|
Seven hydrophobic residues ranging in size from glycine to phenylalanine have
been substituted for the wild-type methionine residue at position 13 in a
15-residue truncated version (S15) of S-peptide, the small component of
ribonuclease S. Complexes of both S-15 and the seven variants with S-protein
yielded isomorphous crystals. The structures of all eight complexes have been
refined to final R-factors in the range of 17-19%. [See Kim, E. E. Varadarajan,
R., Wyckoff, H. W., and Richards, F. M. (1992) Biochemistry (preceding paper in
this issue) for the description of the reference S-15 complex.] Multiple
side-chain conformations were seen for six residues in all of the complexes and
for two to three additional residues in at least some of the complexes. Three of
the complexes, Gly, Ala, and alpha-amino-n-butyric acid (ANB), contained a
single water molecule in the cavity near residue 13 that makes three hydrogen
bonds to protein atoms. Although space is available, no evidence for additional
water in this region, ordered or disordered, was found. The atoms in the cavity
wall tend to shrink the cavity by moving in on the small residues and to swell
the cavity by moving out for the larger Phe substitution. A swelling seen with
leucine was attributed to a shape effect since Leu, Ile, and Met all have the
same volume. A slight volume contraction of the collection of interior residues
outside of the region of position 13 was also noted. (All changes noted are in
the direction to maintain a constant packing density averaged over the whole
protein.) Leu51, a surface hydrophobic residue, moved considerably in the G, A,
and ANB complexes in directionswhich would tend to decrease the cavity volume.
The only other major change in position, 1.5 A, was the 66-69 loop, which is
about 25 A from position 13. His12, Phe120, and Asp121 appear to be involved in
this movement, but the connection with position 13 is not clear at all. The
thermodynamic data on the association reaction for all of these complexes have
been previously reported [Connelly, P. R., Varadarajan, R., Sturtevant, J. M.,
& Richards, F. M. (1990) Biochemistry 29, 6108-6114; Varadarajan, R.,
Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry
31, 1421-1426]. Some comments are offered on our initial attempts to correlate
the structural changes with the changes in the thermodynamic
parameters.(ABSTRACT TRUNCATED AT 400 WORDS)
|
