A Positron Named Priscilla Scientific Discovery at the Frontier (1994) / Chapter Skim
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10 Fold, Spindle, and Regulate: How Proteins Work
10 Fold, Spindle, and Regulate: How Proteins Work
Pages 290-315
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From page 290... ...
The symptoms of genetic disease are caused by defects in proteins. For example, sickle cell anemia results from a defect in the bloodtransporting hemoglobin molecule.
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From page 291... ...
Cellulose, the woody material that prevents humans from grazing with the cattle, and from dining with termites on old, dead trees, is composed of chains of sugar molecules, just like starch. The difference between a two-by-four and potatoes or pasta is largely the result of slight differences in the way the sugar molecules are strung together.
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From page 292... ...
These are also referred to by scientists as "hydrophobic" or just plain "greasy." The difference between covalent bonds and the other forces is analogous to the difference between the strength of the ties of family and friendship. Both the covalent bonds and the various weaker forces are properties of the building blocks of proteins, small molecules called amino acids.
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From page 293... ...
It accomplishes this by revealing the location of electron densities throughout the protein. These correspond to chemical groups on amino acids.
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From page 294... ...
Of atoms that occur naturally in amino acids, only hydrogens can be magnetized. It is possible to set up NMR so that it detects atoms in pairs, because one atom can magnetize another provided the two are within several chemical bond lengths of each other.
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From page 295... ...
But he doubted this. He had noted that, while the hemoglobins of horses and humans are structurally similar, they differ in amino acid sequence by nearly 50 percent.
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From page 296... ...
To further test these ideas, Matthews's postdoctoral student Xue-Tun Zhang systematically substituted the amino acid alanine at each position in the protein, one by one. Alanine is one of the simplest of all the amino acids and lacks the reactive chemical groups that interact with those on other amino acids.
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From page 297... ...
This meant substituting cysteine, the sulfur-containing amino acid, in place of other amino acids on either side of a fold in the protein. Matsumura, now at Scripps Research Institute, built the bridges.
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From page 298... ...
Leucine zippers manage the regulatory process. The work on leucine zippers ultimately would support Matthews's findings that, although most amino acids exert little influence on shape, that of core amino acids can be profound.
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From page 299... ...
Leucine zippers are alpha helices, which are named for the fact that the amino acid leucine appears in the helix at intervals of seven amino acids, or slightly less than two turns of the screw. Moreover, the leucines, and another, similarly hydrophobic amino acid, which also appears at intervals of seven, form a zipper-like structure that binds two alpha helices together (see Figures 10.1 and 10.2~.
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From page 300... ...
The big clue that the leucine zipper was important came when McKnight and his colleagues sequenced a regulatory protein that goes by the evocative acronym C/EBP and discovered via computer search that a segment of 60 amino acids was very similar to segments of the regulatory proteins fos and myc. (Fos and myc are proto-oncogenes, genes that normally play important roles in the body but that contribute to the development of cancer when they undergo certain mutations.
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From page 301... ...
couldn't be correct," says O'Shea. "It takes 3.6 amino acids to make one full turn of a protein helix," she explains.
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From page 302... ...
In 1949 Pauling had proposed that some proteins would form alpha helices. He knew how amino acids fit together, and he could take a protein full of them and manipulate the topology in his mind, and now he and Crick were in a race to find an actual protein that had this struc
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From page 303... ...
Besides proving that the leucine zipper is a coiled coil, the comparison of diffraction patterns showed that the structure of the zipper is similar in detail to that of keratin. But at the time, no one had ever deciphered the fine structure of keratin from the diffraction pattern.
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From page 304... ...
We were very lucky to hit close enough to begin with." They had their crystal within 3 months. Sometimes parts of the protein crystallize poorly or not at all, so that electron clouds of those atoms do not contribute to the diffraction pattern.
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From page 305... ...
Until recently, the x-ray patterns were recorded on ordinary film, and the machine judging of how strong the xray diffraction had been by the shade of spots on the film was imprecise. Now, photographic film has been replaced by electronic film that can literally count photons, greatly increasing accuracy.
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From page 306... ...
But recent advances have made NMR much easier, says Thomas James, a researcher at the University of California, San Francisco. These advances have also allowed researchers to use the technique to examine much bigger proteins: with 150 to 200 amino acids, up from about 80 amino residues.
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From page 307... ...
Since experimental error is inevitable, the structure is analyzed by a program called the distance geometric algorithm, which determines what parts of the protein's structure have been accurately defined, and what parts have been poorly defined. The data are delivered in the form of a "family of structures," which the researcher can compare to one another.
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From page 308... ...
THE COILED COIL RULES OF FOLDING Meanwhile, in 1991, Pehr Harbury, one of Peter Kim's graduate students, set out to determine how structure influences function in the leucine zipper. Leucine and the other hydrophobic amino acids in the zipper are spaced as evenly as possible within an odd-numbered repeating sequence: Four positions from leucine to the other hydrophobe, and back to leucine again is three, and so on.
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From page 309... ...
"Why is that? The only thing that we've changed in these sequences is the geometry of these [amino acids that connect the helices]
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From page 310... ...
And in particular, says Alber, how the amino acids fit together in the core of the coiled coil determines the number of strands. The rule of folding that the results suggest, says Alber, is that amino acids with side chains that branch at the first carbon do not fit the holes in the so-called knob-in-hole packing that leucines occupy in the leucine .
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From page 311... ...
In the leucine zipper, asparagine accomplishes this fine tuning. Most coiled coils are not as regular as leucine zippers, and frequently another hydrophobic amino acid occupies the "leucine position." Harbury hopes to develop a set of rules for predicting the structures and bonding arrangements of this variety of coiled coils, and he is asking such questions as how many substitutions of leucine by isoleucine, one of the so-called beta-branching hydrophobes that fail to fit in the knob 311
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From page 312... ...
The results of experiments now under way will tell. ANOTHER APPROACH IN THE QUEST FOR THE HOLY GRAIL Despite the growing knowledge of the mechanics of lysozyme and leucine zippers, the Holy Grail of protein research, predicting structure from sequence, remains elusive.
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From page 313... ...
That limits the dimensionality of the search." "The second major simplification is that instead of working with a three-dimensional structure, we have simplified that into a one-dimensional string which we can compare to amino acid sequences." ("String" is a computer term meaning things that have been strung out in one dimension.) ~ v v Eisenberg replaces three-dimensionality with the details of the chemical environment of each amino acid position.
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From page 314... ...
A coiled coil that Eisenberg had predicted should be a dimer turned out to be a trimer. And Alber says, "Our finding that the shape of an amino acid makes a difference to the structure suggests that something is missing from his calculations, because he doesn't consider shape at all." "It's not that his method is wrong," Alber hastens to add.
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From page 315... ...
Researchers are only beginning to design novel proteins while sitting at the keyboard. The amino acid chain remains a Rosetta stone with the wealth of information on how proteins fold largely undeciphered.
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