Filip Van Petegem
Relevant Degree Programs
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)
Complete these steps before you reach out to a faculty member!
- Familiarize yourself with program requirements. You want to learn as much as possible from the information available to you before you reach out to a faculty member. Be sure to visit the graduate degree program listing and program-specific websites.
- Check whether the program requires you to seek commitment from a supervisor prior to submitting an application. For some programs this is an essential step while others match successful applicants with faculty members within the first year of study. This is either indicated in the program profile under "Requirements" or on the program website.
- Identify specific faculty members who are conducting research in your specific area of interest.
- Establish that your research interests align with the faculty member’s research interests.
- Read up on the faculty members in the program and the research being conducted in the department.
- Familiarize yourself with their work, read their recent publications and past theses/dissertations that they supervised. Be certain that their research is indeed what you are hoping to study.
- Compose an error-free and grammatically correct email addressed to your specifically targeted faculty member, and remember to use their correct titles.
- Do not send non-specific, mass emails to everyone in the department hoping for a match.
- Address the faculty members by name. Your contact should be genuine rather than generic.
- Include a brief outline of your academic background, why you are interested in working with the faculty member, and what experience you could bring to the department. The supervision enquiry form guides you with targeted questions. Ensure to craft compelling answers to these questions.
- Highlight your achievements and why you are a top student. Faculty members receive dozens of requests from prospective students and you may have less than 30 seconds to pique someone’s interest.
- Demonstrate that you are familiar with their research:
- Convey the specific ways you are a good fit for the program.
- Convey the specific ways the program/lab/faculty member is a good fit for the research you are interested in/already conducting.
- Be enthusiastic, but don’t overdo it.
G+PS regularly provides virtual sessions that focus on admission requirements and procedures and tips how to improve your application.
Graduate Student Supervision
Doctoral Student Supervision (Jan 2008 - Nov 2019)
The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.
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.
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.
No abstract available.
Master's Student Supervision (2010 - 2018)
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.