Tianfang Wang

A Negative Ion Mass Spectrometry Approach to Identify Cross-Linked Peptides Utilizing Characteristic Disulfide Fragmentations

Chemical cross-linking combined with mass spectrometry (MS) is an analytical tool used to elucidate the topologies of proteins and protein complexes. However, identification of the low abundance cross-linked peptides and modification sites amongst a large quantity of proteolytic fragments remains challenging. In this work, we present a strategy to identify cross-linked peptides by negative ion MS for the first time. This approach is based around the facile cleavages of disulfide bonds in the negative mode, and allows identification of cross-linked products based on their characteristic fragmentations. MS3 analysis of the cross-linked peptides allows for their sequencing and identification, with residue specific location of cross-linking sites. We demonstrate the applicability of the commercially available cystine based cross-linking reagent dithiobis(succinimidyl) propionate (DSP) and identify cross-linked peptides from ubiquitin. In each instance, the characteristic fragmentation behavior of the cross-linked species is described. The data presented here indicate that this negative ion approach may be a useful tool to characterize the structures of proteins and protein complexes, and provides the basis for the development of high throughput negative ion MS chemical cross-linking strategies.

Negative ion fragmentations of deprotonated peptides. The unusual case of isoAsp: a joint experimental and theoretical study. Comparison with positive ion cleavages

The following peptides have been examined in this study: GLDFG(OH), caeridin 1.1 [GLLDGLLGLGGL(NH(2))], 11 Ala citropin 1.1 [GLFDVIKKVAAVIGGL(NH(2))], Crinia angiotensin [APGDRIYVHPF(OH)] and their isoAsp isomers. It is not possible to differentiate between Asp- and isoAsp-containing peptides (used in this study) using negative ion electrospray mass spectrometry. This is because the isoAsp residue cleaves to give the same fragment anions as those formed by delta and gamma backbone cleavage of Asp. The isoAsp fragmentations are as follows: RNHCH(CO(2)H)(-)CHCONHR --> [RNH(-)(HO(2)CCH=CHCONHR)] --> RNH(-)+HO(2)CCH=CHCONHR and RNHCH(CO(2)H)(-)CHCONHR --> [RNH(-)(HO(2)CCH=CHCONHR] --> (-)O(2)CCH=CHCONHR+RNH(2). Calculations at the HF/6-31+G(d)//AM1 level of theory indicate that the first of these isoAsp cleavage processes is endothermic (by +115 kJ mol(-1)), while the second is exothermic (-85 kJ mol(-1)). The barrier to the highest transition state is 42 kJ mol(-1). No diagnostic cleavage cations were observed in the electrospray mass spectra of the MH(+) ion of the Asp- and isoAsp-containing peptides (used in this study) to allow differentiation between these two amino acid residues.

Negative ion fragmentations of deprotonated peptides containing post-translational modifications. An unusual cyclisation/rearrangement involving phosphotyrosine; a joint experimental and theoretical study.

The characteristic fragmentations of a pTyr group in the negative ion electrospray mass spectrum of the [M-H](-) anion of a peptide or protein involve the formation of PO(3) (-) (m/z 79) and the corresponding [(M-H)(-)-HPO(3)](-) species. In some tetrapeptides where pTyr is the third residue, these characteristic anion fragmentations are accompanied by ions corresponding to H(2)PO(4) (-) and [(M-H)(-)-H(3)PO(4)](-) (these are fragmentations normally indicating the presence of pSer or pThr). These product ions are formed by rearrangement processes which involve initial nucleophilic attack of a C-terminal -CO(2) (-) [or -C(==NH)O(-)] group at the phosphorus of the Tyr side chain [an S(N)2(P) reaction]. The rearrangement reactions have been studied by ab initio calculations at the HF/6-31+G(d)//AM1 level of theory. The study suggests the possibility of two processes following the initial S(N)2(P) reaction. In the rearrangement (involving a C-terminal carboxylate anion) with the lower energy reaction profile, the formation of the H(2)PO(4) (-) and [(M-H)(-)-H(3)PO(4)](-) anions is endothermic by 180 and 318 kJ mol(-1), respectively, with a maximum barrier (to a transition state) of 229 kJ mol(-1). The energy required to form H(2)PO(4) (-) by this rearrangement process is (i) more than that necessary to effect the characteristic formation of PO(3) (-) from pTyr, but (ii) comparable with that required to effect the characteristic alpha, beta and gamma backbone cleavages of peptide negative ions.

Radical routes to interstellar glycolaldehyde. The possibility of stereoselectivity in gas-phase polymerization reactions involving CH2O and ˙CH2OH

A previous report that the interstellar molecule glycolaldehyde (HOCH(2)CHO) can be made from hydroxymethylene (HOCH:) and formaldehyde has been revisited at the CCSD(T)/6-311++G(3df,2p)//MP2/6-311++G(3df,2p) level of theory. This reaction competes with the formation of acetic acid and methylformate, molecules which have also been detected in interstellar clouds. Other possible modes of formation of glycolaldehyde by radical/radical reactions have been shown to be viable theoretically as follows: HO˙+˙CH2CHO -->HOCH2CHO [ΔG(Γ)(298K)=-303kJ mol⁻¹] HOCH2˙+˙CHO-->HOCH2CHO (-259kJ mol⁻¹). The species in these two processes are known interstellar molecules. Key radicals ˙CH(2)CHO and ˙CH(2)OH in these sequences have been shown to be stable for the microsecond duration of neutralization/reionization experiments in the dual collision cells of a VG ZAB 2HF mass spectrometer. The polymerization reaction HOCH(2)CH˙OH + nCH(2)O → HOCH(2)[CH(OH)](n)˙CHOH (n = 1 to 3) has been studied theoretically and shown to be energetically feasible, as is the cyclization reaction of HOCH(2)[(CH(2)OH)(4)]˙CHOH (in the presence of one molecule of water at the reacting centre) to form glucose. The probability of such a reaction sequence is small even if polymerization were to occur in interstellar ice containing a significant concentration of CH(2)O. The large number of stereoisomers produced by such a reaction sequence makes the formation of a particular sugar, again for example glucose, an inefficient synthesis. The possibility of stereoselectivity occurring during the polymerization was investigated for two diastereoisomers of HOCH(2)[(CHOH)](2)˙CHOH. No significant difference was found in the transition state energies for addition of CH(2)O to these two diastereoisomers, but a barrier difference of 12 kJ mol(-1) was found for the H transfer reactions ˙OCH(2)[(CHOH)](2)CH(2)OH → HOCH(2)[(CHOH)(2)˙CHOH of the two diastereoisomers.

Negative ion fragmentations of deprotonated peptides containing post-translational modifications: diphosphorylated systems containing Ser, Thr and Tyr. A characteristic phosphate/phosphate cyclisation. A joint experimental and theoretical study.

[M-H](-) anions from small diphosphopeptides (phosphate groups on Ser, Thr or Tyr) show characteristic peaks corresponding to m/z 177 (H(3)P(2)O(7) (-)), 159 (HP(2)O(6) (-)) and sometimes [(M-H)(-)-H(4)P(2)O(7)](-). M/z 177 and m/z 159 are major peaks in the spectra of small peptides with 1,2, 1,3, 1,4, 1,5 and 1,6 diphosphate substitution, which means that the decomposing [M-H](-) anions must have flexible structures in order for the two phosphate groups to interact with each other. Peptides where the two phosphate groups are more than six amino acid residues apart have not been studied. Theoretical calculations indicate that m/z 177 is formed in a strongly exothermic reaction involving facile nucleophilic interaction between the two phosphate groups: m/z 159 is formed by loss of water from energised m/z 177.

Backbone fragmentations of [M–H]– anions from peptides. Reinvestigation of the mechanism of the beta prime cleavage

RATIONALEnAn experimental study has shown that the structure of a β ion proposed earlier is incorrect. Backbone cleavage β anions have structures R(NH(-)) from systems [[RNHCH(X)CONHCH(Y)CO(2)H (or C-terminal CONH(2))-H](-) (where R is the rest of the peptide molecule and X and Y represent the α side chains of the individual amino acid residues).nnnMETHODSnAb initio calculations were carried out at the CAM-B3LYP/6-311++g(d,p) level of theory.nnnCONCLUSIONSnThe calculations suggest that RNH(-) ions are formed by S(N)i cyclisation processes involving either (i) the C-terminal CO(2)(-) or C-terminal [CONH](-) as appropriate, or (ii) an enolate ion [-NHC(-)(Y)-] cyclising at the backbone CH of the -CH(X)- group. Concomitant C-N bond cleavage then liberates an RNH(-) ion, processes which can occur along the peptide backbone.

Can collision-induced negative-ion fragmentations of [M-H]- anions be used to identify phosphorylation sites in peptides?

A joint experimental and theoretical investigation of the fragmentation behaviour of energised [M-H](-) anions from selected phosphorylated peptides has confirmed some of the most complex rearrangement processes yet to be reported for peptide negative ions. In particular: pSer and pThr (like pTyr) may transfer phosphate groups to C-terminal carboxyl anions and to the carboxyl anion side chains of Asp and Glu, and characteristic nucleophilic/cleavage reactions accompany or follow these rearrangements. pTyr may transfer phosphate to the side chains of Ser and Thr. The reverse reaction, namely transfer of a phosphate group from pSer or pThr to Tyr, is energetically unfavourable in comparison. pSer can transfer phosphate to a non-phosphorylated Ser. The non-rearranged [M-H](-) species yields more abundant product anions than its rearranged counterpart. If a peptide containing any or all of Ser, Thr and Tyr is not completely phosphorylated, negative-ion cleavages can determine the number of phosphated residues, and normally the positions of Ser, Thr and Tyr, but not which specific residues are phosphorylated. This is in accord with comments made earlier by Lehmann and coworkers.

The gas phase Smiles rearrangement of anions PhO(CH2)nO− (n = 2–4). A joint theoretical and experimental approach

A combination of experimental data [using (18)O labelling fragmentation data together with metastable ion studies in a reverse sector mass spectrometer (from a previous study)] and ab initio reaction coordinate studies at the CCSD(T)/6-31++G(d,p)//B3LYP/6-31++G(d,p) level of theory, have provided the following data concerning the formation of PhO(-) in the gas-phase from energized systems PhO(CH(2))(n)O(-) (n = 2-4). All DeltaG values were calculated at 298 K. (1) PhO(CH(2))(2)O(-) effects an ipso Smiles rearrangement (DeltaG(r) = +35 kJ mol(-1); barrier to transition state DeltaG(#) = +40 kJ mol(-1)) equilibrating the two oxygen atoms. The Smiles intermediate reverts to PhO(CH(2))(2)O(-) which then undergoes an S(N)i reaction to form PhO(-) and ethylene oxide (DeltaG(r) = -24 kJ mol(-1); DeltaG(#) = +54 kJ mol(-1)). (2) The formation of PhO(-) from energized PhO(CH(2))(3)O(-) is more complex. Some 85% of the PhO(-) formed originates via a Smiles intermediate (DeltaG(r) = +52 kJ mol(-1); DeltaG(#) = +61 kJ mol(-1)). This species reconverts to PhO(CH(2))(3)O(-) which then fragments to PhO(-) by two competing processes, namely, (a) an S(N)i process yielding PhO(-) and trimethylene oxide (DeltaG(r) = -27 kJ mol(-1); DeltaG(#) = +69 kJ mol(-1)), and (b) a dissociation process giving PhO(-), ethylene and formaldehyde (DeltaG(r) = -65 kJ mol(-1); DeltaG(#) = +69 kJ mol(-1)). The other fifteen percent of PhO(-) is formed prior to formation of the Smiles intermediate, occurring directly by the S(N)i and dissociation processes outlined above. The operation of two fragmentation pathways is supported by the presence of a composite metastable ion peak. (3) Energized PhO(CH(2))(4)O(-) fragments exclusively by an S(N)i process to form PhO(-) and tetrahydrofuran (DeltaG(r) = -101 kJ mol(-1); DeltaG(#) = +53 kJ mol(-1)). The Smiles ipso cyclization (DeltaG(r) = +64 kJ mol(-1); DeltaG(#) = +74 kJ mol(-1)) is not detected in this system.

A theoretical study of the rearrangement processes of energized CCCB and CCCAl

The rearrangement reactions of energized CCCB and CCCAl have been studied by means of quantum mechanical electronic structure calculations. Potential barriers were determined at UCCSD(T)/aug-cc-pVTZ with optimized molecular geometries and harmonic vibrational frequencies determined at the UB3LYP/6-311 + G(3df) level. Two planar fully cyclized isomers are key intermediates in both systems. One of these is the rhombic structure, (analogous to rhombic C4) which is called the kite isomer. The other fully cyclized structure is called the fan structure. The quartets of CCCB and CCBC are the ground states of these structures [by 49.8 and 7.9 kJ mol(-1) (E values), respectively], whereas the ground state of kite C3B is the doublet (by 131.8 kJ mol(-1)). The rearrangement of doublet CCCB is more energetically favourable than that of the quartet, with a maximum barrier of +68.6 kJ mol(-1) together with the formation of fan C3B (-60.7 kJ mol(-1)), and then CCBC (+40.6 kJ mol(-1)). Quartet CCCB rearranges through fan C3B (+31.4 kJ mol(-1)) to give CCBC (+82.8 kJ mol(-1)) over a maximum barrier of +184.9 kJ mol(-1). The C3Al system is different from C3B in a number of ways. Doublet CCCAl is the ground state (by 116.3 kJ mol(-1)) and rearrangement to fan C3Al requires only 21.8 kJ mol(-1) of excess energy. Fan C3Al (+18.8 kJ mol(-1)) then converts to the kite isomer (-12.1 kJ mol(-1)) over a barrier of 50.2 kJ mol(-1). Conversion to CCAlC is energetically unfavourable requiring some 371 kJ mol(-1) of excess energy [at the UCCSD(T)/aug-cc-pVTZ//UB3LYP/6-311 + G(3df) level of theory]. Rearrangement of quartet CCCAl is more complex, but again, the cyclic kite and fan forms are in equilibrium and ring opening to CCAIC is unfavourable.

Study of the Isomers of Isoelectronic C4, (C3B)−, and (C3N)+: Rearrangements through Cyclic Isomers

Optimized structures of the isoelectronic cumulenes (CCCB)(-), CCCC, and (CCCN)(+) and of their isomers formed by rearrangement have been calculated at the B3LYP/6-311+ G(3df) level of theory with relative energies and electronic states determined at the CCSD(T)/aug-cc-pVTZ level of theory. The ground states of CCCC and (CCCN)(+) are triplets, whereas the ground state of (CCCB)(-) is a quasi-linear singlet structure that is only 0.6 kcal mol(-1) more negative in energy than the linear triplet. When energized, both triplet and singlet CCCC cyclize to planar rhomboids, of which the singlet is the lowest-energy configuration. Ring-opening of rhomboid C(4) reforms CCCC with the carbons partially randomized. Similar rearrangements occur for (CCCB)(-) and (CCCN)(+), but the reactions are different in the detail. In the case of (CCCN)(+), rearrangement of atoms is supported both experimentally and theoretically. Because (CCCB)(-) and (CCCN)(+) are not symmetrical, two fully cyclized forms are possible; the one more resembling a rhomboid structure is called a kite structure, and the other is called a fan structure. The rearrangement of (CCCB)(-) is more favored via the triplet with equilibrating kite and fan structures being formed, whereas the singlet (CCCN)(+) ring closes to give the singlet kite structure, which may ring open to give a mixture of (CCCN)(+) and (CCNC)(+). Intersystem crossing may occur for the triplet and singlet forms of CCCC and (CCCB)(-) but not for (CCCN)(+).