Protein footprinting
Protein footprinting is a term used to refer to a method of biochemical analysis that investigates
Hydroxyl radical protein footprinting
Time-resolved
Unlike nucleic acids, proteins oxidize rather than cleave on these timescales. Analysis of the products by mass spectrometry reveals that proteins are oxidized in a limited manner (some 10–30% of total protein) at a number of amino acid side chains across the proteins. The rate or level of oxidation at the reactive amino acid side chains (Met, Cys, Trp, Tyr, Phe, His, Pro and Leu) provides a measure of their accessibility to the bulk solvent. The mechanisms of side chain oxidation were explored by performing the radiolysis reactions in 18O-labeled water.
Producing OH radicals
A critical feature of these experiments is the need to expose proteins to hydroxyl radicals for limited timescales on the order of 1–50 ms inducing 10-30% oxidation of total protein. A further requirement is to generate hydroxyl radicals from the bulk solvent (i.e. water) (equations 1 and 2) not hydrogen peroxide which can remain to oxidize proteins even without other stimuli.[15]
- H2O → H2O+• + e− + H2O*
- H2O+• + H2O → H3O+ + OH•
Hydroxyl radicals can be produced in solution by an electrical discharge within a conventional atmospheric pressure electrospray ionization (ESI) source. When a high voltage difference (~8 keV) is held between an electrospray needle and a sampling orifice to the mass analyzer, radicals can be produced in solution at the electrospray needle tip. This method was the first employed to apply protein footprinting to the study of a protein complex.[16]
Method
The exposure of proteins to a "white" X-ray beam of synchrotron light or an electrical discharge for tens of milliseconds provides sufficient oxidative modification to the surface amino acid side chains without damage to the protein structure. These products can be easily detected and quantified by mass spectrometry. By adjusting the time for radiolysis or which protein ions spend in the discharge source, a time-resolved approach is possible which is valuable for the study of protein dynamics.
Analysis
A computer program (PROXIMO) has also been written to help model protein complexes using data from the RP-MS/Protein footprinting approach.[17] RP-MS/Protein footprinting studies of protein complexes can also employ computational approaches to assist with this modeling.[18]
Applications
The application of ion mobility mass spectrometry has conclusively demonstrated that the conditions employed in RP-MS/Protein footprinting experiments do not alter the structure of proteins.[19]
Other studies have extended the method to study early onset protein damage given the radical basis of the method and the significance of oxygen based radicals in the pathogenesis of many diseases including neurological disorders and even blindness.[20]
See also
References
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