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C&SP17: NMJ Calcium Signaling

A. Collaborating Investigators: Stephen D. Meriney,1 Tom M. Bartol,2 Terry J. Sejnowski,2 Ivet Bahar,1 Mary H. Cheng, 1 Rozita Lahgaei3 and Greg Hood 3

B. Institutions: 1University of Pittsburgh, 2Salk Institute, 3Pittsburgh Supercomputing Center

C. Funding Status: NINDS5R01-NS090644-02, CRCNS: Transmitter Release Site Organization in Plasticity and Disease at the NMJ (Meriney) 8/1/14-5/31/19

D. Biomedical Research Problem: A significant number of neurological diseases are known to affect synaptic transmission by targeting synaptic organization.19,20 While most studies on this topic focus on postsynaptic adaptations,21 it has become increasingly clear that presynaptic homeostatic changes also play a major role. In particular, presynaptic homeostatic plasticity under normal and disease conditions can be mediated by mechanisms22 that influence the structure and function of the active zone (AZ), the nerve terminal specialization that controls transmitter release.23 Ca2+ influx into AZs is critical to triggering neurotransmitter (NT) release, and alterations in Ca2+ influx are a target for presynaptic homeostatic plasticity.24,25 Thus, a better understanding of the role of presynaptic structure in synaptic function is needed. LEMS (Lambert-Eaton Myasthenic Syndrome) is one of a number of devastating Ca2+ channelopathies26,27 known to alter presynaptic Ca2+ channel number and AZ organization at the NMJ.28,29 The presynaptic plasticity in normal and diseased NMJs provides an excellent opportunity to study the impact of Ca2+ channel-NT release site organization at a model synapse. We hypothesize that major aspects of synaptic function and presynaptic homeostatic plasticity (in control and disease states) can be explained by changes in the number and organization of Ca2+ channels within transmitter release sites.

E. Methods and Procedures Aim 1. Presynaptic activity-dependent homeostatic regulation of structure and function within the NMJ. We hypothesize that homeostatic changes serve to fine-tune the strength of communication with muscle cells as activity patterns and muscle sizes change over time. Using MCell30 modeling and experimental techniques, we will evaluate the impact of homeostatically driven changes in the organization of individual single-vesicle release sites on the probability of release, synaptic latency, and short-term synaptic plasticity. This approach will be an extension of our recently published development of MCell (TR&D2) models to evaluate synaptic function and plasticity.4,6

Aim 2. Presynaptic changes in AZ structure and function in a mouse model of LEMS. LEMS is known to disrupt the normally well-organized AZ at the NMJ (Fig VIII.1). These changes reduce total Ca2+ flux into motor nerve terminals, which results in reduced NT release, and altered short-term synaptic plasticity. Using a combination of physiological, anatomical, and MCell computational approaches, we will elucidate the number and distribution of Ca2+ channels in diseased mouse model LEMS AZs, their probability of opening during an action potential, and the functional coupling between these Ca2+ channels and synaptic vesicle release sites. We will test the hypothesis that LEMS-induced changes in AZ organization underlie functional consequences. This approach expands upon our studies of LEMS31 and will aid in LEMS treatment, and advance our understanding of the functional impact of AZ organization

Fig VIII.1. Mouse NMJ anatomy, AZ organization, synaptic function, and MCell modeling. A. Mouse NMJ stained with bassoon antibodies (green) to identify the location of AZs. Postsynaptic ACh receptors are stained red. B. Mouse AZ in normal and LEMS disease states. C. Tans-mitter release is greatly reduced in LEMS. D. MCell model of mouse AZ.

Aim 3. Integration of presynaptic Ca2+ channel function with the spatio-temporal dynamics of Ca2+ ion action within a multi-active zone MCell model. In collaboration with Dr. Bahar’s group (TR&D1) we will use molecular computational tools for studying normal and drug-modulated Ca2+ channel gating. The structure-based data on functional dynamics will be combined with MCell modeling of spatiotemporal dynamics of intra-terminal Ca2+ ions, to take a multi-scale approach to increasing our understanding of how Ca2+ channel number and gating function can influence synaptic transmitter release within complex nerve terminals. The approach at both molecular and cell levels will allow a more detailed understanding of how ion channel biophysics, our newly developed gating modifier drugs,32,33 and stochastic diffusion and reaction biochemistry combine to regulate the function of motor nerve terminals.

Research Highlights

 

Direct coupling of oligomerization and oligomerization-driven endocytosis of the dopamine transporter to its conformational mechanics and activity

The Bahar (TR&D1) and Sorkin (DBP3) labs published an article in the Journal of Biological Chemistry, selected as one of JBC's "Editors' Picks. Our results demonstrate a direct coupling between conformational dynamics of DAT, functional activity of the transporter and its oligomerization leading to endocytosis. The high specificity of such coupling for DAT makes the TM4-9 hub a new target for pharmacological modulation of DAT activity and subcellular localization. (Read more)

 

 

Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation

Comparison with RNA-seq expression data reveals a strong overlap between highly expressed genes and those distinguished by high mobilities in the present study, in support of the role of the intrinsic spatial dynamics of chromatin as a determinant of cell differentiation. (Read more)

 

 

Nanoscale co-organization and coactivation of AMPAR, NMDAR, and mGluR at excitatory synapses

Work by TR&D2 Investigators and collaborators provide insights into the nanometer scale organization of postsynaptic glutamate receptors using a combination of dual-color superresolution imaging, electrophysiology, and computational modeling. (Read more)

 

 

Parallel Tempering with Lasso for model reduction in systems biology

TR&D3 Investigators and collaborators develop PTLasso, a Bayesian model reduction approach that combines Parallel Tempering with Lasso regularization, to automatically extract minimal subsets of detailed models that are sufficient to explain experimental data. On both synthetic and real biological data, PTLasso is an effective method to isolate distinct parts of a larger signaling model that are sufficient for specific data. (Read more)

 

Image-derived models of cell organization changes during differentiation and drug treatments

Our work on modeling PC12 cells undergoing differentiation into neuron-like morphologies (under C&SP11, completed) has been published in Molecular Biology of the Cell. We have also made the large dataset of 3D images collected in that study available through Dryad. (Read more)

 

Monoamine transporters: structure, intrinsic dynamics and allosteric regulation

T&RD1 investigators Mary Cheng and Ivet Bahar published an invited review article in Nature Structural & Molecular Biology, addressing recent progress in the elucidation of the structural dynamics of MATs and their conformational landscape and transitions, as well as allosteric regulation mechanisms. (Read more)

Trimerization of dopamine transporter triggered by AIM-100 binding

The Bahar (TR&D1) and Sorkin (DBP3) labs explored the trimerization of dopamine transporter (DAT) triggered by a furopyrimidine, AIM-100, using a combination of computational and biochemical methods, and single-molecule live-cell imaging assays. (Read more)

Pre-post synaptic alignment through neuroligin-1 tunes synaptic transmission efficiency

TR&D2 investigators and collaborators describe organizing role of neuroligin-1 to align post-synaptic AMPA Receptors with pre-synaptic release sites into trans-synaptic “nano-columns” to enhance signaling.(Read more)

Inferring the Assembly Network of Influenza Virus

In an article in PLoS Computational Biology, MMBioS TR&D4 members Xiongto Ruan and Bob Murphy collaborated with Seema Lakdawala to address this question of the assembly network of the Influenza virus.(Read more)

PINK1 Interacts with VCP/p97 and Activates PKA to Promote NSFL1C/p47 Phosphorylation and Dendritic Arborization in Neurons

Our findings highlight an important mechanism by which proteins genetically implicated in Parkinson’s disease (PD; PINK1) and frontotemporal dementia (FTD; VCP) interact to support the health and maintenance of neuronal arbors.(Read more)

Improved methods for modeling cell shape

In a recent paper in Bioinformatics, Xiongtao Ruan and Bob Murphy of TR&D4 addressed the question of how best to model cell and nuclear shape.(Read more)

New tool to predict pathogenicity of missense variants based on structural dynamics: RHAPSODY

We demonstrated that the analysis of a protein’s intrinsic dynamics can be successfully used to improve the prediction of the effect of point mutations on a protein functionality. This method employs ANM/GNM tools (Read more)

New method for investigating chromatin structural dynamics.

By adapting the Gaussian Network Model (GNM) protein-modeling framework, we were able to model chromatin dynamics using Hi-C data, which led to the identification of novel cross-correlated distal domains (CCDDs) that were found to also be associated with increased gene co-expression.  (Read more)

 

Structural elements coupling anion conductance and substrate transport identified

We identified an intermediate anion channeling state (iChS) during the global transition from the outward facing (OF) to inward facing state (IFS). Our prediction was tested and validated by experimental study conducted in the Amara lab (NIMH). Critical residues and interactions were analyzed by SCAM, electrophysiology and substrate uptake experiments (Read more)

Integrating MMBioS technologies for multiscale discovery

TR&D teams driven by individual DBPs are naturally joining forces, integrating their tools to respond to the needs of the DBP, and creating integrative frameworks for combining structural and kinetic data and computing technologies at multiple scales.  (Read more)

 

Large scale visualization of rule-based models.

Signaling in living cells is mediated through a complex network of chemical interactions. Current predictive models of signal pathways have hundreds of reaction rules that specify chemical interactions, and a comprehensive model of a stem cell or cancer cell would be expected to have many more. Visualizations of rules and their interactions are needed to navigate, organize, communicate and analyze large signaling models.  (Read more)

Integration of MCellR into MCell/CellBlender

Using spatial biochemical models of SynGAP/PSD95, MMBioS investigators were able to merge the MCellR code-base with the MCell code-base and validate its utility and correctness of this sophisticated technology now easily accessible through the MCell/CellBlender GUI.  (Read more)

 

csp29

Causal relationships of spatial distributions of T cell signaling proteins

The idea is to identify a relationship in which a change in the concentration of one protein in one cell region consistently is associated with a change in the concentration of another protein in the same or a different region. We used the data from our Science Signaling paper reported last year to construct a model for T cells undergoing stimulation by both the T cell receptor and the costimulatory receptor. (Read more...)

T-Cell Receptor Signaling

BioNetGen modeling helps reveal immune system response decision

To attack or to let be is an important decision that our immune systems must make to protect our bodies from foreign invaders or protect bodily tissues from an immune attack. Using modeling and experiments, we have painted a sharper picture of how T cells make these critical decisions.  (Read more)

 

 

distancecell

Tools for determining the spatial relationships between different cell components

An important task for understanding how cells are organized is determining which components have spatial patterns that are related to each other.Read more

 

4d rtd

Pipeline for creation of spatiotemporal maps

Using a combination of diffeomorphic methods and improved cell segmentation, we developed a CellOrganizer pipeline for use in DPB4 to construct models of the 4D distributions of actin and 8 of its regulators during the response of T cells to antigen presentation. Read more

 

Multi-scale Hybrid Methodology

The hybrid methodology, coMD, that we have recently developed [1] has been recently extended to construct the energy landscape near the functional states of LeuT (Fig 1) [2]. This is the first energy landscape constructed for this NSS family member. Read more

 


Insights into the cooperative dynamics of AMPAR

Comparative analysis of AMPAR and NMDAR dynamics reveals striking similarities, opening the way to designing new modulators of allosteric interactions. Read more


Improved Sampling of Cell-Scale Models using the WE Strategy

The WE strategy for orchestrating a large set of parallel simulations has now been extended to spatially resolved cell-scale systems. The WESTPA implementation of WE has been used to control MCell simulations, including models built using a BioNetGen-CellOrganizer pipeline for situating complex biochemistry within spatially realistic cell models. Read more

Mouse visual cortex
Anatomy and Function of an Excitatory Network in the Visual Cortex

MMBioS researcher Greg Hood’s collaboration with Wei-Chung Allen Lee of Harvard University and R. Clay Reid of the Allen Institute for Brain Science concerning the reconstruction of an excitatory nerve-cell network in the mouse brain cortex at a subcellular level using the AlignTK software has been published in Nature. Read more

 

Molecular Mechanism of Dopamine Transport by hDAT

Dopamine transporters (DATs) control neurotransmitter dopamine (DA) homeostasis by reuptake of excess DA, assisted by sodium and chloride ions. The recent resolution of DAT structure (dDAT) from Drosophila permits us for the first time to directly view the sequence of events involved in DA reuptake in human DAT (hDAT). Read more

 

 

 

figure good 170Synaptic Facilitation Revealed

An investigation of several mechanisms of short-term facilitation at the frog neuromuscular junction concludes that the presence of a second class of calcium sensor proteins distinct from synaptotagmin can explain known properties of facilitation. Read more

 

langmead2 200Sparse Graphical Models of Protein:Protein Interactions

DgSpi is a new method for learning and using graphical models that explicitly represent the amino acid basis for interaction specificity and extend earlier classification-oriented approaches to predict ΔG of binding. Read more

 

Picture1 180Advancing Parallel Bio-simulations

A new non-Markovian analysis can eliminate bias in estimates of long-timescale behavior, such as the mean first-passage time for the dissociation of methane molecules in explicit solvent. Read more

 

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