Collision Cross Sections for Structural Proteomics

Marklund, Erik; Degiacomi, Matteo T.; Robinson, Carol V.; Baldwin, Andrew J.; Benesch, Justin L. P.

doi:10.1016/j.str.2015.02.010

Cited by 256 publications

(336 citation statements)

References 54 publications

(83 reference statements)

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“…This observation is in agreement with the calculated CCS of 58.7 nm 2 derived from 225 our crystal structure of the EncFtn sH decamer 22 . By contrast, IM-MS measurements of the 226 .…”

Section: Mass Spectrometry Of the Encftn Assembly 204supporting

confidence: 90%

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments

Hughes

Vanden-Hehir

et al. 2016

Preprint

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22Ferritins are ubiquitous proteins that oxidise and store iron within a protein shell to protect cells 23 from oxidative damage. We have characterized the structure and function of a new member of the 24 ferritin superfamily that is sequestered within an encapsulin capsid. We show that this 25 encapsulated ferritin (EncFtn) has two main alpha helices, which assemble in a metal dependent 26 manner to form a ferroxidase centre at a dimer interface. EncFtn adopts an open decameric 27 structure that is topologically distinct from other ferritins. While EncFtn acts as a ferroxidase, it 28 cannot mineralize iron. Conversely, the encapsulin shell associates with iron, but is not 29 enzymatically active, and we demonstrate that EncFtn must be housed within the encapsulin for 30 iron storage. This encapsulin nanocompartment is widely distributed in bacteria and archaea and 31 represents a distinct class of iron storage system where the oxidation and mineralization of iron are 32 distributed between two proteins.

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“…This observation is in agreement with the calculated CCS of 58.7 nm 2 derived from 225 our crystal structure of the EncFtn sH decamer 22 . By contrast, IM-MS measurements of the 226 .…”

Section: Mass Spectrometry Of the Encftn Assembly 204supporting

confidence: 90%

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments

Hughes

Vanden-Hehir

et al. 2016

Preprint

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“…The low computational cost of the EHSS algorithm has made it the method of choice for many practitioners [3,18,23,65]. Another common approach is the use of rescaled PA data (Ω PA_CORR ), which have been shown to agree well with experimental values [29,56,66]. In this work, we use the rescaling procedure Ω PA_CORR = 1.299 × (Ω PA -81Å 2 ), which produces results consistent with the computationally more expensive trajectory method (TM) [56].…”

Section: Twims Calibrationmentioning

confidence: 95%

“…To a first approximation, Ω represents a rotationally averaged projection area [28,29]. Ion packages are exposed to an electric field in the presence of a background gas.…”

Section: Introductionmentioning

confidence: 99%

Protein Structural Studies by Traveling Wave Ion Mobility Spectrometry: A Critical Look at Electrospray Sources and Calibration Issues

Sun

Vahidi

Sowole

et al. 2015

J. Am. Soc. Mass Spectrom.

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Abstract. The question whether electrosprayed protein ions retain solution-like conformations continues to be a matter of debate. One way to address this issue involves comparisons of collision cross sections (Ω) measured by ion mobility spectrometry (IMS) with Ω values calculated for candidate structures. Many investigations in this area employ traveling wave IMS (TWIMS). It is often implied that nanoESI is more conducive for the retention of solution structure than regular ESI. Focusing on ubiquitin, cytochrome c, myoglobin, and hemoglobin, we demonstrate that Ω values and collisional unfolding profiles are virtually indistinguishable under both conditions. These findings suggest that gas-phase structures and ion internal energies are independent of the type of electrospray source. We also note that TWIMS calibration can be challenging because differences in the extent of collisional activation relative to drift tube reference data may lead to ambiguous peak assignments. It is demonstrated that this problem can be circumvented by employing collisionally heated calibrant ions. Overall, our data are consistent with the view that exposure of native proteins to electrospray conditions can generate kinetically trapped ions that retain solution-like structures on the millisecond time scale of TWIMS experiments.

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“…The number of algorithms to derive theoretical CCSs has boomed in recent years, with new methods appearing nearly every year. 20,21 Significant progress has been made in order to create accurate and efficient algorithms that utilise polyatomic gases (i.e. N2 or CO2), in particular by Campuzano et al, 22 Bleiholder et al 23 and…”

Section: Mason-schamp Equation Whereas Travelling Wave Im-ms (Twims-mentioning

confidence: 99%

A Careful Consideration of the Influence of Structure, Partial charges and Basis Sets on Collision Cross Sections of Monosaccharides when Comparing Values from DFT Calculated Conformers to those Obtained Experimentally

Migas

Gray

Flitsch

et al. 2017

Preprint

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Molecular modelling is routinely employed to assign 3D structures to collision cross sections (CCSs) derived from ion mobility mass spectrometry experiments (IM-MS). The assignment of model structures to the experimental CCSs remains an ambiguous task, where one of several methods may be used to obtain a CCS from a given set of coordinates. The most reliable of the commonly used techniques, the Trajectory Method, starts with atomic coordinates which can be accompanied by partial atomic charges, obtained using ab initio methods. Here, we use lithiated α-and β-glucose ions as exemplar molecules to detect the effect conformational modification and changes to the partial charge distribution have on computed collision cross sections. Six popular charge schemes (Mulliken, APT, CHelpG, MK, HLY and NPA) were examined in combination with three functionals (Hartree-Fock, B3LYP and M05) and five basis sets (STO-3G, 3-21G, 6-31G, 6-31+G and 6-31G*) on twenty unique structures.Our findings indicate that molecular conformation makes a significant contribution to fluctuations of partial charges in Electrostatic Potential (ESP) and Mulliken charge scheme; Partial charges derived using Natural Population Analysis (NPA) and ESP methods are largely independent of functional and basis set selection; and both selection of the charge scheme and functional/basis set combination play a large role in the resultant CCS, often causing few percent fluctuations in the computed values.

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Collision Cross Sections for Structural Proteomics

Cited by 256 publications

References 54 publications

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments

Structural characterization of encapsulated ferritin provides insight into iron storage in bacterial nanocompartments

Protein Structural Studies by Traveling Wave Ion Mobility Spectrometry: A Critical Look at Electrospray Sources and Calibration Issues

A Careful Consideration of the Influence of Structure, Partial charges and Basis Sets on Collision Cross Sections of Monosaccharides when Comparing Values from DFT Calculated Conformers to those Obtained Experimentally

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