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Distance Distributions (distance + distribution)
Selected AbstractsThe Study of Protein Folding and Dynamics by Determination of Intramolecular Distance Distributions and Their Fluctuations Using Ensemble and Single-Molecule FRET Measurements,CHEMPHYSCHEM, Issue 5 2005Elisha Haas Prof. Abstract The folding and dynamics of globular proteins is a multidimensional problem. The structures of the heterogeneous population of refolding protein molecules are characterized by multiple distances and time constants. Deciphering the mechanism of folding depends on studies of the processes rather than the folded structures alone. Spectroscopy is indispensable for these sorts of studies. Herein, it is shown that the determination of intramolecular distance distributions by ensemble and single-molecule FRET experiments enable the exploration of partially folded states of refolding protein molecules. [source] Investigation of nanocrystalline CdS,glutathione particles by radial distribution functionJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2003V. I. Korsounski Using high-energy synchrotron radiation, powder diffraction experiments were carried out on CdS nanocrystals stabilized with glutathione. The radial distribution function was calculated from the data and analysed. The nanoparticle core, of diameter estimated as 15,20,Å, consists of Cd and S atoms in the proportion 1:1. Inside the core, both Cd and S atoms coordinate each other approximately tetrahedrally. The surface S atoms are connected to just two or three Cd atoms of the core and belong to the glutathione molecules of the particle shell. These S atoms are also a part of the core structure and contribute about one half of the total number of S atoms per particle. First-neighbour Cd,S distances are 2.523,Å with a narrow distance distribution. No difference is observed between the lengths of Cd,S bonds involving the sulfur of the glutathione molecules and the sulfur atoms which are solely bound to Cd. The bond angle Cd,S,Cd at the surface bridging S atoms of glutathione is ca 99.5°, i.e. significantly smaller than an average one of 109.5° characteristic of the Cd and S atom packing inside the core. Beyond the range of the near interatomic distances, the influence of the surface and the defects cause a significant distinction of the particle core structure from those of zincblende and wurtzite, characteristic of bulk CdS. [source] Photolysis of Br2 in CCl4 studied by time-resolved X-ray scatteringACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2010Qingyu Kong A time-resolved X-ray solution scattering study of bromine molecules in CCl4 is presented as an example of how to track atomic motions in a simple chemical reaction. The structures of the photoproducts are tracked during the recombination process, geminate and non-geminate, from 100,ps to 10,µs after dissociation. The relaxation of hot Br2* molecules heats the solvent. At early times, from 0.1 to 10,ns, an adiabatic temperature rise is observed, which leads to a pressure gradient that forces the sample to expand. The expansion starts after about 10,ns with the laser beam sizes used here. When thermal artefacts are removed by suitable scaling of the transient solvent response, the excited-state solute structures can be obtained with high fidelity. The analysis shows that 30% of Br2* molecules recombine directly along the X potential, 60% are trapped in the A/A, state with a lifetime of 5.5,ns, and 10% recombine non-geminately via diffusive motion in about 25,ns. The Br,Br distance distribution in the A/A, state peaks at 3.0,Å. [source] The influence of positional errors on the Debye effectsACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2004P. H. Zwart The relation between a Gaussian perturbation of the atomic positional parameters and the average squared structure-factor amplitude is presented. Using an error-dependent radial distance distribution of an atomic protein model, it can be shown that the Debye effects diminish exponentially as a function of increasing positional errors. These relations can be used to estimate the quality of an atomic model and the corresponding phases. The limiting case of equal atoms with an infinitely large coordinate error results in the classical Wilson model. [source] Non-Covalent Interactions of Organic Halogen Compounds with Aromatic Systems , Analyses of Crystal Structure DataEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 6 2005Dariusz Swierczynski Abstract The Cambridge Structural Database showed in mid 2002 about 20.000 structures containing halogen atoms and aryl rests with distances d between the aryl center and the halogen atom, which would allow both hydrogen bonds with the aromatic hydrogens and/or van der Waalsinteractions with the ,-cloud. The latter are characterized by short distances d and by small angles , between the vector along the aryl centroid,halogen line and the perpendicular vector originating in the aryl center (the plane normal). The cases with d < 3.0 Å for F; and d < 3.5 Å for Cl, Br or I (outliers neglected), and , , 10 ± 5°, indicating predominating van der Waals forces, amount to several hundreds. The majority of fragments exhibit larger d and , values, in line with avoidance of electrostatic repulsion between the negative partial charges of the halogens and the ,-cloud center, and with an increasing electrostatic attraction with the aromatic hydrogen atoms. The corresponding hydrogen bonds are characterized by longer distances d and by angle values of , > 60° (about 40 % of the fragments), with only very few cases close to linear hydrogen bonds (then with , = 90°). Compounds containing metal,halogen bonds were omitted in view of possible strong orientational interferences. The structures were screened with four different halogen binding modes, all of them containing the halogen attached to a carbon atom, but with different hybrizations at the connecting carbon centers. The results show only small differences in the distance distributions, with a slight preference for smaller , values for sp2 frameworks. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Linking movement behaviour, dispersal and population processes: is individual variation a key?JOURNAL OF ANIMAL ECOLOGY, Issue 5 2009Colin Hawkes Summary 1Movement behaviour has become increasingly important in dispersal ecology and dispersal is central to the development of spatially explicit population ecology. The ways in which the elements have been brought together are reviewed with particular emphasis on dispersal distance distributions and the value of mechanistic models. 2There is a continuous range of movement behaviours and in some species, dispersal is a clearly delineated event but not in others. The biological complexities restrict conclusions to high-level generalizations but there may be principles that are common to dispersal and other movements. 3Random walk and diffusion models when appropriately elaborated can provide an understanding of dispersal distance relationships on spatial and temporal scales relevant to dispersal. Leptokurtosis in the relationships may be the result of a combination of factors including population heterogeneity, correlation, landscape features, time integration and density dependence. The inclusion in diffusion models of individual variation appears to be a useful elaboration. The limitations of the negative exponential and other phenomenological models are discussed. 4The dynamics of metapopulation models are sensitive to what appears to be small differences in the assumptions about dispersal. In order to represent dispersal realistically in population models, it is suggested that phenomenological models should be replaced by those based on movement behaviour incorporating individual variation. 5The conclusions are presented as a set of candidate principles for evaluation. The main features of the principles are that uncorrelated or correlated random walk, not linear movement, is expected where the directions of habitat patches are unpredictable and more complex behaviour when organisms have the ability to orientate or navigate. Individuals within populations vary in their movement behaviour and dispersal; part of this variation is a product of random elements in movement behaviour and some of it is heritable. Local and metapopulation dynamics are influenced by population heterogeneity in dispersal characteristics and heritable changes in dispersal propensity occur on time-scales short enough to impact population dynamics. [source] Accurate long-range distance measurements in a doubly spin-labeled protein by a four-pulse, double electron,electron resonance methodMAGNETIC RESONANCE IN CHEMISTRY, Issue 12 2008Michela G. Finiguerra Abstract Distance determination in disordered systems by a four-pulse double electron,electron resonance method (DEER or PELDOR) is becoming increasingly popular because long distances (several nanometers) and their distributions can be measured. From the distance distributions eventual heterogeneities and dynamics can be deduced. To make full use of the method, typical distance distributions for structurally well-defined systems are needed. Here, the structurally well-characterized protein azurin is investigated by attaching two (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl) methanethiosulfonate spin labels (MTSL) by site-directed mutagenesis. Mutations at the surface sites of the protein Q12, K27, and N42 are combined in the double mutants Q12C/K27C and K27C/N42C. A distance of 4.3 nm is found for Q12C/K27C and 4.6 nm for K27C/N42C. For Q12C/K27C the width of the distribution (0.24 nm) is smaller than for the K27C/N42C mutant (0.36 nm). The shapes of the distributions are close to Gaussian. These distance distributions agree well with those derived from a model to determine the maximally accessible conformational space of the spin-label linker. Additionally, the expected distribution for the shorter distance variant Q12C/N42C was modeled. The width is larger than the calculated one for Q12C/K27C by 21%, revealing the effect of the different orientation and shorter distance. The widths and the shapes of the distributions are suited as a reference for two unperturbed MTSL labels at structurally well-defined sites. Copyright © 2008 John Wiley & Sons, Ltd. [source] The Study of Protein Folding and Dynamics by Determination of Intramolecular Distance Distributions and Their Fluctuations Using Ensemble and Single-Molecule FRET Measurements,CHEMPHYSCHEM, Issue 5 2005Elisha Haas Prof. Abstract The folding and dynamics of globular proteins is a multidimensional problem. The structures of the heterogeneous population of refolding protein molecules are characterized by multiple distances and time constants. Deciphering the mechanism of folding depends on studies of the processes rather than the folded structures alone. Spectroscopy is indispensable for these sorts of studies. Herein, it is shown that the determination of intramolecular distance distributions by ensemble and single-molecule FRET experiments enable the exploration of partially folded states of refolding protein molecules. [source] | ||||||||||