Protein Folding and Macromolecular Recognition 
and dynamics of short peptides in isolated, well- 
defined conditions such as the gas phase will pro- 
vide a valuable bridge to theoretical simulations. 
Macromolecular Recognition 
In this area, we have focused on the leucine 
zipper class of DNA-binding transcriptional acti- 
vator proteins, originally identified by Steven 
McKnight and co-workers (HHMI, the Carnegie 
Institution) . The leucine zipper regions of these 
proteins are important for homodimer or specific 
heterodimer formation. 
Our approach in this work is to use "protein 
dissection." GCN4, a homodimeric transcription 
factor, serves as a prototype protein. A synthetic 
peptide corresponding to the 33-residue leucine 
zipper region folds as a parallel pair of helices. 
This led us to propose that leucine zippers are 
actually short coiled coils. Recent x-ray crystallo- 
graphic studies of this peptide (with Tom Alber's 
group, University of Utah) confirm that the leu- 
cine zipper of GCN4 is a coiled coil and provide 
the first high-resolution structure of a two- 
stranded parallel coiled coil. We are using NMR 
to investigate the dynamics of the leucine zipper 
dimer by measuring amide proton exchange 
rates. Combinatorial mutagenesis is being used 
(with Robert Sauer's group, Massachusetts Insti- 
tute of Technology) to investigate the sequence 
requirements for dimerization by this leucine 
zipper. 
Proper biological function requires that recog- 
nition between many different macromolecules 
in the cell occurs with exquisite specificity. We 
have found that the isolated leucine zipper re- 
gions from the nuclear oncogene products Fos 
and Jun are sufficient to mediate specific hetero- 
dimer formation. This provides a very simple 
model system for studying the specificity of pro- 
tein-protein interactions: two helices that prefer 
to interact with each other rather than with them- 
selves. We are investigating the mechanism and 
structural basis of this specificity in detail. 
A region of GCN4 rich in basic amino acid resi- 
dues, immediately adjacent to the leucine zipper, 
is involved in DNA recognition. We find that this 
basic region by itself, when dimerized via a flexi- 
ble disulfide linker in place of the leucine zip- 
per, is also capable of sequence-specific DNA 
binding. In addition to simplifying structural 
analysis of this new DNA-binding motif, the find- 
ing provides a new strategy for the design of DNA- 
binding peptides. 
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