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71.
Liu L Michelsen K Kitova EN Schnier PD Klassen JS 《Journal of the American Chemical Society》2010,132(50):17658-17660
The first quantitative comparison of the thermal dissociation rate constants measured for protein-ligand complexes in their hydrated and dehydrated states is described. Rate constants, measured using surface plasmon resonance spectroscopy, are reported for the dissociation of the 1:1 complexes of bovine β-lactoglobulin (Lg) with the fatty acids (FA), palmitic acid (PA), and stearic acid (SA), in aqueous solution at pH 8 and at temperatures ranging from 5 to 45 °C. The rate constants are compared to values determined from time-resolved blackbody infrared radiative dissociation measurements for the gaseous deprotonated (Lg+FA)(n-) ions, where n = 6 and 7, at temperatures ranging from 25 to 66 °C. Notably, the hydrated (Lg+PA) complex is kinetically less stable than the corresponding gas phase (Lg+PA)(n-) ions at all temperatures investigated; the hydrated (Lg+SA) complex is kinetically less stable than the gaseous (Lg+SA)(n-) ions at temperatures <45 °C. The greater kinetic stability of the gaseous (Lg+FA)(n-) ions originates from significantly larger, by 11-12 kcal mol(-1), E(a) values. It is proposed that the differences in the dissociation E(a) values measured in solution and the gas phase reflect the differential hydration of the reactant and the dissociative transition state. 相似文献
72.
Kitova EN El-Hawiet A Schnier PD Klassen JS 《Journal of the American Society for Mass Spectrometry》2012,23(3):431-441
The association-dissociation of noncovalent interactions between protein and ligands, such as other proteins, carbohydrates,
lipids, DNA, or small molecules, are critical events in many biological processes. The discovery and characterization of these
interactions is essential to a complete understanding of biochemical reactions and pathways and to the design of novel therapeutic
agents that may be used to treat a variety of diseases and infections. Over the last 20 y, electrospray ionization mass spectrometry
(ESI-MS) has emerged as a versatile tool for the identification and quantification of protein–ligand interactions in vitro.
Here, we describe the implementation of the direct ESI-MS assay for the determination of protein–ligand binding stoichiometry
and affinity. Additionally, we outline common sources of error encountered with these measurements and various strategies
to overcome them. Finally, we comment on some of the outstanding challenges associated with the implementation of the assay
and highlight new areas where direct ESI-MS measurements are expected to make significant contributions in the future. 相似文献
73.
Jun Li Michele R. Richards Elena N. Kitova John S. Klassen 《Journal of the American Society for Mass Spectrometry》2017,28(10):2054-2065
The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)2+ ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å2 (conformation 1, C1), 708 Å2 (C2), and 737 Å2 (C3). The addition of NH4CH3CO2 produced (2GA + 2Na)2+ and (2GA + H + Na)2+ ions, with Ω similar to those of C1, C2, and C3, as well as (2GA + 2H)2+, (2GA + 2NH4)2+, and (2GA + H + NH4)2+ ions, which adopt a single conformation with a Ω similar to that of C2. These results suggest that the nature of the charging agents, imparted by the ESI process, can influence dimer conformation in the gas phase. Notably, the POPC NDs produced exclusively (2GA + 2NH4)2+ dimer ions; the DMPC NDs produced both (2GA + 2H)2+ and (2GA + 2NH4)2+ dimer ions. While the Ω of (2GA + 2H)2+ is similar to that of C2, the (2GA + 2NH4)2+ ions from NDs adopt a more compact structure, with a Ω of 656 Å2. It is proposed that this compact structure corresponds to the ion conducting single stranded head-to-head helical GA dimer. These findings highlight the potential of NDs, combined with ESI, for transferring transmembrane peptide complexes directly from lipid bilayers to the gas phase. 相似文献
74.
Fentabil MA Daneshfar R Kitova EN Klassen JS 《Journal of the American Society for Mass Spectrometry》2011,22(12):2171-2178
The dissociation pathways, kinetics, and energetics of protonated oligosaccharides in the gas phase were investigated using
blackbody infrared radiative dissociation (BIRD). Time-resolved BIRD measurements were performed on singly protonated ions
of cellohexaose (Cel6), which is composed of β-(1 → 4)-linked glucopyranose rings, and five malto-oligosaccharides (Malx, where x = 4–8), which are composed of α-(1 → 4)-linked glucopyranose units. At the temperatures investigated (85–160 °C),
the oligosaccharides dissociate at the glycosidic linkages or by the loss of a water molecule to produce B- or Y-type ions.
The Y ions dissociate to smaller Y or B ions, while the B ions yield exclusively smaller B ions. The sequential loss of water
molecules from the smallest B ions (B1 and B2) also occurs. Rate constants for dissociation of the protonated oligosaccharides and the corresponding Arrhenius activation
parameters (Ea and A) were determined. The Ea and A-factors measured for protonated Malx (x > 4) are indistinguishable within error (~19 kcal mol−1, 1010 s−1), which is consistent with the ions being in the rapid energy exchange limit. In contrast, the Arrhenius parameters for protonated
Cel6 (24 kcal mol−1, 1012 s−1) are significantly larger. These results indicate that both the energy and entropy changes associated with the glycosidic
bond cleavage are sensitive to the anomeric configuration. Based on the results of this study, it is proposed that formation
of B and Y ions occurs through a common dissociation mechanism, with the position of the proton establishing whether a B or
Y ion is formed upon glycosidic bond cleavage. 相似文献
75.
Martin W. Bredenkamp Cedric W. Holzapfel Renske M. Snyman Wynand J. van Zyl 《合成通讯》2013,43(21):3029-3039
An understanding of the mechanism by which racemization occurs in the Hantzsch reaction preparation of 2-(1-aminoalkyl)thiazoles has enabled the development of a methodology to prevent racemization. N-tBoc-S-dolaphenine (3) is then synthesized using this methodology. 相似文献
76.
Non-Uniform Rational B-Splines (NURBS) are basis functions used in CAD software to describe exact geometric models. The implementation of these basis functions in the context of the Finite Element Analysis (FEA) is known as isogeometric analysis. The concept and definition of NURBS is briefly presented here. Since these functions are implemented as shape functions for the isogeometric analysis, the refinement strategies are discussed. The example of an infinite plate with circular hole serves as a benchmark. Finally, isogeometric analysis is applied to gradient elasticity since NURBS functions are of higher continuity and this is required in gradient elasticity. (© 2010 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim) 相似文献
77.
78.
A comparison for a range of linear equation problems Ax = b between LINSYS, IBMSSP and IMSL is made. 相似文献
79.
Blackbody infrared radiative dissociation (BIRD) and functional group replacement are used to map the location and strength of hydrogen bonds between an antibody single chain fragment (scFv) and its natural trisaccharide receptor, alpha-D-Galp (1-->2)[alpha-D-Abep (1-->3)]alpha-D-Manp1-->OMe (1), in the gaseous, multiply protonated complex. Arrhenius activation parameters (E(a) and A) are reported for the loss of 1 and a series of monodeoxy trisaccharide congeners (5-8 identical with tri) from the (scFv + tri + 10H)(+10) complex. The energetic contribution of the specific oligosaccharide OH groups to the stability of the (scFv + 1 + 10H)(+10) complex is determined from the differences in E(a) measured for the trisaccharide analogues and 1 (55.2 kcal/mol). A decrease of 6 to 11 kcal/mol in E(a), measured for the monodeoxy trisaccharides, indicates that the deleted OH groups interact strongly with the scFv and that they account for a majority of the stabilizing intermolecular interactions. A partial map of the hydrogen bond donor/acceptor groups of 1 and the strength of the interactions is presented for the protonated +10 complex. A comparison of the gas-phase map with the crystal structure indicates that significant structural differences exist. The hydroxyl groups located outside of the binding pocket, and exposed to solvent in solution, participate in new protein-oligosaccharide hydrogen bonds in the gas phase. The decrease in kinetic and energetic stability of the (scFv + 2 + nH)(n)()(+) complex with increasing charge-state is attributed to conformational differences in the binding region induced by electrostatic repulsion. The similarity in the Arrhenius parameters for the +9 and +10 charge states suggests that repulsion effects on the structure of the binding region are negligible below +11. 相似文献
80.