The effect of charge and temperature on gas phase protein conformational landscapes - an ion mobility mass spectrometry investigation

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Abstract

The amino acid sequence of a protein determines its 3D fold, the ease with which its native structure is formed, its function, the conformational preferences sampled and the tendency to interact with itself (aggregation) and binding partners. In addition, certain conformational preferences can lead to dysfunction resulting in different diseased states in organisms. All of these conformations can be described by a protein's energy landscape; a native (functional) state being localised at the energy minimum. As protein dynamics is crucial to function it is important to monitor the sampling of different conformations. Thus the work in this thesis reports on two methods for monitoring protein conformation and conformational change in the gas phase using ion mobility mass spectrometry (IM-MS). The measurement from IM-MS methods allow the determination of a collision cross section (CCS) which is an indicator of a molecule's 3D shape. First, the effect of charge on protein structure is investigated by manipulation of protein charge, post electrospray ionisation (ESI), by exposure to radical anions of the electron transfer reagent, 1,3-dicyanaobenzene; the charge reduced products formed are the result of electron transfer to the charged protein without any dissociation (ETnoD). IM-MS is used to monitor the conformational preferences of the altered and unaltered precursor and its products. Secondly, intermediate (transient) conformers are formed by activating the charged protein in the source region of an instrument post ESI. Activation of the protein precursor allows the sampling of different conformational preferences after energetic barriers have been overcome; IM-MS following activation allows for the monitoring of protein conformational change before and after. Further, variable temperature (VT) IM-MS allows for the deduction of intermediate structures with a focus on measurements at cryogenic temperatures whereby intermediate structures can be 'frozen out' post activation; intermediate structures which would otherwise anneal out at room temperature. With both methods a range of conformer populations are mapped for different protein molecules sampled upon different energetic inputs (via activation) and the disruption of intramolecular neutralising contacts/salt bridges (via charge reduction) one of the main interactions responsible for maintaining the structural integrity (3D fold) of proteins.

Keyword(s)

Charge; Collision cross section; Conformation; ETD/ETnoD; Ion mobility mass spectrometry; Protein; Temperature

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