Testing of the additivity-based protein sequence to reactivity algorithm.
The standard free energies of association (or equilibrium constants) are predicted for 11 multiple variants of the turkey ovomucoid third domain, a member of the Kazal family of protein inhibitors, each interacting with six selected enzymes. The equilibrium constants for 38 of 66 possible interactions are strong enough to measure, and for these, the predicted and measured free energies are compared, thus providing an additional test of the additivity-based sequence to reactivity algorithm. The test appears to be unbiased as the 11 variants were designed a decade ago to study furin inhibition and the specificity of furin differs greatly from the specificities of our six target enzymes. As the contact regions of these inhibitors are highly positive, nonadditivity was expected. Of the 11 variants, one does not satisfy the restriction that either P(2) Thr or P(1)' Glu should be present and all three measurable results on it, as expected, are nonadditive. For the remaining 35 measurements, 22 are additive, 12 are partially additive, and only one is (slightly) nonadditive. These results are comparable to those obtained for a set of 398 equilibrium constants for natural variants of ovomucoid third domains. The expectation that clustering of charges would be nonadditive is modified to the expectation that major nonadditivity will be observed only if the combining sites in both associating proteins involve large charge clusters of the opposite sign. It is also shown here that an analysis of a small variant set can be accomplished with a smaller subset, in this case 13 variants, rather than the whole set of 191 members used for the complete algorithm.
Qasim
M A
MA
Department of Chemistry, Purdue University, 560 Oval Drive, Brown Building, West Lafayette, Indiana 47907-2038, USA.
Lu
Wuyuan
W
Lu
Stephen M
SM
Ranjbar
Michael
M
Yi
ZhengPing
Z
Chiang
Yi-Wen
YW
Ryan
Kevin
K
Anderson
Stephen
S
Zhang
Wenlei
W
Qasim
Sabiha
S
Laskowski
Michael
M
D000465:Algorithms; D000595:Amino Acid Sequence; D001671:Biochemistry / Q000379:methods*; D019992:Databases as Topic; D004926:Escherichia coli / Q000378:metabolism; D007700:Kinetics; D008969:Molecular Sequence Data; D009154:Mutation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D013211:Staphylococcus aureus / Q000201:enzymology; D013816:Thermodynamics
D011506:Proteins