Revealing the quaternary structure of a heterogeneous noncovalent protein complex through surface-induced dissociation

As scientists begin to appreciate the extent to which quaternary structure facilitates protein function, determination of the subunit arrangement within noncovalent protein complexes is increasingly important. While native mass spectrometry shows promise for the study of noncovalent complexes, few developments have been made toward the determination of subunit architecture, and no mass spectrometry activation method yields complete topology information. Here, we illustrate the surface-induced dissociation of a heterohexamer, toyocamycin nitrile hydratase, directly into its constituent trimers. We propose that the single-step nature of this activation in combination with high energy deposition allows for dissociation prior to significant unfolding or other large-scale rearrangement. This method can potentially allow for dissociation of a protein complex into subcomplexes, facilitating the mapping of subunit contacts and thus determination of quaternary structure of protein complexes.     

Application of a genetic algorithm: near optimal estimation of the rate and equilibrium constants of complex reaction mechanisms

In iterative non-linear least-squares fitting, the reliable estimation of initial parameters that lead to convergence to the global optimum can be difficult. Irrespective of the algorithm used, poor parameter estimates can lead to abortive divergence if initial guesses are far from the true values or in rare cases convergence to a local optimum. For determination of the parameters of complex reaction mechanisms, where often little is known about what value these parameters should take, the task of determining good initial estimates can be time consuming and unreliable. In this contribution, the methodology of applying a genetic algorithm (GA) to the task of determining initial parameter estimates that lie near the global optimum is explained. A generalised genetic algorithm was implemented according to the methodology and the results of its application are also given. The parameter estimates obtained were then used as the starting parameters for a gradient search method, which quickly converged to the global optimum. The genetic algorithm was successfully applied to both simulated kinetic measurements where the reaction mechanism contained one equilibrium constant and two rate constants to be fitted, and to kinetic measurements of the complexation of Cu²⁺ by 1,4,8,11-tetraazacyclotetradecane where two equilibrium and two rate constants were fitted. The implementation of the algorithm is such that it can be generally applied to any reaction mechanism that can be expressed by standard chemistry notation. The control parameters of the algorithm can be varied through a simple user interface to account for parameter range and the number of parameters involved.     

Quantitative determination of noncovalent binding interactions using automated nanoelectrospray mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) has proven to be an extremely powerful tool for studying biomolecular structures and noncovalent interactions. Here we report a method using a fully automated, chip-based nanoESI-MS system to determine the dissociation constants (Kd) for the complexes of two different proteins with their ligands. The automated nanoelectrospray system, consisting of the NanoMate and ESI chip, serves functionally as a combination of autosampler and nanoelectrospray ionization source. This system provides all the advantages of conventional nanoelectrospray plus automated, high-throughput analyses without carryover. The automated nanoESI system was used to investigate quantitative noncovalent interactions between ribonuclease A (RNase A) and cytidylic acid ligands (2'-CMP, CTP), a well-characterized model protein-ligand complex, and between an inactive endocellulase mutant (Thermobifida fusca Cel6A D117Acd) and four oligosaccharide ligands (cellotriose, cellotetraose, cellopentaose, cellohexaose). Both titration and competitive binding approaches were performed prior to automated nanoESI-MS analysis with a Q-TOF mass spectrometer. Dissociation constants for each complex were calculated from the sum of ion peak areas of free and complexed proteins during the titration and competition experiments. The measured Kd values for the RNase A-CMP and Cel6A D117Acd-G3 complexes were found to be in excellent agreement with the available published values obtained by standard spectroscopic titration techniques. To our knowledge, this is the first report of using an ESI-MS approach to study the interactions between a cellulase and oligosaccharides. The results provide new insights for understanding the nature of cellulase-cellulose interactions.     

Translational partition functions and equilibrium constants of atomic and molecular particles

Some special features of the calculation of partition functions for the objects possessing finite dimensions are considered. It is shown that atomic, molecular, and more extended clusterlike objects are subject to certain spatial limitations related to the initial assumptions employed in the statistical approach. The values calculated for a material point or an object such as electron are overstated when applied to atomic particles. The classical expressions for the kinetic and statistical equilibrium constants of the reactions of formation and dissociation of diatomic molecules are compared. The observed discrepancies are eliminated by introducing corrections into formulas for the translational partition functions.     

Dynamic titration: determination of dissociation constants for noncovalent complexes in multiplexed format using HPLC-ESI-MS

With recent growth in fields such as life sciences and supramolecular chemistry, there has been an ever increasing need for high-throughput methods that would permit determination of binding affinities for noncovalent complexes of various host-guest systems. These are traditionally measured by titration experiments where concentration-dependent signals of species participating in solution-based binding equilibria are monitored by methods such as UV-vis spectrophotometry, calorimetry, or nuclear magnetic resonance spectrometry. Here we present a new titration technique that unifies and allows chromatographic separation of guests with determination of dissociation constants by electrospray mass spectrometry in a multiplexed format. A theoretical model has been derived that describes the complex formation for the guests eluted from a chromatographic column when hosts are admixed postcolumn. The model takes possible competition equilibria into account; i.e., it can deal with unresolved peaks of guests with the possible addition of multiple hosts in one experiment. This on-line workflow makes determination of binding affinities for large libraries of compounds possible. The potential of the method is demonstrated on the determination of dissociation constants for complexes of beta- and gamma-cyclodextrins with nonsteroidal antiinflammatory drugs ibuprofen, naproxen, and flurbiprofen.     

Chasing equilibrium: measuring the intrinsic solubility of weak acids and bases

A novel procedure is described for rapid (20-80 min) measurement of intrinsic solubility values of organic acids, bases, and ampholytes. In this procedure, a quantity of substance was first dissolved at a pH where it exists predominantly in its ionized form, and then a precipitate of the neutral (un-ionized) species was formed by changing the pH. Subsequently, the rate of change of pH due to precipitation or dissolution was monitored and strong acid and base titrant were added to adjust the pH to discover its equilibrium conditions, and the intrinsic solubility of the neutral form of the compound could then be determined. The procedure was applied to a variety of monoprotic and diprotic pharmaceutical compounds. The results were highly repeatable and had a good correlation to available published values. Data collected during the procedure provided good diagnostic information. Kinetic solubility data were also collected but provided a poor guide to the intrinsic solubility.     

X-ray study of weak interactions in two flavonoids

X-ray diffraction studies were carried out on single crystals of two flavonoids, viz. 5-hydroxy-6,7,4′-trimethoxyflavone, C₁₈H₁₆O₆, (I) and 5-hydroxy-3,7,4′-trimethoxyflavone, C₁₈H₁₆O₆, (II). Crystal structures of both the flavonoids were solved by direct methods and refined by full-matrix least-squares procedures. In both the molecules, the benzopyran moiety is planar. The dihedral angle between the phenyl ring and the benzopyran portion is 5.50(4)° in (I) and 29.11(5)° in (II). In (I), the crystal packing is influenced by O-H…O hydrogen bonds, and weak C-H…O and π…π interactions whereas in (II) the crystal structure is stabilized by the presence of four intermolecular short contacts of the type C-H…O. There is also one C-H…π hydrogen bond with H… centroid distance of <2.7 Å. The molecules are further stabilized by π-π interactions.     

Layer-by-layer assembly through weak interactions and their biomedical applications

The surface design and control of substrates with nanometer- or micrometer-sized polymer films are of considerable interest for both fundamental and applied studies in the biomedical field because of the required surface properties. The layer-by-layer (LbL) technique was discovered in 1991 by Decher and co-workers for the fabrication of polymer multilayers constructed mainly through electrostatic interaction. The scope and applicability of this LbL assembly has been extended by introducing molecularly regular conformations of polymers or proteins by employing, for the first time, weak interactions such as van der Waals interactions and biological recognition. Since these weak interactions are the sum of the attractive or repulsive forces between parts of the same molecule, they allow macromolecules to be easily arranged into the most stable conformation in a LbL film. By applying this characteristic feature, the template polymerization of stereoregular polymers, stereoregular control of surface biological properties, drastic morphological control of biodegradable nano materials, and the development of three-dimensional cellular multilayers as a tissue model were successfully achieved. It is expected that LbL assembly using weak interactions will promote further interest into fundamental and applied studies on the design of surface chemistry in the biomedical field.     

Manufacturer-retail platform interactions in the presence of a weak retailer

Motivated by the emergence of dominant retail platforms operating using a store-within-a-store strategy, we study the interaction of such a retailer's decision on the selling format and a manufacturer's decision on the channel selection. The dominant retailer may elect to operate as a traditional reseller or a retail platform where the manufacturer manages his own store and pays a slotting fee and a portion of the revenue to the platform. The manufacturer makes the channel selection decision between the dominant retailer and a weak reseller. A Stackelberg game with the dominant retailer being the leader is formulated, and five relevant channel options are presented. We solve sub-games and characterise the equilibrium solution of the full game. Numerical studies shed light on the roles of the slotting fee and the outcomes of some prevailing selling formats in business practice. In particular, it is shown that the demand substitution between the dominant retailer and the weak retailer is crucial in determining channel selection.     

Calculating equilibrium constants from spectral data: Reliability of the Benesi-Hildebrand method and its modifications

Equations for statistical evaluation of complex formation in solution were revised and a simple modification of the correct least-squares procedure was advanced. The main difference against the previous treatment is in the uncertainty of the estimated parameters: the equilibrium constant K and extinction coefficient of the complex ε. This uncertainty is always greater, often by an order of magnitude, than that given in the literature using various methods and programs. On a couple of examples, the new method was compared with the previous ones, also with most commonly used procedure of BenesiHildebrand. According to the quality of data, particularly the concentration range and the number of measurements, one can distinguish cases when Benesi-Hildebrand method yields reasonable results and when it is unreliable: in no case it gives any idea about the uncertainty. Many K values determined in this way should be better removed from the literature.     

Measurement of oxygen recombination rate constants by the piezoelectric method

The piezoelectric method is used to measure pressure in a gas flow within a nozzle, measurement results are compared with calculation, and values of the oxygen atom recombination rate constant are obtained for the temperature range 1680–3250°K.Translated from Inzhenerno-Fizicheskii Zhurnal, Vol. 53, No. 3, pp. 437–441, September, 1987.     

On-line dynamic titration: determination of dissociation constants for noncovalent complexes using Gaussian concentration profiles by electrospray ionization mass spectrometry

A new method for determination of dissociation constants (Kd) using on-line titration by electrospray ionization mass spectrometry is presented. Unlike in common titration experiments, where a set of discrete solutions with a fixed concentration of host and increasing concentration of guest is measured, here a continuous Gaussian concentration profile of guest, formed by band-broadening dispersion during passage through a long tubing, is utilized. An equation allowing access to dissociation constant values from experimental data fit to a 1:1 binding model was derived and incorporated into an in-house-written computer program for automated data processing. The new method is demonstrated for noncovalent complexes of cinchona alkaloid carbamate chiral selectors with N-dinitrobenzoylleucine enantiomers and a series of cyclodextrins with sulfonated azo dyes.     

Target dependence of equilibrium mean charge of fast ions emerging from solids

Equilibrium mean charges of H and ⁴He ions emerging from solids were measured for many kinds of target materials, and were found to show an oscillatory dependence on target atomic number. This oscillation was found to be the reflection of electron shell structures of the target atoms. The electron capture cross sections of very fast ³He²⁺ ions were also measured and interpreted on the same physical ground.     

The nature of phosphorylated chrysin-protein interactions involved in noncovalent complex formation by electrospray ionization mass spectroscopy

In the work described in this paper, chrysin was phosphorylated by a modified Atheron-Todd reaction. The structure of phosphorylated chrysin was determined by elemental analysis, NMR, ESI-MS/MS, and X-ray data. Electrospray ionization results showed that the phosphorylated flavonoids could form noncovalent complexes with many proteins, such as lysozyme, myoglobin, bovine insulin, and cytochrome c, while noncovalent complexes were not detected in the mixed solution of the chrysin and proteins. The research shows that the phosphorylated flavonoids possess relatively stronger affinities and form noncovalent complexes with the proteins more easily than the non-phosphorylated compounds.     

Decomposition of atmospheric water content into cluster contributions based on theoretical association equilibrium constants

Water vapor is treated as an equilibrium mixture of water clusters (H₂O)_i using quantum-chemical evaluation of the equilibrium constants of water associations. The model is adapted to the conditions of atmospheric humidity, and a decomposition algorithm is suggested using the temperature and mass concentration of water as input information and used for a demonstration of evaluation of the water oligomer populations in the Earth's atmosphere. An upper limit of the populations is set up based on the water content in saturated aqueous vapor. It is proved that the cluster population in the saturated water vapor, as well as in the Earth's atmosphere for a typical temperature/humidity profile, increases with increasing temperatures.     

Covalent and noncovalent functionalisation and solubilisation of nanodiamond

Covalent functionalisation of nanodiamond has been carried out by employing several methods. One of them involves the reaction of acid-treated nanodiamond with thionyl chloride followed by reaction with a long-chain aliphatic amine to produce the amide derivative. The second method involves reaction of acid-treated nanodiamond with an organosilicon or organotin reagent such as hexadecyltrimethoxysilane, dibutyldimethoxytin, and perfluoro-octyltriethoxysilane. The products of covalent functionalisation produce excellent dispersions in CCl₄ and toluene. SiO₂–and SnO₂–covered nanodiamond are obtained by heating the nanodiamond coated with the organosilane and the organotin reagents, respectively. By interaction of nanodiamond with surfactants such as sodium bis(2-ethylhexyl) sulphosuccinate (AOT), Triton X-100 (TX-100), polyvinyl alcohol (PVA), cetyltrimethylammonium bromide (CTAB), and tert-octylphenoxy poly(oxyethylene)ethanol (IGEPAL) gives good dispersions in water, the best dispersion with the lowest surfactant concentration being obtained with IGEPAL.     

Production and properties of nanoelectrospray emitters used in Fourier transform ion cyclotron resonance mass spectrometry: implications for determination of association constants for noncovalent complexes

Electrospray ionization (ESI) is extensively used in the analysis of biological compounds; yet some fundamental properties of this technique are not completely understood. It is widely recognized that care should be exercised when noncovalent complexes are being studied by ESI, since weak noncovalent binding can be broken or formed during the desolvation process. In the present work, spectra from the noncovalent complex, vancomycin/diacetyl-L-lysyl-D-alanyl-D-alanine, obtained from ESI and from nanoelectrospray ionization (nanoESI), have been compared. The results indicated that the milder desolvation conditions arising as a result of the smaller sizes of droplets produced in the nanoESI source attenuated effects upon weak bonds in the desolvation process. The association constant values calculated from the relative peak intensities suggest that, when using ESI, the analyzed noncovalent complex dissociated in the condensed phase during the spraying process. The influences of experimental parameters such as tip diameter and coating for nanoESI needles were investigated. Principal component analysis, a multivariate analysis method, was applied to achieve a better evaluation of the spectra obtained using different needle diameters and coatings for the analysis of the noncovalent complex vancomycin/diacetyl-L-lysyl-D-alanyl-D-alanine. It was found that 2-microm tip diameter resulted in more reproducible spectra than the larger tip diameters tested (6-20 microm).