PDB Molecules of the Quarter: RNA Polymerase, Hemoglobin, and Green Fluorescent Protein (GFP)

The Molecule of the Month series explores the functions and significance of selected biological macromolecules for a general audience. These features, written and illustrated by Dr. David S. Goodsell of the Scripps Research Institute, are available at www.rcsb.org/pdb/molecules/molecule_list.html.

A sample of the molecules featured during this past quarter are included below:

PDB ID: 1i6h
A.L. Gnatt, P. Cramer, J. Fu, D.A. Bushnell, R.D. Kornberg (2001): Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 ? Resolution. Science 292, p. 1876.
RNA Polymerase: The RNA Factory

April, 2003 -- RNA is a versatile molecule. In its most familiar role, RNA acts as an intermediary, carrying genetic information from the DNA to the machinery of protein synthesis. RNA also plays more active roles, performing many of the catalytic and recognition functions normally reserved for proteins. In fact, most of the RNA in cells is found in ribosomes--our protein-synthesizing machines--and the transfer RNA molecules used to add each new amino acid to growing proteins. In addition, countless small RNA molecules are involved in regulating, processing and disposing of the constant traffic of messenger RNA. The enzyme RNA polymerase carries the weighty responsibility of creating all of these different RNA molecules.

RNA polymerase is a huge factory with many moving parts. The one shown in PDB entry 1i6h is from yeast cells. It is composed of a dozen different proteins. Together, they form a machine that surrounds DNA strands, unwinds them, and builds an RNA strand based on the information held inside the DNA. Once the enzyme gets started, RNA polymerase marches confidently along the DNA copying RNA strands thousands of nucleotides long.

Further information about RNA polymerase can be found at www.rcsb.org/pdb/molecules/pdb40_1.html.

Hemoglobin: Red Blood, Blue Blood

PDB ID: 2dhb
W. Bolton, M.F. Perutz (1970): Three dimensional Fourier synthesis of horse deoxyhaemoglobin at 2.8 ?ngstrom units resolution. Nature 228, p. 551.

May, 2003 -- Ever wondered why blood vessels appear blue? Oxygenated blood is bright red: when you are cut, the blood you see is brilliant red oxygenated blood. Deoxygenated blood is deep purple: when you donate blood or give a blood sample at the doctor's office, it is drawn into a storage tube away from oxygen, so you can see this dark purple color. However, deep purple deoxygenated blood appears blue as it flows through our veins, especially in people with fair skin. This is due to the way that different colors of light travel through skin: blue light is reflected in the surface layers of the skin, whereas red light penetrates more deeply. The dark blood in the vein absorbs most of this red light (as well as any blue light that makes it in that far), so what we see is the blue light that is reflected at the skin's surface. Some organisms like snails and crabs, on the other hand, use copper to transport oxygen, so they truly have blue blood.

Hemoglobin is the protein that makes blood red. It is composed of four protein chains, two alpha chains and two beta chains, each with a ring-like heme group containing an iron atom. Oxygen binds reversibly to these iron atoms and is transported through blood. Each of the protein chains is similar in structure to myoglobin (presented in the January 2000 Molecule of the Month), the protein used to store oxygen in muscles and other tissues. However, the four chains of hemoglobin give it some extra advantages.

Further information about hemoglobin can be found a www.rcsb.org/pdb/molecules/pdb41_1.html.

Green Fluorescent Protein (GFP): Ready-Made

PDB ID: 1gfl
F. Yang, L.G. Moss, G.N. Phillips, Jr. (1996): The molecular structure of green fluorescent protein. Nat. Biotechnol. 14, p. 1246.

June, 2003 -- The green fluorescent protein, shown in 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.

You might be saying: who cares about this obscure little green protein from a jellyfish? It turns out that GFP is amazingly useful in scientific research, because it allows us to look directly into the inner workings of cells. It is easy to find out where GFP is at any given time: you just have to shine ultraviolet light, and any GFP will glow bright green. So here is the trick: you attach the GFP to any object that you are interested in watching. For instance, you can attach it to a virus. Then, as the virus spreads through the host, you can watch the spread by following the green glow. Or, you can attach it to a protein, and watch through the microscope as it moves around inside cells.

Further information about the green fluorescent protein can be found at www.rcsb.org/pdb/molecules/pdb42_1.html.