Title

Quantitative Measurement of the Solvent Accessibility of Histidine Imidazole Groups in Proteins

Document Type

Article

Publication Date

2012

Publication Title

Biochemistry

Abstract

We report a method for expressing the solvent accessibility of histidine imidazole groups in proteins. The method is based on measuring the rate of the hydrogen exchange (HX) reaction of the imidazole Cε1-hydrogen. The rate profile of the HX reaction as a function of pH gives a sigmoidal curve, which reaches the maximal rate constant (kmax) on the alkaline side of the sigmoidal curve. To quantitatively describe the solvent accessibility of imidazole groups in proteins, it is necessary to compare the kmax of the imidazole groups with their intrinsic kmax (ikmax), the maximal rate constants for the given imidazole groups when they are fully exposed to the bulk solvent. However, the mechanism of the HX reaction suggests that the ikmax of an imidazole group differs depending on its pKa, and no systematic study has been conducted to clarify how the ikmax is affected by pKa. We therefore investigated the relationship between ikmax and pKa using four imidazole derivatives at three different temperatures. The experimentally determined pKa-specific ikmax values allowed us to derive a general formula to estimate the ikmax value of any given imidazole group exhibiting a specific pKa at a specific temperature. Using the formula, the protection factors (PF), the ratio of ikmax to kmax, of five imidazole groups in dihydrofolate reductase were obtained and used to express the magnitude of their solvent accessibility. In this definition, the smaller the PF value, the higher the solvent accessibility, and a value of 1 indicates full exposure to the bulk solvent. The solvent accessibility expressed by the PF values agreed well with the solvent accessible surface areas obtained from the X-ray diffraction data.

Comments

This study was supported by National Institutes of Health
Grant P30EY-11373 (Visual Sciences Research Center of Case
Western Reserve University) and funds from Case Western
Reserve University and the Cleveland Foundation.

DOI

10.1021/bi300911d

Volume

51

Issue

36