Once again, these studies suggest that zinc fingers 
will provide a powerful and adaptable framework 
for the design of novel DNA-binding proteins. 
Strategies for Designing 
DNA-binding Proteins 
The laboratory is also developing strategies for 
computer-aided protein design and for genetic se- 
lection of DNA-binding proteins with novel binding 
specificities. The strategies for protein design are 
implemented in a package of programs and subrou- 
tines known as PDB-PROTEUS. These programs, 
which include simple methods for characterizing 
spatial relationships, are being used to compare side 
chain-base interactions and side chain-phosphate 
interactions in all known protein-DNA complexes. 
This systematic analysis of spatial relationships 
should help explain the structure and evolution of 
DNA-binding proteins and should provide a firm 
foundation for designing new regulatory proteins. 
Dr. Pabo's laboratory is also testing several meth- 
ods for experimentally screening large numbers of 
sequence variants. One strategy involves expressing 
DNA-binding proteins on the surface of the fd bacte- 
riophage. This may allow the use of affinity chroma- 
tography to isolate DNA-binding proteins with novel 
specificities, and these screening and selection strat- 
egies should complement computer-aided protein 
design. 
Dr. Pabo is also Professor of Biophysics and 
Structural Biology in the Department of Biology 
at the Massachusetts Institute of Technology. 
Articles 
Clarke, N.D., Beamer, L.J., Goldberg, H.R., Ber- 
kower, C, and Pabo, CO. 1991. The DNA bind- 
ing arm of X repressor: critical contacts from a 
flexible region. Science 25 i •.261-210. 
Godley, L., Pfeifer, J., Steinhauer, D., Ely, B., Shaw, 
G., Kaufmann, R., Suchanek, E., Pabo, C, Skehel, 
J.J., Wiley, D.C., and Wharton, S. 1992. Introduc- 
tion of intersubunit disulfide bonds in the mem- 
brane-distal region of the influenza hemaggluti- 
nin abolishes membrane fusion activity. Cell 
68:635-645. 
Pabo, CO., and Sauer, R.T. 1992. Transcription 
factors: structural families and principles of DNA 
recognition. Annu Rev Biochem 61:1053-1095. 
Wolberger, C, Vershon, A.K., Liu, B., Johnson, 
A.D., and Pabo, CO. 1991 ■ Crystal structure of a 
MATa2 homeodomain-operator complex suggests 
a general model for homeodomain-DNA interac- 
tions. CeW 67:517-528. 
PROTEIN STRUCTURE, FUNCTION, AND MOLECULAR RECOGNITION 
Florante A. QuiocHo, Ph.D., Investigator 
The interaction between a protein and its ligand, 
large or small, forms the basis of biological specific- 
ity. It is responsible for the remarkable selectivities 
exhibited, for example, by enzymes for their sub- 
strates, by transpon proteins for their nutrients, by 
binding proteins for their ligands (e.g., DNA, 
metals), and by antibodies for their antigens. Dr. 
Quiocho and his colleagues are studying the three- 
dimensional structures of a number of proteins in 
order to understand a variety of protein-ligand inter- 
actions at the atomic level. Although x-ray crystal- 
lography is the principal experimental approach, 
other correlative techniques — biochemical, physi- 
cochemical, and recombinant DNA — are also 
employed. 
Calmodulin: Target Enzyme Recognition 
Calmodulin (CaM) is the key calcium-dependent 
regulator of a variety of eukaryotic intracellular pro- 
cesses. In many of these the regulator activates more 
than 20 enzymes, and the CaM-binding domains in 
several of these enzymes have been shown to reside 
in a region consisting of an 1 8-residue peptide seg- 
ment. Although these domains show considerable 
sequence diversity, most are predicted to form am- 
phipathic helices. Synthetic peptides based on the 
CaM-binding domains of the target proteins have 
been shown to bind CaM in a calcium-dependent 
manner with the same stoichiometry and affinity as 
the native protein. 
To understand the atomic details of the mecha- 
nism by which CaM recognizes and binds to target 
proteins, the laboratory has recently determined 
two structures. First, the structure of native CaM has 
been refined to 1.7-A resolution. This is a higher 
resolution structure than those of several other in- 
vestigators. The native structure, like all others de- 
termined previously, reveals a dumbbell-shaped 
molecule in which two structurally similar globular 
domains, each containing a pair of calcium-binding 
STRUCTURAL BIOLOGY 481 
