Measurement of dissociation constants of inhibitors binding to Src SH2 domain protein by non-covalent electrospray ionization mass spectrometry

A mass spectrometric protocol for identifying ligands with a wide range of affinities (3-101 microM) and quantitative spectral analysis for non-covalent interactions have been developed using Src SH2 as a target. Dissociation constants of five compounds, three with a phospho moiety, one with a sulphonic acid group and one with carboxylic acid groups only, were determined using one-ligand one-binding-site, two-ligands one-binding site and one-ligand two-binding-sites models. The Kd values determined by ESI-MS of the three compounds containing the phospho moiety (3.2-7.9 microM) were comparable to those obtained from a solution equilibrium fluorescence polarization assay. The compound with a sulphonate group is a much weaker binding ligand (Kd=101 microM by ESI, >300 microM by FP) towards the Src SH2 protein. Two complexes with different stoichiometric ratios 1:1 and 2:1 (ligand-protein) were observed by ESI-MS for the ligand GIXXX630X. Analysis of binding isotherms indicated the presence of two binding sites for the ligand with Kd values of 9.3 and 193 microM. These data confirmed that, for these polar compounds, non-covalent ESI-MS can measure affinity which very closely reflects the affinity measured under true solution equilibrium conditions. ESI-MS has several key advantages over many solution methods: it can identify the existence of and measure the affinity of complexes other than simple 1:1 ligand-enzyme complexes. Moreover, ESI-MS competition experiments can be readily performed to yield data on whether two ligands bind simultaneously or competitively at the same time as measuring the affinity of the ligand.     

NMR experiments for the sign determination of homonuclear scalar and residual dipolar couplings

A modified version of the JHH-TOCSY experiment, `signed COSY', is presented that allows the determination of the sign of residual dipolar ¹H-¹H coupling constants with respect to the sign of one-bond ¹H-X coupling constants in linear three-spin systems X-¹H-¹H, where X = ¹³C or ¹⁵N. In contrast to the original JHH-TOCSY experiments, the signs of J _HH couplings may be determined for CH₂-CH₂ moieties and for uniformly ¹³C/¹⁵N-labelled samples. In addition, sensitivity is enhanced, diagonal peaks are suppressed and cross peaks are observed only between directly coupled protons, as in a COSY spectrum.     

Nicotinic receptor fourth transmembrane domain: hydrogen bonding by conserved threonine contributes to channel gating kinetics

The fourth transmembrane domain (M4) of the nicotinic acetylcholine receptor (AChR) contributes to the kinetics of activation, yet its close association with the lipid bilayer makes it the outermost of the transmembrane domains. To investigate mechanistic and structural contributions of M4 to AChR activation, we systematically mutated alphaT422, a conserved residue that has been labeled by hydrophobic probes, and evaluated changes in rate constants underlying ACh binding and channel gating steps. Aromatic and nonpolar mutations of alphaT422 selectively affect the channel gating step, slowing the rate of opening two- to sevenfold, and speeding the rate of closing four- to ninefold. Additionally, kinetic modeling shows a second doubly liganded open state for aromatic and nonpolar mutations. In contrast, serine and asparagine mutations of alphaT422 largely preserve the kinetics of the wild-type AChR. Thus, rapid and efficient gating of the AChR channel depends on a hydrogen bond involving the side chain at position 422 of the M4 transmembrane domain.     

Ligand-insensitive State of Cardiac ATP-sensitive K+ Channels : Basis for Channel Opening

The mechanism by which ATP-sensitive K⁺ (K_ATP) channels open in the presence of inhibitory concentrations of ATP remains unknown. Herein, using a four-state kinetic model, we found that the nucleotide diphosphate UDP directed cardiac K_ATP channels to operate within intraburst transitions. These transitions are not targeted by ATP, nor the structurally unrelated sulfonylurea glyburide, which inhibit channel opening by acting on interburst transitions. Therefore, the channel remained insensitive to ATP and glyburide in the presence of UDP. “Rundown” of channel activity decreased the efficacy with which UDP could direct and maintain the channel to operate within intraburst transitions. Under this condition, the channel was sensitive to inhibition by ATP and glyburide despite the presence of UDP. This behavior of the K_ATP channel could be accounted for by an allosteric model of ligand-channel interaction. Thus, the response of cardiac K_ATP channels towards inhibitory ligands is determined by the relative lifetime the channel spends in a ligand-sensitive versus -insensitive state. Interconversion between these two conformational states represents a novel basis for K_ATP channel opening in the presence of inhibitory concentrations of ATP in a cardiac cell.     

Bioremediation Scaleup Effectiveness: A Review

Bioremediation has been applied in laboratory-scale testing to simulate field-scale bioremediation applications. The simulations have focused on the development of concentration-time profile data in the laboratory to be modeled and used for predicting field-scale performance, particularly the time of treatment and the treatment concentration endpoints. This review reports on more than a dozen examples of bioremediation where both the laboratory-scale and field-scale data are provided. These data have been analyzed to examine how well the laboratory-scale kinetics predict the kinetics at field scale. In most cases, the laboratory-scale kinetics exceed field-scale kinetics and underpredict the time of treatment to a given endpoint in excess of 100% and by as much as 11,900%. In some cases, the laboratory-scale kinetic rate constants fall between ±100% of the field-scale kinetics, leading to predictions within 50 to 200% of the time of treatment to a given concentration level. Not enough examples nor details within the references exist to permit a detailed explanation of why these differences exist. However, several hypotheses are given in this review as to why scaleup is often problematic, and comments from other investigators on this topic are presented.     

Physiological changes in, and phosphate uptake by potato plants during development of, and recovery from phosphate deficiency

The development of phosphate deficiency (P-stress) was observed in rooted sprouts of Solanum tuberosum L. cv. Desiree growing in solutions without phosphate. Shoot growth was inhibited by P-stress within 3 to 5 days of terminating the phosphate supply, while significant effects on root growth were not recorded until 7 to 9 days. Thus, the shoot:root dry weight ratio decreased from 4.3 to 2.6 over a 10-day period. Growth in the absence of an exogenous phosphate supply progressively diluted the phosphorus in the plant. The proportional decrease in concentration was similar in roots and shoots over a 7-day period, even though the former were growing more quickly. The potential for phosphate uptake per unit weight of root increased rapidly during the first 3 days of P-stress. When the plants were provided subsequently with a labelled, 1 mol m^?3 phosphate solution, the absorption rate was 3 to 4-fold greater than that of control plants which had received a continuous phosphate supply. The increased rate of uptake by P-stressed plants was accounted for by an increase (3-fold) in the V_max of system 1 for phosphate transport and by a marked increase in the affinity of the system for phosphate (decrease in K_m). In the early stages of P-stress, before marked changes in growth were measured, the proportion of labelled phosphate translocated to the shoots increased slightly relative to the controls when a phosphate supply was restored. In the later stages of stress a greater proportion was retained in the root system of P-stressed plants than in that of controls. In plants with roots divided between solutions containing or lacking a phosphate supply, the increased absorption rate was determined by the general demand for phosphate in the plant and not by the P-status of the particular root where uptake was measured. By contrast, the poportion translocated was strongly dependent on the P-status of the root. The restoration of a phosphate supply to P-stressed plants was marked by a rapid increase in the P concentration in snoots and roots which returned to levels similar to unstressed controls within 24 h. The enhanced uptake rate persisted for at least 5 days, resulting in supra-normal concentrations of P in both shoots and roots, and in the formation of extensive necrotic areas between the veins of mature leaves. Autoradiographs showed accumulations of ³²P in these lesions and at the points where guttation droplets formed on leaves.     

Local helix content in an alanine-rich peptide as determined by the complete set of 3JHNα coupling constants

Summary Alanine-rich peptides serve as models for exploring the factors that control helix structure in peptides and proteins. Scalar CH-NH couplings (³J_HN) are an extremely useful measure of local helix content; however, the large alanine content in these peptides leads to significant signal overlap in the CH region of ¹H 2D NMR spectra. Quantitative determination of all possible ³J_HN values is, therefore, very challenging. Szyperski and co-workers [(1992) J. Magn. Reson., 99, 552–560] have recently developed a method for determining ³J_HN from NOESY spectra. Because ³J_HN may be determined from 2D peaks outside of the CH region, there is a much greater likelihood of identifying resolved resonances and measuring the associated coupling constants. It is demonstrated here that ³J_HN can be obtained for every residue in the helical peptide Ac-(AAAAK)₃A-NH₂. The resulting ³J_HN profile clearly identifies a helical structure in the middle of the peptide and further suggests that the respective helix termini unfold via distinct pathways.Abbreviations ³J_HN three-bond CH-NH scalar coupling constant - NOE nuclear Overhauser enhancement - NOESY two-dimensional nuclear Overhauser spectroscopy - COSY two-dimensional correlated spectroscopy - DQF-COSY two-dimensional double-quantum-filtered correlated spectroscopy - TOCSY two-dimensional total correlation spectroscopy To whom correspondence should be addressed.Deceased March 5, 1996.     

A calbindin D9k mutant containing a novel structural extension: 1H nuclear magnetic resonance studies.

Calbindin D9k is a small, well-studied calcium-binding protein consisting of two helix-loop-helix motifs called EF-hands. The P43MG2 mutant is one of a series of mutants designed to sequentially lengthen the largely unstructured tether region between the two EF-hands (F36-S44). A lower calcium affinity for P43MG was expected on the basis of simple entropic arguments. However, this is not the case and P43MG (-97 kJ.mol-1) has a stronger calcium affinity than P43M (-93 kJ.mol-1), P43G (-95 kJ.mol-1) and even wild-type protein (-96 kJ.mol-1). An NMR study was initiated to probe the structural basis for these calcium-binding results. The 1H NMR assignments and 3JHNH alpha values of the calcium-free and calcium-bound form of P43MG calbindin D9k mutant are compared with those of P43G. These comparisons reveal that little structure is formed in the tether regions of P43MG(apo), P43G(apo) and P43G(Ca) but a helical turn (S38-K41) appears to stabilize this part of the protein structure for P43MG(Ca). Several characteristic NOEs obtained from 2D and 3D NMR experiments support this novel helix. A similar, short helix exists in the crystal structure of calcium-bound wild-type calbindin D9k-but this is the first observation in solution for wild-type calbindin D9k or any of its mutants.     

Distamycin A affects the stability of NF-kappaB p50-DNA complexes in a sequence-dependent manner

The effect of two different DNA minor groove binding molecules, Hoechst 33258 and distamycin A, on the binding kinetics of NF-kappaB p50 to three different specific DNA sequences was studied at various salt concentrations. Distamycin A was shown to significantly increase the dissociation rate constant of p50 from the sequences PRDII (5'-GGGAAATTCC-3') and Ig-kappa B (5'-GGGACTTTCC-3') but had a negligible effect on the dissociation from the palindromic target-kappaB binding site (5'-GGGAATTCCC-3'). By comparison, the effect of Hoechst 33258 on binding of p50 to each sequence was found to be minimal. The dissociation rates for the protein--DNA complexes increased at higher potassium chloride concentrations for the PRDII and Ig-kappaB binding motifs and this effect was magnified by distamycin A. In contrast, p50 bound to the palindromic target-kappaB site with a much higher intrinsic affinity and exhibited a significantly reduced salt dependence of binding over the ionic strength range studied, retaining a K(D) of less than 10 pM at 150 mM KCl. Our results demonstrate that the DNA binding kinetics of p50 and their salt dependence is strongly sequence-dependent and, in addition, that the binding of p50 to DNA can be influenced by the addition of minor groove-binding drugs in a sequence-dependent manner.     

Kinetic model of disaccharide oxidation by Agrobacterium tumefaciens

Disaccharides were microbaially transformed to their corresponding 3-keto-derivatives by resting cells of Agrobacterium tumefaciens NCPPB 396. The kinetics and yield of this highly specific oxidation depend on several factors. The oxygen concentration especially has a major influence on the production of 3-keto-derivatives and was investigated kinetically with respect to low stationary oxygen concentrations in solution. Experiments showed unconventional results that conflicted with normal Michaelis-Menten kinetics. A kinetic model was developed and the kinetic constants were calculated. The model and experimental data for sucrose, maltose, iso-maltulose (palatinose), and leucrose are in good agreement with each other. Initial reaction rates with different sugars using constant oxygen concentrations resulted in a Michaelis-Mentent type function. The complete kinetics, including the effect of disaccharide and oxygen concentrations, are presented. (c) 1995 John Wiley & Sons, Inc.