enzymes interact with their substrates and act as cata- 
lysts? Significant progress has been made in using 
genetic engineering to simplify the protein-folding 
problem and to quantitate the interactions that sta- 
bilize protein structures. The structure of the biotin 
repressor was determined. Related studies of Cro 
and other DNA-binding proteins are revealing the 
structural basis of DNA-protein interaction. 
The laboratory of Associate Investigator Robert 
O. Fox, Ph.D. (Yale University) has developed a 
cysteine-specifiic iron chelator reagent that can ef- 
fect cleavage of peptide bonds. This novel reagent 
has been useful in mapping the structure of protein- 
folding intermediates and of protein-DNA com- 
plexes, particularly a number of nuclease and 
myoglobin variants. In a complementary kinetic 
experiment, progress has been made using nu- 
clear magnetic resonance spectroscopy to identify 
an early folding intermediate of staphylococcal 
nuclease. 
The work of Assistant Investigator John Kuriyan, 
Ph.D. (Rockefeller University) and his colleagues is 
aimed at obtaining atomic-level information about 
how protein molecules perform their diverse and 
specific functions. The major tools used are x-ray 
diffraction and computer simulation. Proteins 
under investigation include electron transfer en- 
zymes, DNA-binding proteins that are important in 
the replication of genetic information, and regula- 
tory proteins involved in carcinogenesis. The struc- 
tures of two new proteins were recently deter- 
mined. One is a part of the DNA polymerase that 
replicates the bacterial chromosome during cell di- 
vision and serves to tether the rest of the replicative 
machinery onto the DNA. The other protein is 
known as the SH2 domain and is a key element in the 
mechanisms used by the cell to respond to external 
signals. 
The general goal of Investigator Thomas A. Steitz, 
Ph.D. (Yale University) and his colleagues has been 
to understand the biological function of macromole- 
cules in terms of their detailed molecular structure. 
The following are among the questions being asked 
about proteins that interact with nucleic acids: How 
do the sequence-specific DNA-binding proteins rec- 
ognize the particular DNA sequence to which they 
bind? What are the common structural themes 
among proteins that interact with nucleic acids? 
How do the template-directed polymerases assure 
high fidelity in the copying of templates? How does 
tRNA binding to human immunodeficiency virus 
(HIV) reverse transcriptase differ from its binding to 
synthetases? The specific systems being studied for 
which crystals exist include the catabolite gene acti- 
vator protein-DNA complexes, Escherichia colt lac 
repressor, T7 RNA polymerase complexed with T7 
lysozyme, the E. coli Klenow fragment complex 
with DNA, HIV reverse transcriptase, T4 gene 
32, single-stranded DNA-binding protein-DNA 
complex, resolvase, recA, ruvC, and GlntRNA 
synthetase-tRNA^'" complex. In order to under- 
stand enzyme mechanisms, site-directed mutagene- 
sis is used to determine the effect of specific muta- 
tions on the activity and the three-dimensional 
structure of the protein and its complexes with sub- 
strates. Using the structure of HIV reverse transcrip- 
tase complexed with appropriate substrate and in- 
hibitor ligands, new inhibitors will be designed that 
may serve as anti-AIDS drugs. 
Assistant Investigator Stephen K. Burley, M.D., 
D.Phil. (Rockefeller University) and his colleagues 
are also interested in developing a detailed under- 
standing of the physical principles that govern the 
general problem of molecular recognition in biolog- 
ical systems. Many important biochemical processes 
rely on precise recognition of one macromolecule, 
usually a protein, by another. The approach of this 
laboratory is to use x-ray crystallography and 
other biophysical methods to determine the three- 
dimensional structures of biological macromole- 
cules and their complexes with DNA, protein, or 
other ligands. These structures contain a wealth of 
detail that can be analyzed to provide a functional 
description of the physical forces that are responsi- 
ble for mediating recognition. 
The laboratory of Investigator Carl O. Pabo, Ph.D. 
(Massachusetts Institute of Technology) is attempt- 
ing to understand how proteins recognize spe- 
cific sites on double-stranded DNA and how the 
bound proteins regulate gene expression. His group 
uses x-ray crystallography to determine the three- 
dimensional structure of protein-DNA complexes. 
Recent work has revealed how two of the major fami- 
lies of eukaryotic DNA-binding proteins (known as 
the homeodomain and the zinc finger) recognize 
their binding sites. This information will eventually 
be used to help design novel DNA-binding proteins 
for research, diagnosis, and therapy. 
During the past year Investigator Johann Deisen- 
hofer, Ph.D. (University of Texas Southwestern 
Medical Center at Dallas) and his research group 
have been working on the analysis of the three- 
dimensional structure of several proteins by x-ray 
diffraction methods. The crystal structure of cy- 
tochrome P450bm-3 was solved, and cytochrome 
P450t-erp, DNA photolyase, a fragment of synapsin I, 
ribonuclease inhibitor, and SecA protein are among 
other proteins under analysis. 
The interaction between a protein and its ligand 
(large or small) forms the basis of biological speci- 
458 
