Gas-Phase Conformations of Proteolytically Derived Protein Fragments: Influence of Solvent on Peptide Conformation

Gas-Phase Dopant-Induced Conformational Changes Monitored with Transversal Modulation Ion Mobility Spectrometry

The potential of a Transversal Modulation Ion Mobility Spectrometry (TMIMS) instrument for protein analysis applications has been evaluated. The Collision Cross Section (CCS) of cytochrome c measured with the TMIMS is in agreement with values reported in the literature. Additionally, it enables tandem IMS-IMS prefiltration in dry gas and in vapor doped gas. The chemical specificity of the different dopants enables interesting studies on the structure of proteins as CCS changed strongly depending on the specific dopant. Hexane produced an unexpectedly high CCS shift, which can be utilized to evaluate the exposure of hydrophobic parts of the protein. Alcohols produced higher shifts with a dual behavior: an increase in CCS due to vapor uptake at specific absorption sites, followed by a linear shift typical for unspecific and unstable vapor uptake. The molten globule +8 shows a very specific transition. Initially, its CCS follows the trend of the compact folded states, and then it rapidly increases to the levels of the unfolded states. This strong variation suggests that the +8 charge state undergoes a dopant-induced conformational change. Interestingly, more sterically demanding alcohols seem to unfold the protein more effectively also in the gas phase. This study shows the capabilities of the TMIMS device for protein analysis and how tandem IMS-IMS with dopants could provide better understanding of the conformational changes of proteins.

Characterizing gaseous peptide structure with action-EET and simulated annealing

Distance-sensitive energy transfer and molecular dynamics are used to generate experimentally corroborated structures for peptides in the gas phase.

Effects of charge states, charge sites and side chain interactions on conformational preferences of a series of model peptide ions

The factors affecting conformational preference of gas phase peptide ions are investigated by IM-MS and molecular dynamics simulation.

Size-to-charge dispersion of collision-induced dissociation product ions for enhancement of structural information and product ion identification

Ion mobility is used to disperse product ions formed by collision-induced dissociation (CID) on the basis of charge state and size-to-charge ratio. We previously described an approach for combining CID with ion mobility mass spectrometry (IM-MS) for dispersing fragment ions along charge state specific trend lines (Zinnel, N. F.; Pai, P. J.; Russell, D. H. Anal. Chem. 2012, 84, 3390; Sowell, R. A.; Koeniger, S. L.; Valentine, S. J.; Moon, M. H.; Clemmer, D. E. J. Am. Soc. Mass Spectrom. 2004, 15, 1341; McLean, J. A.; Ruotolo, B. T.; Gillig, K. J.; Russell, D. H. Int. J. Mass Spectrom. 2005, 240, 301), and this approach was used to assign metal ion binding sites for human metallothionein protein MT-2a (Chen, S. H.; Russell, W. K.; Russell, D. H. Anal. Chem. 2013, 85, 3229). Here, we use this approach to distinguish b-type N-terminal fragment ions from both internal fragment ions and y-type C-terminal fragment ions. We also show that in some cases specific secondary structural elements, viz., extended coils or helices, can be obtained for the y-type fragment ions series. The advantage of this approach is that product ion identity can be correlated to gas-phase ion structure, which provides rapid identification of the onset and termination of extended coil structure in peptides.

A database of alkaline-earth-coordinated peptide cross sections: insight into general aspects of structure

A database of 1470 collision cross sections (666 doubly- and 804 triply-charged) of alkaline-earth-coordinated tryptic peptide ions [where the cation (M(2+)) correspond to Mg(2+), Ca(2+), or Ba(2+)] is presented. The utility of such an extensive set of measurements is illustrated by extraction of general properties of M(2+)-coordinated peptide structures. Specifically, we derive sets of intrinsic size parameters (ISPs) for individual amino acid residues for M(2+)-coordinated peptides. Comparison of these parameters with existing ISPs for protonated peptides suggests that M(2+) binding occurs primarily through interactions with specific polar aliphatic residues (Asp, Ser, and Thr) and the peptide backbone. A comparison of binding interactions for these alkaline-earth metals with interactions reported previously for alkali metals is provided. Finally, we describe a new analysis in which ISPs are used as probes for assessing peptide structure based on amino acid composition.

Non-covalent interactions of alkali metal cations with singly charged tryptic peptides

The complexes formed by alkali metal cations (Cat(+) = Li(+), Na(+), K(+), Rb(+)) and singly charged tryptic peptides were investigated by combining results from the low-energy collision-induced dissociation (CID) and ion mobility experiments with molecular dynamics and density functional theory calculations. The structure and reactivity of [M + H + Cat](2+) tryptic peptides is greatly influenced by charge repulsion as well as the ability of the peptide to solvate charge points. Charge separation between fragment ions occurs upon dissociation, i.e. b ions tend to be alkali metal cationised while y ions are protonated, suggesting the location of the cation towards the peptide N-terminus. The low-energy dissociation channels were found to be strongly dependant on the cation size. Complexes containing smaller cations (Li(+) or Na(+)) dissociate predominantly by sequence-specific cleavages, whereas the main process for complexes containing larger cations (Rb(+)) is cation expulsion and formation of [M + H](+). The obtained structural data might suggest a relationship between the peptide primary structure and the nature of the cation coordination shell. Peptides with a significant number of side chain carbonyl oxygens provide good charge solvation without the need for involving peptide bond carbonyl groups and thus forming a tight globular structure. However, due to the lack of the conformational flexibility which would allow effective solvation of both charges (the cation and the proton) peptides with seven or less amino acids are unable to form sufficiently abundant [M + H + Cat](2+) ion. Finally, the fact that [M + H + Cat](2+) peptides dissociate similarly as [M + H](+) (via sequence-specific cleavages, however, with the additional formation of alkali metal cationised b ions) offers a way for generating the low-energy CID spectra of 'singly charged' tryptic peptides.

Collision cross sections of proteins and their complexes: a calibration framework and database for gas-phase structural biology

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.

Chiral and structural analysis of biomolecules using mass spectrometry and ion mobility-mass spectrometry

This report describes the strategies for gas-phase chiral and structural characterization of biomolecules using mass spectrometry (MS) and ion mobility-MS (IM-MS) techniques. Because both MS and IM-MS do not directly provide chiral selectivity, methodologies for adding a chiral selector are discussed in the context of (i) host-guest (H-G) associations, (ii) diastereomeric collision-induced dissociation (CID) methods, (iii) ion-molecule reactions, and (iv) the kinetic method. MS techniques for the analysis of proteins and protein complexes are briefly described. New advances in performing rapid 2D gas-phase separations on the basis of IM-MS are reviewed with a particular emphasis on the different forms of IM instrumentation and how they are used for chiral and/or structural biomolecular studies. This report is not intended to be a comprehensive review of the field, but rather to underscore the contemporary techniques that are commonly or increasingly being used to complement measurements performed by chiroptical methodologies.

Factors that influence helical preferences for singly charged gas-phase peptide ions: the effects of multiple potential charge-carrying sites

Ion mobility-mass spectrometry is used to investigate the structure(s) of a series of model peptide [M + H](+) ions to better understand how intrinsic properties affect structure in low dielectric environments. The influence of peptide length, amino acid sequence, and composition on gas-phase structure is examined for a series of model peptides that have been previously studied in solution. Collision cross sections for the [M + H](+) ions of Ac-(AAKAA)(n)Y-NH(2) (n = 3-6) and Ac-Y(AEAAKA)(n)F-NH(2) (n = 2-5) are reported and correlated with candidate structures generated using molecular modeling techniques. The [M + H](+) ions of the AAKAA peptide series each exhibit a single, dominant ion mobility arrival time distribution (ATD) which correlates to partial helical structures, whereas the [M + H](+) ions of the AEAAKA ion series are composed of ATDs which correlate to charge-solvated globules (i.e., the charge is coordinated or solvated by polar peptide functional groups). These data raise numerous questions concerning intrinsic properties (amino acid sequence and composition as well as charge location) that dictate gas-phase peptide ion structure, which may reflect trends for peptide ion structure in low dielectric environments, such as transmembrane segments.

The contributions of molecular framework to IMS collision cross-sections of gas-phase peptide ions

Molecular dynamics (MD) is an essential tool for correlating collision cross-section data determined by ion mobility spectrometry (IMS) with candidate (calculated) structures. Conventional methods used for ion structure determination rely on comparing the measured cross-sections with the calculated collision cross-section for the lowest energy structure(s) taken from a large pool of candidate structures generated through multiple tiers of simulated annealing. We are developing methods to evaluate candidate structures from an ensemble of many conformations rather than the lowest energy structure. Here, we describe computational simulations and clustering methods to assign backbone conformations for singly-protonated ions of the model peptide (NH(2)-Met-Ile-Phe-Ala-Gly-Ile-Lys-COOH) formed by both MALDI and ESI, and compare the structures of MIFAGIK derivatives to test the 'sensitivity' of the cluster analysis method. Cluster analysis suggests that [MIFAGIK + H](+) ions formed by MALDI have a predominantly turn structure even though the low-energy ions prefer partial helical conformers. Although the ions formed by ESI have collision cross-sections that are different from those formed by MALDI, the results of cluster analysis indicate that the ions backbone structures are similar. Chemical modifications (N-acetyl, methylester as well as addition of Boc or Fmoc groups) to MIFAGIK alter the distribution of various conformers; the most dramatic changes are observed for the [M + Na](+) ion, which show a strong preference for random coil conformers owing to the strong solvation by the backbone amide groups.

Gas-phase behavior of noncovalent transmembrane segment complexes

Specific helix oligomerization between transmembrane segments (TMSs) is often promoted by motifs like GxxxG. Disruption of this motif in the transmembrane segments of vesicular stomatitis virus G-protein and of glycophorin A results in a reduced dimerization level studied by in vivo systems like ToxR. This paper reports the influence of sequence motifs like GxxxG in solution and the gas phase.The transmembrane segments may behave differently in the gas and liquid phase, because of the absence of surrounding solvent molecules in the gas phase. Comparison of experiments depending on peptide properties performed in the gas and liquid phase discloses that the peptides retain 'some memory' of their liquid-phase structure in the gas phase. A direct correlation has been found between helicity in solution as determined by circular dichroism and dimerization in the gas phase monitored by electrospray mass spectrometry. These results show that a proper folding in solution is required for oligomerization.On the other hand, sequence-specific oligomerization depending on the GxxxG motif was not observed with the mass spectrometric detection. Further on, neither concentration-dependent complex studies nor studies regarding complex stability in the gas phase - via collision-induced dissociation (CID) - led to sequence-specific differences.Finally, the findings show that in mass spectrometric measurements noncovalent interactions of studied TMSs is rather more dependent on the secondary structure and proper folding than on their primary structure.

Relative strengths of NH..O and CH..O hydrogen bonds between polypeptide chain segments

Correlated ab initio calculations are used to compare the energetics when the CH and NH groups of the model dipeptide CHONHCH2CONH2 are each allowed to form a H-bond with the proton acceptor O of a peptide group. When the dipeptide is in its C7 conformation, the NH..O H-bond energy is found to be 7.4 kcal/mol, as compared to only 2.8 kcal/mol for the CH..O interaction. On the other hand, the situation reverses, and the CH..O H-bond becomes stronger than NH..O, when the dipeptide adopts a C5 structure. This reversal is important as C5 is nearly equal in stability to C7 for the dipeptide, and is representative of the commonly observed beta-sheet structure in a protein. Immersing the dipeptide-peptide pair in a model solvent weakens both sorts of H-bonds, and in a fairly uniform manner. Consequently, the trends observed in the in vacuo situation retain their validity in either aqueous solution or the protein interior. Likewise, the desolvation penalty, suffered by removing a H-bonded complex from water and placing it in the less polar interior of a protein, is quite similar for the NH..O and CH..O bonds.

A collision cross-section database of singly-charged peptide ions

A database of ion-neutral collision cross-sections for singly-charged peptide ions is presented. The peptides included in the database were generated by enzymatic digestion of known proteins using three different enzymes, resulting in peptides that differ in terms of amino acid composition as well as N-terminal and C-terminal residues. The ion-neutral collision cross-sections were measured using ion mobility (IM) spectrometry that is directly coupled to a time-of-flight (TOF) mass spectrometer. The ions were formed by a matrix-assisted laser desorption ionization (MALDI) ion source operated at pressures (He bath gas) of 2 to 3 torr. The majority (63%) of the peptide ion collision cross-sections correlate well with structures that are best described as charge-solvated globules, but a significant number of the peptide ions exhibit collision cross-sections that are significantly larger or smaller than the average, globular mobility-mass correlation. Of the peptide ions having larger than average collision cross-sections, approximately 71% are derived from trypsin digestion (C-terminal Arg or Lys residues) and most of the peptide ions that have smaller (than globular) collision cross-sections are derived from pepsin digestion (90%).

Correlated proton motion in hydrogen bonded systems: tuning proton affinities

The theorem of matching proton affinities (PA) has been widely used in the analysis of hydrogen bonds. However, most experimental and theoretical investigations have to cope with the problem that the variation of the PA of one partner in the hydrogen bond severely affects the properties of the interface between both molecules. The B3LYP/d95+(d,p) analysis of two hydrogen bonds coupled by a 5-methyl-1H-imidazole molecule showed that it is possible to change the PA of one partner of the hydrogen bond while maintaining the properties of the interface. This technique allowed us to correlate various properties of the hydrogen bond directly with the difference in the PAs between both partners: it is possible to tune the potential energy surface of the bonding hydrogen atom from that of an ordinary hydrogen bond (localized hydrogen atom) to that of a low barrier hydrogen bond (LBHB, delocalized hydrogen atom) just by varying the proton affinity of one partner. This correlation shows clearly that matching PAs are of lesser importance for the formation of a LBHB than the relative energy difference between the two tautomers of the hydrogen bond.

Molecular dynamics study on the folding and metallation of the individual domains of metallothionein

De novo synthesis of metallothionein (MT) initially forms the metal-free protein, which must, in a posttranslational reaction, coordinate metal ions via the cysteine sulfur ligands to form the fully folded protein structure. In this article, we use molecular dynamics (MD) and molecular mechanics (MM) to investigate the metal-dependent folding steps of the individual domains of recombinant human metallothionein (MT). The divalent metals were removed sequentially from the metal-sulfur M4(Scys)11 and M3(Scys)9 clusters within the alpha- and beta- domains of MT, respectively, after protonation of the previously coordinating sulfurs. With each of the four (alpha) or three (beta) sites defined, an order of metal release could be determined on the basis of a comparison of the strain energies for each combination by selecting the lowest energy demetallated conformations. The effect of an additional noninteracting, 34-residue peptide sequence on the demetallation order was assessed when bound to either the N- or C-termini of the individual domain fragments to identify the differences in cluster stability between one- and two-domain proteins. The N-terminal-bound peptide had no effect on the order of metal removal; however, addition to the C-terminus significantly altered the sequence. The number of hydrogen bonds was calculated for each energy-minimized demetallated structure and was increased on metal removal, indicating a possible stabilization mechanism for the protein structure via a hydrogen-bonding network. On complete demetallation, the cysteinyl sulfurs were shown to move to the exterior surface of the peptide chain.

The structure of gas-phase bradykinin fragment 1-5 (RPPGF) ions: an ion mobility spectrometry and H/D exchange ion-molecule reaction chemistry study

Ion mobility-mass spectrometry (IM-MS) data is interpreted as evidence that gas-phase bradykinin fragment 1-5 (BK1-5, RPPGF) [M + H](+) ions exist as three distinct structural forms, and the relative abundances of the structural forms depend on the solvent used to prepare the matrix-assisted laser desorption ionization (MALDI) samples. Samples prepared from organic rich solvents (90% methanol/10% water) yield ions having an ion mobility arrival-time distribution (ATD) that is dominated by a single peak; conversely, samples prepared using mostly aqueous solvents (10% methanol/90% water) yield an ATD composed of three distinct peaks. The BK1-5 [M + H](+) ions were also studied by gas-phase hydrogen/deuterium (H/D) exchange ion-molecule reactions and this data supports our interpretation of the IM-MS data. Plausible structures for BK1-5 ions were generated by molecular dynamics (MD). Candidate MD-generated structures correlated to measured cross-sections suggest a compact conformer containing a beta-turn whereas a more extended, open form does not contain such an interaction. This study illustrates the importance of intra-molecular interactions in the stabilization of the gas-phase ions, and these results clearly illustrate that solution-phase parameters (i.e., MALDI sample preparation) greatly influence the structures of gas-phase ions.

Structural studies of metal-free metallothionein

We report the first molecular dynamics calculations on the structure of metal-free betaalpha recombinant human metallothionein, with comparison to the two isolated fragments, alpha-rhMT and beta-rhMT, starting from a linear synthesized strand as well as a demetallated conformation. Following a 5000 ps MM3/MD calculation, the cysteine side chains were found to populate the outside surface of the metal-free protein, regardless of the initial conformation. The polypeptide backbone adopted a random coil conformation when starting from the linear strand, however, it retained a significant amount of secondary structure when starting from the demetallated conformation. We propose that the inverted cysteinyl sulfur orientation facilitates the binding of the metal ions to form the proteolytically stable, metallated protein.