Protein Folding and Macromolecular Recognition 
vator proteins, originally identified by Steven 
McKnight and his co-workers (HHMI, 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. X-ray crystal lographic 
studies of this peptide (with Tom Alber's group, 
University^ of California, Berkeley) confirm that 
the leucine zipper of GCN4 is a coiled coil and 
provide the first high-resolution structure of a 
two-stranded parallel coiled coil. The effects of 
amino acid replacements on the stability, struc- 
ture, and dynamics of this leucine zipper are be- 
ing investigated. 
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 
protein-protein interactions: two helices that 
prefer to interact with each other rather than with 
themselves. By making hybrid leucine zipper 
peptides, we found that eight amino acid resi- 
dues from each of the leucine zipper sequences 
are sufficient to mediate specific heterodimer 
formation. The predominant mechanism for spec- 
ificity in this system was found to be electrostatic 
in nature. 
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. This work was supported by a 
grant from the National Institutes of Health. 
Peptide and Protein Design 
Knowledge of the rules involved in protein 
folding and macromolecular recognition can be 
tested by trying to design de novo amino acid 
sequences that fold into specific conformations 
and/or that interact in a predetermined manner 
with other molecules. Toward this end, we have 
begun to analyze the structural hierarchies in nat- 
ural proteins and to design simple "building 
blocks" of peptide structure. 
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