Human islet amyloid polypeptide (hIAPP or Amylin) is a 37 residue hormone that is cosecreted with insulin from the pancreatic islets. The aggregation of hIAPP plays a role in the progression of type 2 diabetes and contributes to the failure of islet cell grafts. Despite considerable effort, little is known about the mode of action of IAPP amyloid inhibitors, and this has limited rational drug design. Insulin is one of the most potent inhibitors of hIAPP fibril formation, but its inhibition mechanism is not understood. In this study, the aggregation of mixtures of hIAPP with insulin, as well as with the separate A and B chains of insulin, were characterized using ion mobility spectrometry-based mass spectrometry and atomic force microscopy. Insulin and the insulin B chain target the hIAPP monomer in its compact isoform and shift the equilibrium away from its extended isoform, an aggregation-prone conformation, and thus inhibit hIAPP from forming β-sheets and subsequently amyloid fibrils. All-atom molecular modeling supports these conclusions.

•PGG inhibits Aβ1-40/Aβ1-42 self-assembly.•PGG selectively interacts with N-terminal metal binding region of amyloid peptides.•Binding sites involve both hydrophilic and hydrophobic interactions.The early oligomerization of amyloid β-protein (Aβ) is a crucial step in the etiology of Alzheimer’s disease (AD), in which soluble and highly neurotoxic oligomers are produced and accumulated inside neurons. In search of therapeutic solutions for AD treatment and prevention, potent inhibitors that remodel Aβ assembly and prevent neurotoxic oligomer formation offer a promising approach. In particular, several polyphenolic compounds have shown anti-aggregation properties and good efficacy on inhibiting oligomeric amyloid formation. 1,2,3,4,6-penta-O-galloyl-β-d-glucopyranose is a large polyphenol that has been shown to be effective at inhibiting aggregation of full-length Aβ1-40 and Aβ1-42, but has the opposite effect on the C-terminal fragment Aβ25-35. Here, we use a combination of ion mobility coupled to mass spectrometry (IMS-MS), transmission electron microscopy (TEM) and molecular dynamics (MD) simulations to elucidate the inhibitory effect of PGG on aggregation of full-length Aβ1-40 and Aβ1-42. We show that PGG interacts strongly with these two peptides, especially in their N-terminal metal binding regions, and suppresses the formation of Aβ1-40 tetramer and Aβ1-42 dodecamer. By exploring multiple facets of polyphenol-amyloid interactions, we provide a molecular basis for the opposing effects of PGG on full-length Aβ and its C-terminal fragments.Download high-res image (163KB)Download full-size image

Evidence suggests that oligomers of the 42-residue form of the amyloid β-protein (Aβ), Aβ42, play a critical role in the etiology of Alzheimer’s disease (AD). Here we use high resolution atomic force microscopy to directly image populations of small oligomers of Aβ42 that occur at the earliest stages of aggregation. We observe features that can be attributed to a monomer and to relatively small oligomers, including dimers, hexamers, and dodecamers. We discovered that Aβ42 hexamers and dodecamers quickly become the dominant oligomers after peptide solubilization, even at low (1 μM) concentrations and short (5 min) incubation times. Soon after (≥10 min), dodecamers are observed to seed the formation of extended, linear preprotofibrillar β-sheet structures. The preprotofibrils are a single Aβ42 layer in height and can extend several hundred nanometers in length. To our knowledge this is the first report of structures of this type. In each instance the preprotofibril is associated off center with a single layer of a dodecamer. Protofibril formation continues at longer times, but is accompanied by the formation of large, globular aggregates. Aβ40, by contrast, does not significantly form the hexamer or dodecamer but instead produces a mixture of smaller oligomers. These species lead to the formation of a branched chain-like network rather than discrete structures.

Ion-mobility mass spectrometry is utilized to examine the metacluster formation of serine, asparagine, isoleucine, and tryptophan. These amino acids are representative of different classes of noncharged amino acids. We show that they can form relatively large metaclusters in solution that are difficult or impossible to observe by traditional solution techniques. We further demonstrate, as an example, that the formation of Ser metaclusters is not an ESI artifact because large metaclusters can be detected in negative polarity and low concentration with similar cross sections to those measured in positive polarity and higher concentration. The growth trends of tryptophan and isoleucine metaclusters, along with serine, asparagine, and the previously studied phenylalanine, are balanced among various intrinsic properties of individual amino acids (e.g., hydrophobicity, size, and shape). The metacluster cross sections of hydrophilic residues (Ser, Asn, Trp) tend to stay on or fall below the isotropic model trend lines whereas those of hydrophobic amino acids (Ile, Phe) deviate positively from the isotropic trend lines. The growth trends correlate well to the predicted aggregation propensity of individual amino acids. From the metacluster data, we introduce a novel approach to score and predict aggregation propensity of peptides, which can offer a significant improvement over the existing methods in terms of accuracy. Using a set of hexapeptides, we show that the strong negative deviations of Ser metaclusters from the isotropic model leads a prediction of microcrystalline formation for the SFSFSF peptide, whereas the strong positive deviation of Ile leads to prediction or fibril formation for the NININI peptide. Both predictions are confirmed experimentally using ion mobility and TEM measurements. The peptide SISISI is predicted to only weakly aggregate, a prediction confirmed by TEM.

Alzheimer’s disease (AD) is a neurodegenerative disease characterized by extracellular deposits of amyloid β protein (Aβ) in the brain. The conversion of soluble monomers to amyloid Aβ fibrils is a complicated process and involves several transient oligomeric species, which are widely believed to be highly toxic and play a crucial role in the etiology of AD. The development of inhibitors to prevent formation of small and midsized oligomers is a promising strategy for AD treatment. In this work, we employ ion mobility spectrometry (IMS), transmission electron microscopy (TEM), and molecular dynamics (MD) simulations to elucidate the structural modulation promoted by two potential inhibitors of Aβ oligomerization, cucurbit[7]uril (CB[7]) and 1,2,3,4,6-penta-O-galloyl-β-d-glucopyranose (PGG), on early oligomer and fibril formation of the Aβ25–35 fragment. One and two CB[7] molecules bind to Aβ25–35 monomers and dimers, respectively, and suppress aggregation by remodeling early oligomer structures and inhibiting the formation of higher-order oligomers. On the other hand, nonselective binding was observed between PGG and Aβ25–35. The interactions between PGG and Aβ25–35, surprisingly, enhanced the formation of Aβ aggregates by promoting extended Aβ25–35 conformations in both homo- and hetero-oligomers. When both ligands were present, the inhibitory effect of CB[7] overrode the stimulatory effect of PGG on Aβ25–35 aggregation, suppressing the formation of large amyloid oligomers and eliminating the structural conversion from isotropic to β-rich topologies induced by PGG. Our results provide mechanistic insights into CB[7] and PGG action on Aβ oligomerization. They also demonstrate the power of the IMS technique to investigate mechanisms of multiple small-molecule agents on the amyloid formation process.Keywords: amyloid β; Amyloids; computational modeling; cucurbiturils; ion-mobility mass spectrometry; polyphenols

The aggregation of human islet amyloid polypeptide (hIAPP) has been closely associated with the pathogeny of type 2 diabetes mellitus (T2DM) and destruction of pancreatic islet β-cells. Several amyloidogenic domains within the hIAPP sequence capable of self-association have been identified. Among them is the 8–20 region of hIAPP, which has formed β-sheet fibrils despite being contained within an α-helical region of full-length hIAPP. To further understand the propensity of this region for self-assembly, two peptide fragments were compared, one consisting of the residues 8–20 (WT8–20) and a mutant fragment with a His18Pro substitution (H18P8–20). The conformational distribution and aggregation propensity of these peptides was determined using a combination of ion mobility mass spectrometry and atomic force microscopy. Our results reveal that the two peptide fragments have vastly differing assembly pathways. WT8–20 produces a wide range of oligomers up to decamer whereas the H18P8–20 mutant produces only low order oligomers. This study confirms the propensity of the 8–20 region to aggregate from its native α-helical structure into amyloid β-sheet oligomers and highlights the significance of the charged His18 in the aggregation process.

Targeting the early oligomerization of amyloid β protein (Aβ) is a promising therapeutic strategy for Alzheimer’s disease (AD). Recently, certain C-terminal fragments (CTFs) derived from Aβ42 were shown to be potent inhibitors of Aβ-induced toxicity. The shortest peptide studied, Aβ(39–42), has been shown to modulate Aβ oligomerization and inhibit Aβ toxicity. Understanding the mechanism of these CTFs, especially Aβ(39–42), is of significance for future therapeutic development of AD and peptidomimetic-based drug development. Here we used ion mobility spectrometry–mass spectrometry to investigate the interactions between two modified Aβ(39–42) derivatives, VVIA-NH2 and Ac-VVIA, and full-length Aβ42. VVIA-NH2 was previously shown to inhibit Aβ toxicity, whereas Ac-VVIA did not. Our mass spectrometry analysis revealed that VVIA-NH2 binds directly to Aβ42 monomer and small oligomers while Ac-VVIA binds only to Aβ42 monomer. Ion mobility studies showed that VVIA-NH2 modulates Aβ42 oligomerization by not only inhibiting the dodecamer formation but also disaggregating preformed Aβ42 dodecamer. Ac-VVIA also inhibits and removes preformed Aβ42 dodecamer. However, the Aβ42 sample with the addition of Ac-VVIA clogged the nanospray tip easily, indicating that larger aggregates are formed in the solution in the presence of Ac-VVIA. Molecular dynamics simulations suggested that VVIA-NH2 binds specifically to the C-terminal region of Aβ42 while Ac-VVIA binds dispersedly to multiple regions of Aβ42. This work implies that C-terminal interactions and binding to Aβ oligomers are important for C-terminal fragment inhibitors.

Amyloid formation by human islet amyloid polypeptide (hIAPP) has long been implicated in the pathogeny of type 2 diabetes mellitus (T2DM) and failure of islet transplants, but the mechanism of IAPP self-assembly is still unclear. Numerous fragments of hIAPP are capable of self-association into oligomeric aggregates, both amyloid and non-amyloid in structure. The N-terminal region of IAPP contains a conserved disulfide bond between cysteines at position 2 and 7, which is important to hIAPP’s in vivo function and may play a role in in vitro aggregation. The importance of the disulfide bond in this region was probed using a combination of ion mobility-based mass spectrometry experiments, molecular dynamics simulations, and high-resolution atomic force microscopy imaging on the wildtype 1-8 hIAPP fragment, a reduced fragment with no disulfide bond, and a fragment with both cysteines at positions 2 and 7 mutated to serine. The results indicate the wildtype fragment aggregates by a different pathway than either comparison peptide and that the intact disulfide bond may be protective against aggregation due to a reduction of inter-peptide hydrogen bonding.

In order to evaluate potential therapeutic targets for treatment of amyloidoses such as Alzheimer’s disease (AD), it is essential to determine the structures of toxic amyloid oligomers. However, for the amyloid β-protein peptide (Aβ), thought to be the seminal neuropathogenetic agent in AD, its fast aggregation kinetics and the rapid equilibrium dynamics among oligomers of different size pose significant experimental challenges. Here we use ion-mobility mass spectrometry, in combination with electron microscopy, atomic force microscopy, and computational modeling, to test the hypothesis that Aβ peptides can form oligomeric structures resembling cylindrins and β-barrels. These structures are hypothesized to cause neuronal injury and death through perturbation of plasma membrane integrity. We show that hexamers of C-terminal Aβ fragments, including Aβ(24–34), Aβ(25–35) and Aβ(26–36), have collision cross sections similar to those of cylindrins. We also show that linking two identical fragments head-to-tail using diglycine increases the proportion of cylindrin-sized oligomers. In addition, we find that larger oligomers of these fragments may adopt β-barrel structures and that β-barrels can be formed by folding an out-of-register β-sheet, a common type of structure found in amyloid proteins.

Phenylalanine is the only amino acid known to self-assemble into toxic fibrillar aggregates. An elevated concentration of phenylalanine in the blood can result in Phenylketonuria, a progressive mental retardation. Ion-mobility mass spectrometry is employed to investigate the structure and distribution of phenylalanine oligomers formed in the early stage of the aggregation cascade. The experimental cross sections indicate that phenyl-alanine self-assembles at neutral pH into oligomers composed of multiple layers of four monomers. The monomers arrange themselves to create a hydrophilic core made of zwitterionic termini and expose hydrophobic aromatic side chains to the outside. At high pH, the interactions between the neutral amino and negatively charged carboxylate of phenylalanine allow a minor population of ladder-like oligomers to be formed and detected in ion-mobility experiments. However, counterions such as ammonium rearrange those structures into the same structures observed at neutral pH. The cytotoxicity of Phe oligomers and fibrils may be due to favorable interactions between the hydrophobic exterior and the cell membrane and strong interactions between the hydrophilic core of Phe oligomers and ions, resulting in ion leakage and cellular damage.

The mechanism and driving forces behind the formation of diphenylalanine (FF) nanotubes have attracted much attention in the past decades. The hollow structure of the nanotubes suggests a role for water during the self-assembly process. Here, we use novel ion-mobility mass spectrometry methods to probe the early oligomers formed by diphenylalanine peptides. Interestingly, water-bound oligomers are observed in nano-electrospray ionization (ESI) mass spectra in the absence of bulk solvent. In addition, ligated water clusters transit the ion mobility cell but (often) dissociate before detection. These water molecules are shown to be essential for the formation of diphenylalanine oligomers larger than the dimer. The ligated water molecules exist in the solvent free environment either as neutral water or as protonated water clusters, depending on the composition of solvent from which they are sprayed. Water adduction helps stabilize conformers that are otherwise energetically unstable ultimately leading to the assembly of FF nanotubes.

An empirically observed correlation between ion mobility cross sections in helium and nitrogen buffer gases was examined as a function of temperature, molecular size, and shape. Experimental cross sections were determined for tetraglycine, bradykinin, angiotensin 2, melittin, and ubiquitin at 300 K and in the range from 80 to 550 K on home-built instruments and calculated by the projection superposition approximation (PSA) method. The PSA was also used to predict cross sections for larger systems such as human pancreatic alpha-amylase, concanavalin, Pichia pastoris lysyl oxidase, and Klebsiella pneumoniae acetolactate synthase. The data show that the ratio of cross sections in helium and nitrogen depends significantly on the temperature of the buffer gas as well as the size and shape of the analyte ion. Therefore, the analysis of the data indicates that a simple formula that seeks to quantitatively relate the momentum transfer cross sections observed in two distinct buffer gases lacks a sound physical basis.

Oligomeric states of the amyloid β-protein (Aβ) appear to be causally related to Alzheimer’s disease (AD). Recently, two familial mutations in the amyloid precursor protein gene have been described, both resulting in amino acid substitutions at Ala2 (A2) within Aβ. An A2V mutation causes autosomal recessive early onset AD. Interestingly, heterozygotes enjoy some protection against development of the disease. An A2T substitution protects against AD and age-related cognitive decline in non-AD patients. Here, we use ion mobility-mass spectrometry (IM-MS) to examine the effects of these mutations on Aβ assembly. These studies reveal different assembly pathways for early oligomer formation for each peptide. A2T Aβ42 formed dimers, tetramers, and hexamers, but dodecamer formation was inhibited. In contrast, no significant effects on Aβ40 assembly were observed. A2V Aβ42 also formed dimers, tetramers, and hexamers, but it did not form dodecamers. However, A2V Aβ42 formed trimers, unlike A2T or wild-type (wt) Aβ42. In addition, the A2V substitution caused Aβ40 to oligomerize similar to that of wt Aβ42, as evidenced by the formation of dimers, tetramers, hexamers, and dodecamers. In contrast, wt Aβ40 formed only dimers and tetramers. These results provide a basis for understanding how these two mutations lead to, or protect against, AD. They also suggest that the Aβ N-terminus, in addition to the oft discussed central hydrophobic cluster and C-terminus, can play a key role in controlling disease susceptibility.Keywords: A2T; A2V; Amyloid β-protein; familial Alzheimer’s disease; ion mobility spectrometry; mass spectrometry; oligomerization

Aggregation of proteins to fiberlike aggregates often involves a transformation of native monomers to β-sheet-rich oligomers. This general observation underestimates the importance of α-helical segments in the aggregation cascade. Here, using a combination of experimental techniques and accelerated molecular dynamics simulations, we investigate the aggregation of a 43-residue, apolipoprotein A-I mimetic peptide and its E21Q and D26N mutants. Our study indicates a strong propensity of helical segments not to adopt cross-β-fibrils. The helix–turn–helix monomeric conformation of the peptides is preserved in the mature fibrils. Furthermore, we reveal opposite effects of mutations on and near the turn region in the self-assembly of these peptides. We show that the E21–R24 salt bridge is a major contributor to helix–turn–helix folding, subsequently leading to abundant fibril formation. On the other hand, the K19–D26 interaction is not required to fold the native helix–turn–helix peptide. However, removal of the charged D26 residue decreases the stability of the helix–turn–helix monomer and consequently reduces the level of aggregation. Finally, we provide a more refined assembly model for the helix–turn–helix peptides from apolipoprotein A-I based on the parallel stacking of helix–turn–helix dimers.

•IMS results at UCSB from 1990 to May 2014 are summarized.•Instrumental innovations in ion mobility are discussed.•Experimental and theoretical symbiosis is emphasized.Ion mobility is not a newly discovered phenomenon. It has roots going back to Langevin at the beginning of the 20th century. Our group initially got involved by accident around 1990 and this paper is a brief account of what has transpired here at UCSB the past 25 years in response to this happy accident. We started small, literally, with transition metal atomic ions and transitioned to carbon clusters, synthetic polymers, most types of biological molecules and eventually peptide and protein oligomeric assembly. Along the way we designed and built several generations of instruments, a process that is still ongoing. And perhaps most importantly we have incorporated theory with experiment from the beginning; a necessary wedding that allows an atomistic face to be put on the otherwise interesting but not fully informative cross section measurements.

The early oligomerization of amyloid β-protein (Aβ) has been shown to be an important event in the pathology of Alzheimer’s disease (AD). Designing small molecule inhibitors targeting Aβ oligomerization is one attractive and promising strategy for AD treatment. Here we used ion mobility spectrometry coupled to mass spectrometry (IMS-MS) to study the different effects of the molecular tweezers CLR01 and CLR03 on Aβ self-assembly. CLR01 was found to bind to Aβ directly and disrupt its early oligomerization. Moreover, CLR01 remodeled the early oligomerization of Aβ42 by compacting the structures of dimers and tetramers and as a consequence eliminated higher-order oligomers. Unexpectedly, the negative-control derivative, CLR03, which lacks the hydrophobic arms of the tweezer structure, was found to facilitate early Aβ oligomerization. Our study provides an example of IMS as a powerful tool to study and better understand the interaction between small molecule modulators and Aβ oligomerization, which is not attainable by other methods, and provides important insights into therapeutic development of molecular tweezers for AD treatment.

Five different mutants of [Leu-5] Enkephalin YGGFL peptide have been investigated for fibril formation propensities. The early oligomer structures have been probed with a combination of ion-mobility mass spectrometry and computational modeling. The two peptides YVIFL and YVVFL form oligomers and amyloid-like fibrils. YVVFV shows an early stage oligomer distribution similar to those of the previous two, but amyloid-like aggregates are less abundant. Atomic resolution X-ray structures of YVVFV show two different modes of interactions at the dry interface between steric zippers and pairs of antiparallel β-sheets, but both are less favorable than the packing motif found in YVVFL. Both YVVFV and YVVFL can form a Class 6 steric zipper. However, in YVVFV, the strands between mating sheets are parallel to each other and in YVVFL they are antiparallel. The overall data highlight the importance of structurally characterizing high order oligomers within oligomerization pathways in studies of nanostructure assembly.

We have investigated at the oligomeric level interactions between Aβ(25–35) and Tau(273–284), two important fragments of the amyloid-β and Tau proteins, implicated in Alzheimer’s disease. We are able to directly observe the coaggregation of these two peptides by probing the conformations of early heteroligomers and the macroscopic morphologies of the aggregates. Ion-mobility experiment and theoretical modeling indicate that the interactions of the two fragments affect the self-assembly processes of both peptides. Tau(273–284) shows a high affinity to form heteroligomers with existing Aβ(25–35) monomer and oligomers in solution. The configurations and characteristics of the heteroligomers are determined by whether the population of Aβ(25–35) or Tau(273–284) is dominant. As a result, two types of aggregates are observed in the mixture with distinct morphologies and dimensions from those of pure Aβ(25–35) fibrils. The incorporation of some Tau into β-rich Aβ(25–35) oligomers reduces the aggregation propensity of Aβ(25–35) but does not fully abolish fibril formation. On the other hand, by forming complexes with Aβ(25–35), Tau monomers and dimers can advance to larger oligomers and form granular aggregates. These heteroligomers may contribute to toxicity through loss of normal function of Tau or inherent toxicity of the aggregates themselves.

Amyloid cascades leading to peptide β-sheet fibrils and plaques are central to many important diseases. Recently, intermediate assemblies of these cascades were identified as the toxic agents that interact with the cellular machinery. The relationship between the transformation from natively unstructured assembly to the β-sheet oligomers to disease is important in understanding disease onset and the development of therapeutic agents. Research on this early oligomeric region has largely been unsuccessful since traditional techniques measure only ensemble average oligomer properties. Here, ion mobility methods are utilized to deduce the modulation of peptide self-assembly pathways in the amyloid-β protein fragment Aβ(25–35) by two amyloid inhibitors (epigallocatechin gallate and scyllo-inositol) that are currently in clinical trials for Alzheimer’s Disease. We provide evidence that suppression of β-extended oligomers from the onset of the conversion into β-oligomer conformations is essential for effective attenuation of β-structured amyloid oligomeric species often associated with oligomer toxicity. Furthermore, we demonstrate the ease with which ion mobility spectrometry–mass spectrometry can guide the development of therapeutic agents and drug evaluation by providing molecular level insight into the amyloid formation process and its modulation by small molecule assembly modulators.

Alzheimer’s disease (AD) is characterized by multiple, intertwined pathological features, including amyloid-β (Aβ) aggregation, metal ion dyshomeostasis, and oxidative stress. We report a novel compound (ML) prototype of a rationally designed molecule obtained by integrating structural elements for Aβ aggregation control, metal chelation, reactive oxygen species (ROS) regulation, and antioxidant activity within a single molecule. Chemical, biochemical, ion mobility mass spectrometric, and NMR studies indicate that the compound ML targets metal-free and metal-bound Aβ (metal–Aβ) species, suppresses Aβ aggregation in vitro, and diminishes toxicity induced by Aβ and metal-treated Aβ in living cells. Comparison of ML to its structural moieties (i.e., 4-(dimethylamino)phenol (DAP) and (8-aminoquinolin-2-yl)methanol (1)) for reactivity with Aβ and metal–Aβ suggests the synergy of incorporating structural components for both metal chelation and Aβ interaction. Moreover, ML is water-soluble and potentially brain permeable, as well as regulates the formation and presence of free radicals. Overall, we demonstrate that a rational structure-based design strategy can generate a small molecule that can target and modulate multiple factors, providing a new tool to uncover and address AD complexity.

The projected superposition approximation (PSA) method was used to theoretically evaluate the factors contributing to the cross section measured in ion mobility experiments and to study how the significance of these factors varies with ion size from diglycine to a 1 μm oil droplet. Thousands of PSA calculations for ∼400 different molecules in the temperature range from 80 to 700 K revealed that the molecular framework made up of atomic hard spheres is, as expected, a major component of the cross section. However, the ion–buffer gas interaction is almost equally important for very small peptides, and although its significance decreases with increasing ion size, interaction is still a factor for megadalton ions. An additional major factor is the ion shape: Fully convex ions drifting in a buffer gas have a minimal frictional resisting force, whereas the resisting force increases with degree of ion surface concaveness. This added resistance is small for peptides and larger for proteins and increases the ion mobility cross section from 0 to greater than 40%. The proteins with the highest degree of concaveness reach a shape-effected friction similar to, and sometimes larger than that of, macroscopic particles such as oil droplets. In summary, our results suggest that the transition from nanoparticle (with Lennard–Jones-like interaction with the buffer gas) to macroscopic particle (with hard sphere-like interaction) occurs at ∼1 GDa.

•The PSA method gives cross sections within experimental error over an extended temperature range for short peptide sequences.•The method is robust for structures derived from different levels of theory.One fundamental problem of IMS-MS based structure elucidation is achieving agreement between experimental cross sections and those predicted by theoretical algorithms for candidate structures for the compound of interest. Recently, the projected superposition approximation (PSA) was introduced specifically to yield accurate ion mobility cross sections for complex macroscopic systems with great computational efficiency. Here, the PSA method is shown to give cross sections within experimental error over an extended temperature range for short peptide sequences of unknown structure. The method is robust for structures derived from different levels of theory. The existing trajectory method (TJM) and projection approximation (PA) method were shown sensitive to the level of theory used to derive the candidate structures. The PSA method is much faster than the TJM for the systems measured here. As ion mobility instrumentation improves and becomes increasingly available, cross section measurements and theoretical modeling can become a routine technique for determination of macromolecular structure under a variety of experimental conditions, given the accuracy of the PSA method.

Parameters for the elements H, C, N, Na, and K for use in conjunction with the projected superposition approximation (PSA) method to compute collision cross sections are derived based on experimental collision cross sections in the temperature range from approximately 80 to 550 K. The application of the PSA method to proteins of up to approximately 300 kDa in weight is discussed based on a set of 396 protein structures downloaded from the protein data bank. The general method allows determination of cross sections with essentially the same accuracy as the trajectory method but at several orders of magnitude less computational cost. In addition, we define an empirical shape factor ρ˜ for proteins that approximates the computationally intensive part of the PSA calculation and can be used to estimate the PSA cross section based on the classical projection approximation. This empirical method reproduces collision cross sections with an accuracy of approximately 10%.Graphical abstractFigure optionsDownload full-size imageDownload high-quality image (82 K)Download as PowerPoint slideHighlights► We derive atomic parameters for use with the projected superposition approximation (PSA). ► We apply the PSA method to 396 protein structures from the Protein Data Bank with up to 300 kDa in weight. ► We define an empirical shape factor to estimate the PSA cross section for proteins. ► The empirical shape factor is accurate to approximately 10%.

Residue mutations have substantial effects on aggregation kinetics and propensities of amyloid peptides and their aggregate morphologies. Such effects are attributed to conformational transitions accessed by various types of oligomers such as steric zipper or single β-sheet. We have studied the aggregation propensities of six NNQQNY mutants: NVVVVY, NNVVNV, NNVVNY, VIQVVY, NVVQIY, and NVQVVY in water using a combination of ion-mobility mass spectrometry, transmission electron microscopy, atomic force microscopy, and all-atom molecular dynamics simulations. Our data show a strong correlation between the tendency to form early β-sheet oligomers and the subsequent aggregation propensity. Our molecular dynamics simulations indicate that the stability of a steric zipper structure can enhance the propensity for fibril formation. Such stability can be attained by either hydrophobic interactions in the mutant peptide or polar side-chain interdigitations in the wild-type peptide. The overall results display only modest agreement with the aggregation propensity prediction methods such as PASTA, Zyggregator, and RosettaProfile, suggesting the need for better parametrization and model peptides for these algorithms.

We have probed the structures and aggregation propensities of chirally substituted [Ala2]-Leu-Enkephalin peptides (i.e., Leu-Enkephalin G2A) with a combination of ion-mobility spectrometry/mass spectrometry and techniques of computational chemistry. Our IMS/MS data reveal a strong correlation between the propensity to form peptide dimers and the subsequent aggregation propensity. This correlation indicates that the dimerization process is fundamental to the overall self-assembly process. Our computational data correlate a conformational conversion during the peptide association process with a reduced experimental dimer formation and subsequent aggregation propensity. Furthermore, our analysis indicates that monomer activation does not precede peptide association and thus suggests that the entire-refolding or gain-in-interaction models are more realistic accounts of the peptide self-assembly process than the monomer-conversion model. In sum, our results suggest that conformational transitions of early peptide oligomers represent bottlenecks of the peptide self-assembly process and thus highlight the importance of structurally characterizing this reaction during amyloid formation.

Peptide oligomerization is necessary but not sufficient for amyloid fibril formation. Here, we use a combination of experiments and simulations to understand how pH influences the aggregation properties of a small hydrophobic peptide, YVIFL, which is a mutant form of [Leu-5]-Enkephalin. Transmission electron microscopy and atomic force microscopy measurements reveal that this peptide forms small aggregates under acidic conditions (pH = 2), but that extensive fibrillization only occurs under basic conditions (pH = 9 and 11). Ion-mobility mass spectrometry identifies key oligomers in the oligomerization process, which are further characterized at an atomistic level by molecular dynamics simulations. These simulations suggest that terminal charges play a critical role in determining aggregation propensity and aggregate morphology. They also reveal the presence of steric zipper oligomers under basic conditions, a possible precursor to fibril formation. Our experiments suggest that multiple aggregation pathways can lead to YVIFL fibrils, and that cooperative and multibody interactions are key mechanistic elements in the early stages of aggregation.

Recently, certain C-terminal fragments (CTFs) of Aβ42 have been shown to be effective inhibitors of Aβ42 toxicity. Here, we examine the interactions between the shortest CTF in the original series, Aβ(39–42), and full-length Aβ. Mass spectrometry results indicate that Aβ(39–42) binds directly to Aβ monomers and to the n = 2, 4, and 6 oligomers. The Aβ42:Aβ(39–42) complex is further probed using molecular dynamics simulations. Although the CTF was expected to bind to the hydrophobic C-terminus of Aβ42, the simulations show that Aβ(39–42) binds at several locations on Aβ42, including the C-terminus, other hydrophobic regions, and preferentially in the N-terminus. Ion mobility–mass spectrometry (IM-MS) and electron microscopy experiments indicate that Aβ(39–42) disrupts the early assembly of full-length Aβ. Specifically, the ion-mobility results show that Aβ(39–42) prevents the formation of large decamer/dodecamer Aβ42 species and, moreover, can remove these structures from solution. At the same time, thioflavin T fluorescence and electron microscopy results show that the CTF does not inhibit fibril formation, lending strong support to the hypothesis that oligomers and not amyloid fibrils are the Aβ form responsible for toxicity. The results emphasize the role of small, soluble assemblies in Aβ-induced toxicity and suggest that Aβ(39–42) inhibits Aβ-induced toxicity by a unique mechanism, modulating early assembly into nontoxic hetero-oligomers, without preventing fibril formation.

Early oligomerization of human IAPP (hIAPP) is responsible for β-cell death in the pancreas and is increasingly considered a primary pathological process linked to Type II Diabetes (T2D). Yet, the assembly mechanism remains poorly understood, largely due to the inability of conventional techniques to probe distributions or detailed structures of early oligomeric species. Here, we describe the first experimental data on the isolated and unmodified dimers of human (hIAPP) and nonamyloidogenic rat IAPP (rIAPP). The experiments reveal that the human IAPP dimers are more extended than those formed by rat IAPP and likely descend from extended monomers. Independent all-atom molecular dynamics simulations show that rIAPP forms compact helix and coil rich dimers, whereas hIAPP forms β-strand rich dimers that are generally more extended. Also, the simulations reveal that the monomer−monomer interfaces of the hIAPP dimers are dominated by β-strands and that β-strands can recruit coil or helix structured regions during the dimerization process. Our β-rich interface contrasts with an N-terminal helix-to-helix interface proposed in the literature but is consistent with existing experimental data on the self-interaction pattern of hIAPP, mutation effects, and inhibition effects of the N-methylation in the mutation region.

A projected superposition approximation (PSA) to compute molecular collision cross sections measured in ion-mobility experiments is developed. In the framework of the PSA, molecular collision cross sections are computed as a projection approximation modified to account for collective size and shape effects. Illustrative calculations on a range of molecular structures demonstrate that the PSA algorithm is able to handle the complex molecular shapes (concave, convex, pores, cavities, channels) as well as the range in molecular size typical to proteins. Our results indicate strong numerical agreement with the accurate trajectory method while only a small fraction of the computational demand is required.Graphical abstractHighlights► We develop the projected superposition approximation (PSA) to compute molecular collision cross sections measured in ion-mobility experiments. ► Molecular collision cross sections are computed as a projection approximation modified to account for collective size and shape effects. ► We show that the PSA algorithm is able to handle the geometries typical to proteins while being computationally highly efficient.

The conformations of desolvated ubiquitin ions, lifted into the gas phase by electrospray ionization (ESI), were characterized by ion mobility spectrometry (IMS) and compared to the solution structures they originated from. The IMS instrument combining a two-meter helium drift tube with a quadrupole time-of-flight mass spectrometer was built in-house. Solutions stabilizing the native state of ubiquitin yielded essentially one family of tightly folded desolvated ubiquitin structures with a cross section matching the size of the native state (1000 Å2). Solutions favoring the A state yielded several well-defined families of significantly unfolded conformations (1800–2000 Å2) matching in size conformations between the A state and a fully unfolded state. On the basis of these results and a wealth of data available in the literature, we conclude that the native state of ubiquitin is preserved in the transition from solution to the desolvated state during the ESI process and survives for >100 ms in a 294 K solvent-free environment. The A state, however, is charged more extensively than the native state during ESI and decays more rapidly following ESI. A state ions unfold on a time scale equal to or shorter than the experiment (≤50 ms) to more extended structures.

Many transmissible spongiform encephalopathies (TSEs) are believed to be caused by a misfolded form of the normal cellular prion protein (PrPC) known as PrPSc. While PrPSc is known to be exceptionally stable and resistant to protease degradation, PrPC has not shown these same unusual characteristics. However, using ion mobility spectrometry mass spectrometry (IMS−MS), we found evidence for at least one very stable conformation of a truncated form of recombinant PrPC consisting of residues 90−231, which resists unfolding in the absence of solvent at high injection energies and at temperatures in excess of 600 K. We also report the first absolute collision cross sections measured for recombinant Syrian hamster prion protein PrP(90−231).

Rigid rectangular, triangular, and prismatic supramolecular assemblies, cyclobis[(2,9-bis[trans-Pt(PEt3)2(PF6)]anthracene)(4,4′-dipyridyl)], cyclotris[(2,9-bis[trans-Pt(PEt3)2(PF6)]phenanthrene)(4,4′-dipyridyl)], and cyclotris[bis[cis-Pt(PEt3)2(CF3SO3)2]tetrakis(4-pyridyl)cyclobutadienecyclopentadienylcobalt(I)], respectively, based on dipyridyl ligands and square planar platinum coordination, have been investigated by ion mobility spectrometry−mass spectrometry (IMS-MS). Electrospray ionization−quadrupole and time-of-flight spectra have been obtained and fragmentation pathways assigned. Ion mobility studies give cross sections that compare very well with cross sections of the supramolecular rectangle and triangle species on the basis of X-ray bond distances. For the larger prism structures, agreement of experimental and calculated cross sections from molecular modeling is very good, indicating IMS-MS methods can be used to characterize complex self-assembled structures where X-ray or other spectroscopic structures are not available.

A series of Polyhedral Oligomeric Silsesquioxane (POSS) propylmethacrylate (PMA) and styryl oligomers were prepared from POSS monomers, R7R'Si8O12, containing 1 functional R’ group for polymerization and 7 inert R-groups where R = isobutyl (i-butyl), phenyl (Ph), cyclohexyl (Cy) or cyclopentyl (Cp). Both standard atom transfer radical polymerization (ATRP) and free radical syntheses, the latter employing azoisobutylnitrile as the free radical initiator were used in the syntheses. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectra were obtained in a new matrix, 4,4′-dihydroxyoctafluoroazobenzene which was especially designed for insoluble and intractable polymeric materials. Well-resolved series of oligomers were observed out to n = ∼13 in both the linear and reflectron modes. Major peaks were assigned based on tandem mass spectrometry (MSMS) fragmentation patterns to give a consistent explanation of the observed spectra. In all cases, ionization of the ATRP products gave cationized parent ions in which the terminal Br atom was replaced by hydrogen. Additional observed peaks were due to loss of POSS side chains from the oligomer backbone. The free radical products were terminated with either one or two isobutylnitrile groups. Electrospray ionization (ESI) spectra were more complex than the MALDI-TOF but showed either identical parent ions or closely related hydroxylated parent ions.We report MALDI-TOF mass spectra and assignments of major peaks for polyhedral oligomeric silsesquioxane (POSS) propylmethacrylate and styryl oligomers, obtained in a new matrix, 4,4′-dihydroxyoctafluoroazobenzene.

Ion mobility techniques, using both traveling wave-based technology and standard drift tube methods, along with molecular modeling were used to examine the gas-phase conformational properties of a series of isomeric oligosaccharides and hydrazine-released N-linked glycans from various sources. Electrospray ionization was used to generate H+ and Na+ adducts of oligosaccharides as well as Na+ and H2PO4− adducts of released N-linked glycans. The ion mobility mass spectrometry techniques were used to separate the isomeric oligosaccharides and the glycan mixtures. Good agreement was obtained between the theoretical and measured collision cross-sections. Glycans common to each glycoprotein were observed to have the same arrival time distribution independent of their source. In some cases support for multiple isomers was observed which correlated well with evidence obtained, where possible, from other experimental techniques. The sensitivity of the traveling wave ion mobility spectrometry (TWIMS) technique, together with the rapid experimental timescale, reproducibility and high information content make this an attractive approach for the characterization of complex mixtures of glycans released from glycoproteins. Successful calibration of the TWIMS arrival times/cross-sections was demonstrated using data from the drift tube instrument.Traveling wave-based and standard drift tube ion mobility techniques were used to examine gas-phase conformations of a series of isomeric oligosaccharides and N-linked glycans from various sources.

A combination of ion mobility and mass spectrometry methods was used to characterize the molecular shape of the protein calmodulin (CaM) and its complexes with calcium and a number of peptide ligands. CaM, a calcium-binding protein composed of 148 amino acid residues, was found by X-ray crystallography to occur both in a globular shape and in the shape of an extended dumbbell. Here, it was found, as solutions of CaM and CaM complexes were sprayed into the solvent-free environment of the mass spectrometer, that major structural features of the molecule and the stoichiometry of the units constituting a complex in solution were preserved in the desolvation process. Two types of CaM structures were observed in our experiments: a compact and an extended form of CaM with measured cross sections in near-perfect agreement with those calculated for the known globular and extended dumbbell X-ray geometries. Calcium-free solutions yielded predominantly an extended CaM conformation. Can2+−CaM complexes were observed in calcium-containing solutions, n = 0−4, with the population of the compact conformation increasing relative to the elongated conformation as n increases. For n = 4, a predominantly compact globular conformation was observed. Solutions containing the peptide CaMKII290−309, the CaM target domain of the Ca2+/calmodulin-dependent protein kinase II (CaMKII) enzyme, yielded predominantly globular Ca42+−CaM−CaMKII290−309 complexes. Similar results were obtained with the 26-residue peptide melittin. For the 14-residue C-terminal melittin fragment, on the other hand, formation of both a 1:1 and a 1:2 CaM−peptide complex was detected. On the basis of the entirety of our results, we conclude that the collapse of extended (dumbbell-like) CaM structures into more compact globular structures occurs upon specific binding of four calcium ions. Furthermore, this calcium-induced structural collapse of CaM appears to be a prerequisite for formation of a particularly stable CaM−peptide complex involving peptides long enough to be engaged in interactions with both lobes of CaM.

A portion of the prion protein, PrP106−126, is highly conserved among various species and is thought to be one of the key domains involving amyloid formation of the protein. We used ion mobility spectrometry−mass spectrometry (IMS−MS) in conjunction with replica exchange molecular dynamics (REMD) to examine the monomeric and oligomeric structures of normal PrP106−126 and two nonaggregating forms of the peptide, an oxidized form in which both methionine residues are oxidized to methionine sulfoxide and a control peptide consisting of the same amino acids as PrP106−126 in a scrambled sequence. Our ion mobility and simulation data indicate the presence of a population of β-hairpin monomers for the normal and oxidized peptides. This is supported by our CD data indicating that a monomer solution of the normal peptide contains ∼46% β-sheet and ∼23% β-turn content, in excellent agreement with our REMD simulations. Oligomerization was seen by IMS−MS for the normal peptide only, not the oxidized peptide or the control sequence. Both our IMS−MS and CD data suggest that this oligomerization results from the association of ordered β-hairpin monomers rather than disordered monomers. Structural analysis shows that the normal and oxidized peptides have similar secondary and tertiary structural properties, suggesting that the inhibition of aggregation caused by methionine oxidation stems from mediating interpeptide interactions rather than by altering the peptide’s monomeric conformation. In contrast, an increase in α-helical and random coil structural components relative to the normal peptide might be responsible for the lack of observed aggregation of the control peptide.

Oligomerization of human islet amyloid polypeptide (IAPP) has been increasingly considered a pathogenic process in type II diabetes. Here structural features of the IAPP monomer have been probed using a combination of ion mobility mass spectrometry (IMS-MS) and all-atom replica exchange molecular dynamics (REMD) simulations. Three distinct conformational families of human IAPP monomer are observed in IMS experiments, and two of them are identified as dehydrated solution structures on the basis of our simulation results: one is an extended β-hairpin structural family, and the second is a compact helix-coil structural family. The extended β-hairpin family is topologically similar to the peptide conformation in the solid-state NMR fibril structure published by Tycko and co-workers. It is absent in both experiments and simulations performed on the non-amyloidogenic rat IAPP, suggesting it may play an important role in the fibrillation pathway of human IAPP. In addition, pH dependence studies show that the relative abundance of the β-hairpin structural family is significantly enhanced at pH 8.0. This observation is consistent with the increased rate of fibrillation at high pH in vitro and offers a possible explanation of the pH dependent fibrillation in vivo. This paper, to the best of our knowledge, presents the first experimental evidence of a significant population of β-hairpin conformers for the IAPP peptide. It is consistent with a previous suggestion in the literature that β-sheet-rich oligomers are assembled from ordered β-hairpins rather than from coiled structures.

Aβ40 and Aβ42 are peptides that adopt similar random-coil structures in solution. Aβ42, however, is significantly more neurotoxic than Aβ40 and forms amyloid fibrils much more rapidly than Aβ40. Here, mass spectrometry and ion mobility spectrometry are used to investigate a mixture of Aβ40 and Aβ42. The mass spectrum for the mixed solution shows the presence of a heterooligomer composed of equal parts of Aβ40 and Aβ42. Ion mobility results indicate that this mixed species comprises an oligomer distribution extending to tetramers. Aβ40 alone produces such a distribution, whereas Aβ42 alone produces oligomers as large as dodecamers. This indicates that Aβ40 inhibits Aβ42 oligomerization.

The A-site of 16S rRNA, which is a part of the 30S ribosomal subunit involved in prokaryotic translation, is a well known aminoglycoside binding site. Full characterization of the conformational changes undergone at the A-site upon aminoglycoside binding is essential for development of future RNA/drug complexes; however, the massiveness of 16S makes this very difficult. Recently, studies have found that a 27 base RNA construct (16S27) that comprises the A-site subdomain of 16S behaves similarly to the whole A-site domain. ESI-MS, ion mobility and molecular dynamics methods were utilized in this study to analyze the A-site of 16S27 before and after the addition of ribostamycin (R), paromomycin (P) and lividomycin (L). The ESI mass spectrum for 16S27 alone illustrated both single-stranded 16S27 and double-stranded (16S27)2 complexes. Upon aminoglycoside addition, the mass spectra showed that only one aminoglycoside binds to 16S27, while either one or two bind to (16S27)2. Ion mobility measurements and molecular dynamics calculations were utilized in determining the solvent-free structures of the 16S27 and (16S27)2 complexes. These studies found 16S27 in a hairpin conformation while (16S27)2 existed as a cruciform. Only one aminoglycoside binds to the single A-site of the 16S27 hairpin and this attachment compresses the hairpin. Since two A-sites exist for the (16S27)2 cruciform, either one or two aminoglycosides may bind. The aminoglycosides compress the A-sites causing the cruciform with just one aminoglycoside bound to be larger than the cruciform with two bound. Non-specific binding was not observed in any of the aminoglycoside/16S27 complexes.ESI-MS, ion mobility and molecular dynamics methods were utilized in this study to analyze the A-site of 16S27 before and after the addition of ribostamycin (R), paromomycin (P) and lividomycin (L).

The secondary structures of DNA hairpins, pseudoknots and cruciforms are of great interest because of their possible role in materials applications and biological functions such as regulating transcription. To determine the stability of these structures, DNA sequences capable of forming each were analyzed with mass spectrometry, ion mobility, and molecular dynamics calculations. Nano-ESI mass spectra indicated that stoichiometries compatible with hairpin, pseudoknot, and cruciform structures were present. Ion mobility spectrometry (IMS) was utilized to obtain experimental collision cross sections for all complexes. These cross sections were compared with structures from molecular dynamics, and in all cases, the lowest-charge states could be matched with a structure for an intact hairpin, pseudoknot, or cruciform. However, as the charge states of the single-stranded hairpins and pseudoknots increased, their structures elongated, and all Watson−Crick pairs were broken.

Using a mass spectrometer equipped with a drift cell, water binding energies of protonated arginine (ArgH+) and protonated lysine (LysH+) were determined in equilibrium experiments and supplementary calculations at the B3LYP/6-311++G** level of theory. The binding energy of the first water molecule was measured to be 10.3 and 10.9 kcal/mol for ArgH+ and LysH+, respectively. Water binding energies decrease with increasing degree of hydration reaching values of 6−7 kcal/mol for the fourth and fifth water molecule. Theory reproduces this trend of decreasing binding energies correctly and theoretical water binding energies agree with experiment quantitatively within 2 kcal/mol. Lowest-energy theoretical structures of ArgH+ and LysH+ are characterized by protonated side chains and neutral α-amino and carboxyl groups which form intramolecular hydrogen bonds to the ionic group (charge solvation or CS structures). The salt bridge (SB) structures with two cationic groups (side chain and α-amine) and one anionic group (carboxyl) are 13.1 and 9.3 kcal/mol higher in energy for ArgH+ and LysH+, respectively. Theory indicated that the first water molecule binds to the ionic group of the CS structures of ArgH+ and LysH+. With increasing degree of hydration intramolecular interactions are replaced one by one with water bridges with water inserted into the intramolecular hydrogen bonds. Whereas the global minima of ArgH+·(H2O)n and LysH+·(H2O)n, n < 7, were calculated to represent CS structures, 7-fold hydrated CS and SB structures, ArgH+·(H2O)7 and LysH+·(H2O)7, are nearly isoenergetic (within <1 kcal/mol).

A new series of encapsulated fluoride polyhedral oligomeric silsesquioxane (POSS) materials, [(CH3)4N+][F−@(R8Si8O12)], where R = vinyl, phenyl, styrenyl, trifluoropropyl, nonafluorohexyl, or tridecafluorooctyl, were synthesized by the reaction of tetramethylammonium fluoride with the R8Si8O12 POSS in tetrahydrofuran. Encapsulation of the fluoride was confirmed with 19F and 29Si NMR spectroscopy. Ion mobility and molecular modeling methods were used to investigate the gas phase conformational properties of these POSS. Theoretical calculations demonstrate that the binding energy of fluoride to the interior of the POSS cage ranges from 70 to 270 kcal/mol as a function of substituent. Sodiated positive ions of the form H+[F−@R8T8]Na+ (T = SiO3/2, R = styrenyl, phenyl, and vinyl) were examined by MALDI; ESI was used to study the negative ions F−@R8T8 (R = styrenyl, phenyl, vinyl, trifluoropropyl, and nonafluorohexyl). The ion mobilities of these species were measured and used to calculate collision cross sections. These cross sections were compared to X-ray crystal structures and theoretical cross sections obtained from molecular mechanics and dynamics calculations. Experimental cross sections were consistent with all of the known X-ray crystal structures (styrenyl, vinyl, and phenyl POSS species). The experimental cross sections also agreed with the calculated cross sections for each species. As a result of the compact nature of the POSS cages, each sample had only one stable conformation, and only one low-energy family of structures was found for each set of sample calculations.

Aggregation of α-synuclein (α-syn), a protein implicated in Parkinson’s disease (PD), is believed to progress through formation of a partially folded intermediate. Using nanoelectrospray ionization (nano-ESI) mass spectrometry combined with ion mobility measurements we found evidence for a highly compact partially folded family of structures for α-syn and its disease-related A53T mutant with net charges of −6, −7, and −8. For the other early onset PD mutant, A30P, this highly compact population was only evident when the protein had a net charge of −6. When bound to spermine near physiologic pH, all three proteins underwent a charge reduction from the favored solution charge state of −10 to a net charge of −6. This charge reduction is accompanied by a dramatic size reduction of about a factor of 2 (cross section of 2600 Å2 (−10 charge state) down to 1430 Å2 (−6 charge state)). We conclude that spermine increases the aggregation rate of α-syn by inducing a collapsed conformation, which then proceeds to form aggregates.

B-DNA is the most common DNA helix conformation under physiological conditions. However, when the amount of water in a DNA solution is decreased, B-to-A helix transitions have been observed. To understand what type of helix conformations exist in a solvent-free environment, a series of poly d(CG)n and mixed sequence DNA duplexes from 18 to 30 bp were examined with circular dichroism (CD), ESI-MS, ion mobility, and molecular dynamics. From the CD spectra, it was observed that all sequences had B-form helices in solution. However, the solvent-free results were more complex. For the poly d(CG)n series, the 18 bp duplex had an A-form helix conformation, both A- and B-helices were present for the 22 bp duplex, and only B-helices were observed for the 26 and 30 bp duplexes. Since these sequences were all present as B-DNA in solution, the observed solvent-free structures illustrate that smaller helices with fewer base pairs convert to A-DNA more easily than larger helices in the absence of solvent. A similar trend was observed for the mixed sequence duplexes where both an A- and B-helix were present for the 18 bp duplex, while only B-helices occur for the larger 22, 26, and 30 bp duplexes. Since the solvent-free B-helices appear at smaller sizes for the mixed sequences than for the pure d(CG)n duplexes, the pure d(CG)n duplexes have a greater A-philicity.

The structural properties of G-quadruplex forming sequences, such as the human telomeric repeat d(T2AG3)n, are of great interest due to their role in cancer and cellular aging. To determine if G-quadruplexes are present in a solvent-free environment, different lengths of the telomeric repeat d(T2AG3)n (where n = 1, 2, 4 and 6) and dTG4T were investigated with mass spectrometry, ion mobility and molecular dynamics calculations. Nano-ESI-MS illustrated quadruplex stoichiometries compatible with G-quadruplex structures for each sequence, with dT2AG3 and dTG4T forming 4-strand complexes with two and three NH4+ adducts, d(T2AG3)2 a 2-strand complex, and d(T2AG3)4 and d(T2AG3)6 remaining single-stranded. Experimental cross sections were obtained for all species using ion mobility methods. In all cases, these could be quantitatively matched to model cross sections with specific strand orientations (parallel/antiparallel) and structures. For each species, the solvent-free structures agreed with the solution CD measurements, but the ion mobility/modeling procedure often gave much more detailed structural information.

The aggregation and conformation of deoxyguanosine (dG) in an ammonium acetate buffer solution were examined using mass spectrometry, ion mobility, and molecular mechanics/dynamics calculations. The nano-ESI mass spectrum indicated that 4 and 6 dGs cluster with 1 NH4+; 11 dGs with 2 NH4+; 14, 16, and 17 dGs with 3 NH4+; and 23 dGs with 4 NH4+. The collision cross sections with helium were measured and compared with calculated cross sections of theoretical structures generated by molecular mechanics/dynamics calculations. Three distinct arrival time distribution (ATD) peaks were observed for (4dG + NH4)+. One peak was assigned to the quadruplex structure of (4dG + NH4)+, while the other two peaks corresponded to the quadruplex structures of (8dG + 2NH4)2+ and (12dG + 3NH4)3+, all with the same m/z. Four ATD peaks were observed for (6dG + NH4)+ and assigned to the globular structure of (6dG + NH4)+, and the quadruplex structures of (12dG + 2NH4)2+, (18dG + 3NH4)3+, and (24dG + 4NH4)4+. Two ATD peaks were observed for (11dG + 2NH4)2+ and assigned to the quadruplex structures of (11dG + 2NH4)2+ and (22dG + 4NH4)4+. All of the other clusters in the mass spectrum (14, 16, and 17 dGs with 3 NH4+ and 23 dGs with 4 NH4+) only had one peak in their ATDs and in all cases the theoretical structures in a quadruplex arrangement agreed with the experimental cross sections. These results provide compelling evidence that quadruplexes are present in solution and retain their structure during the spray process, dehydration, and detection.

Sequence dependent conformations of a series of glycidyl methacrylate/butyl methacrylate (GMA/BMA) copolymers cationized by sodium were analyzed in the gas phase using ion mobility methods. GMA and BMA have the same nominal mass but vary in exact mass by 0.036 Da (CH4 versus O). Matrix assisted laser desorption/ionization (MALDI) was used to form Na+(GMA/BMA) copolymer ions and their collision cross-sections were measured in helium using ion mobility methods. The copolymer sequences from Na+(GMA/BMA)3 to Na+(GMA/BMA)5 (i.e. for the trimer to the pentamer) were studied. Analysis by molecular mechanics/dynamics indicates that each copolymer (regardless of sequence) forms a ring around the sodium ions due to Na+/oxygen electrostatic interactions. However, the structures vary in size, since the epoxy oxygen atoms in the glycidyl groups are attracted to the sodium ions while the carbon-composed butyl groups are not. This allows copolymers with more GMA segments to fold tighter (more spherically) around the sodium ion and have smaller cross-sections than copolymers with a larger amount of BMA segments in the sequence. Due to this cross-sectional difference, the GMA/BMA sequence compositions of the trimer and tetramer could be quantified.

The gas-phase conformations of a series of trinucleotides containing thymine (T) and guanine (G) bases were investigated for the possibility of zwitterion formation. Deprotonated dGTT−, dTGT−, and dTTG− ions were formed by MALDI and their collision cross-sections in helium measured by ion mobility based methods. dTGT− was theoretically modeled assuming a zwitterionic and non-zwitterionic structure while dGTT− and dTTG− were considered “control groups” and modeled only as non-zwitterions. In the zwitterion, G is protonated at the N7 site and the two neighboring phosphates are deprotonated. In the non-zwitterion, G is not protonated and only one phosphate group is deprotonated. Two conformers, whose cross-sections differ by 17 ± 2 Å2, are observed for dTGT− in the 80 K experiments. Multiple conformers are also observed for dGTT− and dTTG− at 80 K, though relative cross-section differences between the conformers could not be accurately obtained. At higher temperatures (>200 K), the conformers rapidly interconvert on the experimental time scale and a single “time-averaged” conformer is observed in the ion mobility data. Theory predicts only one low-energy conformation for the zwitterionic form of dTGT− with a cross-section 8% smaller than experimental values. Additionally, the extra H+ on G does not bridge both phosphates. Thus, dTGT− does not appear to be a stable zwitterion in the gas-phase. Theory does, however, predict two low-energy conformers for the non-zwitterionic form of dTGT− that differ in cross-section by 18 ± 3 Å2, in good agreement with the experiment. In the smaller cross-section form (folded conformer), G and one of the T bases are stacked while the other T folds towards the stacked pair and hydrogen bonds to G. In the larger cross-section form (open conformer), the unstacked T extends away from the T/G stacked pair. Similar folded and open conformers are predicted for all three trinucleotides, regardless of which phosphate is deprotonated.

The gas-phase conformations of poly(styrene) oligomers cationized by Li+, Na+, Cu+, and Ag+ (M+PSn) were examined using ion mobility experiments and molecular mechanics/dynamics calculations. M+PSn ions were formed by MALDI and their ion-He collision cross-sections were measured by ion mobility methods. The experimental collision cross-sections of each M+PS n-mer were similar for all four metal cations and increased linearly with n. Molecular modeling of selected M+PS oligomers cationized by Li+ and Na+ yielded quasi-linear structures with the metal cation sandwiched between two phenyl groups. The relative energies of the structures were ∼2–3 kcal/mol more stable when the metal cation was sandwiched near the middle of the oligomer chain than when it was near the ends of the oligomer. The cross-sections of these theoretical structures agree well with the experimental values with deviations typically around 1–2%. The calculations also show that the metal cation tends to align the phenyl groups on the same side of the CH2CH backbone. Calculations on neutral poly(styrene), on the other hand, showed structures in which the phenyl groups were more randomly positioned about the oligomer backbone. The conformations and metal-oligomer binding energies of M+PS are also used to help explain CID product distributions and fragmentation mechanisms of cationized PS oligomers.

Measurements are reported for sequential clustering of CH4 to Co+ ions under equilibrium conditions. The CH4 cluster bond strengths show a pairwise behavior: −ΔH00 = 23.1 and 25.3 kcal/mol for n = 1 and 2; 7.3 and 5.2 kcal/mol for n = 3 and 4; and ∼2 kcal/mol for both n = 5 and 6. This pairwise behavior is well reproduced by large basis set density functional theory calculations. These calculations indicate n = 1 and n = 2 add on opposite sides of the Co+ ion in η2 configuration and induce significant s/d hybridization on Co+. This hybridization both reduces Pauli repulsion and fosters sigma donation into the 4s orbital on Co+. Clusters n = 3 and n = 4 add at 90° to the n = 1 and 2 line of centers forming a planar system. The s/d hybridization is unfavorable for these clusters resulting in longer Co+–C bond lengths and substantially reduced binding energies. To n = 5 and 6 ligands probably complete a pseudo octahedral complex and are very weakly bound, perhaps defining a second solvation shell. An impurity contributed substantially to the experimental peak at m/z = 123 corresponding to Co+(CH4)4. The impurity was tentatively identified as O2Co+(CH4)2 and experimental protocals were developed to eliminate its impact on the data reported here. It is suggested this impurity could be responsible for published guided ion beam results that found a substantially larger binding energy for n = 4 than for n = 3 in contrast to what is reported here.

A method is developed for measuring collision cross sections of gas-phase biomolecules using a slightly modified commercial triple quadrupele instrument. The modifications allow accurate stopping potentials to be measured for ions exiting the collision region of the instrument. A simple model allows these curves to be converted to cross sections. In order to account for certain poorly defined experimental parameters (exact ion energy, absolute pressure in the collision cell, etc.) variable parameters are included in the model. These parameters are determined on a case by case basis by normalizing the results to the well known cross section of singly charged bradykinin. Two relatively large systems were studied (cytochrome c and myoglobin) so comparisons could be made to literature values. A number of new peptide systems were then studied in the 9–14 residue range. These included singly and doubly charged ions of luteinizing hormone releasing hormone (LHRH) substance P, and bombesin in addition to bradykinin. The experimental cross sections were in very good agreement with predictions from extensive molecular dynamics modeling. One interesting result was the experimental observation that the cross section of the doubly charged ions of LHRH, substance P, and bombesin were all smaller than those of the corresponding singly charged ions. Molecular dynamics did not reproduce this result, predicting doubly charged cross sections of the same magnitude or slightly larger than for the singly charged species. The experimental results appear to be correct, however. Possible shortcomings in the modeling procedure for multiply charged ions were suggested that might account for the discrepancy.

A model was developed to describe the deuterium uptake of gas phase polypeptide ions via H/D exchange with D2O. Ab initio calculations established, for energetic reasons, that the exchange must take place via a “relay” mechanism involving both a charged site and a nearby basic site. Molecular dynamics simulations indicated that the D2O molecule did not penetrate the core of the example peptide, protonated bradykinin (Bk+H)+, and hence the relay mechanism must occur on the peptide surface. Two factors were deemed to be important: (1) The surface accessibility of the charged sites and the basic sites and (2) the distances between them. An algorithm was developed that accounted for these features using the absolute exchange rate as a free parameter. Excellent agreement was obtained with experiment when equal weight was given to an ensemble of low energy conformations of (Bk+H)+, assumed to have a salt bridge primary structure. Single conformations, or other protonated forms, did not allow good agreement with experiment for any value of the absolute exchange rate constant.

The geometrical shapes of the sodiated and cesiated amino acids glycine and arginine were probed in the gas phase by using the ion mobility based ion chromatography method. The data were compared to those obtained for alkali cationized methyl esters and for all the protonated species. Molecular mechanics, semiempirical, and ab initio/density functional theory (DFT) calculations were carried out to generate model structures for comparison with experiment and to determine the relative energies of different structures. For alkali cationized glycine the experimental cross sections agreed with charge solvation structures which were found by calculation to be the most stable forms as well. Both experiment and theory indicated that sodium is solvated by both the amino and the carbonyl groups, while cesium is solvated by one or both oxygen(s) of the carboxyl group. Alkali cationized arginine was found to form a salt bridge structure. The carboxylate group is stabilized by both the charged guanidinium group and the alkali ion. High level (6-311++G∗∗ and DZVP) ab initio/DFT calculations carried out on sodiated and rubidiated N amidinoglycine, which contains a guanidino group and which was used as a model for the larger arginine molecule, indicated that the salt bridge structures are ∼10 kcal/mol more stable than the charge solvation forms for both alkali ions. The structure of protonated arginine, i.e. salt bridge or charge solvation, could not be unambiguously determined.

Collision cross sections of gas phase valinomycin–alkali ion complexes were measured in helium using the ion mobility based ion chromatography technique. For the lithiated and sodiated species a value of 267 Å2 was measured whereas the cross sections for the potassiated, rubidiated, and cesiated complexes were larger 272, 277, and 279 Å2, respectively. The systematic increase with ion size indicates that the backbone folding of the cyclic valinomycin molecule is dependent on the choice of alkali ion. This result is in good agreement with theoretical cross sections of model structures obtained by molecular mechanics simulations. The model structures demonstrate that the valinomycin host completely encapsulates the alkali ion with five or six of the polar carbonyl groups in the first solvation sphere of the alkali ion. The polar core of the complex is shielded by the aliphatic valinomycin side chains, which were found to be predominant on the complex surface. The lithium ion is solvated by a fivefold carbonyl coordination sphere with at least four of the five carbonyls belonging to valine units. The sodiated species exhibits a five- to sixfold carbonyl coordination with highly excited O…Na+ vibrations at 300 K. In the potassiated and cesiated complexes the alkali ion is coordinated by six valine carbonyl groups in a near octahedral arrangement causing the valinomycin backbone to fold in a quasi-S6 symmetric fashion. These results demonstrate that the overall size and shape of the complex is not quite the same for different alkali ions, in contrast to conclusions made from solution salt extraction experiments and assumptions made in previous molecular mechanics calculations. However, our results were found to be in good agreement with earlier spectroscopic studies carried out on alkali salt valinomycin crystals and solutions thereof in organic solvents. Relative alkali ion–valinomycin binding energies extracted from the molecular mechanics data were able to qualitatively explain the experimentally observed preference of valinomycin for hosting potassium over lithium and sodium.

B-DNA is the most common DNA helix conformation under physiological conditions. However, when the amount of water in a DNA solution is decreased, B-to-A helix transitions have been observed. To understand what type of helix conformations exist in a solvent-free environment, a series of poly d(CG)n and mixed sequence DNA duplexes from 18 to 30 bp were examined with circular dichroism (CD), ESI-MS, ion mobility, and molecular dynamics. From the CD spectra, it was observed that all sequences had B-form helices in solution. However, the solvent-free results were more complex. For the poly d(CG)n series, the 18 bp duplex had an A-form helix conformation, both A- and B-helices were present for the 22 bp duplex, and only B-helices were observed for the 26 and 30 bp duplexes. Since these sequences were all present as B-DNA in solution, the observed solvent-free structures illustrate that smaller helices with fewer base pairs convert to A-DNA more easily than larger helices in the absence of solvent. A similar trend was observed for the mixed sequence duplexes where both an A- and B-helix were present for the 18 bp duplex, while only B-helices occur for the larger 22, 26, and 30 bp duplexes. Since the solvent-free B-helices appear at smaller sizes for the mixed sequences than for the pure d(CG)n duplexes, the pure d(CG)n duplexes have a greater A-philicity.

The C-terminus of amyloid β-protein (Aβ) 42 plays an important role in this protein's oligomerization and may therefore be a good therapeutic target for the treatment of Alzheimer's disease. Certain C-terminal fragments (CTFs) of Aβ42 have been shown to disrupt oligomerization and to strongly inhibit Aβ42-induced neurotoxicity. Here we study the structures of selected CTFs [Aβ(x–42); x = 29–31, 39] using replica exchange molecular dynamics simulations and ion mobility mass spectrometry. Our simulations in explicit solvent reveal that the CTFs adopt a metastable β-structure: β-hairpin for Aβ(x–42) (x = 29–31) and extended β-strand for Aβ(39–42). The β-hairpin of Aβ(30–42) is converted into a turn-coil conformation when the last two hydrophobic residues are removed, suggesting that I41 and A42 are critical in stabilizing the β-hairpin in Aβ42-derived CTFs. The importance of solvent in determining the structure of the CTFs is further highlighted in ion mobility mass spectrometry experiments and solvent-free replica exchange molecular dynamics simulations. A comparison between structures with solvent and structures without solvent reveals that hydrophobic interactions are critical for the formation of β-hairpin. The possible role played by the CTFs in disrupting oligomerization is discussed.

Human islet amyloid polypeptide (hIAPP or Amylin) is a 37 residue hormone that is cosecreted with insulin from the pancreatic islets. The aggregation of hIAPP plays a role in the progression of type 2 diabetes and contributes to the failure of islet cell grafts. Despite considerable effort, little is known about the mode of action of IAPP amyloid inhibitors, and this has limited rational drug design. Insulin is one of the most potent inhibitors of hIAPP fibril formation, but its inhibition mechanism is not understood. In this study, the aggregation of mixtures of hIAPP with insulin, as well as with the separate A and B chains of insulin, were characterized using ion mobility spectrometry-based mass spectrometry and atomic force microscopy. Insulin and the insulin B chain target the hIAPP monomer in its compact isoform and shift the equilibrium away from its extended isoform, an aggregation-prone conformation, and thus inhibit hIAPP from forming β-sheets and subsequently amyloid fibrils. All-atom molecular modeling supports these conclusions.