Sunday, September 26, 2010

Mah Rabbu Ma'asecha Hashem!!! - A Portal to Cell & Molecular Animation
By Scientific Area    |    By Animator / Studio
 Adhesion / Extracellular Matrix
Angiogenesis / Metastasis
Cell Division / Cell Cycle 
Chemistry / Organic Synthesis 
Cytoskeleton / Molecular Motors 
Developmental Processes 
Disease / Immune System 
DNA / Chromatin 
Drug / Mechanism of Action 
Evolution / Origins of Life 
Metabolic / Respiration
Neuronal Signaling

Protein Folding & Stability
RNA Stability / RNAi 
RTKs & Signal Transduction
Stem Cells
Viruses / Infectious Disease
Cell Invasions    |   Jason Sharpe, Donald Ly, Charles Lumsden et al
This Maya animation provides a visual simulation of fibroblasts moving through extracellular matrix - the 3D matrix and behavior of the cell population through the matrix are based on mathematical models implemented in MEL.
The Inner Life of the Cell    |   XVIVO & Harvard Univeristy
This Siggraph award-winning animation depicts the molecular players and signaling processes underlying leukocyte migration, adhesion and extravasation. Structural components of the cytoskeleton and the extracellular matrix, in particular, are highlighted.
T-Cell Mobility from Blood to Lymph    |   Marc Dryer
An interpretative visualization of T-cell mobility from blood to lymph through the thymus-dependent zone of the lymph node using evidence-based research.
Angiogenesis   |   Drew Berry
This animation shows the process by which tumors recruit new blood vessels thereby facilitating the metastatic behavior of stray cells that enter the circulation.
Angiogenesis   |   Greg Leuenberger / Sabertooth Productions
A solid tumor secretes angiogenic molecules that induce new blood vessels to form in the vicinity of the mass. These new vessels eventually grow into the tumor providing it with the necessary oxygen and nutrients for continued growth.
Apoptosis   |   Drew Berry
This stunning Maya animation covers the death receptor signaling pathway that originates with binding of the Fas/TNF family of ligands, triggering of the caspase cascade, cytochrome C release from the mitochondria, apoptosome activation, and ensuing signal amplification.
Bacterial Septosome    |   Damien Lariviere
A 3D model of the cell-division machinery. In bacteria like E. coli, FtsZ proteins assembles into the Z ring at the cell centre. The ring then recruits at least ten membrane-associated proteins to assemble the cell-division protein machinery.
Diversity Oriented Synthesis    |   Eric Keller
A step-by-step depiction of a diversity-oriented organic synthesis reaction on beads (created for Professor Stuart Schreiber at Harvard/Broad). At the same time as the camera follows the reaction in 3D showing bond rearrangements, the viewer can simultaneously follow the reaction in standard stick notation at the bottom of the screen.

Melamine-PTCDI Self-Assembly on Si(111)-Ag Surface    |   Yan Liang
The first part of the animation describes the structure of Si(111)-Ag surface, which is another surface that took the surface science community 25 years to determine. The second part describes the melamine-PTCDI self-assembly on this surface.

Si(111) Surface 7x7 Reconstruction    |   Yan Liang
The Si(111) 7×7 reconstruction was one of the most intriguing problems in surface science. It took surface scientists over 25 years to determine its structure. This 4-minute long animation tries to help the viewers understand and enjoy the beauty of this complicated surface structure.
Actin Polymerization & Spire    |   Janet Iwasa
Spire mechanism - The protein Spire contains 4 WH2 domains which are each able to bind an actin monomer. A conformational change in linker 3 is thought to catalyze the formation of an actin nucleus.

Actin Polymerization - Model for Spire & Formin    |   Janet Iwasa
Spire & formin - The formin cappucino binds to Spire's KIND domain. While bound to Spire, cappucino is unable to act as an actin nucleator, but does not inhibit Spire's nucleation activity.

Cell Quakes - Actin & Actinin    |   Anthony Zielinksi, Charles Lumsden et al
This movie presents a simulation of the behavior of selected cytoskeletal components as external forces are applied to the model (representing the forces of cell migration).

Dynamics of ParM Filaments    |   Janet Iwasa
ParM polymerization dynamics - ParM polymerizes bidirectionally at the same rate at either end. ATP hydrolysis (shown as color change to red) occurs spontaneously. When a filament end loses its ATP 'cap,' the filament undergoes rapid depolymerization from that end in a process termed dynamic instability.
Kinesin Mechanism   |   Graham Johnson
Kinesin walking along a microtubule protofilament demonstrating how energy exchanges combine with binding events to create forward motion.

Microtubules: Structure, Function & Dynamics   |   Geordie Martinez, Steve Davy
Stylus Visuals
This Maya animation depicts the dynamic self-assembly and dissassembly processes of microtubules. The animation incoporates atomic resolution structural information for tubulin (as it undergoes a GTP vs GDP-induced conformational change), as well as cryoEM data for 'protofilament peels' and 'helical ribbons' from the Nogales lab.
Myosin Mechanism   |   Graham Johnson
This animation describes the translation of chemical bond energy of ATP into the sliding motion of thick/thin filaments in our muscle fibers.

ParM and Plasmid Segregation    |   Janet Iwasa
DNA segregation by ParM - ParM binds to DNA-binding proteins, called ParR (orange proteins) around which segments of genomic DNA are coiled. Sister plasmid segregation is achieved through bidirectional insertional polymerization of the ParM filaments.
Tensegrity Model    |   Eddy Xuan
Mechanotransduction through the cytoskeleton: a hypothetical model of mechano-biochemical conversion through protein-protein interaction. This animation depicts the tensegrity model of the cell's cytoskeleton. 
Embryonic Development    |   Blake Porch, HHMI /
Covers the early stages of embyronic development (including fertilization, cleavage, blastocyst formation, implantation, cell migration in the inner cell mass and formation of the embryo's germ layers and neural tube formation).
Embryonic Germ Layers    |   Blake Porch, HHMI /
This animation briefly summarizes the early stages of development and highlights/maps the organ systems in the adult that result from the 3 embryonic germ layers.
Clonal Selection Theory    |   Etsuko Uno
‘Fighting Infection by Clonal Selection’ was created to commemorate the 50th anniversary of a revolutionary theory called ‘Clonal Selection’ by Nobel Laureate, Sir Frank Macfarlane Burnet.  The animation shows how clonal selection works during a bacterial infection of the throat.
Crohn's Disease    |   Gardenia Gonzalez Gil / Living Pixels
The first two parts of this animation illustrate  features of innate and adaptive immunity relevant to Crohn's disease. The third part describes the mechanism of action of lipoxin resolving infection and inflammation, leading to restoration of healthy  gastrointestinal function.
DIabetes (type I)    |   Etsuko Uno
Approximately 25 million people worldwide, many of them children, suffer from type 1 diabetes.  There is currently no cure for diabetes and those affected with this disease must endure daily insulin injections for the duration of their lives.  This animation illustrates how insulin is normally produced in the body and how its production is destroyed in this disease.
Multiple Sclerosis    |   Gardenia Gonzalez Gil / Living Pixels
This Maya animation describes some immunological and brain barrier defects found in patients with Multiple Sclerosis. It illustrates how these defects progressively deteriorate neuronal signal transmission.
Chromatin   |   Drew Berry
This animation shows the different levels of chromatin packing - starting with wrapping of DNA around histone octamers and nucleosome assembly, all the way to chromosome condensation during mitosis. 
DNA structure    |   Drew Berry
A series of short animations highlighting the structureand flexibility of the DNA double-helix.

Restriction Endonuclease Digestion & Ligation   |   Drew Berry
This animation depicts the proces of DNA recombination. The DNA plasmid is first digested with the restriction endonuclease enzyme ecoRI. Then, a piece of DNA encoding a gene is inserted into the plasmid by DNA ligase.
Rapamycin, FKBP12 & FRAP    |   Eric Keller /
Dimerization of FKBP12 & FRAP is shown upon binding of the small molecule rapamycin.

Fatty Acid Formation in a Geyser    |   Janet Iwasa
This animation illustrates a theoretical means by which fatty acids may have been synthesized along the sides of mineral walls of hydrothermal vents or (in this case) a geyser

Fatty Acid Vesicle Formation    |   Janet Iwasa
De novo vesicle formation from fatty acid micelles - Protons are represented by the small glowing spheres. Upon protonation, the micelle structure becomes more fluid and may allow for larger numbers of micelles to join together. Vesicle formation occurs by chance after the fatty acid sheet has reached a threshold surface area.
Fatty Acid Vesicle Dynamics    |   Janet Iwasa
Although the vesicle structure itself as a whole is extremely stable, individual fatty acids within vesicles are extremely dynamic and are constantly joining and leaving the vesicle membrane.  Protonated fatty acids (shown by the glowing hydrogen in the head group and the lighter colored tail) readily flip between the inner and outer leaflets of the membrane.
Vesicle Entry of Adenosine Mono-Phosphate   |   Janet Iwasa
Polar molecules such as AMP may enter fatty acid vesicles through interactions between the fatty acid head groups and the small molecule.

ATP Synthase    |   Graham Johnson
This animation describes the transfer of chemiosmotic energy into rotational energy, and ultimately into the chemical bond energy of ATP.

ATP Synthase - Part I    |   Said Sannuga
The rotary mechanism of mitochondrial ATP synthase.

ATP Synthase - Part II    |   Said Sannuga
View from above and then below the F1 domain along the rotating γ-subunit.

ATP Synthase - Part III    |   Said Sannuga
How the rotating γ-subunit imposes the conformational states on a β-subunit required for substrate binding, ATP formation and ATP release.

ATP Synthase - Part IV    |   Said Sannuga
Three conformations of a catalytic β-subunit produced by 120º rotations of the central γ-subunit.

ATP Synthase - Part V    |   Said Sannuga
Changes in the positions of sidechains in the catalytic site of F1-ATPase bringing about binding and subsequent hydrolysis of ATP.

F1-F0 ATPase - Part I    |   Dale Muzzey
This Maya animation describes the mechanism of the F1-Fo ATPase.

F1-F0 ATPase - Part II    |   Dale Muzzey
A fly-through of the morphing ATPase structure in surface representation

F1-F0 ATPase - Part III    |   Dale Muzzey
A detailed atomic look at the molecular interactions that stabilize ADP/ATP in the F1-F0 ATPase active site.

Hemoglobin    |   Janet Iwasa
A series of short movies decribing the structure of hemoglobin and the conformational changes that accompany binding of oxygen. Page also includes other useful resources.

Sickle Cell Hemoglobin    |   Drew Berry
This animation depicts hemoglobin molecules binding to oxygen. The mutant form of hemoglobin is also shown and results in the assembly of the long stiff protein fibers characteristic of the disease sickle cell anemia.
Villus Capillary - Hemoglobin    |   Gaël McGill
An animation that takes the viewer from the tissue level (i.e. a capillary inside a gut villus) all the way to the molecular level (by taking a look at the conformational changes that occur as a result of oxygen release by hemoglobin). 
Neural Long Term Potentiation (LTP)    |   Jason Raine
A 3D animation depicting the early molecular events underlying long term potentiation in the spinal cord of pain pathways. (Click on the icon in the "Master's Research Project Examples 2002-2005 area of the page).
The Whole Brain Catalog   |   Drew Berry
A visualization of the possibilities of the Whole Brain Catalog (, an open source, multi-scale virtual catalog of the mouse brain.
Bacterial Flagellum    |   ERATO
This series of animations depicts the processes of flagellar motion and assembly in molecular detail (also called the "Protonic Nanomachine Project").

E. coli Cytoplasm Brownian Dynamics Simulation  |  Sean McGuffee & Adrian Elcock
The simulation shows 1000 individual macromolecules diffusing, colliding and transiently associating with each other over the course of 10 microseconds of simulation; the translational diffusion coefficient of the GFP in this model is in agreement with experimental measurements.
E. coli Cytoplasm    |   Julio Ortiz
This 3DS Max fly-through animation uses experimentally-derived concentrations of the 50 most abundant components of the E. coli cytoplasm (not counting DNA).
Spiroplasma Tomography    |   Julio Ortiz
This animation shows the mapping of 70S ribosome positioning and orientation data from a tomogram of Sprioplasma melliferum using pattern recognition.
Proteasome   |   Janet Iwasa
This Maya animation provides an introduction to proteasome structure as well as an explanation for proteasome-mediated degradation of a target protein (including potential "wobble" of the regulatory particle as it interacts with the core particle).

Proteasome & Ataxin    |   Eric Keller / - HHMI
This Maya animation depicts the process of ubiquitin-dependent degradation in the proteasome. The effect of mutant ataxin no this process is also shown.

Replication   |   Drew Berry
Still one of the more complex and beautiful molecular animations ever made, this movie shows the components and dynamic processes involved in the replication of both the leading and lagging strands of DNA. 

T7 Primase/Helicase    |   David Gohara / SciAna FilmWorks
This animation shows the dancing heptameric complex responsible for unwinding the DNA double helix in bacteriophage and how it is subsequently used as a site for primer synthesis.

Tri Nucleotide Repeat    |   Drew Berry / - HHMI
This animation shows how a tri-nucletoide repeat can cause the DNA polymerase to 'slip' and incorporate additional nucleotides during the replication process.
Dicer   |   Steve Davy, Geordie Martinez / Stylus Visuals
This Maya animation shows cleavage of double-stranded RNA into short RNA fragements by the Dicer ribonuclease.

RNA Folding    | - HHMI
A short animated sequence showing how RNA can fold back onto itself (through the formation of intramolecula base-pairing).

Clathrin Mediated Receptor Endocytosis    |   Janet Iwasa
Dynamics of Lck in the T cell synapse - Upon T cell activation, clusters of signaling proteins form microdomains in the cell membrane. Some proteins, like the tyrosine kinase Lck (white) can freely diffuse between these clusters. Interactions between Lck and proteins in the signalling cluster can cause Lck to become immobilized.
Protein Expressions - Study N3    |   Monica Zoppe/Scientific Visualization Unit
"The video PROTEIN EXPRESSIONS - Study N. 3D is the third (and last) re-elaboration of the movie on which we have been developing our studies in the last two years.

CSF Receptor    |   Drew Berry
A molecular view of the surface of a stem cell highlighting the binding of G-CSF by its receptor, dimerization, signal transduction and the resulting effect on cell division and growth.

Intestinal Crypt Stem Cells - A Clonal Conveyor Belt    |   Eric Keller / Digizyme Inc.
This animation, created for Hans Clevers' lab, shows how the entire surface of the intestine is populated via a "clonal conveyor belt" mechanism. Daughter cells born from stem cells located at the base of the crypts travel up and differentiate, thereby pushing existing cells up towards the villus tip (the oldest cells are jetisoned via apoptosis at the villus tip). Adenoma formation is also shown.
Stem Cell Differentiation & Division    |   Drew Berry
An animation showing stem cell colonies expanding in the bone marrow. Some daughter cells differentiate intowhite blood cells and migrate into the blood, while others remain stem cells.

Stem Cell Introduction    |   Arkitek Studios
A series of animations with audio and text commentary that clearly explain the basics od stem cell biology (including their unique characteristics, pluripotency in the early embryo, presence in adult tissues and embryonic stem cels in culture).

Introduction to Transcription - part I    |   Drew Berry
Transcription factors assemble at a DNA promoter region found at the start of a gene. Promoter regions are characterised by the DNA's base sequence, which contains the repetition TATATA É and for this reason is known as the "TATA box".
Introduction to Transcription - part II    |   Drew Berry
The RNA polymerase unzips a small portion of the DNA helix exposing the bases on each strand. One of the strands acts as a template for the synthesis of an RNA molecule. The base-sequence code is transcribed by matching these DNA bases with RNA subunits, forming a long RNA polymer chain.
MECP2 transcription factor    |   Eric Keller / - HHMI
This animation show the effects of MECP2 DNA methylation (CpG islands) on recruitment of Sina3/HDAC, nuclesome modification and gene silencing.

p53 transcription factor    |   Eric Keller / - HHMI
This animation highlights the structure of p53 protein and its binding to a cognate promoter. Recruitment of RNA polymerase and transcription are also shown.

Polymerase mechanism   |   David Gohara / SciAna FilmWorks
A detailed animation highlighting the key residues and side chains within a polymerase active site and the polymerization mechanism.

PPAR Delta transcription factor    |   Eric Keller / - HHMI
Shows the effects of drug-binding to the PPAR-delta transcription factor receptor on DNA - a repressor is released thereby turning on the muscle delta network on genes. Oxidative metabolism is activated and leads to reduction of fat pads in adipose tissue.
PPAR Gamma transcription factor    |   Eric Keller / - HHMI
Shows fat cells in the adipose tissue adjacent to muscle - storage / breakdown of the cell's fat droplet affects the balance of secreted adiponectin and resistin hormones. The effect of drugs against PPAR gamma is also shown to affect this balance and resulting insulin sensitivity.
Elongation Cycle of Protein Biosynthesis    |   A.H. Whiting, J. Frank, R. Agarwal
This visualization rotates the assembled ribosome and then shows (using a cut-away) the path of entry of the tRNA during the elongation cycle.

Elongation Factor Tu   |   Graham Johnson
An animation highlighting the structural domains of elongation factor Tu and the surface involved in tRNA binding. The conformational change in the switch helix that occurs as a result of GTP hydrolysis results in the release of the tRNA.
Golgi /ER Visualization    |   Drew Berry
A visualization of a cell's cytosplasm derived from electron tomography data from Brad Marsh's laboratory. The different components - nucleus, microtubules, mitochondria, ribosomes, smooth ER, rough ER, Golgi - are highlighted in separate 'passes' and then overaid as one. A great reminder of how crowded cellular interiors are!
IRES   |   Stylus Visuals
This animation compares the structure of ribosome complexes in either IRES-mRNA (Internal RIbosome Entry Sequence) or capped-mRNA conformations.

Ribosome Function    |   Said Sannuga
A detailed animation that covers all the central steps in prokaryotic translation (including initiation, elongation and termination steps with many of the invidual protein factors involved in each).
RIbosome Molecular Ratchet Motion    |   A.H. Whiting, J. Frank, R. Agarwal
Shows the 70S ribosome conformation change that occurs upon binding of elongation factor G.

Signal Recognition Particle    |   Eric Keller, Steve Davy / Stylus Visuals
This Maya animation depicts the process by which the translating ribosome is halted by the signal recognition particle (SRP). The ribosome is subsequently brought to the membrane and docked with a channel to translocate the nascent polypeptide chain.
Translation   |   Drew Berry
Part 3 in Drew Berry's "Central Dogma" animations - the mRNA (yellow) is decoded inside the ribosome (purple and light blue) and translated into a chain of amino acids (red) as aminoacyl-tRNAs (green) deliver each amino-acid cargo (red/pink tip) to the ribosome.
tRNA-Ribosome Molecular Dynamics Simulation    |   K.Y. Sanbomatsu et al.
One of the largest molecular dynamic simulations in biology - studies the interactions of tRNA as it enters the ribosome.

tRNA acts as a flexible molecular spring during codon recognition    |   Yu Chen
A movie showing how aminoacyl-tRNA acts as a flexible molecular spring during codon recognition and accomodation.

Bacteriophage T4    |   Seyet, LLC
An accurate visualization of the Bacteriophage T4 based on Cryo-EM datasets of the virus. The scope of the animation is to show the infection process of T4 into an E. coli cell. All scientific data sets and motion based off of research from Michael Rossmann Laboratory (Purdue University).

Capsid Molecular Dynamics Simulation    |   Geordie Martinez / Stylus Visuals
A Maya-rendered visualization of a VMD molecular dynamics simulation. Created for David Chandler's lab at UC Berkeley, this movie depicts the physics of viral capsid formation while summarizing some of the technical steps involved in its creation.
Dengue Virus Entry    |   Janet Iwasa, Gaël McGill (Digizyme) & Michael Astrachan (XVIVO)
A narrated animation depicting the events that lead to Dengue virus entry into a host cell. In particular, rearrangements and conformational changes in the Dengue glycoprotein E are shown. These lead to membrane fusion and subsequent release of the viral payload into the host cell cytoplasm. Created for WGBH.
HIV Assembly, Budding and Maturation    |   Ken VanderStoep
A visualization of the capsid protein lattice structure that forms during the assembly of immature HIV-1 particles. (Click on the icon in the "Master's Research Project Examples 2002-2005 area of the page).

HIV Entry - gp41-mediated membrane fusion    |   Gaël McGill
This Maya animation depicts the process by which HIV's gp41 protein mediates the fusion of viral and cellular membranes during virus entry. In addition, strategies for inhibiting this process with peptide or small molecule inhibitors are shown.

The Lifecycle of Malaria (Part 1)    |   Drew Berry
This animation represents part-1 of a 2-part series depicting the events of the malaria parasite lifecycle.
The parasite is shown entering the human host following a mosquito bite and we follow its progression initially to the liver and subsequently targeting erythrocytes on a large scale.

The Lifecycle of Malaria (Part 2)    |   Drew Berry
Part 2 depicts events in the mosquito host.
The malaria parasite is shown reproducing in the mosquito's stomach followed by the development of cysts and infection of the salivary glands.

Poliovirus    |   Art Olson, Dan Bloch
This 1985 animation (programmed in GRAMPS) describes the structure of the poliovirus (seen here at near-atomic resolution). Icoshedral symmetry of the capsid, positioning and interaction of each of the V 1 - 4 proteins is described in detail. 
Pseudomonas    |   Graham Johnson
A sequence depicting Pseudomonas infection of lung epithelial cells.

Reovirus Entry    |   Dale Muzzey / Digizyme
This animation highlights the structure of the reovirus - we follow the virus as it gets cleaved/activated in the gut lumen, undergoes endocytosis and subsequently begins replication and export of its viral RNA once in the cytosol of the target cell.
Early Events in Reovirus Entry    |   Gaël McGill, Janet Iwasa
A more in-depth look at the early events of reovirus entry. This current version highlights each of the 8 proteins that make up the virus as well as its icosahedral symmetry. The virus is activated upon trypsin 'attack' and cleavage of the outer protein layer. The virus then binds to and enters the cell via the JAM-1 receptor and clathrin-mediated endocytosis.
Tomato Bushy Stunt Virus    |   Art Olson
This 1981 landmark molecular animation was programmed in GRAMPS and captured from a computer screen with a Bolex 16 mm movie camera. Elegantly choreographed and paced, the movie presents the structure of the tomato bushy stunt virus (TBSV) - the first viral structure solved at atomic-resolution (2.9 angstroms) by Steve Harrison in 1978. Morphing animations of capsid proteins are also shown and explain the swelling of the viral particle observed at high pH.
Viral DNA Packaging - Part I    |   Eric Keller / Stylus Visuals
This 2-part Maya animation depicts the process of nucleic acid packing/assembly into the viral capsid. Part I shows the process simultaneous with the measured kinetics of packing and force (displayed on the right). 
Viral DNA Packaging - Part II    |   Eric Keller / Stylus Visuals
This 2-part Maya animation depicts the process of nucleic acid packing/assembly into the viral capsid. Part II focuses on the molecular machinery responsible for pulling the nucleic aacid strand inside the capsid.
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