provide very detailed insights in the disease process. Current projects include congenital cardiac arrhythmias (CPVT, LongQT, Brugada Syndromes) and epilepsy (Dravet Syndrome)

I support public scholarship, e.g. through the Public Scholars Initiative, and am available to supervise students and Postdocs interested in collaborating with external partners as part of their research.
I am open to hosting Visiting International Research Students (non-degree, up to 12 months).
I am interested in hiring Co-op students for research placements.

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Graduate Student Supervision

Doctoral Student Supervision

Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.

The role of STAC proteins in regulation of calcium channels and skeletal muscle excitation-contraction coupling (2023)

The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.

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Moment-to-moment regulation of voltage-gated potassium channel function (2020)

Kv1.2 channels are prominently expressed in neurons where they help to set the threshold of action potential firing. While we have a good understanding of the mechanism of voltage sensing and gating, we have comparatively little information on the compendium of regulatory molecules that can impact Kv1.2 expression and function. Kv1.2 channels are subject to a unique mechanism of regulation whereby a train of brief, repetitive depolarizations elicit increasing amounts of current, a phenotype we term ‘use-dependent activation’. In heterologous cells expressing Kv1.2 and primary hippocampal cultures from rats, there is remarkable diversity in this phenotype. While use-dependent activation is absent in all other Kv1 channels, it persists in heteromeric channels containing at least one Kv1.2 subunit. Exposing cells expressing Kv1.2 to reducing conditions causes a dramatic shift in use-dependent activation where there is very little or no current elicited by the first pulse, but over the course of the train there is a hundred-fold or more increase in current. Additionally, reducing conditions cause a depolarizing shift in the activation curve of Kv1.2 by +64 mV. Taken together, we postulate that use-dependence arises from an extrinsic, redox-sensitive inhibitory regulator that associates with Kv1.2 preferentially in the closed, reduced state. We have identified a new regulator of Kv1.2 function, Slc7a5, an amino acid transporter. Co-expression of these two proteins decreases Kv1.2 expression and produces a hyperpolarizing shift of the activation and inactivation curves. Together these effects result in Kv1.2 channels being caught in an ‘inactivation trap’. These effects of Slc7a5 can be rescued by co-expressing a third protein, Slc3a2, which is known to heterodimerize with the Slc7a5 channel. Using BRET we show that Slc7a5 and Kv1.2 can be within 10 nm of each other. Other Kv1 channels we have tested (Kv1.1 and Kv1.5) are insensitive to the activation shift produced by Slc7a5, however Kv1.1 channels are exquisitely sensitive to current inhibition. Overall, the work in this thesis expands our knowledge of how Kv1.2 channels are regulated and opens the door to examining how these interactions contribute to normal neuronal function.

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Structural insights into calmodulin regulation and dysregulation of the L-type voltage-gated calcium channel (2020)

Calmodulinopathies are life-threatening arrhythmia syndromes that arise from mutations in calmodulin (CaM), a calcium-sensing protein whose sequence is completely conserved across vertebrates. Although these mutations have been shown to interfere with the function of cardiac ion channels including the voltage-gated calcium channel CaV1.2, in a mutation-specific manner, direct structural insights into any CaM disease variant have been lacking. Here, we utilize X-ray crystallography, NMR, and binding assays to probe the interaction of CaM disease variants with the IQ domain of CaV1.2 from a structural and biophysical standpoint.We present crystal structures of several C-lobe mutants and an N-lobe mutant in complex with the IQ domain. Surprisingly, two variants (D95V and N97I) cause major distortion of the C-lobe, resulting in a new pathological conformation not reported before. These structural changes result in altered interactions with IQ domain. Ca²⁺ binding to EF-hands normally proceeds with high cooperativity, but we find N97S CaM can adopt different conformations with either one or two Ca²⁺ ions bound to the C-lobe, possibly disrupting cooperativity. Another mutation (D129G) results in complete separation of EF-hands within the C-lobe and loss of Ca²⁺-binding in EF-hand 4. Q135P CaM has severely reduced affinity for the IQ domain, and shows changes in the CD spectra under Ca²⁺-saturating conditions when unbound to IQ domain. F141L CaM exhibits structural changes in the Ca²⁺-free state that increase affinity for IQ domain. An N-lobe variant (N53I) does not display major changes in complex with the IQ domain, providing a structural basis for why this mutant does not affect function of CaV1.2. These findings demonstrate that different CaM mutants have distinct effects on both CaM structure and interactions with protein targets, and act via distinct pathological mechanisms to cause disease.We also investigate a binding site for CaM in the intracellular linker between domains I and II of CaV1.1 and CaV1.2. We describe crystal structures of Ca²⁺/CaM in complex with I-II loops and examine binding thermodynamics via isothermal titration calorimetry, revealing a high affinity CaM-binding site in the cytoplasmic I-II loop of L-type calcium channels which may contribute to the complex CaM-mediated regulation of the channel.

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Structural and biochemical insights into the cardiac and skeletal muscle excitation-contraction coupling machinery (2018)

Excitation-contraction (EC) coupling describes the process whereby the depolarizing action potential is transduced into a rapid increase of cytosolic calcium (Ca²⁺) that initiates muscle contraction. Proper execution of EC coupling relies on the coordinated communication between two calcium channels: plasma membrane-bound, L-type voltage-gated calcium channels (CaVs) and the intracellular Ryanodine Receptors (RyRs). CaVs respond to membrane depolarization by conveying an intracellular signal to the RyR. In skeletal muscle, CaV1.1 mechanically couples to the RyR; in cardiac tissue, extracellular Ca²⁺ entry via CaVs trigger RyR opening. The net effect of RyR activation is elevation of intracellular Ca²⁺ levels, activating the contractile machinery. In skeletal muscle, the nature of the physical CaV-RyR coupling has been an area of intense interest: do the channels directly interact or are auxiliary proteins required? Recently, a novel adaptor protein, STAC3, has been identified as playing a role in trafficking and maintaining components of the EC coupling machinery in a functional state. Indeed, STAC3-null mice and fish exhibit failure of skeletal muscle EC coupling. Chapter 2 presents x-ray crystallographic and isothermal titration calorimetry (ITC) data showing a direct interaction between STAC3 and CaV1.1. EC coupling assays reveal the importance of this interaction in EC coupling. The CaV1.1-STAC3 interaction is perturbed by the Native American Myopathy STAC3 mutation. L-type voltage-gated calcium channels fulfill dual roles as voltage-sensors for EC coupling and calcium ion conduits. In non-muscle cells, STAC3 facilitates CaV1.1’s functional membrane expression and alters the current properties of CaV1.2, suggesting a role of STAC proteins as a CaV regulator. Chapter 3 presents electrophysiology data illustrating the significant effect of STAC3 on modulating CaV1.2 currents. Detection of an interaction to Calmodulin (CaM), a well-known CaV regulator, suggests that STAC proteins may exert its effect on ion conduction via CaM. Genetic defects in the EC coupling machinery underlie numerous congenital myopathies and life-threatening cardiac arrhythmias. Chapter 4 explores the implications of disease-associated mutations within the cardiac Ryanodine Receptor (RyR2) using structural, spectroscopic, and thermal stability assays. An anion binding site within the N-terminal RyR2 region and maintenance of proper domain interfaces are key to RyR2 stability and normal functioning.

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Binding and Structural Insights of the Ryanodine Receptor (2014)

Ryanodine Receptors (RyR) are large ion channels that are responsible for the release of Ca²⁺ from the sarco/endoplasmic reticulum. The channel consists of a large cytosolic cap which functions as a giant allosteric protein, capable of being modulated by an assortment of binding partners and small molecules. To understand its function and mechanisms one needs to dissect the channel to its smallest parts. Using a combination of isothermal titration calorimetry and x-ray crystallography, two areas have been analyzed: binding by calmodulin (CaM) and the structure of a RyR domain, SPRY2.Calmodulin (CaM) is a Ca²⁺ binding protein that can regulate RyR under conditions of both high and low Ca²⁺ by tuning their Ca²⁺ sensitivity to channel opening and closing in an isoform-specific manner. I analyze the binding of CaM and its individual domains to three different RyR CaM binding regions using isothermal titration calorimetry. I compared binding to skeletal muscle (RyR1) and cardiac (RyR2) isoforms, under both Ca²⁺-loaded and Ca²⁺ free conditions. I find that CaM is able to bind all three regions, but with different binding modes, between the isoforms. Disease mutations target one of the three sites and affect CaM binding and energetics.The SPRY2 domain is one of three repeats of the same fold that are present within the RyR. It has been suggested as a key protein interaction site with dihydropyridine receptors to mediate excitation-contraction coupling in skeletal muscle tissue. RyR1 and RyR2 SPRY2 domains were crystallized and reveal differences with several other known SPRY domain structures. Docking of the RyR1 SPRY2 structure places it in between the central rim and the clamp region. The structure of a disease mutant causing cardiomyopathy is also determined and shows local misfolding. Finally, RyR1 SPRY2 binding to the DHPR II-III loops is undetectable by isothermal titration calorimetry.

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Structural and biochemical characterizations of the skeletal muscle and cardiac ryanodine receptor n-terminal disease associated mutants (2014)

Ryanodine receptors (RyRs) are calcium release channels located in the endo/sarcoplasmic reticulum that play a crucial role in the excitation-contraction coupling. Over 500 mutations have been found in the skeletal muscle (RyR1) and cardiac (RyR2) isoforms that cause severe muscle disorders or life-threatening arrhythmias. Mechanisms of these mutations have remained elusive largely due to the lack of high-resolution structures. Here, we compare pseudo-atomic models of the N-terminal region of RyR1 in the open and closed states together with crystal structures and thermal melts of multiple disease-associated mutants. We describe a model in which the intersubunit interface at the N-terminal region acts as a brake in channel opening. Next, we depict crystal structures of mutants at the intersubunit interface of RyR2 N-terminal region that perturb the structure of a loop targeted by multiple mutations. Furthermore, the crystal structure of the N-terminal domains of RyR2 reveals a unique, central anion-binding site. This anion binding is ablated in a disease-associated mutant that targets one of the anion-coordinating arginine residues, resulting in domain reorientations. Several other disease-causing mutations destabilize the protein. Taken together, the results illustrate a common theme across the RyR isoforms and their homologous IP₃ receptors that conformational changes at the N-terminal region caused by the destabilization of the interfaces are allosterically coupled to channel opening.

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The basis for calcium regulation of the cardiac sodium channel (2012)

No abstract available.

Master's Student Supervision

Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.

Crystallographic advancements in the study of junctophilin proteins (2022)

Heartbeats and locomotion require muscle contraction, which is governed by the transport of calcium ions across membrane compartments within cells. Excitation-contraction coupling (ECC) is an essential process that connects extracellular signals to intracellular ion channels. Cells from excitable tissue have specialized ultrastructure in the form of transverse (T) tubules, where the plasma membrane comes into proximity with the sarcoplasmic reticulum (SR), an intracellular calcium reservoir. Voltage-gated calcium channels (CaV) in the plasma membrane and ryanodine receptors (RyR) in the SR membrane coordinate calcium release during ECC. Auxiliary proteins regulate and maintain the channels within the junctional membrane complex (JMC), including the junctophilin (JPH) proteins. JPH proteins form a bridge between membranes and have direct interactions with calcium channels; the skeletal isoform JPH1 and the cardiac isoform JPH2 are essential for muscle ECC. Mutations in JPH2 lead to severe diseases including hypertrophic cardiomyopathy (HCM). In this thesis, the goals are to elucidate the structures of JPH proteins using X-ray crystallography, study the interaction between JPH and CaV using a combination of X-ray crystallography and ITC, and study the lipid-binding function of JPH using protein-lipid overlay assays. The structures of JPH1 and JPH2 were determined at resolutions of 1.31 Å and 2.35 Å, respectively. ITC data showed that JPH1/JPH2 binds to the C-terminal domain of skeletal CaV1.1 with an affinity of 1-2 μM, and the structure of JPH2 in complex with the CaV1.1 binding site was determined at a resolution of 2.03 Å. Over 80 variants were mapped onto the JPH2 structure, most of which are HCM-causing mutations, and a subset of mutations target the JPH/CaV interaction site. Co-crystallization and ITC experiments showed no binding between JPH and short-chain phospholipids. Protein-lipid overlay assays demonstrate that high ionic strength disrupts the interaction between JPH and phospholipids, and clusters of positive residues on the surface of JPH affect lipid-binding.

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Crystallographic exploration into the regulation of the cardiac voltage-gated sodium channel by its protein partners (2021)

The human heartbeat is governed by a series of tightly controlled action potentials (APs) leading to the coordinated contractions of distinct groups of cardiac cells. Ion channel proteins are the cornerstones to this process, generating the different phases of the AP. Specifically, the cardiac voltage-gated sodium channel, Nav1.5, is responsible for generating the rapid depolarization phase of the AP. The channel possesses several domains and motifs which allow for an additional layer of control via cytosolic protein partners such as calmodulin (CaM) and fibroblast growth factor homologous factors (FHFs or FGF11-14). Dysregulation of either the channel or its protein partners can give rise to life-threatening arrhythmia syndromes. The goal of this thesis is to study the effects of calmodulin mutants, specifically F141L CaM on the structure and function of Nav1.5 and explore how FGFs engage Nav1.5. ITC data showed no significant difference between WT CaM and F141L CaM binding to the Nav1.5 CTD in either the presence or absence of Ca²⁺. The ternary structure complexes of the Nav1.5 CTD, WT apo/CaM, and FGF14 and Nav1.5 CTD, F141L apo/CaM, and FGF14 were determined at a resolution of 2.20Å and 1.60Å, respectively. The F141L mutation resulted in a destabilization of a hydrophobic pocket within the C-lobe causing a conformational change of a loop within EF-hand IV of CaM. The interface between FGF14 and Nav1.5 EF-hand domain revealed the absence of two salt bridges present at the interface of FGF13U and FGF12B with the Nav1.5 EF-hand supporting the observed decreased affinity. Moreover, ITCs showed that under Ca²⁺-saturating conditions, the change in enthalpy during titrations between FGF14 and CaM-bound Nav1.5 CTD was 2-fold lower than between FGF14 and Nav1.5 CTD. This points to differences in the binding of FGF14 in the Ca²⁺-saturated condition in support of a model where the Ca²⁺/C-lobe is bound to a position that would clash with a 180 rotation of the Nav1.5 EF-hand. ITCs between FGF14 and CaM-bound Nav1.5 CTD in the apo condition demonstrated a more complex two-site binding model suggesting the presence of two conformations of the apo/CaM-Nav1.5 CTD complex with which FGF14 can interact.

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Crystallographic Investigation and Characterization of the Interaction between presynaptic voltage-gated calcium channels and SNARE proteins (2010)

Voltage-gated calcium channels (Cay) have functions ranging from regulatingrelease of hormones and neurotransmitters, generating cardiac action potentials, andexcitation-contraction coupling. At nerve terminals, N- and P/Q- type Cavs convert theaction potential into aC²⁺ signal that in turn triggers neurotransmitter release.Neurotransmitter release requires several components, such as SNARE proteins.SNAREs, as well as many other presynaptic proteins, can interact with Cavs and inhibitthem by increasing their inactivation. The interaction is localized in the intracellular loopbetween domains II and III of the CL 1 subunit, in a domain termed ‘synprint’ (synapticprotein interaction site). In this study, we tried to solve the structure of the synprint siteby crystallography. To date, long needle-shape crystals were obtained; however, thequality of these crystals was not good enough for X-ray diffraction. in addition,isothermal titration calorimetry (ITC) was used to determine the interaction betweenSNARE protein syntaxinlA and the synprint site. It turned out that not any binding wasdetected, suggesting that the interaction between SNARE proteins and the presynapticCas, if at all present, is weak.

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