Quantitation of the Calcium and Membrane Binding Properties of the C2 Domains of Dysferlin

Dysferlin is a large membrane protein involved in calcium-triggered resealing of the sarcolemma after injury. Although it is generally accepted that dysferlin is Ca²⁺ sensitive, the Ca²⁺ binding properties of dysferlin have not been characterized. In this study, we report an analysis of the Ca²⁺ and membrane binding properties of all seven C2 domains of dysferlin as well as a multi-C2 domain construct. Isothermal titration calorimetry measurements indicate that all seven dysferlin C2 domains interact with Ca²⁺ with a wide range of binding affinities. The C2A and C2C domains were determined to be the most sensitive, with K_d values in the tens of micromolar, whereas the C2D domain was least sensitive, with a near millimolar K_d value. Mutagenesis of C2A demonstrates the requirement for negatively charged residues in the loop regions for divalent ion binding. Furthermore, dysferlin displayed significantly lower binding affinity for the divalent cations magnesium and strontium. Measurement of a multidomain construct indicates that the solution binding affinity does not change when C2 domains are linked. Finally, sedimentation assays suggest all seven C2 domains bind lipid membranes, and that Ca²⁺ enhances but is not required for interaction. This report reveals for the first time, to our knowledge, that all dysferlin domains bind Ca²⁺ albeit with varying affinity and stoichiometry.     

Structural Basis for the Distinct Membrane Binding Activity of the Homologous C2A Domains of Myoferlin and Dysferlin

Dysferlin has been implicated in acute membrane repair processes, whereas myoferlin's activity is maximal during the myoblast fusion stage of early skeletal muscle cell development. Both proteins are similar in size and domain structure; however, despite the overall similarity, myoferlin's known physiological functions do not overlap with those of dysferlin. Here we present for the first time the X‐ray crystal structure of human myoferlin C2A to 1.9 Å resolution bound to two divalent cations, and compare its three-dimensional structure and membrane binding activities to that of dysferlin C2A. We find that while dysferlin C2A binds membranes in a Ca²⁺-dependent manner, Ca²⁺ binding was the rate-limiting kinetic step for this interaction. Myoferlin C2A, on the other hand, binds two calcium ions with an affinity 3-fold lower than that of dysferlin C2A; and, surprisingly, myoferlin C2A binds only marginally to phospholipid mixtures with a high fraction of phosphatidylserine.     

Modular Dispensability of Dysferlin C2 Domains Reveals Rational Design for Mini-dysferlin Molecules

Dysferlin is a large transmembrane protein composed of a C-terminal transmembrane domain, two DysF domains, and seven C2 domains that mediate lipid- and protein-binding interactions. Recessive loss-of-function mutations in dysferlin lead to muscular dystrophies, for which no treatment is currently available. The large size of dysferlin precludes its encapsulation into an adeno-associated virus (AAV), the vector of choice for gene delivery to muscle. To design mini-dysferlin molecules suitable for AAV-mediated gene transfer, we tested internally truncated dysferlin constructs, each lacking one of the seven C2 domains, for their ability to localize to the plasma membrane and to repair laser-induced plasmalemmal wounds in dysferlin-deficient human myoblasts. We demonstrate that the dysferlin C2B, C2C, C2D, and C2E domains are dispensable for correct plasmalemmal localization. Furthermore, we show that the C2B, C2C, and C2E domains and, to a lesser extent, the C2D domain are dispensable for dysferlin membrane repair function. On the basis of these results, we designed small dysferlin molecules that can localize to the plasma membrane and reseal laser-induced plasmalemmal injuries and that are small enough to be incorporated into AAV. These results lay the groundwork for AAV-mediated gene therapy experiments in dysferlin-deficient mouse models.     

Structure and Ca2+-Binding Properties of the Tandem C2 Domains of E-Syt2

1. Download : Download high-res image (204KB)
2. Download : Download full-size image

     

Serum Binding of Calcium and the Red Cell Membrane in Cystic Fibrosis

THERE is evidence for a factor in the serum of cystic fibrosis patients which may play a role in the pathological manifestation of the genetic syndrome: serum of patients with cystic fibrosis alters the cilia movement of rabbit trachea in vitro¹ and of oyster cilia². This activity is apparently associated with the immunoglobulin fraction^3,4. Balfe et al.⁵ reported a modification of sodium flux in red cells obtained from patients with cystic fibrosis. In the course of searching for evidence of interaction of serum with red cells in cystic fibrosis, we found that there is a substantial increase in serum calcium binding in patients with cystic fibrosis. This seems to be associated with a modified membrane protein electrophoretic pattern of cystic fibrosis red cells in specified experimental conditions.     

Neurogranin Alters the Structure and Calcium Binding Properties of Calmodulin

Neurogranin (Ng) is a member of the IQ motif class of calmodulin (CaM)-binding proteins, and interactions with CaM are its only known biological function. In this report we demonstrate that the binding affinity of Ng for CaM is weakened by Ca²⁺ but to a lesser extent (2–3-fold) than that previously suggested from qualitative observations. We also show that Ng induced a >10-fold decrease in the affinity of Ca²⁺ binding to the C-terminal domain of CaM with an associated increase in the Ca²⁺ dissociation rate. We also discovered a modest, but potentially important, increase in the cooperativity in Ca²⁺ binding to the C-lobe of CaM in the presence of Ng, thus sharpening the threshold for the C-domain to become Ca²⁺-saturated. Domain mapping using synthetic peptides indicated that the IQ motif of Ng is a poor mimetic of the intact protein and that the acidic sequence just N-terminal to the IQ motif plays an important role in reproducing Ng-mediated decreases in the Ca²⁺ binding affinity of CaM. Using NMR, full-length Ng was shown to make contacts largely with residues in the C-domain of CaM, although contacts were also detected in residues in the N-terminal domain. Together, our results can be consolidated into a model where Ng contacts residues in the N- and C-lobes of both apo- and Ca²⁺-bound CaM and that although Ca²⁺ binding weakens Ng interactions with CaM, the most dramatic biochemical effect is the impact of Ng on Ca²⁺ binding to the C-terminal lobe of CaM.     

DOC2B,C2 Domains,and Calcium: A Tale of Intricate Interactions

Ca⁺²-dependent exocytosis involves vesicle docking, priming, fusion, and recycling. This process is performed and regulated by a vast number of synaptic proteins and depends on proper protein–protein and protein–lipid interactions. Double C2 domain (DOC2) is a protein family of three isoforms found while screening DNA libraries with a C2 probe. DOC2 has three domains: the Munc13-interacting domain and tandem C2s (designated C2A and C2B) connected by a short polar linker. The C2 domain binds phospholipids in a Ca²⁺-dependent manner. This review focuses on the ubiquitously expressed isoform DOC2B. Sequence alignment of the tandem C2 protein family in mouse revealed high homology (81%) between rabphilin-3A and DOC2B proteins. We created a structural model of DOC2B's C2A based on the crystal structure of rabphilin-3A with and without calcium and found that the calcium-binding loops of DOC2B move upon calcium binding, enabling efficient plasma membrane penetration of its C2A. Here, we discuss the potential relation between the DOC2B bioinformatical model and its function and suggest a possible working model for its interaction with other proteins of the exocytotic machinery, including Munc13, Munc18, and syntaxin.     

Ubiquitin Interacts with the Tollip C2 and CUE Domains and Inhibits Binding of Tollip to Phosphoinositides

A large number of cellular signaling processes are directed through internalization, via endocytosis, of polyubiquitinated cargo proteins. Tollip is an adaptor protein that facilitates endosomal cargo sorting for lysosomal degradation. Tollip preferentially binds phosphatidylinositol 3-phosphate (PtdIns(3)P) via its C2 domain, an association that may be required for endosomal membrane targeting. Here, we show that Tollip binds ubiquitin through its C2 and CUE domains and that its association with the C2 domain inhibits PtdIns(3)P binding. NMR analysis demonstrates that the C2 and CUE domains bind to overlapping sites on ubiquitin, suggesting that two ubiquitin molecules associate with Tollip simultaneously. Hydrodynamic studies reveal that ubiquitin forms heterodimers with the CUE domain, indicating that the association disrupts the dimeric state of the CUE domain. We propose that, in the absence of polyubiquitinated cargo, the dual binding of ubiquitin partitions Tollip into membrane-bound and membrane-free states, a function that contributes to the engagement of Tollip in both membrane trafficking and cytosolic pathways.     

The Calcium-Dependent and Calcium-Independent Membrane Binding of Synaptotagmin 1: Two Modes of C2B Binding

The Ca²⁺-independent membrane interactions of the soluble C2 domains from synaptotagmin 1 (syt1) were characterized using a combination of site-directed spin labeling and vesicle sedimentation. The second C2 domain of syt1, C2B, binds to membranes containing phosphatidylserine and phosphatidylcholine in a Ca²⁺-independent manner with a lipid partition coefficient of approximately 3.0 × 10² M^− 1. A soluble fragment containing the first and second C2 domains of syt1, C2A and C2B, has a similar affinity, but C2A alone has no detectable affinity to phosphatidylcholine/phosphatidylserine bilayers in the absence of Ca²⁺. Although the Ca²⁺-independent membrane affinity of C2B is modest, it indicates that this domain will never be free in solution within the cell. Site-directed spin labeling was used to obtain bilayer depth restraints, and a simulated annealing routine was used to generate a model for the membrane docking of C2B in the absence of Ca²⁺. In this model, the polybasic strand of C2B forms the membrane binding surface for the domain; however, this face of C2B does not penetrate the bilayer but is localized within the aqueous double layer when C2B is bound. This double-layer location indicates that C2B interacts in a purely electrostatic manner with the bilayer interface. In the presence of Ca²⁺, the membrane affinity of C2B is increased approximately 20-fold, and the domain rotates so that the Ca²⁺-binding loops of C2B insert into the bilayer. This Ca²⁺-triggered conformational change may act as a switch to modulate the accessibility of the polybasic face of C2B and control interactions of syt1 with other components of the fusion machinery.     

The C2 Domains of Human Synaptotagmin 1 Have Distinct Mechanical Properties

Synaptotagmin 1 (Syt1) is the Ca⁺² receptor for fast, synchronous vesicle fusion in neurons. Because membrane fusion is an inherently mechanical, force-driven event, Syt1 must be able to adapt to the energetics of the fusion apparatus. Syt1 contains two C2 domains (C2A and C2B) that are homologous in sequence and three-dimensional in structure; yet, a number of observations have suggested that they have distinct biochemical and biological properties. In this study, we analyzed the mechanical stability of the C2A and C2B domains of human Syt1 using single-molecule atomic force microscopy. We found that stretching the C2AB domains of Syt1 resulted in two distinct unfolding force peaks. The larger force peak of ∼100 pN was identified as C2B and the second peak of ∼50 pN as C2A. Furthermore, a significant fraction of C2A domains unfolded through a low force intermediate that was not observed in C2B. We conclude that these domains have different mechanical properties. We hypothesize that a relatively small stretching force may be sufficient to deform the effector-binding regions of the C2A domain and modulate the affinity for soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptors (SNAREs), phospholipids, and Ca⁺².     

Calcium Ion Binding Properties of Medicago truncatula Calcium/Calmodulin-Dependent Protein Kinase

A calcium/calmodulin-dependent protein kinase (CCaMK) is essential in the interpretation of calcium oscillations in plant root cells for the establishment of symbiotic relationships with rhizobia and mycorrhizal fungi. Some of its properties have been studied in detail, but its calcium ion binding properties and subsequent conformational change have not. A biophysical approach was taken with constructs comprising either the visinin-like domain of Medicago truncatula CCaMK, which contains EF-hand motifs, or this domain together with the autoinhibitory domain. The visinin-like domain binds three calcium ions, leading to a conformational change involving the exposure of hydrophobic surfaces and a change in tertiary but not net secondary or quaternary structure. The affinity for calcium ions of visinin-like domain EF-hands 1 and 2 (K(d) = 200 ± 50 nM) was appropriate for the interpretation of calcium oscillations (～125-850 nM), while that of EF-hand 3 (K(d) ≤ 20 nM) implied occupancy at basal calcium ion levels. Calcium dissociation rate constants were determined for the visinin-like domain of CCaMK, M. truncatula calmodulin 1, and the complex between these two proteins (the slowest of which was 0.123 ± 0.002 s(-1)), suggesting the corresponding calcium association rate constants were at or near the diffusion-limited rate. In addition, the dissociation of calmodulin from the protein complex was shown to be on the same time scale as the dissociation of calcium ions. These observations suggest that the formation and dissociation of the complex between calmodulin and CCaMK would substantially mirror calcium oscillations, which typically have a 90 s periodicity.     

Conformational Changes Produced by ATP Binding to the Plasma Membrane Calcium Pump

The aim of this work was to study the plasma membrane calcium pump (PMCA) reaction cycle by characterizing conformational changes associated with calcium, ATP, and vanadate binding to purified PMCA. This was accomplished by studying the exposure of PMCA to surrounding phospholipids by measuring the incorporation of the photoactivatable phosphatidylcholine analog 1-O-hexadecanoyl-2-O-[9-[[[2-[¹²⁵I]iodo-4-(trifluoromethyl-3H-diazirin-3-yl)benzyl]oxy]carbonyl]nonanoyl]-sn-glycero-3-phosphocholine to the protein. ATP could bind to the different vanadate-bound states of the enzyme either in the presence or in the absence of Ca²⁺ with high apparent affinity. Conformational movements of the ATP binding domain were determined using the fluorescent analog 2′(3′)-O-(2,4,6-trinitrophenyl)adenosine 5′-triphosphate. To assess the conformational behavior of the Ca²⁺ binding domain, we also studied the occlusion of Ca²⁺, both in the presence and in the absence of ATP and with or without vanadate. Results show the existence of occluded species in the presence of vanadate and/or ATP. This allowed the development of a model that describes the transport of Ca²⁺ and its relation with ATP hydrolysis. This is the first approach that uses a conformational study to describe the PMCA P-type ATPase reaction cycle, adding important features to the classical E₁-E₂ model devised using kinetics methodology only.     

N-Terminal Domains of Cardiac Myosin Binding Protein C Cooperatively Activate the Thin Filament

1. Download high-res image (363KB)
2. Download full-size image

     

Eisosomes Are Dynamic Plasma Membrane Domains Showing Pil1-Lsp1 Heteroligomer Binding Equilibrium

Eisosomes are plasma membrane domains concentrating lipids, transporters, and signaling molecules. In the budding yeast Saccharomyces cerevisiae, these domains are structured by scaffolds composed mainly by two cytoplasmic proteins Pil1 and Lsp1. Eisosomes are immobile domains, have relatively uniform size, and encompass thousands of units of the core proteins Pil1 and Lsp1. In this work we used fluorescence fluctuation analytical methods to determine the dynamics of eisosome core proteins at different subcellular locations. Using a combination of scanning techniques with autocorrelation analysis, we show that Pil1 and Lsp1 cytoplasmic pools freely diffuse whereas an eisosome-associated fraction of these proteins exhibits slow dynamics that fit with a binding-unbinding equilibrium. Number and brightness analysis shows that the eisosome-associated fraction is oligomeric, while cytoplasmic pools have lower aggregation states. Fluorescence lifetime imaging results indicate that Pil1 and Lsp1 directly interact in the cytoplasm and within the eisosomes. These results support a model where Pil1-Lsp1 heterodimers are the minimal eisosomes building blocks. Moreover, individual-eisosome fluorescence fluctuation analysis shows that eisosomes in the same cell are not equal domains: while roughly half of them are mostly static, the other half is actively exchanging core protein subunits.     

The Plasma Membrane Ca2+ ATPase and the Plasma Membrane Sodium Calcium Exchanger Cooperate in the Regulation of Cell Calcium

Calcium is an ambivalent signal: it is essential for the correct functioning of cell life, but may also become dangerous to it. The plasma membrane Ca²⁺ ATPase (PMCA) and the plasma membrane Na⁺/Ca²⁺ exchanger (NCX) are the two mechanisms responsible for Ca²⁺ extrusion. The NCX has low Ca²⁺ affinity but high capacity for Ca²⁺ transport, whereas the PMCA has a high Ca²⁺ affinity but low transport capacity for it. Thus, traditionally, the PMCA pump has been attributed a housekeeping role in maintaining cytosolic Ca²⁺, and the NCX the dynamic role of counteracting large cytosolic Ca²⁺ variations (especially in excitable cells). This view of the roles of the two Ca²⁺ extrusion systems has been recently revised, as the specific functional properties of the numerous PMCA isoforms and splicing variants suggests that they may have evolved to cover both the basal Ca²⁺ regulation (in the 100 nM range) and the Ca²⁺ transients generated by cell stimulation (in the μM range).Ca²⁺ controls critical cellular responses in all eukaryotic organisms. It controls both short-term biological processes that occur in milliseconds, such as muscle contraction, as well as long-term processes that require longer times, such as cell proliferation and organ development. The specificity of cellular Ca²⁺ signals is controlled by a sophisticated “toolkit” comprising numerous ion channels, pumps, and exchangers that drive the fluxes of Ca²⁺ ions across the plasma membrane and across the membranes of intracellular organelles (Berridge et al. 2003).The plasma membrane contains several types of channels that mediate Ca²⁺ entry from the extracellular ambient, and two systems for Ca²⁺ extrusion: a low affinity, high capacity Na⁺/Ca²⁺ exchanger (NCX), and a high-affinity, low-capacity Ca²⁺-ATPase (the plasma membrane Ca²⁺ pump (PMCA)) (Fig. 1). The type of channels and the relative proportions of NCX and PMCA vary with the cell type, the NCX being particularly abundant in excitable tissues, e.g., heart and brain. The regulated opening of the Ca²⁺ channels by either voltage gating, interaction with ligands or the emptying of intracellular stores, allows a limited amount of Ca²⁺ to enter the cell to transmit signals to its designated targets. Thereafter, the Ca²⁺ transients must be dissipated: its extrusion from the cell is mediated by the NCX and the PMCA pump, but Ca²⁺ is also restored to basal levels by sequestration in the endo/sarcoplasmic reticulum via the SERCA pump and in the mitochondria by the electrophoretic uniporter. The NCX has also been found at the inner membrane of the nuclear envelope (NE) and has been proposed to mediate Ca²⁺ flux between the nucleoplasm and the NE (Xie et al. 2002), and then to the ER (Wu et al. 2009) in neuronal and certain other cell types. Ca²⁺ binding proteins also contributed to Ca²⁺ buffering: In this review, we will not cover them, as we will only discuss the systems that extrude Ca²⁺ out of the cell.Open in a separate windowFigure 1.A schematic representation of the structures involved in cellular Ca²⁺ homeostasis. The model shows a cell with its Ca²⁺-transporting systems: Ca²⁺-ATPases (plasma membrane and sarco/endoplasmic reticulum, PMCA and SERCA), plasma membrane (PM) Ca²⁺ channels, Na⁺/Ca²⁺ exchangers (NCX and NCLX), 1,4,5-triphosphate receptor (IP₃R) and ryanodine receptor (RyR), the electrophoretic mitochondrial uptake uniporter (U). Mitochondria are drawn as yellow ellipses, nucleus as orange circle and endoplasmic reticulum is colored in red. The different Ca²⁺-transporting systems cooperate to maintain the Ca²⁺ concentration gradient between the extracellular and the intracellular ambient.The PMCA pump is a minor component of the total protein of the plasma membrane (less than 0.1% of it). Quantitatively, it is overshadowed by the more powerful NCX in excitable tissue like heart; however, even cells in which the NCX predominates, the PMCA pump is likely to be the fine tuner of cytosolic Ca²⁺, as it can operate in a concentration range in which the low affinity NCX is relatively very inefficient.The PMCA was discovered in erythrocytes (Schatzmann 1966), and was then described and characterized in numerous other cell types. It was purified in 1979 using a calmodulin affinity column (Niggli et al. 1979), and cloned about 10 years later (Shull and Greeb 1988; Verma et al. 1988). It shows the same essential membrane topology properties of the SERCA pump. Molecular modeling work using the structure of the SERCA pump as a template (Toyoshima et al. 2000) predicts the same general features of the latter, with 10 transmembrane domains and the large cytosolic headpiece divided into the three main cytosolic A, N, and P domains. The Na⁺/Ca²⁺ cotransport process was discovered at about the same time as PMCA by two independent groups working on heart (Reuter and Seitz 1968) and on the squid giant axon (Baker et al. 1969). The exchanger was cloned in 1990 (Nicoll et al. 1990). The sequence was initially predicted to correspond to a protein with 11 transmembrane domains and one large cytosolic loop linking transmembrane domain five and six but a revised model predicting only nine transmembrane domains is now generally accepted.     

Lipid Segregation and Membrane Budding Induced by the Peripheral Membrane Binding Protein Annexin A2

The formation of dynamic membrane microdomains is an important phenomenon in many signal transduction and membrane trafficking events. It is driven by intrinsic properties of membrane lipids and integral as well as membrane-associated proteins. Here we analyzed the ability of one peripherally associated membrane protein, annexin A2 (AnxA2), to induce the formation of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P₂)-rich domains in giant unilamellar vesicles (GUVs) of complex lipid composition. AnxA2 is a cytosolic protein that can bind PI(4,5)P₂ and other acidic phospholipids in a Ca²⁺-dependent manner and that has been implicated in cellular membrane dynamics in endocytosis and exocytosis. We show that AnxA2 binding to GUVs induces lipid phase separation and the recruitment of PI(4,5)P₂, cholesterol and glycosphingolipids into larger clusters. This property is observed for the full-length monomeric protein, a mutant derivative comprising the C-terminal protein core domain and for AnxA2 residing in a heterotetrameric complex with its intracellular binding partner S100A10. All AnxA2 derivatives inducing PI(4,5)P₂ clustering are also capable of forming interconnections between PI(4,5)P₂-rich microdomains of adjacent GUVs. Furthermore, they can induce membrane indentations rich in PI(4,5)P₂ and inward budding of these membrane domains into the lumen of GUVs. This inward vesiculation is specific for AnxA2 and not shared with other PI(4,5)P₂-binding proteins such as the pleckstrin homology (PH) domain of phospholipase Cδ1. Together our results indicate that annexins such as AnxA2 can efficiently induce membrane deformations after lipid segregation, a mechanism possibly underlying annexin functions in membrane trafficking.     

大鼠脊髓细胞膜胰岛素受体的结合特性

大鼠脊髓细胞膜胰岛素受体的结合特性朱尚权,徐明华,张新堂,叶莺（中国科学院上海生物化学研究所,２０００３１）姜新建,林淑琼（上海市第一人民医院康复科,２０００８５）关键词胰岛素受体,脊髓细胞膜免疫组织化学、放射免疫自显影和放射受体测定技术已证明脑各区...