March 31, 2001
Molecules of the Quarter:
|PDB ID: 1htb
G. J. Davis, W. F. Bosron, C. L. Stone, K. Owusu-Dekyi, T. D. Hurley (1996): X-ray structure of human beta3beta3 alcohol dehydrogenase. The contribution of ionic interactions to coenzyme binding. J. BIOL. CHEM. 271, p. 17057.
Our bodies create at least nine different forms of alcohol dehydrogenase, each with slightly different properties. Most of these are found primarily in the liver, including the beta3 form (PDB entry 1htb) and the similar enzyme from horse liver (PDB entry 6adh). The sigma form, available in PDB entry 1agn, is found in the lining of the stomach. Each enzyme is composed of two subunits, and quite remarkably, you can mix and match subunits between these different forms, creating mixed dimers that are still active. Ethanol is not the only target of these enzymes; they also make important modifications to retinol, steroids, and fatty acids. The range of different types of alcohol dehydrogenase ensures that there will always be one that is perfect for the current task.
Alcohol dehydrogenase provides a line of defense against a common toxin in our environment. But this protection carries with it some dangers. Alcohol dehydrogenase also modifies other alcohols, often producing dangerous products. For instance, methanol, which is commonly used to "denature" ethanol, rendering it undrinkable, is converted into formaldehyde by alcohol dehydrogenase. The formaldehyde then does the damage, attacking proteins and embalming them. Small amounts of methanol cause blindness, as the sensitive proteins in the retina are attacked, and larger amounts, perhaps a glassful, lead to widespread damage and death.
Alcohol dehydrogenase also plays a central role in the most ancient business of biotechnology: alcoholic fermentation. Yeast and many bacteria build a larger alcohol dehydrogenase, like the one shown on the right (PDB entry 1ykf). It performs the last step in the conversion of food into metabolic energy, creating ethanol instead of detoxifying it. Sugars are broken down and used for energy, forming ethanol as the waste product, which is excreted into liquid surrounding the cell. We have harnessed this process to produce alcoholic beverages: yeast is allowed to ferment grain sugars to form beer, and yeast is allowed to ferment grape juice to form wine.
Alcohol dehydrogenase uses two molecular "tools" to perform its reaction on ethanol. The first is a zinc atom, which is used to hold and position the alcoholic group on ethanol. The second is a large NAD cofactor (constructed using the vitamin niacin), which actually performs the reaction. PDB entry 1adc contains ethanol molecules bound to the two active sites. A slightly modified version of NAD was used in the structure analysis, so that the enzyme would not immediately attack the ethanol. The zinc atom is cradled by three amino acids from the protein: cysteine 46, cysteine 174, and histidine 67. The ethanol binds to the zinc and is positioned next to the NAD cofactor.
Insulin: A Molecular Messenger
|PDB ID: 4ins
E. N. Baker, T. L. Blundell, J. F. Cutfield, S. M. Cutfield, E. J. Dodson, G. G. Dodson, D. M. Hodgkin, R. E. Hubbard, N. W. Isaacs, C. D. Reynolds, et al. (1988): The structure of 2Zn pig insulin crystals at 1.5 A resolution. PHILOS. TRANS. R. SOC. LOND. B. BIOL. SCI. 319, p. 369.
Insulin is a tiny protein. It moves quickly through the blood and is easily captured by receptors on cell surfaces, delivering its message. Small proteins pose a challenge to cells: it is difficult to make a small protein that will fold into a stable structure. Our cells solve this problem by synthesizing a longer protein chain, which folds into the proper structure. Then, the extra piece is clipped away, leaving two small chains in the mature form. The structure is further stabilized by three disulfide bridges.
When insulin function is impaired, either by damage to the pancreas or by the rigors of aging, glucose levels in the blood rise dangerously, leading to diabetes mellitus. For people totally deficient in insulin, such as children who develop diabetes early in life, this can be acutely dangerous. High glucose levels lead to dehydration as the body attempts to flush out the excess sugar in urine, and life-threatening changes in blood pH as the body turns to other acidic molecules for delivery of energy. Diabetes mellitus has severe long-term effects as well. It is one of the major chronic diseases in the industrialized world. Lowered levels of insulin that may occur as we age allow elevated levels of sugar in the blood over extended periods of time. Sugar molecules attach to proteins throughout the body, compromising their function, and sugars derived from glucose build up, distorting and clogging cells.
Diabetes mellitus may be treated by manually replacing the insulin that is missing in the blood. Of course, we need a plentiful source of insulin for use in these treatments. Fortunately, insulin from pigs (PDB entry 4ins) differs from human insulin (PDB entry 2hiu) by only one amino acid: a threonine at the end of the chain in human insulin is replaced by alanine in pig insulin. Insulin from cows is also very similar, differing in only three positions. Because of their similarity, these forms of insulin are also recognized by our own cells and may be used in therapy. Today, human insulin is also created by biotechnology, using engineered bacteria to produce a protein exactly identical to our own protein.
Insulin is a perfect molecule for exploring protein structure. It is small enough that you can display all of the atoms and still have a picture that is not too confusing. Human insulin, PDB entry 1trz, contains four chains, labeled A, B, C, and D. When looking at this structure, you'll want to display only the A and B chains, which together compose one monomer of insulin. In the structure, you can see many of the key features that stabilize protein structure. Notice the cluster of carbon-rich amino acids, like leucine and isoleucine, that cluster in the middle of insulin, forming a hydrophobic core. Notice that the surface is covered with the charged amino acids lysine, arginine, and glutamate. These amino acids interact favorably with the surrounding water. Also notice the three disulfide bridges between cysteine amino acids, which stabilize this tiny protein.
Transfer RNA: The Translator of Genetic Sequence
|PDB ID: 4tna
B. Hingerty, R. S. Brown, A. Jack (1978): Further refinement of the structure of yeast tRNAPhe. J. MOL. BIOL. 124, p. 523.
March, 2001 -- Since the process of DNA-directed protein synthesis was discovered, scientists and philosophers have searched, more or less seriously, for a relationship between the triplet nucleic acid codons and the chemical nature of the amino acids. These attempts have been uniformly unsuccessful, but remain an occasional topic of speculation because of their possible insights into the origins of life. There does not appear to be a specific interaction between the codons and the amino acids themselves. Instead, the match is made by transfer RNA, the Rosetta Stone that translates the nucleotide language of codons into the amino acid language of proteins. This translation is physical and direct: at one end of each tRNA is an anticodon that recognizes the genetic code, and at the other end is the appropriate amino acid for that code.
Errors in the production of proteins can occur at both ends of the tRNA. The proper amino acid must be added to the tip of tRNA, ready to be added to a growing protein chain. A battery of enzymes, termed amino-acyl tRNA synthases, are in charge of this job. They generally make a mistake in about one out of every ten thousand tRNA molecules that they charge with an amino acid. We'll look more carefully at these fascinating proteins next month. Errors may also occur at the other end of the tRNA, when the anticodon matches up with a codon. It may simply match improperly--this happens about one time in five hundred. Or, because each codon is three nucleotides long, it may associate in a shifted position, instead of the proper reading frame. This will throw off the rest of the protein, as each successive tRNA lines up in the wrong position after the shifted one. Fortunately, when genetic sequences are read in the wrong frame, they are filled with STOP codons, so the protein synthesis will be aborted after a few dozen more amino acids are added.
Biological evolution is remarkable in its ability to benefit from shortcomings. If there is any way that a problem can be made into an asset, the process of natural selection will find it eventually. Errors in protein synthesis are no exception. Both the mismatch of codon with anticodon and the shifting of reading frames play special functional roles in certain organisms. In many places, different codons are used as START signals. The codons may be GUG, UUG, or AUU, but all use the same methionine tRNA, which normally recognizes the codon AUG. In order for these proteins to be made, the methionine tRNA must pair with these erroneous codons. Shifting of the reading frame is essential in the life-cycle of HIV. When making the long polyprotein that contains all of the proteins that are found inside the virus, ribosomes make a mistake in one place about 5% of the time, aligning a tRNA incorrectly and shifting the reading frame. This causes the ribosome to miss the normal STOP codon, so a much longer protein is made. These occasional errors are critical for the life of the virus, because the longer proteins contain the enzymes that transcribe the viral genome.
Transfer RNA molecules are composed of one short chain of RNA, 70-90 nucleotides in length, folded into a trefoil shape. Two different examples of this structure can be found in phenylalanine tRNA (PDB entry 4tna) and aspartate tRNA (PDB entry 2tra). The two ends of the RNA chain are close to one another at the pointed end of the L-shaped structure. The amino acid is also added at this end. The center of the chain forms the rounded leg of the L, exposing the three nucleotides that form the anticodon. The other two loops of the trefoil are bundled into the elbow, where they provide structure to the whole molecule. The four normal RNA bases--adenine, uracil, guanine and cytosine--obviously do not provide enough latitude to form a sturdy structure, because many of the bases are modified to enhance their structures. To see two particularly exotic examples, look at the base next to the anticodon, number 37, in the initiator methionine tRNA (PDB entry 1yfg) or the phenylalanine tRNA (PDB entries 4tna and 6tna).
For more information on Transfer RNA, please see the list of references at http://www.rcsb.org/pdb/molecules/pdb15_4.html.