scholarly journals Dynamic Control of Ca2+ Binding in the C2 Domains of Synaptotagmin 1

2018 ◽  
Author(s):  
Patrick J. Rock ◽  
Austin G. Meyer ◽  
Chantell S. Evans ◽  
Edwin R. Chapman ◽  
R. Bryan Sutton
Keyword(s):  
Structural Changes ◽  
Dynamic Control ◽  
Point Mutations ◽  
Binding Pocket ◽  
Snare Complex ◽  
C2 Domains ◽  
Domain Interactions ◽  
Synaptotagmin 1 ◽  
Binding Pockets ◽  
Dynamics Simulations

AbstractSynaptotagmin senses fluctuations in the Ca2+ environment of neurons near active zones and transduces a signal to the SNARE complex to initiate exocytosis at the presynaptic terminus. The 3D structures of the two tandem C2 domains of synaptotagmin have been determined to high resolution; however, it is currently unclear how each domain dynamically interacts with Ca2+ at the atomic level. To study the mechanistic consequences of the lethal mutations at the AD3 locus, we introduced tyrosine to asparagine point mutations in both the C2A and C2B domains of synaptotagmin 1, and we have constructed a model that describes the relationship between Ca2+ -binding and the structural changes within each C2 domain. We show that the mobility of loop 3 in the Ca2+ binding pocket increases markedly in C2A, while the mobility of loop 1 changes in C2B with the AD3 mutation. This increase in loop mobility results in an increase in the average volume and variance of the Ca2+ -binding pockets of C2A and C2B. The volume of the unbound Ca2+ -binding pocket in C2A is usually restrained by intra-domain interactions between the tyrosine residue at the AD3 locus and residues on loop 3; however, the AD3 mutation decouples the restraint and results in a larger, more variable Ca2+ -binding pocket in C2A. C2B maintains a more compact Ca2+ -binding pocket; however, its volume also fluctuates significantly with the AD3 mutation. Changes in binding pocket volume that involve more variable Ca2+ binding loops would likely affect Ca2+ affinity in the neurons of the affected organism. Using molecular-dynamics simulations, we show that mutations at the AD3 locus alter the mobility of the Ca2+ -binding loops by removing a key stabilization mechanism that is normally present in C2 domains. The lack of loop stabilization results in a net increase in the volume of the Ca2+ -binding pocket and provides an explanation for the observed lethal phenotype.

scholarly journals Polybasic patches in both C2 domains of Synaptotagmin-1 are required for evoked neurotransmitter release

2021 ◽  
Author(s):  
Zhenyong Wu ◽  
Lu Ma ◽  
Nicholas A Courtney ◽  
Jie Zhu ◽  
Yongli Zhang ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Calcium Binding ◽  
Neurotransmitter Release ◽  
Transmembrane Domain ◽  
Snare Complex ◽  
Critical Feature ◽  
C2 Domains ◽  
Electrophysiological Recordings ◽  
Synaptotagmin 1

Synaptotagmin-1 (Syt1) is a vesicular calcium sensor required for synchronous neurotransmitter release. It is composed of a single-pass transmembrane domain linked to two tandem C2 domains (C2A and C2B) that bind calcium, acidic lipids, and SNARE proteins that drive fusion of the synaptic vesicle with the plasma membrane. Despite its essential role, how Syt1 couples calcium entry to synchronous release is not well understood. Calcium binding to C2B, but not to C2A, is critical for synchronous release and C2B additionally binds the SNARE complex. The C2A domain is also required for Syt1 function, but it is not clear why. Here we asked what critical feature of C2A may be responsible for its functional role, and compared this to the analogous feature in C2B. We focused on highly conserved poly-lysine patches located on the sides of C2A (K189-192) and C2B (K324-327). We tested effects of charge-neutralization mutations in either region (Syt1K189-192A and Syt1K326-327A) side-by-side to determine their relative contributions to Syt1 function in cultured cortical mouse neurons and in single-molecule experiments. Combining electrophysiological recordings and optical tweezers measurements to probe dynamic single C2 domain-membrane interactions, we show that both C2A and C2B polybasic patches contribute to membrane binding, and both are required for evoked release. The readily releasable vesicle pool or spontaneous release were not affected, so both patches are specifically required for synchronization of release. We suggest these patches contribute to cooperative binding to membranes, increasing the overall affinity of Syt1 for negatively charged membranes and facilitating evoked release.

scholarly journals The protein-binding pocket of Botulinum neurotoxin B accommodates a preassembled synaptotagmin / ganglioside complex

2021 ◽  
Author(s):  
Jorge Ramirez-Franco ◽  
Fodil Azzaz ◽  
Marion Sangiardi ◽  
G&eacuteraldine Ferracci ◽  
Fahamoe Youssouf ◽  
...  
Keyword(s):  
Botulinum Neurotoxin ◽  
Transmembrane Domain ◽  
Binding Pocket ◽  
Lipid Binding ◽  
Membrane Topology ◽  
Neuronal Membranes ◽  
Natural Variant ◽  
Synaptotagmin 1 ◽  
Binding Pockets ◽  
Serotype B

Botulinum neurotoxin serotype B (BoNT/B) uses two separate protein and polysialoglycolipid-binding pockets to interact with synaptotagmin 1/2 and gangliosides. However, an integrated model of this therapeutic tool bound to its neuronal receptors in a native membrane topology is still lacking. Using a panel of in silico and experimental approaches, we present here a new model for BoNT/B binding to neuronal membranes, in which the toxin binds to a preassembled synaptotagmin-ganglioside GT1b complex and a free ganglioside. This interaction allows a lipid-binding loop of BoNT/B to engage in a series of concomitant interactions with the glycone part of GT1b and the transmembrane domain of synaptotagmin. Furthermore, our data provide molecular support for the decrease in BoNT/B sensitivity in Felidae that harbor the natural variant synaptotagmin2-N59Q. These results reveal multiple interactions of BoNT/B with gangliosides and support a novel paradigm in which a toxin recognizes a protein/ganglioside complex.

scholarly journals Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion

2021 ◽  
Vol 77 (5) ◽  
pp. 645-662
Author(s):  
Risako Tamura-Sakaguchi ◽  
Rie Aruga ◽  
Mika Hirose ◽  
Toru Ekimoto ◽  
Takuya Miyake ◽  
...  
Keyword(s):  
Complex Formation ◽  
Structure Determination ◽  
Structural Changes ◽  
Insertion Site ◽  
3D Structure ◽  
Binding Pocket ◽  
Crystallographic Analysis ◽  
Stable Complex ◽  
X Ray Crystallography ◽  
Dynamics Simulations

Antibody labeling has been conducted extensively for structure determination using both X-ray crystallography and electron microscopy (EM). However, establishing target-specific antibodies is a prerequisite for applying antibody-assisted structural analysis. To expand the applicability of this strategy, an alternative method has been developed to prepare an antibody complex by inserting an exogenous epitope into the target. It has already been demonstrated that the Fab of the NZ-1 monoclonal antibody can form a stable complex with a target containing a PA12 tag as an inserted epitope. Nevertheless, it was also found that complex formation through the inserted PA12 tag inevitably caused structural changes around the insertion site on the target. Here, an attempt was made to improve the tag-insertion method, and it was consequently discovered that an alternate tag (PA14) could replace various loops on the target without inducing large structural changes. Crystallographic analysis demonstrated that the inserted PA14 tag adopts a loop-like conformation with closed ends in the antigen-binding pocket of the NZ-1 Fab. Due to proximity of the termini in the bound conformation, the more optimal PA14 tag had only a minor impact on the target structure. In fact, the PA14 tag could also be inserted into a sterically hindered loop for labeling. Molecular-dynamics simulations also showed a rigid structure for the target regardless of PA14 insertion and complex formation with the NZ-1 Fab. Using this improved labeling technique, negative-stain EM was performed on a bacterial site-2 protease, which enabled an approximation of the domain arrangement based on the docking mode of the NZ-1 Fab.

scholarly journals Interference of pH buffer with Pb2+-peripheral domain interactions: obstacle or opportunity?

Metallomics ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 164-172 ◽  
Author(s):  
Sachin Katti ◽  
Tatyana I. Igumenova
Keyword(s):  
Metal Ion ◽  
Membrane Association ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
C2 Domains ◽  
Domain Interactions ◽  
Synaptotagmin 1 ◽  
Ph Buffer ◽  
Peripheral Domain

Pb2+-Chelating pH buffer Bis–Tris enables identification of factors that determine the cooperative metal-ion binding response and membrane association of the Synaptotagmin 1 C2 domains.

scholarly journals Crystal Structure of the Cytosolic C2a-C2b Domains of Synaptotagmin III

1999 ◽  
Vol 147 (3) ◽  
pp. 589-598 ◽  
Author(s):  
R. Bryan Sutton ◽  
James A. Ernst ◽  
Axel T. Brunger
Keyword(s):  
Crystal Structure ◽  
Divalent Cations ◽  
Protein A ◽  
Binding Pocket ◽  
Snare Complex ◽  
Accessory Proteins ◽  
Binding Properties ◽  
C2 Domains ◽  
Electrostatic Surface Potential ◽  
Binding Partners

Synaptotagmins are synaptic vesicle-associated, phospholipid-binding proteins most commonly associated with Ca+2-dependent exocytotic and Ca+2- independent endocytotic events. Synaptotagmin III is a 63.2-kD member of the synaptotagmin homology group; one of its characteristic properties is the ability to bind divalent cations and accessory proteins promiscuously. In the cytosolic portion of this protein, a flexible seven–amino acid linker joins two homologous C2 domains. The C2A domain binds to phospholipid membranes and other accessory proteins in a divalent cation-dependent fashion. The C2B domain promotes binding to other C2B domains, as well as accessory proteins independent of divalent cations. The 3.2 Å crystal structure of synaptotagmin III, residues 295–566, which includes the C2A and C2B domains, exhibits differences in the shape of the Ca+2-binding pocket, the electrostatic surface potential, and the stoichiometry of bound divalent cations for the two domains. These observations may explain the disparate binding properties of the two domains. The C2A and the C2B domains do not interact; synaptotagmin, therefore, covalently links two independent C2 domains, each with potentially different binding partners. A model of synaptotagmin's involvement in Ca+2-dependent regulation of membrane fusion through its interaction with the SNARE complex is presented.

scholarly journals Binding of Azobenzene and p-Diaminoazobenzene to the Human Voltage-Gated Sodium Channel NaV1.4

2020 ◽  
Author(s):  
Vito F. Palmisano ◽  
Carlos Gómez-Rodellar ◽  
Hannah Pollak ◽  
Gustavo Cárdenas ◽  
Ben Corry ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Hydrophobic Interactions ◽  
Binding Pocket ◽  
Internal Cavity ◽  
Amino Groups ◽  
Voltage Gated ◽  
Accelerated Molecular Dynamics ◽  
Binding Pockets ◽  
Voltage Gated Ion Channels ◽  
Dynamics Simulations

The activity of voltage-gated ion channels can be controlled by the binding of photoswitches inside their internal cavity and subsequent light irradiation. We investigated the binding of azobenzene and p-diaminoazobenzene to the human Na<sub>V</sub>1.4 channel in the inactivated state by means of Gaussian accelerated molecular dynamics simulations and free-energy computations. Three stable binding pockets were identified for each of the two photoswitches. In all the cases, the binding is controlled by the balance between the favorable hydrophobic interactions of the ligands with the nonpolar residues of the protein and the unfavorable polar solvation energy. In addition, electrostatic interactions between the ligand and the polar aminoacids are also relevant for p-diaminoazobenzene due to the presence of the amino groups on the benzene moieties. These groups participate in hydrogen bonding in the most favorable binding pocket and in long-range electrostatic interactions in the other pockets. The thermodinamically preferred binding sites found for both photoswitches are close to the selectivity filter of the channel. Therefore, it is very likely that the binding of these ligands will induce alterations in the ion conduction through the channel.

scholarly journals Structural insights on the effects of mutation of a charged binding pocket residue on phosphopeptide binding to 14-3-3 ζ Protein

2021 ◽  
Author(s):  
Sreevidya T S ◽  
Somavally Dalvi ◽  
Prasanna Venkatraman ◽  
Satyavani Vemparala
Keyword(s):  
Electrostatic Interactions ◽  
Structural Changes ◽  
Structural Integrity ◽  
Peptide Binding ◽  
Limited Proteolysis ◽  
Binding Pocket ◽  
Mutant Protein ◽  
Amino Acid Residues ◽  
Salt Bridges ◽  
Dynamics Simulations

Mutation of an invariant aspartate residue in the binding pocket of 14-3-3ζ isoform to alanine dramatically reduced phosphopeptide binding and induced opening of the binding pocket. Here we use extensive molecular dynamics simulations to understand the role of D124 residue in ligand binding. The simulations show that in the absence of phosphopeptide, the D124A mutation leads to binding pocket reorganization including widening up of the binding pocket at the major groove and repositioning of N173, a key residue that interacts with the main chain of phosphopeptide. These structural changes would interfere with the efficient binding of the peptide, corroborating the experimental observations. Both gain and loss of electrostatic interactions in the form of salt bridges strongly indicate a rearrangement of the network of interactions within the binding pocket. Limited proteolysis coupled mass spectrometry (lip-MS) of the apo and holo forms of WT and mutant protein shows a peptide binding helix otherwise buried in the WT protein was particularly accessible to trypsin in the apo form of the mutant protein and the region was mapped to 158-186 amino acid residues of 14-3-3ζ. These results further confirm the dynamic nature of D124A mutant. Unlike other basic residues, the invariant D124 facilitates peptide binding by maintaining the geometry of interacting residues and by enforcing the structural integrity of amphipathic pocket.

scholarly journals Synaptotagmin-1 C2B domains cooperatively stabilize the fusion stalk via a master-servant mechanism

2021 ◽  
Author(s):  
Ary Lautaro Di Bartolo ◽  
Diego Masone
Keyword(s):  
Free Energy ◽  
Membrane Fusion ◽  
Membrane Binding ◽  
Vesicle Fusion ◽  
Fusion Process ◽  
Total Work ◽  
C2 Domains ◽  
Domain Interactions ◽  
Synaptotagmin 1 ◽  
Data Point

Synaptotagmin-1 is a low-affinity Ca2+ sensor that triggers synchronous vesicle fusion. It contains two similar C2 domains (C2A and C2B) that cooperate in membrane binding, being the C2B domain the main responsible for the membrane fusion process due to its polybasic patch KRLKKKKTTIKK (321-332). In this work, a master-servant mechanism between two identical C2B domains is shown to control the formation of the fusion stalk. Two regions in C2B are essential for the process, the well-known polybasic patch and a recently described pair of arginines (398,399). The master domain shows strong PIP2 interactions with its polybasic patch and its pair of arginines. At the same time, the servant analogously cooperates with the master to reduce the total work to form the fusion stalk. The strategic mutation (T328E,T329E) in both master and servant domains disrupts the cooperative mechanism, drastically increasing the free energy needed to induce the fusion stalk, however with negligible effects on the master domain interactions with PIP2. These data point to a difference in the behavior of the servant domain, which is unable to sustain its PIP2 interactions neither through its polybasic patch nor through its pair of arginines, in the end losing its ability to assist the master in the formation of the fusion stalk.

scholarly journals Druggability Assessment in TRAPP using Machine Learning Approaches

2019 ◽  
Author(s):  
Jui-Hung Yuan ◽  
Sungho Bosco Han ◽  
Stefan Richter ◽  
Rebecca C. Wade ◽  
Daria B. Kokh
Keyword(s):  
Conformational Changes ◽  
Drug Targets ◽  
Binding Pocket ◽  
Superior Performance ◽  
Protein Crystal ◽  
Data Sets ◽  
Learning Approaches ◽  
Factors Affecting ◽  
Binding Pockets ◽  
Dynamics Simulations

AbstractAccurate protein druggability predictions are important for the selection of drug targets in the early stages of drug discovery. Due to the flexible nature of proteins, the druggability of a binding pocket may vary due to conformational changes. We have therefore developed two statistical models, a logistic regression model (TRAPP-LR) and a convolutional neural network model (TRAPP-CNN), for predicting druggability and how it varies with changes in the spatial and physicochemical properties of a binding pocket. These models are integrated into TRAPP (TRAnsient Pockets in Proteins), a tool for the analysis of binding pocket variations along a protein motion trajectory. The models, which were trained on publicly available and self-augmented data sets, show equivalent or superior performance to existing methods on test sets of protein crystal structures, and have sufficient sensitivity to identify potentially druggable protein conformations in trajectories from molecular dynamics simulations. Visualization of the evidence for the decisions of the models in TRAPP facilitates identification of the factors affecting the druggability of protein binding pockets.

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