suring individual amide-proton exchange rates in 
two-dimensional nuclear magnetic resonance ex- 
periments. Initial results indicate that there can be 
significant differences in the dynamic properties of 
BPTI variants, even when the overall structure is the 
same. This research was supported by a grant from 
the National Institutes of Health. 
A large part of the protein-folding problem is the 
identification and characterization of subdomains of 
native proteins. Accordingly, protein architecture 
and protein structure hierarchies are being analyzed 
and algorithms developed to predict autonomously 
folding domains and subdomains of proteins. In ad- 
dition, proteins are "dissected" experimentally to 
identify minimal folding units and to test predic- 
tions of these algorithms. Protein fragments that 
correspond to minimal folding units have been 
identified and are being characterized. In other pro- 
tein-folding efforts, electrostatic interactions at the 
termini of a helices are being studied in isolated 
peptides. The properties of 13 sheets are being inves- 
tigated in a small |8-sheet-rich domain of protein G, 
the Fc receptor from Streptococcus. 
Macromolecular Recognition 
A second focus of Dr. Kim's laboratory is in macro- 
molecular recognition, which is central to much of 
molecular physiology. The laboratory is particularly 
interested in the leucine zipper class of DNA-bind- 
ing proteins, originally identified by Dr. Steven 
McKnight (HHMI, Carnegie Institution) and his 
co-workers. The leucine zipper regions of these 
proteins are important for homodimer or specific 
heterodimer formation. The long-term goal is to un- 
derstand the "code" for specificity and stability of 
leucine zipper interactions. 
GCN4, a homodimeric transcription factor, serves 
as a prototype protein. A synthetic peptide corre- 
sponding to the 3 3 -residue leucine zipper region of 
GCN4 has been shown to be a two-stranded parallel 
coiled coil. X-ray crystallographic studies of this 
peptide (in collaboration with Dr. Tom Alber, Uni- 
versity of California, Berkeley) provide the first 
high-resolution structure of this motif in isolation. 
The effects of amino acid replacements and/or dele- 
tions on the stability, structure, dynamics, and oli- 
gomerization of this leucine zipper, as well as the 
effects on DNA binding in the context of a larger 
domain, are being investigated. 
The isolated leucine zipper regions from the nu- 
clear oncogene products Fos and Jun are sufficient 
to mediate specific heterodimer formation. The Fos 
homodimer contains several acidic residues that 
lead to substantial electrostatic repulsion at neutral 
pH. It is the destabilization of the Fos homodimer 
that provides a major thermodynamic driving force 
for heterodimer formation. (This research was sup- 
ported by a grant from the National Institutes of 
Health.) 
Peptide and Protein Design 
Knowledge of the rules involved in protein fold- 
ing and macromolecular recognition can be tested 
by trying to design amino acid sequences that fold 
into specific conformations and/or interact in a pre- 
determined manner with other molecules. Based on 
studies of the mechanism of heterodimer formation 
between the Fos and Jun leucine zippers described 
above, two peptides with Velcro-like properties 
have been designed; each by itself is predominantly 
unfolded in aqueous solution, but when mixed they 
form a stable heterodimeric coiled coil. 
Efforts to modify the hydrophobic interface of the 
GCN4 homodimeric coiled coil led to surprises. 
Simply changing the nature of the hydrophobic resi- 
dues at the 4-3 hydrophobic repeat position (i.e., 
while keeping all other residues the same) can 
change the oligomerization state of the peptides 
from dimer to trimer to tetramer. The structure of 
the tetramer has been solved by x-ray crystallogra- 
phy (in collaboration with Dr. Alber) . This structure 
corresponds to a new structural motif, the parallel 
four-helix coiled coil, containing a small channel 
coincident with the superhelix axis. 
Other protein design efforts include alteration of 
the surface of a small water-soluble protein without 
changing the hydrophobic core, in an attempt to 
design a model intrinsic membrane protein. 
Dr. Kim is also Member of the Whitehead Insti- 
tute for Biomedical Research, Associate Professor 
of Biology at Massachusetts Institute of Technol- 
ogy, and Assistant Molecular Biologist at Massa- 
chusetts General Hospital, Boston. 
Articles 
Goodman, E.M., and Kim, P.S. 1991. Periodicity of 
amide proton exchange rates in a coiled-coil leu- 
cine zipper peptide. Biochemistry 30:11615- 
11620. 
Lin, T.-Y., and Kim, P.S. 1991. Evaluating the ef- 
fects of a single amino acid substitution on both 
the native and denatured states of a protein. Proc 
Natl Acad Sci USA 88:10573-10577. 
Lockhart, D.J., and Kim, P.S. 1992. Internal stark 
effect measurement of the electric field at the 
amino-terminus of an a-helix. Science 257:947- 
951. 
O'Shea, E.K., Klemm, J.D., Kim, P.S., and Alber, T. 
1991. X-ray structure of the GCN4 leucine zip- 
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