Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

462 Chapter 8: Analyzing Cells, Molecules, and Systems
Figure 8–22 NMR spectroscopy.
(A) An example of the data from an NMR
machine. This two-dimensional NMR
spectrum is derived from the C-terminal
domain of the enzyme cellulase. The spots
represent interactions between hydrogen
atoms that are near neighbors in the
protein and hence reflect the distance
that separates them. Complex computing
methods, in conjunction with the known
amino acid sequence, enable possible
compatible structures to be derived.
(B) Ten structures of the enzyme, which all
satisfy the distance constraints equally well,
are shown superimposed on one another,
giving a good indication of the probable
three-dimensional structure. (Courtesy of
P. Kraulis.)
(A)
(B)
sequence, it is possible in principle to compute the three-dimensional structure
of the protein (Figure 8–22).
For technical reasons, the structure of small proteins of about 20,000 daltons or
less can be most readily determined by NMR spectroscopy. Resolution decreases
as the size of a macromolecule increases. But recent technical advances have now
pushed the limit to about 100,000 daltons, thereby making the majority of proteins
accessible for structural analysis MBoC6 by m8.29/8.25 NMR.
Because NMR studies are performed in solution, this method also offers a convenient
means of monitoring changes in protein structure, for example during
protein folding or when the protein binds to another molecule. NMR is also used
widely to investigate molecules other than proteins and is valuable, for example,
as a method to determine the three-dimensional structures of RNA molecules
and the complex carbohydrate side chains of glycoproteins.
A third major method for the determination of protein structure, and particularly
the structure of large protein complexes, is single-particle analysis by electron
microscopy. We discuss this approach in Chapter 9.
Protein Sequence and Structure Provide Clues About Protein
Function
Having discussed methods for purifying and analyzing proteins, we now turn to
a common situation in cell and molecular biology: an investigator has identified
a gene important for a biological process but has no direct knowledge of the biochemical
properties of its protein product.
Thanks to the proliferation of protein and nucleic acid sequences that are cataloged
in genome databases, the function of a gene—and its encoded protein—
can often be predicted by simply comparing its sequence with those of previously
characterized genes. Because amino acid sequence determines protein structure,
and structure dictates biochemical function, proteins that share a similar amino
acid sequence usually have the same structure and usually perform similar biochemical
functions, even when they are found in distantly related organisms. In
modern cell biology, the study of a newly discovered protein usually begins with
a search for previously characterized proteins that are similar in their amino acid
sequences.
Searching a collection of known sequences for similar genes or proteins is
typically done over the Internet, and it simply involves selecting a database and
entering the desired sequence. A sequence-alignment program—the most popular
is BLAST—scans the database for similar sequences by sliding the submitted