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Collision Cross Sections of Proteins and Their Complexes: A Calibration Framework and Database for Gas-Phase Structural Biology

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Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom, Waters Corporation, Floats Road, Wythenshawe, Manchester M23 9LZ, United Kingdom, and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
* To whom correspondence should be addressed. E-mail: [email protected] (C.V.R.), [email protected] (B.T.R.).
†University of Oxford.
‡Waters Corporation.
§University of Michigan.
Cite this: Anal. Chem. 2010, 82, 22, 9557–9565
Publication Date (Web):October 27, 2010
https://doi.org/10.1021/ac1022953
Copyright © 2010 American Chemical Society
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    Abstract

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    Collision cross sections in both helium and nitrogen gases were measured directly using a drift cell with RF ion confinement inserted within a quadrupole/ion mobility/time-of-flight hybrid mass spectrometer (Waters Synapt HDMS, Manchester, U.K.). Collision cross sections for a large set of denatured peptide, denatured protein, native-like protein, and native-like protein complex ions are reported here, forming a database of collision cross sections that spans over 2 orders of magnitude. The average effective density of the native-like ions is 0.6 g cm−3, which is significantly lower than that for the solvent-excluded regions of proteins and suggests that these ions can retain significant memory of their solution-phase structures rather than collapse to globular structures. Because the measurements are acquired using an instrument that mimics the geometry of the commercial Synapt HDMS instrument, this database enables the determination of highly accurate collision cross sections from traveling-wave ion mobility data through the use of calibration standards with similar masses and mobilities. Errors in traveling-wave collision cross sections determined for native-like protein complexes calibrated using other native-like protein complexes are significantly less than those calibrated using denatured proteins. This database indicates that collision cross sections in both helium and nitrogen gases can be well-correlated for larger biomolecular ions, but non-correlated differences for smaller ions can be more significant. These results enable the generation of more accurate three-dimensional models of protein and other biomolecular complexes using gas-phase structural biology techniques.

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    Method for calculating effective densities, Tables S1−S3, and Figures S1 and S2. This material is available free of charge via the Internet at http://pubs.acs.org.

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