Symmetrical gas-phase dissociation of noncovalent protein complexes via surface collisions

Previous gas-phase dissociation experiments of protein-protein complexes have resulted in product ion distributions that are asymmetric by charge and mass, providing limited insight into the chemical nature of subunit organization and interaction. In these experiments, a symmetric charge distribution results from an "energy sudden" collision of protein-protein complexes with a surface, indicating that it may be possible to probe the suboligomeric structure of noncovalent complexes in the gas phase. It is proposed that energy sudden surface activation of cytochrome C homodimers results in dissociation without significant unfolding of one of the monomeric subunits. Previously proposed mechanisms for the dissociation of protein-protein complexes are discussed in the context of these results. These experiments demonstrate the potential to preserve the structural details of subunit interaction within a protein-protein complex and help elucidate the asymmetric nature of macromolecular dissociation in the gas phase.     

Separation-based approach to study dissociation kinetics of noncovalent DNA-multiple protein complexes

Noncovalent binding of DNA with multiple proteins is pivotal to many regulatory cellular processes. Due to the lack of experimental approaches, the kinetics of assembly and disassembly of DNA-multiple proteins complexes have never been studied. Here, we report on a first method capable of measuring disassembly kinetics of such complexes. The method is based on continuous spatial separation of different complexes. The kinetics of multiple complex dissociation processes are also spatially separated, which in turn facilitates finding their rate constants. Our separation-based approach was compared with a conventional no-separation approach by using computer simulation of dissociation kinetics. It proved to be much more accurate than the no-separation approach and to be a powerful tool for testing hypothetical mechanisms of the disassembly of DNA-multiple proteins complexes. An experimental implementation of the separation-based approach was finally demonstrated by using capillary electrophoresis as a separation method. The interaction between an 80 nucleotide long single-stranded DNA and single-stranded DNA binding protein was studied. DNA-protein complexes with one and two proteins were observed, and rate constants of their dissociation were determined. We foresee that a separation approach will be also developed to study the kinetics of the formation of DNA-multiple protein complexes.     

Effects of size of noncovalent complexes on their stability during collision-induced dissociation

The size-dependent stability of noncovalent complexes under collision-induced dissociation (CID) conditions was studied on a quadrupole ion trap mass spectrometer. Complexes of heme, tetraphenylporphyrin iron(III) (TPP-Fe), and tetraphenylporphyrin manganese(III) (TPP-Mn) with several histidine-containing peptides and model compounds were formed by electrospray ionization (ESI) and their stability was probed by variable-energy CID. It was found that the stability of complexes with the same (or nearly the same) binding energy has a linear dependence on the complex size (or total number of degrees of freedom). This approach will allow comparisons of variable-energy CID data for noncovalent complexes with different binding energies and could be used to help in structural elucidation of some complexes formed by multidentate ligands. The linearity of size effects on the stability of the complexes was also tested in three crown ether/protonated primary amine systems.     

Quantitative classification of covalent and noncovalent H-bonds

The covalent nature of interactions within various hydrogen bonded molecular aggregates has been characterized by the two entirely different computational methods: Bader analysis of the electron density and variation-perturbation partitioning of the intermolecular interaction energy. Analysis of 34 complexes representing different types of hydrogen bonds indicates that the proton-acceptor distance approximately 1.8 A and the ratio of delocalization and electrostatic terms approximately 0.45 constitutes approximately a borderline between covalent and noncovalent hydrogen bonds. The latter ratio could be used to characterize quantitatively the degree of the covalent nature of transition state interactions with active site residues, a quantity essential for an enzyme catalytic activity.     

Agreement between experiment and hybrid DFT calculations for O--H bond dissociation enthalpies in manganese complexes

Information on the accuracy of DFT functionals for redox reactions in transition metal systems is rather limited. To analyze the performance of some popular functionals for redox reactions in manganese systems, calculated O--H bond dissociation enthalpies for Mn-ligands in six different complexes are compared to experimental results. In this benchmark, B3LYP performs well with a mean absolute error of 3.0 kcal/mol. B98 gives similar results to B3LYP (error of 3.8 kcal/mol). B3LYP* gives lower O--H bond strengths than B3LYP and has a mean error of 5.0 kcal/mol. Compared to B98 and B3LYP, B3LYP* has an error trend for the manganese ligands that is more similar to the error for a free water molecule. The nonhybrid functional BLYP consistently and significantly underestimates the O--H bond strengths by approximately 20 kcal/mol. HCTH407 has a rather large mean error of 9.4 kcal/mol and shows no consistent trend. The results support the use of hybrid functionals and the present computational method for large model systems containing manganese. An example is the oxygen evolving complex in photosystem II where hybrid functionals predict the appearance of a Mn(IV)-oxyl radical before the O--O bond formation step.     

The use of heated capillary dissociation and collision-induced dissociation to determine the strength of noncovalent bonding interactions in gas-phase peptide-cyclodextrin complexes

Complexes of four peptides and permethylated-β-cyclodextrin are produced in the gas phase by using electrospray ionization. The four peptides—bradykinin (BK), des-Arg-1 bradykinin (dR¹BK), des-Arg-9-bradykinin (dR⁹BK), and Gly-5-Gly-8-bradykinin (G⁵G⁸BK)—were chosen because the relative inclusion and protonation sites varied with each peptide. Collision-induced dissociation (CID) was performed to determine the dissociation threshold of the four complexes. Heated capillary dissociation (HCD) was used to determine the dissociation temperatures of the peptide complexes. CID and HCD indicate the same ordering of stability in the complexation of the peptides to the oligosaccharides. Increasing strength of interaction follows the order dR⁹BK < BK < dR¹BK ≈ G⁵G⁸BK. The absence of Arg-9 destabilizes the complex, whereas the absence of Arg-1 stabilizes it relative to BK. Replacing both Phe residues with Gly similarly strengthens the interaction, suggesting that the Phe destabilizes the complex. CID and HCD are useful methods for obtaining relative strengths of interaction in noncovalent bound complexes.     

Computational study of noncovalent complexes between formamide and formic acid

The geometries and binding energies of 1:1, 1:2, and 1:4 formic acid-formamide complexes (FA-FMA) are calculated by quantum chemical procedures. Vibrational spectra and intermolecular distances of the most stable FA-FMA dimers as well as the influence of the basis set superposition error (BSSE) on the geometries and energies of the dimers are also discussed. All FA-FMA dimers are optimized at the B3LYP/cc-pVTZ, the MP2/cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ levels of theory to study the influence of the level of theory on the calculated geometries and energies. CCSD(T)/cc-pVTZ single-point calculations at the MP2/aug-cc-pVTZ-optimized geometries were performed as reference for estimating the quality of lower level calculations. These calculations allow us to qualitatively describe the competition between different types of hydrogen-bonding interactions in FA-FMA complexes. FA-FMA dimers are compared to other formamide complexes and to the FA-FMA crystal structure.     

First examples of a covalent bond between gold and selenophene

1. Download : Download high-res image (45KB)
2. Download : Download full-size image

     

Relationship between bond dissociation energies and activation energies for bond scission reactions

Bond dissociation energies are frequently derived from values of the high pressure activation energy for bond scission reactions. The value derived depends on the transition state structure chosen for the reaction. We consider several models of the transition state and show that the variation in derived BDE values can be quite substantial, 3 to 6 kcal/mol at the high temperatures of pyrolysis kinetics. Application of the restricted Gorin model of the transition state results in BDE values in good agreement with current thermochemistry, while the other models tested result in lower to much lower values. © 1994 John Wiley & Sons, Inc.     

Evaluation of noncovalent interactions between peptides and polyether compounds via energy-variable collisionally activated dissociation

Energy-variable collisionally activated dissociation (CAD) was used to analyze noncovalent interactions of protonated peptide/polyether complexes in a quadrupole ion trap complexes were formed with a series of four polyether host molecules and thirteen peptide molecules. Comparison of dissociation thresholds revealed correlations between the gas-phase basicities of the peptides and polyether molecules and the onset of dissociation. The dissociation thresholds of complexes containing the tripeptides or pentapeptides were inversely proportional to the gas-phase basicities of the sites of protonation of the peptides. Intramolecular hydrogen bonding of the pentapeptides affected the observed dissociation thresholds as well. The dissociation thresholds also scaled proportionally to the gas-phase basicities of the polyethers in the complexes, and the importance of the conformational flexibility of the polyether ligand was confirmed for one of the histidine-containing tripeptide complexes.     

Adiabatic and nonadiabatic bond cleavages in Norrish type I reaction

One of the fundamental photoreactions for ketones is Norrish type I reaction, which has been extensively studied both experimentally and theoretically. Its α bond-cleavage mechanisms are usually explained in an adiabatic picture based on the involved excited-state potential energy surfaces, but scarcely investigated in terms of a nonadiabatic picture. In this work, the S(1) α bond-cleavage reactions of CH(3)OC(O)Cl have been investigated by using the CASSCF and MRCI-SD calculations, and the ab initio based time-dependent quantum wavepacket simulation. The numerical results indicate that the photoinduced dissociation dynamics of CH(3)OC(O)Cl could exhibit strong nonadiabatic bond-fission characteristics for the S(1) α C-Cl bond cleavage, while the dynamics of the S(1) α C-O bond cleavage is mainly of adiabatic characteristics. This nonadiabatic mechanism for Norrish type I reaction of CH(3)OC(O)Cl is uncovered for the first time. The quantum wavepacket dynamics, based on the reduced-dimensional coupled potential energy surfaces, to some extent illustrates the significance of the nonadiabatic effect in the transition-state region on the dynamics of Norrish type I reaction.     

Hydride donor abilities and bond dissociation free energies of transition metal formyl complexes

The hydride complex [Pt(dmpe)2H]+ (dmpe = 1,2-bis(dimethylphosphino)ethane) reversibly transfers H- to the rhenium carbonyl complex [CpRe(PMe3)(NO)(CO)]+, giving the formyl CpRe(PMe3)(NO)(CHO). From the equilibrium constant for the hydride transfer (16.2), the DeltaGdegrees for the reaction was determined (-1.6 kcal/mol), as was the hydride-donating ability of the formyl (44.1 kcal/mol). The hydride-donating ability, DeltaGdegrees(H-), is defined as the energy required to release the hydride ion into solution by the formyl complex [i.e. M(CHO) right arrow M(CO)+ + H-]. Subsequently, the hydride-donating ability of a series of formyl complexes was determined, ranging from 44 to 55 kcal/mol. With use of this information, two rhenium carbonyl complexes, [CpRe(NO)(CO)2]+ and [Cp*Re(NO)(CO)2]+, were hydrogenated to formyls, employing [Pt(dmpp)2]2+ and Proton-Sponge. Finally, the E(1/2)(I/0) values for five rhenium carbonyl complexes were measured by cyclic voltammetry. Combined with the known DeltaGdegrees(H-) values for the complexes, the hydrogen atom donating abilities could be determined. These values were all found to be approximately 50 kcal/mol.     

Backbone and side-chain cleavages in electron detachment dissociation (EDD)

Ab-initio electronic structure methods are used to explore potential energy profiles pertinent to the fragmentations of gas-phase radicals thought to be formed in the new negative-ion mode EDD mass spectroscopic studies of peptides. Barriers to fragmentation as well as the associated overall energy differences are computed for the observed Calpha-C backbone bond cleavage as well as for side-chain loss for a variety of side chains (valine, arginine, glutamic acid, and tyrosine). It is found that Calpha-C bond cleavage is favored over side-chain loss, although loss of a tyrosine side chain may compete with Calpha-C cleavage because the tyrosine radical formed can delocalize its unpaired electron over its aromatic ring. In addition, it is found that fragmentation of the nitrogen-centered radicals formed in EDD results in cleavage to produce so-called a*/x fragments rather than a/x* fragments both because producing the former involves a significantly smaller barrier and is nearly thermoneutral, while cleavage to yield a/x* is significantly endothermic.     

Energy-resolved in-source collisionally induced dissociation for the evaluation of the relative stability of noncovalent complexes in the gas phase

Energy-resolved in-source collisionally induced dissociation (CID) studies on the complexation of alkali metal cations by some crown ethers, nucleic acid bases, and amino acids have been performed. It has been shown that the cone voltage corresponding to the maximum ion abundance (V(c,Imax)) of the breakdown curve is characteristic of a given ion and not influenced by the cone desolvation process or the composition of the solution. Very good agreement of the V(c,Imax) value with the bond strength of the ion has been observed. Determination of the V(c,Imax) values for different ionic species is a useful, simple, and inexpensive way to obtain their relative stabilities in in-source CID conditions.     

Flexible square supramolecular rings with hydrogen-bonded bushing in solid-state oxalurate complexes: versatility of the oxalurate ligand in covalent and noncovalent binding

Isotypic pseudooctahedral complexes of Co, Ni, and Cu with two chelating oxalurate ligands and two water molecules, trans-[M(oxalurate)(2)(H(2)O)(2)], have been synthesized and isolated by a novel progressive crystallization technique. Diffraction analyses reveal that the three complexes form isotypic solid-state structures in which the molecular connectivity and complex network of noncovalent interactions are qualitatively identical throughout the series. The oxalurate groups form unbounded chains through two different self-recognition patterns-a typical DA-AD motif and an unusual DDA'-A'DD form (D = hydrogen bond donor, A' = double acceptor). The unsymmetrical oxalurate group possesses the topological properties necessary to form aggregates of higher symmetry, and the "M(oxalurate)(2)" fragments form a rhombic 2-D motif with hydrogen-bonded corners and with hydrogen-bond acceptors directed to the inside of the cyclic aggregate. The 2-D net is stacked to form a channeled 3-D structure, in which the coordinated aqua ligands form the principal interlayer interactions. The slanted channels are occupied by the axial waters and by waters of crystallization, which are hydrogen bonded to the channel walls to form an ordered bushing. The extensive 3-D hydrogen-bonded superstructure is flexible enough to accommodate the distortion produced by the Jahn-Teller effect in the copper compound without requiring a qualitative structural change. The bonds affected by Jahn-Teller distortion in the Cu complex [Cu-O = 2.3788(15) A] are significantly longer than their analogues in the Co and Ni complexes [Co-O = 2.175(2), Ni-O = 2.094(9) A].     

Characterization of specific noncovalent complexes between guanidinium derivatives and single-stranded DNA by MALDI

Noncovalently bound complexes between highly basic sites of 12 guanidinium compounds and single-stranded DNA were studied using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. 6-Aza-2-thiothymine (ATT) was used as the matrix in the presence of ammonium citrate, and spectra were recorded in the positive ion mode. Detailed control experiments confirmed unambiguously the high selectivity and specificity of the guanidinium moiety for phosphate groups of DNA. The results verify the binding stoichiometry and show preferential binding of hydrophobic binders (pyrene and anthracene guanidinium derivatives) to all sequences examined. In addition, we demonstrate that electrostatic noncovalent interactions are strengthened with phosphorothioate analogs of DNA. These results clearly highlight the structure-directing role of the self-assembling organic species and strongly emphasize the significance of concentration, hydrophobicity, hydrogen-bonding, and pi-pi interactions of the artificial receptor in the formation of these noncovalent complexes. Because of the ability of DNA-binding compounds to influence gene expression, and therefore cell proliferation and differentiation, the interactions described above could be important in providing a better understanding of the mechanism of action of these noncovalent genetic regulators.     

Localization of noncovalent complexes in MALDI-preparations by CLSM

The unambiguous detection of noncovalent complexes (NCCs) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is still a far cry from being routine. For protein NCCs such as their quaternary structure it has been reported that signals of the intact complex are only obtained for the first or at most the first few laser exposures of a given sample area. This observation was called the first-shot phenomenon. In the present study, this first-shot phenomenon has been investigated for the hexameric protein complex allophycocyanine (APC) by two independent methods, MALDI-MS with a (nearly) pH-neutral matrix 6-aza-2-thiothymine (6-ATT) and by imaging the fluorescence of the complex in APC-6-ATT preparations by confocal laser scan microscopy (CLSM). The intact APC heterohexamer loses its visible fluorescence upon dissociation into its subunits. Both methods consistently show that intact APC complexes are precipitated at the matrix crystal surface, but dissociate upon incorporation into the matrix crystals.     

Electron capture dissociation of complexes of diacylglycerophosphocholine and divalent metal ions: Competition between charge reduction and radical induced phospholipid fragmentation

Divalent metal complexes of phosphocholines, [Metal(II)(L)(n)](2+) (where Metal=Cu(2+), Co(2+), Mg(2+), and Ca(2+), L=1,2-dihexanoyl-sn-glycero-3-phosphocholine [6:0/6:0GPCho] and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine [16:0/18:1GPCho] and n=2-5), were formed upon electrospray ionization mass spectrometry (ESI/MS) of 8 mM solution of phosphocholine (L) with 4 mM metal salt (Metal). The electron capture dissociation (ECD) reactions of these [Metal(II)(L)(n)](2+) complexes were examined via Fourier-transform ion-cyclotron resonance mass spectrometry. A rich and complex chemistry was observed, including charge reduction and fragmentation involving losses of a methyl radical, trimethylamine, and the acyl chains. The predominant reaction channel was dependent on the size (n) of the complex, the metal and ligand used, and the size of the acyl chain. Thus charge reduction dominates the ECD spectra of the larger phosphocholine, 16:0/18:1GPCho, but is largely absent in the smaller 6:0/6:0GPCho. For complexes of 16:0/18:1GPCho, n=4-5, fragmentation from the head group mainly occurs via loss of the methyl radical and trimethylamine. At n=3, the relative abundance of fragments due to loss of acyl chain radicals increases. The abundances of ions arising from these radical losses increase further for the n=2 complexes, thereby providing information on the composition and position of the 16:0 and 18:1 acyl groups. Thus ECD of metal complexes provides structurally useful information on the phosphocholine, including the nature of the head group, the acyl chains, and the positions of the acyl chains.