Intrinsic Ca2+ affinities of peptides: Application of the kinetic method to analogs of calcium-binding site III of rabbit skeletal troponin C

We extended the kinetic method to determine the intrinsic affinities of nonvolatile organic molecules with divalent metal ions and then applied the amended method to determine the calcium affinities of peptide analogs of the calcium-binding site III of rabbit skeletal troponin C. Metal-bis(peptide) complexes of the composition ([H2Pi + H2Pii] - H + Ca)+, where H2P is a neutral peptide, were introduced into the gas phase by fast atom bombardment. The extended kinetic method recognizes that the dissociation characteristics of a singly charged, bis(peptide) complexes of divalent metal ions are determined by not only the metal-ion affinity but also the proton affinities of the neutral and deprotonated peptides. The modified method requires one to measure the relative abundances of [H2P - H + Ca]+, [H2P + H]+, and [H2P - H]- ions that form upon collisional activation of mixed peptide/metal complexes, proton-bound peptide dimers, and deprotonated peptide dimers, respectively. We found, by using the modified method, that the set of peptides has a different affinity order than that in solution. Peptides with one aspartic acid have a higher intrinsic Ca2+ affinity than those with two aspartates. The location of the aspartic acid (Asp) residues at various positions also affects the Ca2+ affinity. Those peptides with one Asp in the middle of the chain have higher Ca2+ affinities than those with Asp on the end because the former peptides offer greater polarizability to stabilize the charge. Peptides with two Asp's located in close proximity have higher intrinsic calcium affinities than those with aspartates positioned further apart.     

气相中碱金属离子与丝氨酸、亮氨酸和赖氨酸五肽复合物的裂解反应简

为了探索金属离子对含有不同侧链的多肽气相解离的影响,采用质谱法研究了碱金属离子Li+,Na+,K+,Rb+和Cs+分别与丝氨酸、亮氨酸和赖氨酸五肽(分别简写为S5,L5和K5)形成的复合物的裂解反应. 质谱定性结果表明,5种碱金属离子均可以在气相中与丝氨酸、亮氨酸和赖氨酸五肽形成配合比为1：1 和2：1的非共价复合物;竞争反应结果表明,随着碱金属离子半径的增加,它们与3种五肽的结合能力逐渐减弱. 质谱定量结果表明,K+与丝氨酸、亮氨酸和赖氨酸五肽复合物的结合常数分别为8.94×104,2.83×104和2.50×103 L/mol,表明K+与五肽复合物的结合强度按照丝氨酸、亮氨酸和赖氨酸的顺序依次减小. 含不同侧链碱金属离子-五肽复合物的碰撞诱导解离结果表明,复合物的碎裂主要发生在骨架上,丝氨酸五肽复合物最易碎裂,亮氨酸五肽复合物其次,赖氨酸五肽复合物则较难碎裂,且3种复合物的侧链断裂情况也呈现明显差异. 此外,研究了Na+与亮氨酸五肽复合物所产生的碎片离子,分析了不同离子之间的来源关系,并以Dunbar的复合物理论模型为依据,推测在碎裂过程中,碱金属离子可能向五肽的碳端或氮端偏移. 质谱碎片分析结果表明,在2：1的非共价复合物中,第一个碱金属离子与五肽上4个酰胺键的羰基结合,第二个碱金属离子与五肽的羧基氧原子结合.     

Gas-phase investigation of Pd(II)-alanine complexes with small native and derivatized peptides containing histidine

We report here the generation of gas-phase complexes containing Pd(II), a ligand (deprotonated alanine, A-), and/or N-terminus derivatized peptides containing histidine as one of the amino acids. The species were produced by electrospray ionization, and their gas-phase reactions were investigated using ion-trap tandem mass spectrometry. Pd(II) forms a stable diaqua complex in the gas phase of the formula, [Pd(A-) (H(2)O)(2)]+, (where A- = deprotonated alanine) along with ternary complexes containing A- and peptide. The collision-induced dissociation (CID) patterns of the binary and ternary complexes were investigated, and the dissociation patterns for the ternary complexes suggest that: (a) the imidazole ring of the histidine side group may be the intrinsic binding site of the metal ion, and (b) the peptides fragment primarily by cleavage of the amide bond to the C-terminal side of the histidine residues. These observations are in accord with previous solution-state studies in which Pd(II) was shown to cause hydrolysis of an amide bond of a peptide at the same position.     

气相中碱金属离子与丝氨酸、 亮氨酸和赖氨酸五肽复合物的裂解反应

为了探索金属离子对含有不同侧链的多肽气相解离的影响, 采用质谱法研究了碱金属离子Li⁺, Na⁺, K⁺, Rb⁺和Cs⁺分别与丝氨酸、 亮氨酸和赖氨酸五肽(分别简写为S5, L5和K5)形成的复合物的裂解反应. 质谱定性结果表明, 5种碱金属离子均可以在气相中与丝氨酸、 亮氨酸和赖氨酸五肽形成配合比为1∶1 和2∶1的非共价复合物; 竞争反应结果表明, 随着碱金属离子半径的增加, 它们与3种五肽的结合能力逐渐减弱. 质谱定量结果表明, K⁺与丝氨酸、 亮氨酸和赖氨酸五肽复合物的结合常数分别为8.94×10⁴, 2.83×10⁴和2.50×10³ L/mol, 表明K⁺与五肽复合物的结合强度按照丝氨酸、 亮氨酸和赖氨酸的顺序依次减小. 含不同侧链碱金属离子-五肽复合物的碰撞诱导解离结果表明, 复合物的碎裂主要发生在骨架上, 丝氨酸五肽复合物最易碎裂, 亮氨酸五肽复合物其次, 赖氨酸五肽复合物则较难碎裂, 且3种复合物的侧链断裂情况也呈现明显差异. 此外, 研究了Na⁺与亮氨酸五肽复合物所产生的碎片离子, 分析了不同离子之间的来源关系, 并以Dunbar的复合物理论模型为依据, 推测在碎裂过程中, 碱金属离子可能向五肽的碳端或氮端偏移. 质谱碎片分析结果表明, 在2∶1的非共价复合物中, 第一个碱金属离子与五肽上4个酰胺键的羰基结合, 第二个碱金属离子与五肽的羧基氧原子结合.     

Gas phase hydrogen/deuterium exchange of arginine and arginine dipeptides complexed with alkali metals

The hydrogen/deuterium (H/D) exchange of protonated and alkali-metal cationized Arg-Gly and Gly-Arg peptides with D(2)O in the gas phase was studied using electrospray ionization quadropole ion trap mass spectrometry. The Arg-Gly and Gly-Arg alkali metal complexes exchange significantly more hydrogens than protonated Arg-Gly and Gly-Arg. We propose a mechanism where the peptide shifts between a zwitterionic salt bridge and nonzwitterionic charge solvated conformations. The increased rate of H/D exchange of the alkali metal complexes is attributed to the peptide metal complexes' small energy difference between the salt-bridge conformation and the nonzwitterionic charge-solvated conformation. Implications for the applicability of this mechanism to other zwitterionic systems are discussed.     

MS<Superscript>n</Superscript> characterization of protonated cyclic peptides and metal complexes

MSⁿ experiments involving low energy collisionally activated dissociation (CAD) in a quadrupole ion trap were used to characterize the fragmentation of alkali, alkaline earth and transition metal complexes of five cyclic peptides, and the results were compared with those obtained for protonated cyclic peptides. Complexes with metal ions produced enhanced abundances of the most diagnostic fragments for elucidating the primary structures. For cyclosporin A, nickel and lithium complexes gave additional sequence information compared with the protonated peptide. For depsipeptides, sodium and lead complexes were superior to the protonated peptide or other metal complexes for sequencing residues, and CAD of the lead complexes led to preferential cleavage of two residues at a time. For cyclic lipopeptides, complexes with silver, nickel and strontium ions provided enhanced abundances of key fragment ions.     

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.     

Selective molecular recognition of arginine by anionic salt bridge formation with bis-phosphate crown ethers: implications for gas phase peptide acidity from adduct dissociation

Arginine forms a stable noncovalent anionic salt bridge complex with DP (a crown ether which contains two endocyclic dialkylhydrogenphosphate esters). Abundant adduct formation with DP is observed for complexes with arginine, YAKR, HPPGFSPFR, AAKRKAA, RR, RPPGFSPFR, RYLGYL, RGDS, and YGGFMRGL in electrospray ionization mass spectrometry (ESI-MS) experiments. DFT calculations predict a hydrogen bonded salt bridge structure with a protonated guanidinium flanked by two deprotonated phosphates to be the lowest energy structure. Dissociation of DP/peptide adducts reveals that, in general, the relative gas phase acidity of a peptide is dependent on peptide length, with longer peptides being more acidic. In particular, peptides that are six residues or more in length can stabilize the deprotonated C-terminus by extensive hydrogen bonding with the peptide backbone. Dissociation of DP/peptide complexes often yields the deprotonated peptide, allowing for the facile formation of anionic peptides that otherwise would be difficult to generate in high abundance. Although DP has a preference for binding to arginine residues in peptides, DP is also observed to form less abundant complexes with peptides containing multiple lysines. Lys-Xxx-Lys and Lys-Lys sequences form low abundance anionic adducts with DP. For example, KKKK exclusively forms a double adduct with one net negative charge on the complex.     

Complexes of silver(I) with peptides and proteins as produced in electrospray mass spectrometry

Silver(I) forms aqueous phase complexes with both sulfur and nonsulfur containing peptides and proteins. These complexes were introduced into the gas phase via electrospray, and their structures probed by means of tandem mass spectrometry. Experiments with di-, tri-, and oligopeptides show that the abundance of silver(I)-containing ions increases relative to that of proton-containing ions as peptide length increases. This increase is much more dramatic for methionine-containing peptides. Collision-induced dissociation of silver-peptide complexes yields a multitude of product ions that are silver containing. However, even for methioninecontaining peptides, very few of these product ions contain the methionine residue. The solution-phase structure and the gas-phase structure of the silver/peptide complex are not identical. The methionine sulfur acts as the silver anchoring point in solution. Desolvation in the gas phase leads to a rearrangement of the silver/peptide complex such that the silver ion becomes chelated to the nitrogen and oxygen atom on the peptide backbone in addition to the methionine sulfur. This rearrangement decreases the importance of the silver/sulfur bond to the extent that it is frequently broken upon collision activation and leads to the formation of silver/peptide product ions that are nonsulfur bearing.     

Negative ion production from peptides and proteins by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry

Negative ion production from peptides and proteins was investigated by matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry. Although most research on peptide and protein identification with ionization by MALDI has involved the detection of positive ions, for some acidic peptides protonated molecules are not easily formed because the side chains of acidic residues are more likely to lose a proton and form a deprotonated species. After investigating more than 30 peptides and proteins in both positive and negative ion modes, [M–H]⁻ ions were detected in the negative ion mode for all peptides and proteins although the matrix used was 2,5‐dihydroxybenzoic acid (DHB), which is a good proton donor and favors the positive ion mode production of [M+H]⁺ ions. Even for highly basic peptides without an acidic site, such as myosin kinase inhibiting peptide and substance P, good negative ion signals were observed. Conversely, gastrin I (1‐14), a peptide without a highly basic site, will form positive ions. In addition, spectra obtained in the negative ion mode are usually cleaner due to absence of alkali metal adducts. This can be useful during precursor ion isolation for MS/MS studies. Copyright © 2008 John Wiley & Sons, Ltd.     

碱金属离子对甘氨酸五肽气相解离过程的影响

为了获得更多的多肽结构信息,采用结构简单的甘氨酸五肽(简写为GGGGG或G5)作为模型,研究了碱金属离子(Li+、Na+、K+、Rb+)对甘氨酸五肽GGGGG气相解离过程的影响.将一定化学计量比的甘氨酸五肽分别和四种碱金属盐溶液混合后,静置10h,使反应达到平衡.电喷雾质谱结果表明,四种碱金属离子均可以在溶液中与甘氨酸五肽形成非共价复合物,其中主要组分为碱金属离子与G5配合比为1:1和2:1的非共价复合物.质谱碰撞诱导解离(CID)时的碰撞能量为25eV.气相碰撞诱导解离实验结果表明,在配合比为1:1的复合物中,其碎片化程度按照Li+、Na+、K+、Rb+的次序依次减小,Rb+的复合物碎裂过程中生成了不常见的c、z离子;在配合比为2:1的复合物中,其碎片化程度按照Li+、Na+、K+、Rb+的次序依次增大.与1:1的非共价复合物相比,Na+、K+、Rb+的2:1复合物的气相解离显得更加容易.除Li+外,两个碱金属离子对G5的活化能力明显较单个碱金属离子强,它们可以诱导多肽在更多位点断裂,生成更多类型的碎片离子.     

A density functional theory (DFT) study on gas-phase proton transfer reactions of derivatized and underivatized peptide ions generated by matrix-assisted laser desorption ionization

In this study, classic molecular dynamics (MD) simulations followed by density functional theory (DFT) calculations are employed to calculate the proton transfer reaction enthalpy shifts for native and derivatized peptide ions in the MALDI plume. First, absolute protonation and deprotonation enthalpies are calculated for native peptides (RPPGF and AFLDASR), the corresponding hexyl esters and three common matrices α-cyano-4-hydroxycinnamic acid (4HCCA), 2,5-dihydroxybenzoic acid (DHB), and 6 aza-2-thiothymine (ATT). From the proton exchange reaction calculations, protonation and deprotonation of the neutral peptides are thermodynamically favorable in the gas phase as long as the corresponding protonated/deprotonated matrix ions are present in the plume. Moreover, the gain in proton affinity shown by the ester ions suggests that the increase in ion yield is likely to be related to an easier proton transfer from the matrix to the peptide.     

Gas-phase peptide/protein cationizing agent switching via ion/ion reactions

Polypeptide ions comprising different cationizing agents show distinct fragmentation behavior in the gas phase. Thus, it is desirable to be able to form ions with different cationizing agents such as protons and metal ions. Usually, metal-cationized peptide/protein ions are introduced to the mass spectrometer by electrospraying solutions containing a mixture of the peptide/protein of interest and a metal salt. A new technique for generating metal-containing polypeptide ions that involves gas-phase ion/ion reactions is described. In this strategy, solutions of metal-containing ions and solutions of proteins are each electrosprayed into separate ion sources. The approach allows for independent maximization of ion signal and selection of ions prior to gas-phase reactions. Selected ions are stored in a quadrupole ion trap where reactions of ions of opposite polarity form metal-cationized peptides and proteins in the gas phase by cation switching. This approach affords a high degree of flexibility in forming metal-containing peptide and protein ions via the ability to mass-select reactant ions. The ability to form a variety of peptide/protein ions with various cationizing reagents in the gas phase is attractive both for the study of intrinsic interactions of metal ions with polypeptides and for maximizing the structural information available from tandem mass spectrometry of peptides and proteins.     

Stereoselectivity in the collision-activated reactions of gas phase salt complexes

The collision-activated dissociations (CAD) of gas phase salt complexes composed of chiral ions were studied in a quadrupole ion trap mass spectrometer. Because both partners in the salt are chiral, diastereomeric complexes can be formed (e.g., RR, RS). Two general types of complexes were investigated. In the first, the complex was composed of deprotonated binaphthol and a chiral bis-tetraalkylammonium dication. CAD of these complexes leads to the transfer of a proton or an alkyl cation to the binaphtholate leading to a singly-charged tetraalkylammonium cation. During CAD, diastereomeric complexes give significantly different product distributions indicating reasonable stereoselectivity in the process. In the second system, the complexes involved a peptide dianion and a chiral tetraalkylammonium cation. These systems may be viewed as very simple models for the interactions of peptides/proteins with small chiral molecules. Again, stereoselectivity was evident during CAD, but the extent was dependent on the nature of the peptide and not observable in some cases. To better understand the structural features needed to achieve stereoselectivity in gas phase salt complexes, representative transition states were modeled computationally. The results suggest that it is critical for the asymmetry of the nucleophile (i.e., anion) to be well represented in the vicinity of its reactive center.     

Gas phase hydrogen deuterium exchange reactions of a model peptide: FT-ICR and computational analyses of metal induced conformational mutations

We utilized gas phase hydrogen/deuterium (H/D) exchange reactions and ab initio calculations to investigate the complexation between a model peptide (Arg-Gly-AspRGD) with various alkali metal ions. The peptide conformation is drastically altered upon alkali metal ion complexation. The associated conformational changes depend on both the number and type of complexing alkali metal ions. Sodium has a smaller ionic diameter and prefers a multidentate interaction that involves all three amino acids of the peptide. Conversely, potassium and cesium form different types of complexes with the RGD. The [RGD + 2Cs − H]⁺ species exhibit the slowest H/D exchange reactivity (reaction rate constant of 6 × 10⁻¹³ cm³molecule⁻¹s⁻¹ for the fastest exchanging labile hydrogen with ND₃). The reaction rate constant of the protonated RGD is two orders of magnitude faster than that of the [RGD + 2Cs − H]⁺. Addition of the first cesium to the RGD reduces the H/D exchange reaction rate constant (i.e., D₀) by a factor of seven whereas sodium reduces this value by a factor of thirty. Conversely, addition of the second alkali metal ions has the opposite effect; the rate of D₀ disappearance for all [RGD + 2Met − H]⁺ species (MetNa, K, and Cs) decreases with the alkali metal ion size.     

Ca2+‐complex stability of GAPAGPLIVPY peptide in gas and aqueous phase,investigated by affinity capillary electrophoresis and molecular dynamics simulations and compared to mass spectrometric results

Strong, sequence‐specific gas‐phase bindings between proline‐rich peptides and alkaline earth metal ions in nanoESI‐MS experiments were reported by Lehmann et al. (Rapid Commun. Mass Spectrom. 2006, 20, 2404–2410), however its relevance for physiological‐like aqueous phase is uncertain. Therefore, the complexes should also be studied in aqueous solution and the relevance of the MS method for binding studies be evaluated. A mobility shift ACE method was used for determining the binding between the small peptide GAPAGPLIVPY and various metal ions in aqueous solution. The findings were compared to the MS results and further explained using computational methods. While the MS data showed a strong alkaline earth ion binding, the ACE results showed nonsignificant binding. The proposed vacuum state complex also decomposed during a molecular dynamic simulation in aqueous solution. This study shows that the formed stable peptide–metal ion adducts in the gas phase by ESI‐MS does not imply the existence of analogous adducts in the aqueous phase. Comparing peptide–metal ion interaction under the gaseous MS and aqueous ACE conditions showed huge difference in binding behavior.     

Influences of peptide side chains on the metal ion binding site in metal ion-cationized peptides: Participation of aromatic rings in metal chelation

Aromatic side chains on amino acids influence the fragmentations of cationic complexes of doubly charged metal ions and singly deprotonated peptides. The metal ion interacts with an aromatic side chain and binds to adjacent amide nitrogens. When fragmentation occurs, this bonding leads to the formation of abundant metal-containing a-type ions by reactions that occur at the sites of amino acids that contain the aromatic side chain. Furthermore, formation of metal-containing immonium ions of the amino acids that contain the aromatic side chain also are formed. The abundant a-type ions may be useful in interpretation strategies in which it is necessary to locate in a peptide the position of an amino acid that bears an aromatic side chain.     

Effects of acidic peptide size and sequence on trivalent praseodymium adduction and electron transfer dissociation mass spectrometry

Using the lanthanide ion praseodymium, Pr(III), metallated ion formation and electron transfer dissociation (ETD) were studied for 25 biological and model acidic peptides. For chain lengths of seven or more residues, even highly acidic peptides that can be difficult to protonate by electrospray ionization will metallate and undergo abundant ETD fragmentation. Peptides composed of predominantly acidic residues form only the deprotonated ion, [M + Pr ‐ H]²⁺; this ion yields near complete ETD sequence coverage for larger peptides. Peptides with a mixture of acidic and neutral residues generate [M + Pr]³⁺, which cleaves between every residue for many peptides. Acidic peptides that contain at least one residue with a basic side chain also produce the protonated ion, [M + Pr + H]⁴⁺; this ion undergoes the most extensive sequence coverage by ETD. Primarily metallated and non‐metallated c‐ and z‐ions form for all peptides investigated. Metal adducted product ions are only present when at least half of the peptide sequence can be incorporated into the ion; this suggests that the metal ion simultaneously attaches to more than one acidic site. The only site consistently lacking dissociation is at the N‐terminal side of a proline residue. Increasing peptide chain length generates more backbone cleavage for metal‐peptide complexes with the same charge state. For acidic peptides with the same length, increasing the precursor ion charge state from 2+ to 3+ also leads to more cleavage. The results of this study indicate that highly acidic peptides can be sequenced by ETD of complexes formed with Pr(III). Copyright © 2017 John Wiley & Sons, Ltd.     

Covalent and non‐covalent binding in the ion/ion charge inversion of peptide cations with benzene‐disulfonic acid anions

Protonated angiotensin II and protonated leucine enkephalin‐based peptides, which included YGGFL, YGGFLF, YGGFLH, YGGFLK and YGGFLR, were subjected to ion/ion reactions with the doubly deprotonated reagents 4‐formyl‐1,3‐benzenedisulfonic acid (FBDSA) and 1,3‐benzenedisulfonic acid (BDSA). The major product of the ion/ion reaction is a negatively charged complex of the peptide and reagent. Following dehydration of [M + FBDSA‐H]^? via collisional‐induced dissociation (CID), angiotensin II (DRVYIHPF) showed evidence for two product populations, one in which a covalent modification has taken place and one in which an electrostatic modification has occurred (i.e. no covalent bond formation). A series of studies with model systems confirmed that strong non‐covalent binding of the FBDSA reagent can occur with subsequent ion trap CID resulting in dehydration unrelated to the adduct. Ion trap CID of the dehydration product can result in cleavage of amide bonds in competition with loss of the FBDSA adduct. This scenario is most likely for electrostatically bound complexes in which the peptide contains both an arginine residue and one or more carboxyl groups. Otherwise, loss of the reagent species from the complex, either as an anion or as a neutral species, is the dominant process for electrostatically bound complexes. The results reported here shed new light on the nature of non‐covalent interactions in gas phase complexes of peptide ions that can be used in the rationale design of reagent ions for specific ion/ion reaction applications. Copyright © 2012 John Wiley & Sons, Ltd.