Synaptotagmin rings as high-sensitivity regulators of synaptic vesicle docking and fusion

Chemoproteomics Sheds Light on Epigenetic Targets of [11C]Martinostat in the Human Brain

Initiation of research programs to investigate binding specificity based on in vivo positron emission tomography (PET) imaging results can provide rich opportunities to improve data interpretation, gain biological insight, and inform hypothesis development. Here, we profile the binding specificity of the neuroepigenetic imaging probe, [11C]Martinostat. In vivo neuroimaging studies using [11C]Martinostat have uncovered differential regional uptake in relation to age and biological sex and in patients with schizophrenia, bipolar disorder, Alzheimer's disease, and low-back pain compared to healthy controls. Previous studies using recombinant proteins and thermal shift assays in postmortem tissue indicate that [11C]Martinostat engages class I and putatively class IIb histone deacetylases (HDACs). While HDACs serve multiple functions, including regulation of chromatin remodeling and gene transcription, it is not known how differences in HDAC expression may arise across brain regions. HDACs functionally interact with a diverse array of multisubunit complexes, and engagement with associated binding partners may contribute to these differences. To further assess target engagement of [11C]Martinostat, we designed a synthetic probe based on the inhibitor structural scaffold for use in competition experiments followed by proteomic analysis in postmortem tissue. The synthetic probe, called Compound 4, appears to interact with the class I HDAC paralog HDAC2 and the class IIb paralog HDAC6 in a robust manner. We also uncovered unique interacting partners, including synaptic proteins from the synaptotagmin (SYT) family of proteins and neuronal pentraxin 2 (NPTX2). Further work to investigate HDAC associations with interacting proteins across regions of the human brain is needed to better understand neuroepigenetic dysregulation in psychiatric and neurological conditions.

Independently engaging protein tethers of different length enhance synaptic vesicle trafficking to the plasma membrane

Synaptic vesicle (SV) trafficking toward the plasma membrane (PM) and subsequent SV maturation are essential for neurotransmitter release. These processes, including SV docking and priming, are co-ordinated by various proteins, such as SNAREs, Munc13 and synaptotagmin (Syt), which connect (tether) the SV to the PM. Here, we investigated how tethers of varying lengths mediate SV docking using a simplified mathematical model. The heights of the three tether types, as estimated from the structures of the SNARE complex, Munc13 and Syt, defined the SV-PM distance ranges for tether formation. Geometric considerations linked SV-PM distances to the probability and rate of tether formation. We assumed that SV tethering constrains SV motility and that multiple tethers are associated by independent interactions. The model predicted that forming multiple tethers favours shorter SV-PM distances. Although tethers acted independently in the model, their geometrical properties often caused their sequential assembly, from longer ones (Munc13/Syt), which accelerated SV movement towards the PM, to shorter ones (SNAREs), which stabilized PM-proximal SVs. Modifying tether lengths or numbers affected SV trafficking. The independent implementation of tethering proteins enabled their selective removal to mimic gene knockout (KO) situations. This showed that simulated SV-PM distance distributions qualitatively aligned with published electron microscopy studies upon removal of SNARE and Syt tethers, whereas Munc13 KO data were best approximated when assuming additional disruption of SNARE tethers. Thus, although salient features of SV docking can be accounted for by independent tethering alone, our results suggest that functional tether interactions not yet featured in our model are crucial for biological function. KEY POINTS: A mathematical model describing the role of synaptic protein tethers to localize transmitter-containing vesicles is developed based on geometrical considerations and structural information of synaptotagmin, Munc13 and SNARE proteins. Vesicle movement, along with tether association and dissociation, are modelled as stochastic processes, with tethers functioning independently of each other. Multiple tethers cooperate to recruit vesicles to the plasma membrane and keep them there: Munc13 and Syt as the longer tethers accelerate the movement towards the membrane, whereas short SNARE tethers stabilize them there. Model predictions for situations in which individual tethers are removed agree with the results from experimental studies upon gene knockout. Changing tether length or copy numbers affects vesicle trafficking and steady-state distributions.

Biomarkers of mature neuronal differentiation and related diseases

The nervous system regulates perception, cognition and behavioral responses by serving as the body's primary communication system for receiving, regulating and transmitting information. Neurons are the fundamental structures and units of the nervous system. Their differentiation and maturation processes rely on the expression of specific biomarkers. Neuron-specific intracellular markers can be used to determine the degree of neuronal maturation. Neuronal cytoskeletal proteins dictate the shape and structure of neurons, while synaptic plasticity and signaling processes are intricately associated with neuronal synaptic markers. Furthermore, abnormal expression levels of biomarkers can serve as diagnostic indicators for nervous system diseases. This article reviews the markers of mature neuronal differentiation and their relationship with nervous system diseases.

Vesicle docking and fusion pore modulation by the neuronal calcium sensor Synaptotagmin-1

Synaptotagmin-1 (Syt1) is a major calcium sensor for rapid neurotransmitter release in neurons and hormone release in many neuroendocrine cells. It possesses two tandem cytosolic C2 domains that bind calcium, negatively charged phospholipids, and the neuronal SNARE complex. Calcium binding to Syt1 triggers exocytosis, but how this occurs is not well understood. Syt1 has additional roles in docking dense-core vesicles (DCVs) and synaptic vesicles to the plasma membrane and in regulating fusion pore dynamics. Thus, Syt1 perturbations could affect release through vesicle docking, fusion triggering, fusion pore regulation, or a combination of these. Here, using a human neuroendocrine cell line, we show that neutralization of highly conserved polybasic patches in either C2 domain of Syt1 impairs both DCV docking and efficient release of serotonin from DCVs. Interestingly, the same mutations resulted in larger fusion pores and faster release of serotonin during individual fusion events. Thus, Syt1's roles in vesicle docking, fusion triggering, and fusion pore control may be functionally related.

Synaptotagmin-1 undergoes phase separation to regulate its calcium-sensitive oligomerization

Synaptotagmin-1 (Syt1) is a calcium sensor that regulates synaptic vesicle fusion in synchronous neurotransmitter release. Syt1 interacts with negatively charged lipids and the SNARE complex to control the fusion event. However, it remains incompletely understood how Syt1 mediates Ca2+-trigged synaptic vesicle fusion. Here, we discovered that Syt1 undergoes liquid-liquid phase separation (LLPS) to form condensates both in vitro and in living cells. Syt1 condensates play a role in vesicle attachment to the PM and efficiently recruit SNAREs and complexin, which may facilitate the downstream synaptic vesicle fusion. We observed that Syt1 condensates undergo a liquid-to-gel-like phase transition, reflecting the formation of Syt1 oligomers. The phase transition can be blocked or reversed by Ca2+, confirming the essential role of Ca2+ in Syt1 oligomer disassembly. Finally, we showed that the Syt1 mutations causing Syt1-associated neurodevelopmental disorder impair the Ca2+-driven phase transition. These findings reveal that Syt1 undergoes LLPS and a Ca2+-sensitive phase transition, providing new insights into Syt1-mediated vesicle fusion.

Vesicle docking and fusion pore modulation by the neuronal calcium sensor Synaptotagmin-1

Synaptotagmin-1 (Syt1) is a major calcium sensor for rapid neurotransmitter release in neurons and hormone release in many neuroendocrine cells. It possesses two tandem cytosolic C2 domains that bind calcium, negatively charged phospholipids, and the neuronal SNARE complex. Calcium binding to Syt1 triggers exocytosis, but how this occurs is not well understood. Syt1 has additional roles in docking dense core vesicles (DCV) and synaptic vesicles (SV) to the plasma membrane (PM) and in regulating fusion pore dynamics. Thus, Syt1 perturbations could affect release through vesicle docking, fusion triggering, fusion pore regulation, or a combination of these. Here, using a human neuroendocrine cell line, we show that neutralization of highly conserved polybasic patches in either C2 domain of Syt1 impairs both DCV docking and efficient release of serotonin from DCVs. Interestingly, the same mutations resulted in larger fusion pores and faster release of serotonin during individual fusion events. Thus, Syt1's roles in vesicle docking, fusion triggering, and fusion pore control may be functionally related.

Exploring the structural dynamics of the vesicle priming machinery

Various cell types release neurotransmitters, hormones and many other compounds that are stored in secretory vesicles by exocytosis via the formation of a fusion pore traversing the vesicular membrane and the plasma membrane. This process of membrane fusion is mediated by the Soluble N-ethylmaleimide-Sensitive Factor Attachment Proteins REceptor (SNARE) protein complex, which in neurons and neuroendocrine cells is composed of the vesicular SNARE protein Synaptobrevin and the plasma membrane proteins Syntaxin and SNAP25 (Synaptosomal-Associated Protein of 25 kDa). Before a vesicle can undergo fusion and release of its contents, it must dock at the plasma membrane and undergo a process named 'priming', which makes it ready for release. The primed vesicles form the readily releasable pool, from which they can be rapidly released in response to stimulation. The stimulus is an increase in Ca2+ concentration near the fusion site, which is sensed primarily by the vesicular Ca2+ sensor Synaptotagmin. Vesicle priming involves at least the SNARE proteins as well as Synaptotagmin and the accessory proteins Munc18, Munc13, and Complexin but additional proteins may also participate in this process. This review discusses the current views of the interactions and the structural changes that occur among the proteins of the vesicle priming machinery.

Making the cut: Multiscale simulation of membrane remodeling

Biological membranes are dynamic heterogeneous materials, and their shape and organization are tightly coupled to the properties of the proteins in and around them. However, the length scales of lipid and protein dynamics are far below the size of membrane-bound organelles, much less an entire cell. Therefore, multiscale modeling approaches are often necessary to build a comprehensive picture of the interplay of these factors, and have provided critical insights into our understanding of membrane dynamics. Here, we review computational methods for studying membrane remodeling, as well as passive and active examples of protein-driven membrane remodeling. As the field advances towards the modeling of key aspects of organelles and whole cells - an increasingly accessible regime of study - we summarize here recent successes and offer comments on future trends.

The expanding roles of PI4P and PI(4,5)P2 at the plasma membrane: Role of phosphatidylinositol transfer proteins

Phosphoinositides are phosphorylated derivatives of phosphatidylinositol, a phospholipid that is synthesised at the endoplasmic reticulum. The plasma membrane contains the enzymes to phosphorylate phosphatidylinositol and is therefore rich in the phosphorylated derivatives, PI4P and PI(4,5)P2. PI(4,5)P2 is a substrate for phospholipase C and during cell signaling, PI(4,5)P2 levels are reduced. Here I discuss a family of proteins, phosphatidylinositol transfer proteins (PITPs) that can restore PI(4,5)P2 levels.

Mechanisms of SNARE proteins in membrane fusion

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are a family of small conserved eukaryotic proteins that mediate membrane fusion between organelles and with the plasma membrane. SNAREs are directly or indirectly anchored to membranes. Prior to fusion, complementary SNAREs assemble between membranes with the aid of accessory proteins that provide a scaffold to initiate SNARE zippering, pulling the membranes together and mediating fusion. Recent advances have enabled the construction of detailed models describing bilayer transitions and energy barriers along the fusion pathway and have elucidated the structures of SNAREs complexed in various states with regulatory proteins. In this Review, we discuss how these advances are yielding an increasingly detailed picture of the SNARE-mediated fusion pathway, leading from first contact between the membranes via metastable non-bilayer intermediates towards the opening and expansion of a fusion pore. We describe how SNARE proteins assemble into complexes, how this assembly is regulated by accessory proteins and how SNARE complexes overcome the free energy barriers that prevent spontaneous membrane fusion.

Synaptotagmin 7 C2 domains induce membrane curvature stress via electrostatic interactions and the wedge mechanism

Synaptotagmin 7 (Syt-7) is part of the synaptotagmin protein family that regulates exocytotic lipid membrane fusion. Among the family, Syt-7 stands out by its membrane binding strength and stabilization of long-lived membrane fusion pores. Given that Syt-7 vesicles form long-lived fusion pores, we hypothesize that its interactions with the membrane stabilize the specific curvatures, thicknesses, and lipid compositions that support a metastable fusion pore. Using all-atom molecular dynamics simulations and FRET-based assays of Syt-7's membrane-binding C2 domains (C2A and C2B), we found that Syt-7 C2 domains sequester anionic lipids, are sensitive to cholesterol, thin membranes, and generate lipid membrane curvature by two competing, but related mechanisms. First, Syt-7 forms strong electrostatic contacts with the membrane, generating negative curvature stress. Second, Syt-7's calcium binding loops embed in the membrane surface, acting as a wedge to thin the membrane and induce positive curvature stress. These curvature mechanisms are linked by the protein insertion depth as well as the resulting protein tilt. Simplified quantitative models of the curvature-generating mechanisms link simulation observables to their membrane-reshaping effectiveness.

Requirement of Cholesterol for Calcium-Dependent Vesicle Fusion by Strengthening Synaptotagmin-1-Induced Membrane Bending

Cholesterol is essential for neuronal activity and function. Cholesterol depletion in the plasma membrane impairs synaptic transmission. However, the molecular mechanisms by which cholesterol deficiency leads to defects in vesicle fusion remain poorly understood. Here, it is shown that cholesterol is required for Ca2+ -dependent native vesicle fusion using the in vitro reconstitution of fusion and amperometry to monitor exocytosis in chromaffin cells. Purified native vesicles are crucial for the reconstitution of physiological Ca2+ -dependent fusion, because vesicle-mimicking liposomes fail to reproduce the cholesterol effect. Intriguingly, cholesterol has no effect on the membrane binding of synaptotagmin-1, a Ca2+ sensor for ultrafast fusion. Cholesterol strengthens local membrane deformation and bending induced by synaptotagmin-1, thereby lowering the energy barrier for Ca2+ -dependent fusion to occur. The data provide evidence that cholesterol depletion abolishes Ca2+ -dependent vesicle fusion by disrupting synaptotagmin-1-induced membrane bending, and suggests that cholesterol is an essential lipid regulator for Ca2+ -dependent fusion.

Cofilin-Membrane Interactions: Electrostatic Effects in Phosphoinositide Lipid Binding

The actin cytoskeleton interacts with the cell membrane primarily through the indirect interactions of actin-binding proteins such as cofilin-1. The molecular mechanisms underlying the specific interactions of cofilin-1 with membrane lipids are still unclear. Here, we performed coarse-grain molecular dynamics simulations of cofilin-1 with complex lipid bilayers to analyze the specificity of protein-lipid interactions. We observed the maximal interactions with phosphoinositide (PIP) lipids, especially PIP₂ and PIP₃ lipids. A good match was observed between the residues predicted to interact and previous experimental studies. The clustering of PIP lipids around the membrane bound protein leads to an overall lipid demixing and gives rise to persistent membrane curvature. Further, through a series of control simulations, we observe that both electrostatics and geometry are critical for specificity of lipid binding. Our current study is a step towards understanding the physico-chemical basis of cofilin-PIP lipid interactions.

SNARE Proteins in Synaptic Vesicle Fusion

Neurotransmitters are stored in small membrane-bound vesicles at synapses; a subset of synaptic vesicles is docked at release sites. Fusion of docked vesicles with the plasma membrane releases neurotransmitters. Membrane fusion at synapses, as well as all trafficking steps of the secretory pathway, is mediated by SNARE proteins. The SNAREs are the minimal fusion machinery. They zipper from N-termini to membrane-anchored C-termini to form a 4-helix bundle that forces the apposed membranes to fuse. At synapses, the SNAREs comprise a single helix from syntaxin and synaptobrevin; SNAP-25 contributes the other two helices to complete the bundle. Unc13 mediates synaptic vesicle docking and converts syntaxin into the permissive "open" configuration. The SM protein, Unc18, is required to initiate and proofread SNARE assembly. The SNAREs are then held in a half-zippered state by synaptotagmin and complexin. Calcium removes the synaptotagmin and complexin block, and the SNAREs drive vesicle fusion. After fusion, NSF and alpha-SNAP unwind the SNAREs and thereby recharge the system for further rounds of fusion. In this chapter, we will describe the discovery of the SNAREs, their relevant structural features, models for their function, and the central role of Unc18. In addition, we will touch upon the regulation of SNARE complex formation by Unc13, complexin, and synaptotagmin.