Biophysical Society 2008 NCRR Booth Schedule

Using Virtual Cell to Explore Quantitative Models of PIP2 Signaling in Cerebellar Purkinje Spines

Presenter:Sherry-Ann Brown, Frank Morgan, James Watras, Leslie Loew

Abstract:

We used Virtual Cell to develop a quantitative 3D model of PIP2 signaling in Cerebellar Purkinje spines. Specifically, we modeled the hydrolysis of PIP2 resulting in IP3 production, and focused our efforts on exploring sources of abundant PIP2 supply. We also virtually photobleached PIP2 in patches of dendrite and in spines, to analyze lateral diffusion of PIP2 in the spiny dendrite membrane. In addition to our 3D spatial model, we created a 1D model that gives similar results to simulations run in our constructed and our experimentally derived 3D geometries. We obtained time-dependent boundary conditions for IP3 from the 1D models, based on the length of each respective 3D geometry, and used those boundary conditions in our 3D models. We also used IP3 output from spatial simulations in our constructed 3D geometry as input for a 0D compartmental model previously published by our group in order to investigate the behavior of calcium transients dependent on the IP3 signal. The compartmental model considers molecules, reactions, and fluxes occurring in separate compartments with specific surface/volume ratios. It runs faster than the 1D and 3D models, because it does not explicitly treat diffusion. Simulation results indicate that both stimulated PIP2 synthesis (consistent with a similar mechanism established in earlier work for neuroblastoma cells) and local PIP2 sequestration produce large amplitudes of IP3 and significant calcium transients. (Supported by NIH Grant RR013186)

Demo will provide details of the model behind the platform presentation (1841-Plat), "Analysis of PIP2 Signaling in Cerebellar Purkinje Spines", which will occur on Tuesday at 4pm, in Platform AR: Calcium Signaling. Visitors to the booth may:

Learn how to create compartmental, 1D, and 3D models;
Learn how to photobleach membrane or cytosolic molecules in Virtual Cell;
Gain an introduction to the Virtual Cell modeling and simulation environment.

Title:

The Structure-Function Linkage Database: A resource for exploring enzyme superfamilies

Presenter:Shoshana Brown

Abstract:

The Structure-Function Linkage Database (SFLD) provides highly curated information about the relationships between protein sequence, structure and function. The SFLD currently focuses on enzymes, using a superfamily-centric organization designed to allow users to easily investigate how conserved folds and active sites are able to perform a wide variety of chemical reactions. The information within the SFLD includes sequences, structures, enzyme reactions (including partial reactions), the specific residues of each enzyme that participate in the reaction (and their role when known), hidden Markov models based on family and superfamily classifications, and literature references. In an effort to make assignments of function, superfamily, etc. transparent, assignment evidence codes and extensive metadata are easily accessible. Users can search the database using a sequence (useful in determining the function of a newly sequenced enzyme), a full or partial reaction (useful in identifying a template for enzyme engineering), or through a variety of keyword searches. We are in the process of integrating the SFLD with the network analysis program Cytoscape, to allow users to visualize overall sequence relationships in diverse superfamilies as well as to place a sequence of interest in the context of its superfamily, thus facilitating functional classification. The SFLD is freely available via a web interface at http://sfld.rbvi.ucsf.edu.

Title:

The Dynamics Energy Landscape Capturing Conformational Population Shift in Oligomerization

Presenter:Jennifer M. Bui

Abstract:

Unlike native protein-protein interactions, conversions of natural proteins into aberrant forms that self-assemble into amyloid fibrils have been known to associate many pathological conditions. The formation of oligomeric proteins by a process of monomer assembly and conformational rearrangements is investigated using immunoglobulin-binding domain β1 of streptococcal protein G (Gβ1), a 56 amino acids, stable, single-domain protein, as a model to obtain dynamics information that lead to oligomerization. Two 0.1 µs molecular dynamics trajectories at atomistic levels under pH of 4.0 and 7.0 were conducted. Backbone dynamic order parameters computed using the model-free approach with a double exponential fitting function are highly correlated to those obtained from experimental residual dipole coupling measurements; this demonstrates the system is well sampled and mimic dynamics accessible at long scale dynamics. At lower pH, there is a population shift from a moneric states to a hyperstable state in which the protein is more compact with highly complementary hydrophobic interactions of its core. From the free energy calculations, conformational equilibria between the hyperstable and monermic states, the monomeric and dimeric states, as well as the dimeric and tetrameric states are established. Highly concerted motions of core residues which facilitate in opening or closing of the hydrophobic core of the protein indicated by a distance between the β-strand 1 and 2 and the α-helix lead to transitions between the different conformational states. Conformational populations shift from dimeric state to the dominant tetrameric state when the dimeric mutant (L5V/F30V/Y33F/A34F) is converted to tetramer by an additional mutation at A26F, as also observed in a protein engineering study.

Title:

Visualizing 3-D Electron Microscopy Data with UCSF Chimera

Presenter: Thomas Goddard

Abstract:

I'll demonstrate some new capabilities of the UCSF Chimera visualization program ( www.cgl.ucsf.edu/chimera) including tracing surfaces of intracellular membranes or virus layers in electron microscopy density maps, extracting density within surfaces, slicing tomography data at arbitrary angles to show nuclear pores, and displaying data cross-sections as topographic relief surfaces.

UCSF Chimera is an interactive molecular graphics program for analysis of proteins, nucleic acids, volumetric and sequence data. and for creating publication images. The density map display and analysis capabilities are being developed for studying single particle reconstructions and EM tomography. Chimera runs on Windows, Mac, and Linux operating systems, is free for academic use, and is developed by the Resource for Biocomputing, Visualization and Informatics.

Title:

Resources for teaching quantitative cell biology at undergraduate and graduate levels.

Presenter:Raquell M. Holmes

Abstract:

Introducing quantitative cell biology and modeling into undergraduate and graduate biology courses faces a key challenge of access to appropriate teaching materials. In this demo, visitors to the booth will be introduced to:

publicly accessible models in the Virtual Cell that can be used to teach simple and complex biological behaviors
classroom assignments and exercises that make use of models and modeling to teach modeling cell biology
a prototype format and TWiki for the development of modules in Quantitative Cell Biology.

Quantitative Cell Biology involves moving from existing knowledge and experimental data to a proposed model that embodies hypotheses in mathematical form. The models are used to run simulations from which new experiments maybe designed and results predicted. The Virtual Cell, developed by the NIH designated National Resource for Cell Analysis and Modeling (NRCAM), is designed for biologists to develop models and simulations of cellular processes. It can be used to teach students to model and the significance of quantitative experiments. The models, research projects, and exercises presented have been used in undergraduate and graduate courses to teach students how to construct models, understand biological systems, and analyze complex experimental data such as FRAP experiments. Examples of publicly accessible biological models in Virtual Cell include nuclear transport, calcium dynamics, and signal transduction. Accessible models are one part of a framework for computational cell biology teaching modules proposed by attendees of the Kavli Institute for Theoretical Physics course on Biological Switches and Clocks. These modules are meant to facilitate the introduction of quantitative cell biology to undergraduate biology courses. An initial TWiki has been created to foster development of the computational cell biology teaching modules. Teaching modules will make use of the Virtual Cell and other simulation tools. (Supported by NIH grants P41-RR13186, U54-RR022232, and by NSF grants PACI 6245-7 and PHY05-51164)

Title:

Cryo-EM of Molecular Machines at 0.4 nm Resolution

Presenter:Htet Khant

Abstract:

The National Center of Macromolecular Imaging (http://ncmi.bcm.edu) is dedicated to push the resolution of single particle cryo-EM towards atomic resolution via innovative use of modern electron cryomicroscopes and development of new algorithms for automated data collection, electronic notebook, data processing and structure analysis. All of our technology developments are driven by biological applications initiated by our Center collaborators.

The most notable and recent achievements are the successful tracing of the Cα backbone of the GroEL (in collaboration with Dr. David Chuang at UT Southwestern Medical School) and of the epsilon15 bacteriophage (in collaboration with Wen Jiang at Purdue University and Jonathan King at MIT). The models of these proteins are built from the cryoEM density maps without reference to any crystal structures. These cryo-EM structures also reveal novel biological insights previously not seen at low resolution cryo-EM maps.

Title:

Cooperative permeation of ions and water through the selectivity filter of the KcsA potassium ion channel: A ggaHFB transition path ensemble study

Presenter:Ilja V. Khavrutskii

Abstract:

Ion channels are important for maintaining proper ionic balance within cells and polarizing the cell membrane to ensure nerve impulse conduction and other essential operations. Potassium ion channels such as KcsA are the most intriguing as they solve a nontrivial problem of selecting larger K⁺ ions over smaller Na+ ions. Despite considerable efforts aiming at understanding these channels, the origin of the ion selectivity remains poorly understood. Previously we have demonstrated the functional importance of the local contraction/dilation of the channel at the V76 carbonyl ring of the signature peptide TATTVGYG from the selectivity filter of the KcsA ion channel, and proposed two basic ion selectivity mechanisms. In particular, we suggested a way of reducing kinetic barrier for ion permeation by means of incommensurate passage of coupled ion pairs through a periodic filter, and active impeding of co-translation of the water molecules adjacent to the ions due to electrostatic contraction of the channel by the ions. Here we provide atomic level mechanical details of the channel operation during the cooperative ion-water permeation. We identify a functional unit within the selectivity filter that consists of three carbonyl rings, with the V76 ring in the center. The central ring contracts and dilates breaking the channel symmetry to allow triangular formations of either K⁺-H2O-K⁺ or H2O-K⁺-H2O within the unit. These non-linear triads strongly resemble the metastable K⁺(H2O)2K⁺ quadrupole structures observed in solution and correspond to permeation transition states.

Title:

Gfit Demo: Universal Approach to global fitting of data from multiple types of experiments to computational models.

Presenter:Mikhail Levin

Abstract:

In this demonstration I will show how to globally fit multiple experiments into a computational model. Global fitting allows us to verify that the model is consistent with all experimental observations and to estimate the parameters of the model. To simplify global fitting of many experiments of different types we have developed gfit, an open source program (http://gfit.sf.net). Computational models used by gfit may implement any algorithm for simulating experiments performed with the system. By reading the interface description, gfit discovers how to execute the model and how to interpret the experimental data. The interface description language is simple, but flexible enough to accommodate complex experiments as well as rule-based models. Our approach has been used for creating models and for global analysis of data from many different sources including rapid stopped-flow and quench-flow, fluorescence correlation spectroscopy, and surface plasmon resonance. Visitors will be shown how gfit interacts with models, how to create a model, and how to analyze multiple experiments taking into account different experimental conditions. More information about this approach can be found in poster 2463.06-Pos/B577.06

Title:

Using Virtual Cell to generate and explore quantitative model of actin polymerization at the leading edge of cells.

Presenter:Les Loew

Abstract:

This Demo will provide details of the model behind poster 3165-Pos/B468, "A Quantitative Model of Actin Polymerization at the Cell Leading Edge", which will be displayed on Wednesday. It will offer an opportunity for visitors to the booth to:

Learn about the components of the model in detail.
Interact with the model by changing parameters or mechanisms.
Gain an introduction to the Virtual Cell modeling and simulation environment.

The original abstract of the poster provides a summary of the model and simulation results: Branching of actin filaments through the action of the Arp2/3 complex nucleates new polymerization in the lamellipodium of cells. This active polymer growth pushes the branched network of filaments rearward and contributes to the protrusive force that propels the cell's leading edge forward. In this work, we have constructed a quantitative 3D spatial model based on the mechanisms of actin polymerization using the Virtual Cell software. The model explicitly incorporates the following mechanisms: inter-conversions between the ATP, ADP and ADP-Pi forms of both monomeric G-actin and filamentous F-actin; assembly and disassembly of these 3 nucleotide-bound monomer forms to each of the 3 forms of barbed and pointed ends; acceleration of nucleotide exchange on G-actin by profilin; profilin-mediated delivery of G-actin to barbed ends; capping of the 3 forms of barbed ends; annealing and fragmentation of actin filaments; buffering of G-actin by thymosin-β4; severing and accelerated disassembly of actin filaments by cofilin; branching and nucleation of actin filaments by activated Arp2/3; activation of Arp2/3 at the cell membrane and dissociation of Arp2/3 branches in the cytoplasm. The model recapitulates many observations including the high spatial gradient of F-actin between the cell leading edge and the interior. In particular, speckle microscopy data has revealed that while actin filament assembly is highly concentrated at the leading edge of cells, a sharp transition to strong actin filament disassembly occurs just 1µm away; further into the cell interior, assembly and disassembly are approximately balanced. The model shows that this arises from the interplay of retrograde F-actin flow and branch dissociation, which exposes a high concentration of disassembling pointed ends that peaks 2µm away from the activated edge. (supported by NIH grants U54RR022232, P41RR13186 and U54GM64346)

Title:

New Features in UCSF Chimera

Presenter:Elaine Meng, Eric Pettersen

Abstract:

UCSF Chimera is an interactive molecular graphics program with a wide variety of features. Applications include structure analysis (hydrogen bonding, contacts, clashes), structure superposition and comparison, ensemble analysis (trajectory playback, ensemble clustering), analysis in the context of other types of data (sequence alignments, density maps), and making high-quality images and movies.

Recently added features include display and incorporation of amino acid sidechain rotamers from backbone-dependent and -independent libraries, creation of "morph trajectories" between different conformations of a protein or even different proteins, and generating shadowed images with POV-Ray, which is embedded in Chimera. We will demonstrate these features as well as other features (whether new or not) upon request.

Chimera is available for Windows, Mac, Linux and other platforms and can be downloaded free of charge for noncommercial use (www.cgl.ucsf.edu/chimera).

Title:

Optimizing Cardiac Excitation-Metabolic Model By Using Parallel Grid Computing

Presenter:Anushka Michailova

Abstract:

We have extended the Shannon-Bers model in order to investigate excitation-contraction coupling in rabbit epicardial and endocardial ventricular myocytes. We couple cytosolic metabolism to the cell electrical activity and include rate expressions for Mg²⁺-nucleotide regulation of ATP-sensitive K⁺ channel, L-type Ca²⁺ channel, sarcolemmal and sarcoplasmic Ca²⁺-ATPases, and Na⁺/K⁺ pump. The work was performed with a distributed parameter optimization tool (Nimrod) to search for stable model solutions. The Nimrod experiment involved validation of the updated model by varying (a) input current parameters to stabilize the normal epi- and endocardial Ca²⁺ transients for time interval of 3 min at 0.5Hz, (b) input metabolic constants to fit the predicted normal ionic currents to be as close as possible to the experimentally suggested. The results suggest that the distribution of ATP-sensitive K⁺ channels might be important mechanism regulating the excitation-contraction coupling during ischemia.

Title:

The Virtual Cell: Tutorial on new capabilities

Presenter:Ion I. Moraru

Abstract:

The Virtual Cell (VCell—http://www.vcell.org/) has been developed from the beginning with the vision of providing an easy access for cell biologists to sophisticated and powerful computational tools. It has been developed and deployed as a web-based, distributed, client-server system. VCell provides a separation of layers representing biological models, physical mechanisms, geometry, mathematical models and numerical methods. This separation clarifies the impact of modeling decisions, assumptions, and approximations. The result is a physically consistent, mathematically rigorous, spatial modeling and simulation framework for cell biology. VCell can formulate and solve reaction-diffusion-advection-electrophysiological problems in arbitrary geometries (as well as in compartmental approximations using ODE-only simulations), using either deterministic or stochastic algorithms. Users create biological models and VCell will automatically generate an appropriate mathematical encoding for running a simulation, and also automatically generate and compile the appropriate computer code. Using the VCell database, models and model components can be reused and updated, as well as privately shared among collaborating groups, or published. To date, more than 1,500 independent users worldwide have created and run simulations with VCell.

VCell has been continuously and rapidly growing in capabilities and complexity over the past several years. The presentation sessions will include: (i) a short talk presenting the concepts and abstractions underlying the design of the VCell platform, and (ii) demonstrations of a typical workflows of building models, creating applications, running simulations, viewing and exporting results, with special emphasis on recently introduced capabilities: stochastic simulations, membrane diffusion, parameter scans and optimization, field data, and rule-based modeling via BioNetGen integration. We will also introduce upcoming developments, such as: a new, open-source, extensible architecture, grid computing via OpenScienceGrid, and the Virtual Experiment framework. Participants can try out the VCell client and interactively discuss features and technical details.

Title:

Introduction to the UCSF Chimera molecular modeling package

Presenter: Scooter Morris

Abstract:

UCSF Chimera is a program for interactive molecular graphics and modeling. It provides standard graphics features as well as more unique, domain-specific tools; the menu and command-line interfaces provide a rich and overlapping set of functionality. The Introduction to Chimera shows frequently used coloring and display options, including molecular representations such as ribbons, "pipes and planks," surfaces, and abstract renderings of nucleotides. Other general features shown are distance measurements, bond angle rotations, H-bond identification, and display of the corresponding amino acid and/or nucleotide sequences. Attributes such as B-factors and hydrophobicities can be rendered visually with colors, atomic radii, and "worm" thickness. Chimera includes detailed user documentation and is available for Windows, Linux, Mac OS X (with X11), IRIX, and Tru64 Unix. Chimera is free for academic, government, and non-profit use and can be downloaded from http://www.cgl.ucsf.edu/chimera.

Title:

structureViz: Linking Cytoscape to Chimera

Presenter: Scooter Morris

Abstract:

UCSF structureViz is a Cytoscape plugin that links the visualization of biological networks (and biological relationships expressed as networks) provided by Cytoscape with the visualization and analysis of macromolecular structures and sequences provided by UCSF Chimera. structureViz provides commands to open structures in Chimera, manipulate those structures, and align open structures using Chimera's Sequence/Structure tools. n order to load a structure associated with a node, the Protein Databank (PDB) identifier (or identifiers if there are more than one) must be present as an attribute of that node. Currently, structureViz will look for an attribute named Structure, pdb, or pdbFileName. When a structure is opened, structureViz provides an alternative interface to Chimera: the Cytoscape Molecular Structure Navigator. This interface uses a tree-based paradigm to allow users to select and effect the display of models, chains, and residues, mostly through the use of context menus. Additional commands allow for selection by chemistry (Ligand, Ions, Solvent, Secondary Structure, and in the model context menu, Functional Residues). Users can also take advantage of Chimera's structural alignment capabilities by using the "Align" command. structureViz is available for download at http://www.rbvi.ucsf.edu/Research/cytoscape/structureViz/.

Title:

Exploring Biomolecular Machines with NAMD and VMD

Presenter:Yi Wang

Abstract:

The Theoretical and Computational Biophysics Group, located at the Beckman Institute of the University of Illinois at Urbana-Champaign, operates the NIH Resource for Macromolecular Modeling and Bioinformatics. The Resource brings advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance through direct collaboration with experimental researchers, the distribution of user-friendly cutting-edge software, and a broad range of training and dissemination activities.

The flagship software packages NAMD and VMD, both distributed free of charge with source code, facilitate the discovery process from analysis, through modeling, to visualization of the molecular apparatus in biological cells:

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code used regularly to simulate systems of 1,000,000 atoms and beyond on both large supercomputers and inexpensive Linux clusters.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using hardware-accelerated 3-D graphics and built-in scripting.

Title:

Multiscale Modeling of Ventricular Myocytes: Image Analysis and Geometric Processing

Presenter:Zeyun Yu

Abstract:

In compliance with the particular needs during cell-type specifications, mammalian cells have developed a unique membrane structure, called Ttubules (or transverse tubules). These deep invaginations of plasma membranes are found only in adult mammalian ventricular cardiomyocytes and skeletal muscle cells, and play an important role in rapid propagation of depolarization from surface membranes to interiors of these cells. The membrane depolarization triggers Ca²⁺ influxes through L-type Ca²⁺channels (LCCs, also known as dihydropyridine receptors or DHPRs), about 50% of which are found on T-tubular membranes. The initial Ca²⁺influxes through LCCs then activate the adjacent ryanodine receptors (RyRs) on the sarcoplasmic reticulum (SR) membranes, yielding a bulk of Ca²⁺ released from the SR into the cytosol. This tightly-coupled process, known as Ca²⁺-induced Ca²⁺ release (CICR), is carried out in uniquely shaped narrow Casignaling micro-domains (or dyads) that span about 10 nm between T-tubules and junctional SR (jSR). The dyads and their structural details present a key objective in studying the local Ca²⁺ release and furthermore understanding the quantal nature of E-C coupling in cardiac myocytes. On the other hand, the cell-wide excitation and contraction are governed by the beat-by-beat global Ca²⁺ change that is known to be the temporal and spatial summation of local Ca²⁺ releasing events due to the propagation of membrane excitation through the T-tubule network. In fact, T-tubule disarray has been linked to the dyssynchrony of local Ca²⁺ releases during Ca²⁺ transients and abnormal Ca²⁺ wave propagation in failing hearts. For this reason, it is also crucial to understand the cell-wide organization of T-tubules in cardiac cells. Here we report the successful combination of advanced microscopic imaging technologies and computational approaches for multiscale anatomical modeling of T-tubules and jSR. Specifically, ventricular myocytes are imaged with both electron microscopic (EM) tomography and 2-photon microscopy (T-PM). Three-dimensional (3D) maps reconstructed from EM tomographic data or stacks of T-PM images are pre-processed by contrast enhancement and anisotropic filtering methods. T-tubules and jSR are extracted using automatic image analysis techniques including boundary segmentation and skeleton (median axis) detection. High-quality meshes are generated from the extracted T-tubules and jSR, yielding multiscale, realistic geometries that are useful for numerical simulation of local and global Ca²⁺ regulations in ventricular myocytes.

Biophysical Society 2008 NCRR Booth Schedule
NIH NCRR Exhibitor Booth Talks

Booth #719

Abstracts

Biophysical Society 2008 NCRR Booth Schedule NIH NCRR Exhibitor Booth Talks

Booth #719

Abstracts

Biophysical Society 2008 NCRR Booth Schedule
NIH NCRR Exhibitor Booth Talks