A study of peptide—Peptide interactions using MALDI ion mobility o-TOF and ESI mass spectrometry

Matrix-assisted laser desorption ionization ion mobility coupled to orthogonal time-of-flight mass spectrometry (MALDI-IM-oTOF MS) is evaluated as a tool for studying non-covalent complex (NCX) formation between peptides. The NCX formed between dynorphin 1-7 and Mini Gastrin I is used as a model system for comparison to previous MALDI experiments (Woods, A. S.; Huestis, M. A. J. Am. Soc. Mass Spectrom. 2001, 12, 88-96). The dynorphin 1-7/Mini Gastrin I complex is stable after more than a ms drift time through the He filled mobility cell. Furthermore, the effects of solution pH on NCX ion signal intensity is measured both by MALDI-IM-MS analysis and by nanoelectrospray mass spectrometry. When compared to the previous MALDI study this work shows that all three techniques give similar results. In addition, fragmentation can be observed from of the non-covalent complex parent ion that occurs prior to TOF mass analysis but after mobility separation, thus providing NCX composition information.     

Quantifying the role of water in protein-carbohydrate interactions

Water-mediated interactions play a key role in carbohydrate-lectin binding, where the interactions involve a conserved water that is separated from the bulk solvent and present a bridge between the side chains of the protein and the carbohydrate ligand. To apply quantum mechanical methods to examine the role of conserved waters, we present an analysis in which the relevant carbohydrate atoms are modeled by methanol, and in which the protein is replaced by a limited number of amino acid side chains. Clusters containing a conserved water and a representative amino acid fragment were also examined to determine the influence of amino acid side chains on interaction energies. To quantify the differential binding energies of methanol versus water, quantum mechanical calculations were performed at the B3LYP/6-311++G(3df,3pd)//B3LYP/6-31+G(d) level in which either a methanol molecule was bound to the conserved water (liganded state) or in which a water molecule replaces the methanol (unliganded state). Not surprisingly, the binding of a water to clusters containing charged amino acid side chains was more favorable by 1.55 to 7.23 kcal/mol than that for the binding of a water to the corresponding pure water clusters. In contrast, the binding energy of water to clusters containing polar-uncharged amino acid side chains ranged from 4.35 kcal/mol less favorable to 4.72 kcal/mol more favorable than for binding to the analogous pure water clusters. The overall trend for the binding of methanol versus water, in any of the clusters, favored methanol by an average value of 1.05 kcal/mol. To extend these studies to a complex between a protein (Concanavalin A) and its carbohydrate ligand, a cluster was examined that contained the side chains of three key amino acids, namely asparagine, aspartate, and arginine, as well as a key water molecule, arranged as in the X-ray diffraction structure of Con A. Again, using methanol as a model for the endogenous carbohydrate ligand, energies of -5.94 kcal/mol and -5.70 kcal/mol were obtained for the binding of methanol and water, respectively, to the Con A-water cluster. The extent to which cooperativity enhanced the binding energies has been quantified in terms of nonadditive three-body contributions. In general, the binding of water or methanol to neutral dimers formed cooperative clusters; in contrast, the cooperativity in charged clusters depended on the overall geometry as well as the charge.     

Macrocyclic β-sheet peptides that inhibit the aggregation of a tau-protein-derived hexapeptide

This paper describes studies of a series of macrocyclic β-sheet peptides 1 that inhibit the aggregation of a tau-protein-derived peptide. The macrocyclic β-sheet peptides comprise a pentapeptide "upper" strand, two δ-linked ornithine turn units, and a "lower" strand comprising two additional residues and the β-sheet peptidomimetic template "Hao". The tau-derived peptide Ac-VQIVYK-NH(2) (AcPHF6) aggregates in solution through β-sheet interactions to form straight and twisted filaments similar to those formed by tau protein in Alzheimer's neurofibrillary tangles. Macrocycles 1 containing the pentapeptide VQIVY in the "upper" strand delay and suppress the onset of aggregation of the AcPHF6 peptide. Inhibition is particularly pronounced in macrocycles 1a, 1d, and 1f, in which the two residues in the "lower" strand provide a pattern of hydrophobicity and hydrophilicity that matches that of the pentapeptide "upper" strand. Inhibition varies strongly with the concentration of these macrocycles, suggesting that it is cooperative. Macrocycle 1b containing the pentapeptide QIVYK shows little inhibition, suggesting the possibility of a preferred direction of growth of AcPHF6 β-sheets. On the basis of these studies, a model is proposed in which the AcPHF6 amyloid grows as a layered pair of β-sheets and in which growth is blocked by a pair of macrocycles that cap the growing paired hydrogen-bonding edges. This model provides a provocative and appealing target for future inhibitor design.     

A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies

The accurate prediction of absolute protein-ligand binding free energies is one of the grand challenge problems of computational science. Binding free energy measures the strength of binding between a ligand and a protein, and an algorithm that would allow its accurate prediction would be a powerful tool for rational drug design. Here we present the development of a new method that allows for the absolute binding free energy of a protein-ligand complex to be calculated from first principles, using a single simulation. Our method involves the use of a novel reaction coordinate that swaps a ligand bound to a protein with an equivalent volume of bulk water. This water-swap reaction coordinate is built using an identity constraint, which identifies a cluster of water molecules from bulk water that occupies the same volume as the ligand in the protein active site. A dual topology algorithm is then used to swap the ligand from the active site with the identified water cluster from bulk water. The free energy is then calculated using replica exchange thermodynamic integration. This returns the free energy change of simultaneously transferring the ligand to bulk water, as an equivalent volume of bulk water is transferred back to the protein active site. This, directly, is the absolute binding free energy. It should be noted that while this reaction coordinate models the binding process directly, an accurate force field and sufficient sampling are still required to allow for the binding free energy to be predicted correctly. In this paper we present the details and development of this method, and demonstrate how the potential of mean force along the water-swap coordinate can be improved by calibrating the soft-core Coulomb and Lennard-Jones parameters used for the dual topology calculation. The optimal parameters were applied to calculations of protein-ligand binding free energies of a neuraminidase inhibitor (oseltamivir), with these results compared to experiment. These results demonstrate that the water-swap coordinate provides a viable and potentially powerful new route for the prediction of protein-ligand binding free energies.     

Electrospray sample deposition for matrix-assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI mass spectrometry with attomole detection limits

Electrospray sample deposition was explored for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). In this method, nanoliter volumes of matrix/analyte mixture were electrosprayed from a high voltage biased (1-2 kV) fused-silica capillary onto a grounded MALDI plate mounted 100-500 microm from the capillary outlet. Electrospray deposition with these conditions produced sample spots 200-300 microm in diameter thus matching the laser spot size. Varying spray voltage and distance resulted in different crystal sizes and volatilization rates for alpha-cyano-4-hydroxycinnamic acid matrix. Best results were obtained when the sample was deposited as wet droplets as opposed to deposition as dried solid. Under 'wet-spray' conditions, 2-4 microm diameter crystals were formed and detection limits for several neuropeptides were 0.7-25 amol. Samples could be pre-concentrated on the plate by spraying continuously and allowing sample to evaporate in a small spot. Sample volumes as large as 580 nL were deposited yielding a detection limit of 35 pM for neurotensin 1-11. Electrospray sample deposition yielded similar results when using atmospheric pressure-MALDI coupled with a quadrupole ion trap mass spectrometer, except that the sensitivity was approximately seven-fold worse.     

Hemilability of 2-(1H-imidazol-2-yl)pyridine and 2-(oxazol-2-yl)pyridine ligands: Imidazole and oxazole ring Lewis basicity,Ni(II)/Pd(II) complex structures and spectra

Fourteen new organic molecules A1–A4, B1–B5, C1–C4 and D and a series of transition metal(II) complexes (Ni1–Ni9 and Pd1–Pd2b) were synthesized and studied in order to characterize the hemilability of 2-(1H-imidazol-2-yl)pyridine and 2-(oxazol-2-yl)pyridine ligands (A1–A4 = 2-R²-6-(4,5-diphenyl-1R¹-imidazol-2-yl)pyridines, R¹ = H or CH₃, R² = H or CH₃; B1–B5 = 1-R²-2-(pyridin-2-yl)-1R¹-phenanthro[9,10-d]imidazoles/oxazoles, R¹ = H or CH₃, R² = H or CH₃; C1–C4 = 2-(6-R²-pyridin-2-yl)-1H-imidazo/oxazo[4,5-f][1,10]phenanthrolines, R² = H or CH₃; D = 2-mesityl-1H-imidazo[4,5-f][1,10]phenanthroline). They were also used to study the substituent effects on the donor strengths as well as the coordination chemistries of the imidazole/oxazole fragments of the hemilabile ligands.All the observed protonation–deprotonation processes found within pH 1–14 media pertain to the imidazole or oxazole rings rather than the pyridyl Lewis bases. The donor characteristics of the imidazole/oxazole ring can be estimated by spectroscopic methods regardless of the presence of other strong N donor fragments. The oxazoles possessed notably lower donor strengths than the imidazoles. The electron-withdrawing influence and capacity to hinder the azole base donor strength of 4,5-azole substituents were found to be in the order phenanthrenyl (B series) > 4,5-diphenyl (A series) > phenanthrolinyl (C series). An X-ray structure of Ni5b gave evidence for solvent induced ligand reconstitution while the structure of Pd2b provided evidence for solvent induced metal–ligand bond disconnection.Interestingly, alkylation of 1H-imidazoles did not necessarily produce the anticipated push of electron density to the donor nitrogen. Furthermore, substituents on the 4,5-carbons of the azole ring were more important for tuning donor strength of the azole base. DFT calculations were employed to investigate the observed trends. It is believed that the information provided on substituent effects and trends in this family of ligands will be useful in the rational design and synthesis of desired azole-containing chelate ligands, tuning of donor properties and application of this family of ligands in inorganic architectural designs, template-directed coordination polymer preparations, mixed-ligand inorganic self-assemblies, etc.     

MOCVD过程中金属有机源(C~3H~7)~2Te和(CH~3)~2Cd热裂解机理 质谱实时研究

采用质谱技术实时研究了金属有机源DIPTe和DMCd在MOCVD反应器中热裂解的性质。着重分析了可能发生的气相反应及热裂解机理,并探讨了在CdTe,HgCdTe实际生长条件下两个有机源之间可能发生的相互作用及其对热裂解温度的影响。     

Accessing lanthanide-based,in situ illuminated optical turn-on probes by modulation of the antenna triplet state energy

Luminescent lanthanides possess ideal properties for biological imaging, including long luminescent lifetimes and emission within the optical window. Here, we report a novel approach to responsive luminescent Tb(iii) probes that involves direct modulation of the antenna excited triplet state energy. If the triplet energy lies too close to the ⁵D₄ Tb(iii) excited state (20 500 cm⁻¹), energy transfer to ⁵D₄ competes with back energy transfer processes and limits lanthanide-based emission. To validate this approach, a series of pyridyl-functionalized, macrocyclic lanthanide complexes were designed, and the corresponding lowest energy triplet states were calculated using density functional theory (DFT). Subsequently, three novel constructs L3 (nitro-pyridyl), L4 (amino-pyridyl) and L5 (fluoro-pyridyl) were synthesized. Photophysical characterization of the corresponding Gd(iii) complexes revealed antenna triplet energies between 25 800 and 30 400 cm⁻¹ and a 500-fold increase in quantum yield upon conversion of Tb(L3) to Tb(L4) using the biologically relevant analyte H₂S. The corresponding turn-on reaction can be monitored using conventional, small-animal optical imaging equipment in presence of a Cherenkov radiation emitting isotope as an in situ excitation source, demonstrating that antenna triplet state energy modulation represents a viable approach to biocompatible, Tb-based optical turn-on probes.

The rational, analyte-mediated modulation of the relative energy of the lanthanide-sensitizing triplet state produces Tb-based luminescence, observable by a conventional optical imager in presence of the Cherenkov radiation emitting radioisotope ¹⁸F.