Dynamics of biological responses are controlled through networks of interacting components. This concept lies at the heart of systems biology. The Aitchison laboratory exploits yeast to develop systems approaches to interrogate, model and understand complex biological processes, and applies the advances of systems biology to infectious diseases critical to global health.
Exploring Protein Folding Landscapes by Circular Permutation
The composition and movement of individual protein complexes can be measured simultaneously using total internal reflection fluorescence (TIRF) microscopy. Here, single Dam1 complexes (green) bind and move along a microtubule filament (red) without detaching. This observation shows that Dam1 can contribute to chromosome-microtubule coupling during cell division without necessarily forming a sixteen-membered ring encircling the filament.
The crystal structure of a de novo designed protein is nearly identical to the in silico model.
Understanding the molecular evolution of proteins and viruses.
Surface of the nerve terminal at the electric organ synapse. The red is the alpha subunit of the voltage-gated calcium channel. The green is the synaptic vesicle protein SV2 on the surface of the nerve terminal awaiting endocytosis.
Assembly of an Infectious Virus. The terminase enzyme assembles at a cos site in a multi-genome concatemer. This maturation complex nicks the duplex and then binds to the portal ring of a procapsid shell to afford the packing motor complex. The motor packages DNA into the capsid to liquid-crystalline density generating over 30 atmospheres of pressure. Addition of finishing proteins and the phage tail complete the infectious virus.
Investigating the effect of histone modifications on chromatin
structure and function
Two-color fluorescence (top panels) and atomic force microscopy (bottom panels) images of individual synaptic vesicles
The enzyme phospholipase A2 sitting on the membrane interface. This is an interfacial enzyme that must bind to the phospholipid bilayer to access its water-insoluble phospholipid substrate. The x-ray structure of the enzyme was used together with a novel EPR method developed in the Gelb and Robinson labs to position the enzyme on the membrane surface.
TRPV1 channels diffusing laterally through plasma membrane of F11 cells.
Structure for one form of the complex between the transcription activator Gcn4 and the coactivator Gal11 - figure credit Steven Hahn and Rachel Klevit
Type II secretion system from Vibrio cholera, which translocates cholera toxin (yellow in the center) across the outer membrane.
Figure shows two-color fluorescence (top panels) and atomic force microscopy (bottom panels) images of individual synaptic vesicles; here, we developed a quantitative microscopy technique for counting the number of membrane proteins on synaptic vesicles.
Cryo-electron tomography reveals influenza virus architecture including the virus' hemagglutinin fusion protein spikes on the surface. This technique is being used to understand how the viral membrane and a target host membrane fuse together during cell invasion.
Grand-canonical computer simulation of two actin filament bundles polymerizing into the cell membrane.
Protein kinases are dynamic enzymes that can exist in several different
conformations. This image shows a fluorescently labeled probe binding to
SRC kinase in the DFG-out conformation. This binding event causes an
increase in fluorescence, which allows the thermodynamics and kinetics of
this interaction to be determined.
Key proteins in eukaryotic pathogens can be intriguingly
different from their human homologs, making them suitable
targets for structure-based drug design.
Membrane tethering and fusion systems in eukaryotic cells. A range of biochemical and biophysical approaches are applied to understand how small G proteins and multisubunit tethering complexes control the assembly of membrane fusion machines.
Cardiac muscle sarcomere thin and thick filaments
Midget and parasol ganglion cells, two of the primary outputs of the retina.
Embryonic zebrafish neuromasts labeled with fluorescent dyes serve as a useful screening model system for identification of compounds that protect mammalian auditory hair cells against drug-induced toxicity.
Smart Polymer-Enzyme Conjugates. Stimuli-responsive polymers are
conjugated to engineered sites near the enzyme active site and used to
switch enzyme activity via pH or temperature controlled structural
transitions.
Diffraction pattern from x-ray crystallography
Crystal structure of the I-AniI LAGLIDADG homing endonuclease. This protein and others like it are used for gene targeting in a number of biotechnology and medical applications
Siderocalin is an antibacterial, innate immune system defense protein that functions by sequestering essential iron away from invading pathogens as complexes with bacterial siderophores - discovered completely serendipitously when recombinant protein co-crystallized with ferric enterochelin, the primary siderophore of E. coli.
The bacterial adhesive protein FimH is a mechanical force sensor that switches to a tight-binding state when stretched
By using ultrafast NMR methods, it is possible to observe changes in RNA spectra in real time with resolution of just a few seconds and establish the conformational pathway by which RNA changes structure in atomic detail.
Model of T. brucei MetRS with potent inhibitor docked in the active site.
Micrograph of BK proteoliposomes tethered to a streptavidin crystal
TIRF image of a GFP-labeled kinesins implicating in modulating the dynamics of microtubule ends (Motors: green; Microtubules: red).
Image of fluorescent ion channels in the membrane of a patch-clamp
electrode. These recordings allow us to measure ion channel function with
electrophysiology and structural rearrangements with fluorescence
measurements simultaneously.
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