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Quantitative Proteomics of the Cav2 Channel Nano- Environments in The Quantitative proteomics of the Cav2 channel nano- FEATURE ARTICLE environments in the mammalian brain Catrin Swantje Müllera, Alexander Haupta,c, Wolfgang Bildla, Jens Schindlera, Hans-Günther Knausd, Marcel Meissnere, Burkhard Rammnerf, Jörg Striessnigg, Veit Flockerzie, Bernd Faklera,b,1, and Uwe Schultea,c,1 aInstitute of Physiology II, University of Freiburg, 79108 Freiburg, Germany; bCenter for Biological Signaling Studies, 79104 Freiburg, Germany; cLogopharm GmbH, 79108 Freiburg, Germany; dDivision of Molecular and Cellular Pharmacology, Medical University Innsbruck, A-6020 Innsbruck, Austria; eExperimentelle und Klinische Pharmakologie und Toxikologie, Universität des Saarlandes, 66421 Homburg, Germany; fScimotion, 22761 Hamburg, Germany; and gDepartment of Pharmacology and Toxicology, Center of Molecular Biosciences, University of Innsbruck, A-6020 Innsbruck, Austria This Feature Article is part of a series identified by the Editorial Board as reporting findings of exceptional significance. Edited by William A. Catterall, University of Washington School of Medicine, Seattle, WA, and approved June 24, 2010 (received for review April 29, 2010) Local Ca2+ signaling occurring within nanometers of voltage-gated investigation, mostly because of technical limitations precluding Ca2+ (Cav) channels is crucial for CNS function, yet the molecular their comprehensive proteomic analysis. Such unbiased analysis, composition of Cav channel nano-environments is largely unre- however, is ultimately required for molecular understanding of solved. Here, we used a proteomic strategy combining knockout- the Cav2-mediated signaling. controlled multiepitope affinity purifications with high-resolution Proteomic analysis of membrane-associated signaling networks quantitative MS for comprehensive analysis of the molecular represents a major technical challenge, particularly when native nano-environments of the Cav2 channel family in the whole rodent (not genetically manipulated) tissue is used as source material. brain. The analysis shows that Cav2 channels, composed of pore- Antibody-based affinity purification (AP) combined with quanti- α β forming 1 and auxiliary subunits, are embedded into protein tative MS is a target-directed approach, which, theoretically, allows networks that may be assembled from a pool of ∼200 proteins with for strong enrichment of both target proteins and more stably as- distinct abundance, stability of assembly, and preference for the sociated partners with tight control of specificity and interaction three Cav2 subtypes. The majority of these proteins have not pre- PHYSIOLOGY stringency (16). In fact, AP-based proteomics were successfully viously been linked to Cav channels; about two-thirds are dedicated fi to the control of intracellular Ca2+ concentration, including G protein- used for identi cation of accessory subunits and regulators of var- – coupled receptor-mediated signaling, to activity-dependent cytoskel- ious ion-channel proteins (17 23). Notwithstanding, there remain eton remodeling or Ca2+-dependent effector systems that comprise several sources of error that are aggravated considerably when a high portion of the priming and release machinery of synaptic approaching protein networks such as those comprising nano- vesicles. The identified protein networks reflect the cellular processes environments. First, solubilization conditions, generally a compro- that can be initiated by Cav2 channel activity and define the molec- mise between efficiency and preservation of protein–protein in- ular framework for organization and operation of local Ca2+ signal- teractions, must be carefully adjusted. Second, specificity and ing by Cav2 channels in the brain. selection biases of antibodies (ABs) must be well-controlled, be- cause protein networks offer an increased surface for nonspecific calcium channel | Ca2+ signaling | proteome | biochemistry | mass binding and may obscure access of ABs to their epitopes. Finally, spectrometry reliable identification of less-abundant or smaller proteins requires high-resolution quantitative MS (24). In the light of these concerns, n CNS neurons, voltage-activated calcium (Cav) channels ini- previous efforts to identify proteins associated with Cav channels Itiate a multitude of signaling processes by delivering calcium (25, 26) might have missed important components or contained 2+ ions (Ca ) to the cytoplasm that serve as second messengers false-positive interactors. 2+ (1, 2). Despite this rather unselective trigger mechanism, Ca - Here, we use a proteomic approach that combines a multi- dependent signaling is endowed with high specificity and re- pronged AP using optimized solubilization conditions, multiple 2+ liability by tightly restricting the Ca signal, a transient increase ABs to distinct epitopes, and source material from wild-type 2+ 2+ in the intracellular Ca concentration ([Ca ]i) to very local (WT) and knockout animals together with high-resolution quan- spatiotemporal domains by means of a variety of Ca2+ buffer fl – 2+ titative nano ow tandem MS (nano LC-MS/MS) and a tiered systems (3, 4). Within such local domains, [Ca ]i drops from data-analysis procedure to identify proteins reconstituting the hundreds of micromolar at the inner vestibule of the channel to nano-environments of Cav2 channels in the mammalian brain. values below 10 μM at a distance of several tens of nanometers The identified Cav2 channel proteome provides a comprehensive from the Cav channel (3–5). Consequently, most Ca2+-depen- set of data that serves as a roadmap for ultra-structural and dent signaling systems necessarily reside within these spatial functional analyses of local Ca2+ signaling by these key channels boundaries (5–7) that may be termed nano-environments. Nano-environments are of particular relevance for a number of of synaptic transmission and plasticity. processes in the dendritic and synaptic compartments, including neurotransmitter release, regulation of excitability, excitation– transcription coupling, synaptic plasticity, or axonal growth (5, 8– Author contributions: V.F., B.F., and U.S. designed research; C.S.M., A.H., W.B., J. Schindler, H.-G.K., B.R., B.F., and U.S. performed research; H.-G.K., M.M., and J. Striess- 11). Many of these and a number of further processes are trig- nig contributed new reagents/analytic tools; C.S.M., A.H., W.B., B.R., B.F., and U.S. ana- gered by the subfamily 2 of Cav channels comprising the three lyzed data; and V.F., B.F., and U.S. wrote the paper. members Cav2.1, 2.2, and 2.3 that conduct P/Q-type, N-type, and The authors declare no conflict of interest. 2+ R-type Ca currents, respectively (12). These channels are This article is a PNAS Direct Submission. α thought to be assembled from pore-forming 1 subunits and two Freely available online through the PNAS open access option. β β α δ δ distinct types of auxiliary subunits, Cav 1- 4 and 2 1- 4; 1To whom correspondence may be addressed. E-mail: [email protected] Cavγ2-γ8 have also been suggested as accessory subunits (13–15). freiburg.de or [email protected]. Although the channel core complex has been extensively studied, This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. the nano-environments of Cav2 channels have escaped direct 1073/pnas.1005940107/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1005940107 PNAS Early Edition | 1of8 Downloaded by guest on September 28, 2021 Results targeted the Cav γ2 and γ3 proteins (anti-γ2/3) (22). This mul- Isolation and Analysis of Cav2 Channel Nano-Environments. The ex- tiepitope strategy was used to eliminate the errors frequently perimental approach used to determine the nano-environments introduced into APs of protein complexes by individual ABs fi of Cav2 channels is illustrated in Fig. 1A. because of their speci c binding properties. Thus, ABs are often Plasma membrane-enriched protein fractions were prepared selective for complexes of particular subunit compositions over from total brain of adult rats, WT mice, and mice with targeted others, and/or they interfere with the integrity of complexes by fi deletions of either Cav2 α1 or Cav β subunits [Cav2.1 (27), high-af nity interaction with their target epitope (35). Off-target Cav2.2 (28), Cav2.3 (29), Cavβ2 (30), Cavβ3 (31), and Cavβ4 effects inherent to ABs through direct binding of proteins dif- (32)]. To optimize solubilization conditions that retained intact ferent from their target (cross-reactivity) were circumvented by nano-environments, membrane fractions were solubilized with the parallel use of Cav2 subunit knockout animals. Complete eluates of all APs obtained with the different ABs a set of detergent buffers of variable stringency (Material and from solubilized membrane fractions of WT and knockout ani- Methods) and centrifuged under conditions leaving micelles with mals were analyzed by high-resolution nano–LC-MS/MS on an estimated size (diameter) of up to ∼70 nm in the supernatant α a hybrid linear ion trap/Fourier transform mass spectrometer (Fig. S1). The yield of solubilized Cav2 1 protein displayed (LTQ-FT Ultra). This provided data on both the identity (through a wide range as visualized by Western-probed gel separations. fragmentation MS/MS spectra recorded by the ion trap) and the Thus, digitonin (33) solubilized only small amounts of the Cav2 α amount (through MS spectra over time measured in the ICR cell) 1 protein in the membrane fractions, whereas buffers CL-91 of proteins in each of the eluates. The amount
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