Kinetic Intermediates of Holo- and Apo-Myoglobin Studied Using HDX-TIMS-MS and Molecular Dynamic Simulations

Schenk, Emily R.; Almeida, Raybel; Mikšovská, Jaroslava; Ridgeway, Mark E.; Park, Melvin A.; Fernandez-Lima, Francisco

doi:10.1007/s13361-014-1067-9

Cited by 52 publications

(72 citation statements)

References 61 publications

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“…TWIMS values obtained from calibration represent 9% of the CCS values, 114–117 while the remaining values are from other IM techniques such as DMA 82,83 and TIMS. 118–121 …”

Section: Composition Of Measurementsmentioning

confidence: 99%

Ion Mobility Collision Cross Section Compendium

2016

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In this review, we focus on an important aspect of ion mobility (IM) research, namely the reporting of quantitative ion mobility measurements in the form of the gas-phase collision cross section (CCS), which has provided a common basis for comparison across different instrument platforms and offers a unique form of structural information, namely size and shape preferences of analytes in the absence of bulk solvent. This review surveys the over 24,000 CCS values reported from IM methods spanning the era between 1975 to 2015, which provides both a historical and analytical context for the contributions made thus far, as well as insight into the future directions that quantitative ion mobility measurements will have in the analytical sciences. The analysis was conducted in 2016, so CCS values reported in that year are purposely omitted. In another few years, a review of this scope will be intractable, as the number of CCS values which will be reported in the next three to five years is expected to exceed the total amount currently published in the literature.

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“…TWIMS values obtained from calibration represent 9% of the CCS values, 114–117 while the remaining values are from other IM techniques such as DMA 82,83 and TIMS. 118–121 …”

Section: Composition Of Measurementsmentioning

confidence: 99%

Ion Mobility Collision Cross Section Compendium

2016

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“…TIMS-MS provides complementary information separating samples in two dimensions: size-to-charge and mass-to-charge separation on a very limited time scale of analysis (hundreds of milliseconds) (Fernandez-Lima et al 2011a; Hernandez et al 2014). We have previously used TIMS-MS for detection of small molecules within complex matrices (McKenzie-Coe et al 2015), the separation of polyaromatic hydrocarbons (Benigni et al 2015a; Castellanos et al 2014), targeted analysis of endocrine disruptors (Benigni et al 2015b) and the analysis of the conformational dynamics of small molecules and biomolecules (Frost et al 2015; Gonzalez et al 2016; Molano-Arevalo et al 2014; Schenk et al 2015a; Schenk et al 2014a; Schenk et al 2015b; Schenk et al 2014b; Silveira et al 2014). …”

Section: Introductionmentioning

confidence: 99%

Isomer separation of polybrominated diphenyl ether metabolites using nanoESI-TIMS-MS

Adams

Montero

Aga

et al. 2016

Int. J. Ion Mobil. Spec.

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In this paper, high-resolution nano-electrospray ionization-trapped ion mobility spectrometry coupled to mass spectrometry (nESI-TIMS-MS) is used for the study of hydroxylated polybrominated diphenyl ether (OH-PBDE) metabolites. In particular, experimental ion-neutral collision cross sections (CCS) were measured for five structural OH-PBDE isomers using TIMS-MS. Candidate structures were proposed for each IMS band observed in good agreement with the experimental CCS measurements (5% error). The analytical power of TIMS-MS to baseline and partially separate structural isomers of OH-BDE in binary and ternary mixtures is shown for single charge species with a mobility resolving power of RIMS ~ 400. This work provides the proof of concept for the analysis of low concentration OH-PBDE in environmental samples based on accurate collision cross section and mass measurements without the need for derivatization and pre-fractionation protocols, thus significantly reducing the cost and analysis time.

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“…TIMS’ mode of operation and its advantages over traditional IMS are described in ref 19, 30, 31 . We have shown the use of TIMS for the study of isomerization kinetics of small molecules 32–34 , peptides 35, 36 , and proteins 37–42 , the influence of the collision partner on the molecular structure 43 , and the factors that affect molecular-adduct complex lifetime and stability during TIMS measurements 44 .…”

Section: Introductionmentioning

confidence: 99%

Structures of the kinetically trapped i-motif DNA intermediates

Garabedian

Butcher

Lippens

et al. 2016

Phys. Chem. Chem. Phys.

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In the present work, the conformational dynamics and folding pathways of i-motif DNA were studied in solution and in the gas-phase as a function of the solution pH conditions using circular dichroism (CD), photoacoustic calorimetry analysis (PAC), trapped ion mobility spectrometry - mass spectrometry (TIMS-MS), and molecular dynamics (MD). Solution studies showed at thermodynamic equilibrium the existence of a two-state folding mechanism, whereas during the pH = 7.0 → 4.5 transition a fast and slow phase (ΔHfast+ ΔHslow = 43 ± 7 kcal mol−1) with a volume change associated with the formation of hemiprotonated cytosine base pairs and concomitant collapse of the i-motif oligonucleotide into a compact conformation were observed. TIMS-MS experiments showed that gas-phase, kinetically trapped i-motif DNA intermediates produced by nanoESI are preserved, with relative abundances depending on the solution pH conditions. In particular, a folded i-motif DNA structure was observed in nanoESI-TIMS-MS for low charge states in both positive and negative ion mode (e.g., z = +/− 3 to +/−5) at low pH conditions. As solution pH increases, the cytosine deprotonation leads to the loss of cytosine-cytosine+ (C•CH+) base pairing in the CCC strands and in those conditions we observe partially unfolded i-motif DNA conformations in nanoESI-TIMS-MS for higher charge states (e.g., z = − 6 to −9). Collisional induced activation prior TIMS-MS showed the existence of multiple local free energy minima, associated with the i-motif DNA unfolding at z = −6 charge state. For the first time, candidate gas-phase structures are proposed based on mobility measurements of the i-motif DNA unfolding pathway. Moreover, the inspection of partially unfolded i-motif DNA structures (z = −7 and z = −8 charge states) showed that the presence of inner cations may or may not induce conformational changes in the gas-phase. For example, incorporation of ammonium adducts does not lead to major conformational changes while sodium adducts may lead to the formation of sodium mediated bonds between two negatively charged sides inducing the stabilization towards more compact structures in new local, free energy minima in the gas-phase.

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Kinetic Intermediates of Holo- and Apo-Myoglobin Studied Using HDX-TIMS-MS and Molecular Dynamic Simulations

Cited by 52 publications

References 61 publications

Ion Mobility Collision Cross Section Compendium

Ion Mobility Collision Cross Section Compendium

Isomer separation of polybrominated diphenyl ether metabolites using nanoESI-TIMS-MS

Structures of the kinetically trapped i-motif DNA intermediates

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