Structural View of Biology
Structures in the PDB reveal how cells use chemical energy, light energy, electrical energy and mechanical energy to power the processes of life. Cells must continually interconvert different forms of energy. Energy is obtained from many sources, including light and food. Molecular machines then use this energy to build new molecules, to power motion, to transport molecules to the proper place, to generate heat and light, and to regulate all of the processes occurring in the cell.
Creating and Capturing Light
When needed, cells build molecules to create and focus light. Our eyes build special molecules that act like glass, focusing but not scattering light. Other organisms build molecules that create or modify light.
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As you read this Molecule of the Month, the light from the page is being focused in your eyes by a concentrated solution of crystallin proteins. The lenses in your eyes are built of long cells that, early in their development, filled themselves with crystallins and then made the major sacrifice, ejecting their nuclei and mitochondria and leaving only a smooth, transparent solution of protein. We then rely on these proteins to see for the rest of our lives.
Discussed StructuresalphaA crystallinalphaB crystallinbeta crystallingamma crystallindelta crystallinepsilon crystallinlambda crystallin
Twenty years ago, green fluorescent protein (GFP) was first used to reveal the location of proteins inside living cells, and since then, it has emerged as an invaluable tool for cell biologists. GFP is a small, stable, and brightly fluorescent protein. A gene encoding GFP can be added to a cell and used to synthesize GFP, which then creates its own internal chromophore that fluoresces when illuminated with ultraviolet light, without consuming cellular energy. And perhaps most importantly, GPF can be fused to another protein without perturbing its normal function, creating a highly visible tag that allows the protein of interest to be tracked throughout the cell.
The green fluorescent protein, shown here from PDB entry 1gfl, is found in a jellyfish that lives in the cold waters of the north Pacific. The jellyfish contains a bioluminescent protein-- aequorin--that emits blue light. The green fluorescent protein converts this light to green light, which is what we actually see when the jellyfish lights up. Solutions of purified GFP look yellow under typical room lights, but when taken outdoors in sunlight, they glow with a bright green color. The protein absorbs ultraviolet light from the sunlight, and then emits it as lower-energy green light.
Discussed Structuresgreen fluorescent proteinengineered fluorescent protein
Do you remember the first time that you saw a firefly? If you live anywhere between the Rocky Mountains and the east coast of the US, you have probably chased fireflies since you were a child. If you live in other parts of the world, like me, you may have had the pleasure of discovering fireflies during a summer vacation. They are one of the delightful wonders of warm summer evenings.
Discussed Structuresfirefly luciferasebacterial luciferasedinoflagellate luciferase
Our eyes are biological cameras, complete with a deformable lens to focus light, an adjustable iris to control the exposure, and a retina that acts like a digital sensor to record the focused image. It is filled with amazing refinements, such as a layer of dark black cells behind the retina that reduce reflection and keep the image sharp. Rhodopsin plays the central role in this camera: it is the molecule that senses light.
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