Binding States (binding + states)

Distribution by Scientific Domains

Selected Abstracts

What is the biological relevance of the specific bond properties revealed by single-molecule studies?,

Philippe Robert
Abstract During the last decade, many authors took advantage of new methodologies based on atomic force microscopy (AFM), biomembrane force probes (BFPs), laminar flow chambers or optical traps to study at the single-molecule level the formation and dissociation of bonds between receptors and ligands attached to surfaces. Experiments provided a wealth of data revealing the complexity of bond response to mechanical forces and the dependence of bond rupture on bond history. These results supported the existence of multiple binding states and/or reaction pathways. Also, single bond studies allowed us to monitor attachments mediated by a few bonds. The aim of this review is to discuss the impact of this new information on our understanding of biological molecules and phenomena. The following points are discussed: (i) which parameters do we need to know in order to predict the behaviour of an encounter between receptors and ligands, (ii) which information is actually yielded by single-molecule studies and (iii) is it possible to relate this information to molecular structure? Copyright 2007 John Wiley & Sons, Ltd. [source]

X-ray spectromicroscopy in soil and environmental sciences

J. Thieme
X-ray microscopy is capable of imaging particles in the nanometer size range directly with sub-micrometer spatial resolution and can be combined with high spectral resolution for spectromicroscopy studies. Two types of microscopes are common in X-ray microscopy: the transmission X-ray microscope and the scanning transmission X-ray microscope; their set-ups are explained in this paper. While the former takes high-resolution images from an object with exposure times of seconds or faster, the latter is very well suited as an analytical instrument for spectromicroscopy. The morphology of clusters or particles from soil and sediment samples has been visualized using a transmission X-ray microscope. Images are shown from a cryo-tomography experiment based on X-ray microscopy images to obtain information about the three-dimensional structure of clusters of humic substances. The analysis of a stack of images taken with a scanning transmission X-ray microscope to combine morphology and chemistry within a soil sample is shown. X-ray fluorescence is a method ideally applicable to the study of elemental distributions and binding states of elements even on a trace level using X-ray energies above 1,keV. [source]

Modelling approaches to compare sorption and degradation of metsulfuron-methyl in laboratory micro-lysimeter and batch experiments

Maik Heistermann
Abstract Results of laboratory batch studies often differ from those of outdoor lysimeter or field plot experiments,with respect to degradation as well as sorption. Laboratory micro-lysimeters are a useful device for closing the gap between laboratory and field by both including relevant transport processes in undisturbed soil columns and allowing controlled boundary conditions. In this study, sorption and degradation of the herbicide metsulfuron-methyl in a loamy silt soil were investigated by applying inverse modelling techniques to data sets from different experimental approaches under laboratory conditions at a temperature of 10 C: first, batch-degradation studies and, second, column experiments with undisturbed soil cores (28 cm length 21 cm diameter). The column experiments included leachate and soil profile analysis at two different run times. A sequential extraction method was applied in both study parts in order to determine different binding states of the test item within the soil. Data were modelled using ModelMaker and Hydrus-1D/2D. Metsulfuron-methyl half-life in the batch-experiments (t1/2 = 66 days) was shown to be about four times higher than in the micro-lysimeter studies (t1/2 about 17 days). Kinetic sorption was found to be a significant process both in batch and column experiments. Applying the one-rate-two-site kinetic sorption model to the sequential extraction data, it was possible to associate the stronger bonded fraction of metsulfuron-methyl with its kinetically sorbed fraction in the model. Although the columns exhibited strong significance of multi-domain flow (soil heterogeneity), the comparison between bromide and metsulfuron-methyl leaching and profile data showed clear evidence for kinetic sorption effects. The use of soil profile data had significant impact on parameter estimates concerning sorption and degradation. The simulated leaching of metsulfuron-methyl as it resulted from parameter estimation was shown to decrease when soil profile data were considered in the parameter estimation procedure. Moreover, it was shown that the significance of kinetic sorption can only be demonstrated by the additional use of soil profile data in parameter estimation. Thus, the exclusive use of efflux data from leaching experiments at any scale can lead to fundamental misunderstandings of the underlying processes. Copyright 2003 Society of Chemical Industry [source]

Folding and binding cascades: Dynamic landscapes and population shifts

Sandeep Kumar
Abstract Whereas previously we have successfully utilized the folding funnels concept to rationalize binding mechanisms (Ma B, Kumar S, Tsai CJ, Nussinov R, 1999, Protein Eng 12:713,720) and to describe binding (Tsai CJ, Kumar S, Ma B, Nussinov R, 1999, Protein Sci 8:1181,1190), here we further extend the concept of folding funnels, illustrating its utility in explaining enzyme pathways, multimolecular associations, and allostery. This extension is based on the recognition that funnels are not stationary; rather, they are dynamic, depending on the physical or binding conditions (Tsai CJ, Ma B, Nussinov R, 1999, Proc Natl Acad Sci USA 96:9970,9972). Different binding states change the surrounding environment of proteins. The changed environment is in turn expressed in shifted energy landscapes, with different shapes and distributions of populations of conformers. Hence, the function of a protein and its properties are not only decided by the static folded three-dimensional structure; they are determined by the distribution of its conformational substates, and in particular, by the redistributions of the populations under different environments. That is, protein function derives from its dynamic energy landscape, caused by changes in its surroundings. [source]