Influence of systematic error on the shape of the scatchard plot of tRNAPhe binding to eukaryotic ribosomes

Structures of Anabaena calcium-binding protein CcbP: insights into Ca2+ signaling during heterocyst differentiation

Ca2+-binding proteins play pivotal roles in both eukaryotic and prokaryotic cells. CcbP from cyanobacterium Anabaena sp. strain PCC 7120 is a major Ca2+-binding protein involved in heterocyst differentiation, a process that forms specialized nitrogen-fixing cells. The three-dimensional structures of both Ca2+-free and Ca2+-bound forms of CcbP are essential for elucidating the Ca2+-signaling mechanism. However, CcbP shares low sequence identity with proteins of known structures, and its Ca2+-binding sites remain unknown. Here, we report the solution structures of CcbP in both Ca2+-free and Ca2+-bound forms determined by nuclear magnetic resonance spectroscopy. CcbP adopts an overall new fold and contains two Ca2+-binding sites with distinct Ca2+-binding abilities. Mutation of Asp38 at the stronger Ca2+-binding site of CcbP abolished its ability to regulate heterocyst formation in vivo. Surprisingly, the β-barrel subdomain of CcbP, which does not participate in Ca2+-binding, topologically resembles the Src homology 3 (SH3) domain and might act as a protein-protein interaction module. Our results provide the structural basis of the unique Ca2+ signaling mechanism during heterocyst differentiation.

Determination of calcium-binding constants of caseins, phosphoserine, citrate and pyrophosphate: A modelling approach using free calcium measurement

Dairy products contain large amount of calcium which is bound to caseins and different chelating agents like citrate and polyphosphates. The present study aimed to determine the calcium-binding capacities of phosphoserine (SerP), caseinophosphopeptide (CPP), β-casein, caseinate, citrate and pyrophosphate in the same conditions of temperature, pH and ionic strength. The free calcium (Ca(2+)) was measured using a calcium ion-selective electrode and plotted as a function of total calcium concentration. The association constants and the number of calcium-binding sites were determined by fitting the experimental data to a theoretical model. The phosphate groups of caseins were the main binding sites with evidence for participation of carboxylate groups. The intrinsic association constants determined by the best fit of the data were in the order: pyrophosphate (557×10(3)M(-1))>citrate (20×10(3)M(-1))>β-casein (5×10(3)M(-1))>caseinate, CPP and SerP (∼10(3)M(-1)). These findings may be of interest for the development of calcium-enriched products to overcome calcium deficiency in specific populations.

Structural and mechanistic insights into nerve growth factor interactions with the TrkA and p75 receptors

Nerve growth factor engages two structurally distinct transmembrane receptors, TrkA and p75, which have been proposed to create a "high-affinity" NGF binding site through formation of a ternary TrkA/NGF/p75 complex. To define a structural basis for the high-affinity site, we have determined the three-dimensional structure of a complete extracellular domain of TrkA complexed with NGF. The complex reveals a crab-shaped homodimeric TrkA structure, but a mechanism for p75 coordination is not obvious. We investigated the heterodimerization of membrane-bound TrkA and p75, on intact mammalian cells, using a beta-gal protein-protein interaction system. We find that NGF dimerizes TrkA and that p75 exists on the cell surface as a preformed oligomer that is not dissociated by NGF. We find no evidence for a direct TrkA/p75 interaction. We propose that TrkA and p75 likely communicate through convergence of downstream signaling pathways and/or shared adaptor molecules, rather than through direct extracellular interactions.

Effects of non-covalent interactions with 5-O-caffeoylquinic acid (chlorogenic acid) on the heat denaturation and solubility of globular proteins

The non-covalent interactions between the monomeric phenolic compound chlorogenic acid (5-CQA) and bovine serum albumin (BSA), lysozyme, and alpha-lactalbumin were characterized, and their effect on protein properties was examined. 5-CQA had a low affinity for all three proteins, and these interactions seemed to show a negative cooperativity. 5-CQA-BSA binding decreased with increasing temperature, whereas pH (pH 3.0 compared to pH 7.0) and ionic strength had no pronounced effect. At high 5-CQA/protein molar ratios, both the denaturation enthalpy and temperature of BSA increased; however, covalent bonds were created at high temperatures. The presence of 5-CQA had no effect on the solubility of BSA and alpha-lactalbumin as a function of pH, whereas it decreased lysozyme solubility at alkaline pH due to covalent interactions. These results indicate that the non-covalent interactions with 5-CQA do not have pronounced effects on the functional properties of globular proteins in food systems.

The result of equilibrium-constant calculations strongly depends on the evaluation method used and on the type of experimental errors

The determination of equilibrium constants is a widespread tool both to understand and to characterize protein-protein interactions. A variety of different methods, among them Scatchard analysis, is used to calculate these constants. Although more than 1000 articles dealing with equilibrium constants are published every year, the effects of experimental errors on the results are often disregarded when interpreting the data. In the present study we theoretically analysed the effect of various types of experimental errors on equilibrium constants derived by three different methods. A computer simulation clearly showed that certain experimental errors, namely inaccurate background correction, inexact calibration, saturation effects, slow kinetics and simple scattering, can adversely affect the result. The analysis further revealed that, for a given type of error, the same data set can produce different results depending on the method used.