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Solvation and the hidden thermodynamics of a zinc finger probed by nonstandard repair of a protein crevice
Author(s) -
Lachenmann Marcel J.,
Ladbury John E.,
Qian Xiuqi,
Huang Kun,
Singh Rupinder,
Weiss Michael A.
Publication year - 2004
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.04866404
Subject(s) - chemistry , solvation , enthalpy , conformational entropy , entropy (arrow of time) , zinc finger , thermodynamics , phenylalanine , crystallography , configuration entropy , stereochemistry , solvent , molecule , physics , amino acid , biochemistry , organic chemistry , gene , transcription factor
The classical Zn finger contains a phenylalanine at the crux of its three architectural elements: a β‐hairpin, an α‐helix, and a Zn 2+ ‐binding site. Surprisingly, phenylalanine is not required for high‐affinity Zn 2+ binding, but instead contributes to the specification of a precise DNA‐binding surface. Substitution of phenylalanine by leucine leads to a floppy but native‐like structure whose Zn affinity is maintained by marked entropy–enthalpy compensation (Δ Δ H −8.3 kcal/mol and − T Δ Δ S 7.7 kcal/mol). Phenylalanine and leucine differ in shape, size, and aromaticity. To distinguish which features correlate with dynamic stability, we have investigated a nonstandard finger containing cyclohexanylalanine at this site. The structure of the nonstandard finger is similar to that of the native domain. The cyclohexanyl ring assumes a chair conformation, and conformational fluctuations characteristic of the leucine variant are damped. Although the nonstandard finger exhibits a lower affinity for Zn 2+ than does the native domain (Δ Δ G −1.2 kcal/mol), leucine‐associated perturbations in enthalpy and entropy are almost completely attenuated (Δ Δ H −0.7 kcal/mol and − T Δ Δ S −0.5 kcal/mol). Strikingly, global changes in entropy (as inferred from calorimetry) are in each case opposite in sign from changes in configurational entropy (as inferred from NMR). This seeming paradox suggests that enthalpy–entropy compensation is dominated by solvent reorganization rather than nominal molecular properties. Together, these results demonstrate that dynamic and thermodynamic perturbations correlate with formation or repair of a solvated packing defect rather than type of physical interaction (aromatic or aliphatic) within the core.