Adhesion / Extracellular Matrix

The Inner Life of the Cell    |    Harvard University, XVIVO

xvivo_innerlife

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.

» View the animation at Harvard BioVisions

Cell Invasions    |    Charles Lumsden, Donald Ly, Jason Sharpe

Cell Invasions

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.

» View the animation

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Angiogenesis / Metastasis

Metastatic Bone Pain    |    Geoffrey Cheung

cheung_metastaticBonePain

underlying peripheral pain mechanisms resulting from metastatic bone cancer.

» View the animation

Angiogenesis    |    Drew Berry

berry_cancer

This animation shows the process by which tumors recruit new blood vessels thereby facilitating the metastatic behavior of stray cells that enter the circulation.

» View the animation

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Apoptosis

Apoptosis    |    Drew Berry

berry_apoptosis

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.

» View the animation

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Cell Division / Cell Cycle

Protein Expressions – Study N3    |    Monica Zoppe, Scientific Visualization Unit

zoppe_proteinstudy3

“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.”

» View the animation

Bacterial Septosome    |    Damien Lariviere

lariviere_septosome

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.

» View the animation

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Chemistry / Organic Synthesis

Si(111) Surface 7×7 Reconstruction    |    Yan Liang

liang_Si111

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.

» View the animation

Melamine-PTCDI Self-Assembly on Si(111)-Ag Surface    |    Yan Liang

liang_melamine

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.

» View the animation

Diversity Oriented Synthesis    |    Eric Keller

keller_DOS

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.

» View the animation at Bloopatone

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Cytoskeleton / Molecular Motors

Fantastic Vesicle Traffic    |    Daniel von Wangenheim

showcase_dVonWangenheim

How do plant cells deliver new material to their growing root hair tip? A combination of time-lapse photography, fluorescence live cell imaging and animation shows the molecular mechanisms in the context of the entire organism.

» View the animation

ParM and Plasmid Segregation    |    Janet Iwasa

iwasa_ParMplasmid

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.

» View the animation at OneMicron

Myosin Mechanism    |    Graham Johnson

johnson_myosin

This animation describes the translation of chemical bond energy of ATP into the sliding motion of thick/thin filaments in our muscle fibers.

» View the animation

Microtubules: Structure, Function & Dynamics    |    Geordie Martinez, Steve Davy, Stylus Visuals

martinez_microtubules

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.

» View the animation

Dynamics of ParM Filaments    |    Janet Iwasa

iwasa_ParMdynamics

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.

» View the animation at OneMicron

Kinesin Mechanism    |    Graham Johnson

johnson_kinesin

Kinesin walking along a microtubule protofilament demonstrating how energy exchanges combine with binding events to create forward motion.

» View the animation

Cell Quakes – Actin & Actinin    |    Anthony Zielinksi, Charles Lumsden

zielinski_cellquakes

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).

» View the animation at U. Toronto

Actin Polymerization – Model for Spire & Formin    |    Janet Iwasa

iwasa_spireformin

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.

» View the animation at OneMicron

Tensegrity Model    |    Eddy Xuan

xuan_tensegrity

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.

» View the animation

Actin Polymerization & Spire    |    Janet Iwasa

iwasa_spireactinpoly

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.

» View the animation at OneMicron

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Developmental Processes

Embryonic Germ Layers    |    Biointeractive.org, Blake Porch, HHMI

hhmi_germlayers

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.

» View the animation at HHMI

Embryonic Development    |    Biointeractive.org, Blake Porch, HHMI

hhmi_embyronicdev

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).

» View the animation at HHMI

Chick Embryo Development    |    AXS studio

AXS_chickEmbryoDev

Animation of the 21 day development of a chicken embryo in the egg.

» View the animation

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Disease / Immune System

Clostridium tetani and Tetanus    |    Maja Divjak

showcase_tetanus

This animation describes the process of infection with Clostridium tetani and how the toxin it releases interrupts nervous control of our muscles, leading to tetanus.

» View the animation

Bordetella pertussis & Whooping Cough    |    Maja Divjak

showcase_pertussis

This animation opens with normal respiratory function, then demonstrates how a bacterium, Bordetella pertussis, causes whooping cough by damaging ciliated airway cells.

» View the animation

Diabetes (type I)    |    Etsuko Uno

etsukoUno_diabetes

This animation explores insulin production both in the normal case as well as in the development of Type 1 Diabetes, when insulin production is disrupted.

» View the animation

Multiple Sclerosis    |    Gardenia Gonzalez Gil, Living Pixels

gil_multipleSclerosis

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.

» View the animation

Crohn’s Disease    |    Gardenia Gonzalez Gil, Living Pixels

gil_crohns

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.

» View the animation at Living Pixels

Clonal Selection Theory    |    Etsuko Uno

etsukoUno_clonalSelection

‘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.

» View the animation

Cancer is Not One Disease    |    Kate Patterson

patterson_cancerNotOneDisease

This animation draws on the experience of a patient living with pancreatic cancer to show some of the complexities of cancer. Over a long period of time, thousands of molecular ‘mistakes’ can accumulate in a cell and increase the risk of cancer. Now, these specific mistakes can be detected in individual cancer patients, thereby offering new hope for the future of personalised treatments.

» View the animation

Insulin Receptor & Type II Diabetes    |    Maja Divjak

divjak_insulinType2Diabetes

This animation describes the role of the insulin receptor in type 2 diabetes. It focuses on the very recent discovery of how the hormone insulin actually binds to the receptor on the surface of cells, as determined by Professor Mike Lawrence’s laboratory at the Walter and Eliza Hall Institute.

» View the animation

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DNA / Chromatin

The Structure of DNA    |    Betsy Skrip, Sera Thornton

showcase_structDNA2

An exploration of the structure of deoxyribonucleic acid, or DNA.
This video was created for MITx 7.28.1x Molecular Biology: DNA Replication & Repair, offered on edX.

» View the animation at MITx BIO

Introduction to Epigenetics (for the Boston Museum of Science)    |    Digizyme

Digizyme_MoS_Epigenetics

This animation explains how environmental conditions can influence the expression genes. We begin with a simplified view of gene transcription, mRNA synthesis and translation of the corresponding protein. We also observe how epigenetic ‘tags’ (chemical modifications to the DNA) can alter whether or not a gene is expressed.

» View the animation at Digizyme

Restriction Endonuclease Digestion & Ligation    |    Drew Berry

berry_ecoRI

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.

» View the animation at WEHI

DNA structure    |    Drew Berry

berry_DNA

A series of short animations highlighting the structureand flexibility of the DNA double-helix.

» View the animation at WEHI

Chromatin    |    Drew Berry

berry_chromatin

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.

» View the animation at WEHI

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Drug / Mechanism of Action

Rapamycin, FKBP12 & FRAP    |    Biointeractive.org, Eric Keller

hhmi_rapamycin

Dimerization of FKBP12 & FRAP is shown upon binding of the small molecule rapamycin.

» View the animation

DNA Nanorobot (Wyss)    |    Digizyme

digizyme_dnaNanorobotWyss

This animation depicts the structure and function of a drug delivery device created entirely of DNA. The therapeutic payload (in this case antibodies) is protected from the environment until a target protein (in this case PDGF, in green) competes for binding of the aptamer latches and triggers opening of the clamshell-like device.

» View the animation

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Evolution / Origins of Life

Vesicle Entry of Adenosine Mono-Phosphate    |    Janet Iwasa

iwasa_vesicleadenosineentry

Polar molecules such as AMP may enter fatty acid vesicles through interactions between the fatty acid head groups and the small molecule.

» View the animation

Fatty Acid Vesicle Dynamics    |    Janet Iwasa

iwasa_vesicleFAdynamics

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.

» View the animation

Fatty Acid Vesicle Formation    |    Janet Iwasa

iwasa_vesicleformation

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.

» View the animation

Fatty Acid Formation in a Geyser    |    Janet Iwasa

iwasa_geyserFAformation

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.

» View the animation

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Metabolic / Respiration

Villus Capillary – Hemoglobin    |    Gaël McGill

mcgill_villuscap

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).

» View the animation

Sickle Cell Hemoglobin    |    Drew Berry

berry_hemosicklecell

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.

» View the animation at WEHI

Hemoglobin    |    Janet Iwasa

iwasa_hemoglobin

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.

» View the animation

F1-F0 ATPase – Part III    |    Dale Muzzey

muzzey_F1F0ATPase3

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

» View the animation

F1-F0 ATPase – Part II    |    Dale Muzzey

muzzey_F1F0ATPase2

A fly-through of the morphing ATPase structure in surface representation.

» View the animation

F1-F0 ATPase – Part I    |    Dale Muzzey

muzzey_F1F0ATPase1

This Maya animation describes the mechanism of the F1-Fo ATPase.

» View the animation

ATP Synthase – Part V    |    Said Sannuga

sannuga_ATPsynthase5

Changes in the positions of sidechains in the catalytic site of F1-ATPase bringing about binding and subsequent hydrolysis of ATP.

» View the animation at MRC

ATP Synthase – Part IV    |    Said Sannuga

sannuga_ATPsynthase4

Three conformations of a catalytic β-subunit produced by 120º rotations of the central γ-subunit.

» View the animation at MRC

ATP Synthase – Part III    |    Said Sannuga

sannuga_ATPsynthase3

How the rotating γ-subunit imposes the conformational states on a β-subunit required for substrate binding, ATP formation and ATP release.

» View the animation at MRC

ATP Synthase – Part II    |    Said Sannuga

sannuga_ATPsynthase2

View from above and then below the F1 domain along the rotating γ-subunit.

» View the animation at MRC

ATP Synthase    |    Graham Johnson

johnson_ATPsynthase

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

» View the animation

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Neuronal Signaling

An Atomic View of Brain Activity    |    Burkhard Rammner

showcase_atomicBrain

A 3D molecular-scale computational model of a synapse based on a combination of electron microscopy, super-resolution microscopy and biochemical data.

» View the animation at Science

The Whole Brain Catalog    |    Drew Berry

berry_braincatalog

A visualization of the possibilities of the Whole Brain Catalog (http://wholebraincatalog.org), an open source, multi-scale virtual catalog of the mouse brain.

» View the animation

Neural Long Term Potentiation (LTP)    |    Jason Raine

raine_neuralLTP

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).

» View the animation at U. Toronto

Alzheimer’s Enigma    |    Christopher Hammang

hammang_alzheimersEnigma

A beautiful 3D animation that takes us deep into the brain to understand how plaque build-up on brain cells occurs during Alzheimer’s disease.

» View the animation

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Other

Entomology Animated Episode 1: RIFA Madness    |    Eric Keller

keller_entomologyAnim

A stunning and humorous animation that explains the venom of the infamous fire ant species Solenopsis invicta.

» View the animation

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Physiology

Heart simulation    |    Supercomputational Life Science & Sciement

SCLS_heartSimulation

A highly realistic heart simulation that models heart function, contraction and relaxation of muscle based on the statistical behavior of molecules, which in turn are strongly coupled with the computation of blood flow and pressure.

» View the animation

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Prokaryotes

Spiroplasma Tomography    |    Julio Ortiz

ortiz_ribosomes

This animation shows the mapping of 70S ribosome positioning and orientation data from a tomogram of Sprioplasma melliferum using pattern recognition.

» View the animation

E. coli Cytoplasm    |    Julio Ortiz

ortiz_Ecolicytoplasm

This 3DS Max fly-through animation uses experimentally-derived concentrations of the 50 most abundant components of the E. coli cytoplasm (not counting DNA).

» View the animation

E. coli Cytoplasm Brownian Dynamics Simulation    |    Adrian Elcock, Sean McGuffee

elcock_Ecolicyto

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.

» View the animation

Bacterial Flagellum    |    ERATO

erato_flagellum

This series of animations depicts the processes of flagellar motion and assembly in molecular detail (also called the “Protonic Nanomachine Project”).

» View the animation

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Protein Folding & Stability

Simulated ‘time-lapse’ of a nascent peptide    |    Barth van Rossum, Chris Spronk

showcase_bVanRossum

A beautiful animation showing a steered trajectory from a coarse-grained (no water) Molecular Dynamics/MD simulation of a peptide folding upon exit from the ribosome. The trajectory was calculated in Yasara, imported and morphed with Molecular Maya (mMaya) and rendered in Maya.

» View the animation at Spronk Studio

Proteasome    |    Janet Iwasa

iwasa_proteosome

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).

» View the animation

Proteasome & Ataxin    |    Biointeractive.org, Eric Keller, HHMI

keller_proteasome

This Maya animation depicts the process of ubiquitin-dependent degradation in the proteasome. The effect of mutant ataxin no this process is also shown.

» View the animation

From Milk to Yogurt    |    Yan Liang

liang_milkToYogurt

A beautiful animation depicting how changing acidity conditions due to the presence of yogurt bacteria can affect the protein and fatty components of milk and induce formation of yogurt.

» View the animation

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Replication

Tri Nucleotide Repeat    |    Biointeractive.org, Drew Berry, HHMI

berry_trinucrepeat

This animation shows how a tri-nucletoide repeat can cause the DNA polymerase to ‘slip’ and incorporate additional nucleotides during the replication process.

» View the animation at HHMI

T7 Primase/Helicase    |    David Gohara, SciAna FilmWorks

gohara_T7

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.

» View the animation at SciAnaFilms

Replication    |    Drew Berry

berry_replication

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.

» View the animation at WEHI

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RNA Stability & RNAi

RNA Folding    |    Biointeractive.org, HHMI

hhmi_RNAfolding

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

» View the animation

Dicer    |    Geordie Martinez, Steve Davy, Stylus Visuals

martinez_dicer

This Maya animation shows cleavage of double-stranded RNA into short RNA fragements by the Dicer ribonuclease.

» View the animation

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RTKs & Signal Transduction

Clathrin Mediated Receptor Endocytosis    |    Janet Iwasa

iwasa_clathrin

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.

» View the animation

Yeast Mating Pathway    |    Janet Iwasa

iwasa_yeastMatingPathway

A 3D nimation depicting the step by step signaling transduction process of the mating pathway in yeast.

» View the animation

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Stem Cells

The Origin of Breast Cancer    |    Drew Berry, Etsuko Uno

BreastCancer

This animation visualises research published in Nature Medicine (Vol 15, Issue 8, 2009) by the laboratory of Jane Visvader and Geoffrey Lindeman. The mammary gland is comprised of three main cell types; alveolar, ductal and myoepithelial cells. Breast stem cells can develop into any of the three cell types through a series of intermediate cell stages. One intermediate is the luminal progenitor cell, which develops into either alveolar or ductal cells. The paper describes how an aberrant form of a luminal progenitor cell is involved in the development of some forms of breast cancer.

» View the animation

The Control of Breast Stem Cells    |    Drew Berry, Etsuko Uno

ControlStemCells

This animation illustrates how breast stem cells respond to steroid hormone despite the cells not having any steroid receptors. The animation illustrates the research published in Nature (Vol 465, Issue 7299, 2010) by the laboratory of Jane Visvader and Geoffrey Lindeman.

» View the animation

Breast Stem Cells    |    Drew Berry, Etsuko Uno

BreastStemCells

An overview of the human mammary gland with a focus on the role of breast stem cells during pregnancy. The primary function of the mammary gland is to produce milk to nourish young offspring. The mammary gland is comprised of three main cell types; alveolar, ductal and myoepithelial cells. During pregnancy, the mammary gland increases in size due to the action of breast stem cells, which can mature into any of the three mammary gland cell types.

» View the animation

Stem Cell Introduction    |    Arkitek Studios

arkitek_stemcells

A series of animations with audio and text commentary that clearly explain the basics of stem cell biology (including their unique characteristics, pluripotency in the early embryo, presence in adult tissues and embryonic stem cells in culture).

» View the animation

Stem Cell Differentiation & Division    |    Drew Berry

berry_stemcells

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.

» View the animation at WEHI

Intestinal Crypt Stem Cells – A Clonal Conveyor Belt    |    Digizyme, Eric Keller

kellermcgill_conveyorbelt

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.

» View the animation

CSF Receptor    |    Drew Berry

berry_CSFreceptor

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.

» View the animation at WEHI

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Transcription

PPAR Gamma transcription factor    |    Biointeractive.org, Eric Keller, HHMI

keller_ppargamma

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.

» View the animation at HHMI

PPAR Delta transcription factor    |    Biointeractive.org, Eric Keller, HHMI

keller_ppardelta

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.

» View the animation at HHMI

p53 transcription factor    |    Biointeractive.org, Eric Keller, HHMI

keller_p53

This animation highlights the structure of p53 protein and its binding to a cognate promoter. Recruitment of RNA polymerase and transcription are also shown.

» View the animation at HHMI

MECP2 transcription factor    |    Biointeractive.org, Eric Keller, HHMI

keller_mecp2

This animation show the effects of MECP2 DNA methylation (CpG islands) on recruitment of Sina3/HDAC, nuclesome modification and gene silencing.

» View the animation at HHMI

Introduction to Transcription – part II    |    Drew Berry

berry_transcription2

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.

» View the animation at WEHI

Introduction to Transcription – part I    |    Drew Berry

berry_transcription1

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”.

» View the animation at WEHI

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Translation

tRNA-Ribosome Molecular Dynamics Simulation    |    K.Y. Sanbomatsu

sanbonmatsu_tRNAMD

One of the largest molecular dynamic simulations in biology – studies the interactions of tRNA as it enters the ribosome.

» View the animation

Translation    |    Drew Berry

berry_translation

Part 2 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.

» View the animation at WEHI

Signal Recognition Particle    |    Eric Keller, Steve Davy, Stylus Visuals

keller_SRP

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.

» View the animation at Bloopatone

Ribosome Molecular Ratchet Motion    |    A.H. Whiting, J. Frank, R. Agarwal

whiting_ratchet

Shows the 70S ribosome conformation change that occurs upon binding of elongation factor G.

» View the animation

Ribosome Function    |    Said Sannuga

sannuga_ribosome

A detailed animation that covers all the central steps in prokaryotic translation (including initiation, elongation and termination steps with many of the individual protein factors involved in each).

» View the animation

IRES    |    Stylus Visuals

martinez_IRES

This animation compares the structure of ribosome complexes in either IRES-mRNA (Internal RIbosome Entry Sequence) or capped-mRNA conformations.

» View the animation

Golgi / ER Visualization    |    Drew Berry

berry_golgi

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!

» View the animation

Elongation Factor Tu    |    Graham Johnson

johnson_EFTu

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.

» View the animation

Elongation Cycle of Protein Biosynthesis    |    A.H. Whiting, J. Frank, R. Agarwal

whiting_elongationcycle

This visualization rotates the assembled ribosome and then shows (using a cut-away) the path of entry of the tRNA during the elongation cycle.

» View the animation

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Viruses / Infectious Disease

Viral DNA Packaging – Part II    |    Eric Keller, Stylus Visuals

keller_viralDNApackaging2

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.

» View the animation at Bloopatone

Viral DNA Packaging – Part I    |    Eric Keller, Stylus Visuals

keller_viralDNApackaging1

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).

» View the animation at Bloopatone

Tomato Bushy Stunt Virus    |    Art Olson

olson_tbsv

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.

» View the animation

Early Events in Reovirus Entry    |    Gaël McGill, Janet Iwasa

mcgilliwasa_reovirus

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.

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Reovirus Entry    |    Dale Muzzey, Digizyme

muzzey_reovirus

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.

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Pseudomonas    |    Graham Johnson

johnson_pseudomonas

A sequence depicting Pseudomonas infection of lung epithelial cells.

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Poliovirus    |    Art Olson

olson_polio

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.

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The Lifecycle of Malaria (Part 2)    |    Drew Berry

berry_malaria_p2

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.

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The Lifecycle of Malaria (Part 1)    |    Drew Berry

berry_malaria_p1

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.

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HIV Entry – gp41-mediated membrane fusion    |    Gaël McGill

mcgill_gp41

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.

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Dengue Virus Entry    |    Digizyme, Gaël McGill, Janet Iwasa, Michael Astrachan, XVIVO

iwasamcgill_dengue

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.

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Capsid Molecular Dynamics Simulation    |    Geordie Martinez, Stylus Visuals

martinez_MD

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.

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Bacteriophage T4    |    LLC

seyet_t4

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).

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