A graphical method for the analysis of anisotropic rotational diffusion in proteins

A graphical method for the analysis of relaxation data is presented. It allows a fast estimation of the range of values of the components of the axially symmetric rotational diffusion tensor that are compatible with the experimental relaxation data. The graphical method clearly shows the contribution of different experimental relaxation parameters to the measured anisotropy. In particular, for proteins with moderate anisotropy, data from at least two N-H bonds forming angles close to 0° and 90° with respect to the principal axis of the rotational diffusional tensor are needed. For very anisotropic systems, combination of different relaxation parameters from a single residue is enough to characterize the local anisotropy.     

The inherent properties of DNA four-way junctions: comparing the crystal structures of holliday junctions

Holliday junctions are four-stranded DNA complexes that are formed during recombination and related DNA repair events. Much work has focused on the overall structure and properties of four-way junctions in solution, but we are just now beginning to understand these complexes at the atomic level. The crystal structures of two all-DNA Holliday junctions have been determined recently from the sequences d(CCGGGACCGG) and d(CCGGTACCGG). A detailed comparison of the two structures helps to distinguish distortions of the DNA conformation that are inherent to the cross-overs of the junctions in this crystal system from those that are consequences of the mismatched dG.dA base-pair in the d(CCGGGACCGG) structure. This analysis shows that the junction itself perturbs the sequence-dependent conformational features of the B-DNA duplexes and the associated patterns of hydration in the major and minor grooves only minimally. This supports the idea that a DNA four-way junction can be assembled at relatively low energetic cost. Both structures show a concerted rotation of the adjacent duplex arms relative to B-DNA, and this is discussed in terms of the conserved interactions between the duplexes at the junctions and further down the helical arms. The interactions distant from the strand cross-overs of the junction appear to be significant in defining its macroscopic properties, including the angle relating the stacked duplexes across the junction.     

Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR

HYDRONMR is an implementation of state of the art hydrodynamic modeling to calculate the spectral density functions for NH or C-H vectors in a rigid protein structure starting from an atomic level representation. Thus HYDRONMR can be used to predict NMR relaxation times from a rigid model and to compare them with the experimental results. HYDRONMR contains a single adjustable parameter, the atomic element radius. A protocol to determine the value that gives the best agreement between calculated and experimental T₁/T₂values is described. For most proteins, the value of the atomic element radius ranges between 2.8 Å and 3.8 Å with a distribution centered at 3.3 Å. Deviations from the usual range towards larger values are associated to aggregation in several proteins. Deviations to lower values may be related to large-scale motions or inappropriate model structures.If the average structure is correct, deviations between experimental T₁/T₂values and those calculated with HYDRONMR can be used to distinguish residues affected by anisotropic motion from those that are involved in chemical exchange.     

Analysis of highly phosphorylated inositols in avian and crocodilian erythrocytes

Both morphological and paleontological characteristics support the hypothesis of a monophyletic origin of crocodilian and avian groups. However, while the erythrocytes of all birds studied to date are reported to contain high levels of inositol pentakisphosphate (InsP(5)), which acts as an allosteric effector of hemoglobin, this molecule has not been reported in crocodilian erythrocytes. In this study we compare the highly phosphorylated inositols in crocodilian and avian erythrocytes using a particularly sensitive analytical procedure. Our aim was to obtain new data which might provide further evidence for the monophyletic origin, or otherwise, of crocodiles and birds. We studied three avian and three crocodilian species. The erythrocytes of the three bird species contained low levels of inositol-3,4,5,6-tetrakisphosphate and inositol-1,3,4,6-tetrakisphosphate, thought to be precursors of Ins(1,3,4,5,6)P(5). The crocodilian erythrocytes studied contained Ins(1,3,4,5,6)P(5) and InsP(6) in higher concentrations than those found in mammal erythrocytes and in other more active cells such as macrophages. Our data provide further evidence of the similarity between crocodilian and avian groups and agree with the hypothesis that both groups evolved from a common ancestor. The process by which the function of inositol phosphates changed from that of intracellular signaling to hemoglobin allosteric effector is discussed.     

Changes in mitochondrial electron partitioning in response to herbicides inhibiting branched-chain amino acid biosynthesis in soybean

The adaptation of the respiratory metabolism in roots of soybean (Glycine max L. Merr. cv Ransom) treated with herbicides that inhibit the enzyme acetolactate synthase (ALS) was analyzed. A new gas phase dual-inlet mass spectrometry system for simultaneous measurement of 34O2 to 32O2 and O2 to N2 ratios has been developed. This system is more accurate than previously described systems, allows measurements of much smaller oxygen gradients, and, as a consequence, works with tissues that have lower respiration rates. ALS inhibition caused an increase of the alternative oxidase (AOX) protein and an accumulation of pyruvate. The combination of these two effects is likely to induce the activation of the alternative pathway and its participation in the total respiration. Moreover, the start of the alternative pathway activation and the increase of AOX protein were before the decline in the activity of cytochrome pathway. The possible role of AOX under ALS inhibition is discussed.     

MIPSIM: similarity analysis of molecular interaction potentials

SUMMARY: MIPSIM is a computational package designed to analyse and compare 3D distributions of molecular interaction potentials (MIP) of series of biomolecules.     

EFFECT OF GRAZING-ASSOCIATED INFOCHEMICALS ON GROWTH AND MORPHOLOGICAL DEVELOPMENT IN SCENEDESMUS ACUTUS (CHLOROPHYCEAE)

Populations of the phenotypically plastic alga Scenedesmus acutus Meyen were cultured in standard medium or in medium with filtered water from a Daphnia culture to examine the expression of ecomorphs in both water types. A rapid formation of four- and eight-celled coenobia was observed in the presence of Daphnia water, but not in standard medium. Moreover, cell dimensions were increased in the Daphnia water containing medium. Population growth rates were comparable in both water types; however, the carrying capacity appeared significantly lower in Daphnia water. Daphnia needed to feed on digestible food to produce the colony-inducing chemicals; medium from starved animals and Daphnia fed polystyrene beads appeared inactive. Neither suspensions of homogenate of Scenedesmus and Cryptomonas nor auxins affected colony formation or growth rate in S. acutus. The colony-inducing infochemicals are probably not constituents of the algae themselves; however, modification of algal constituents in the digestive system of daphniids may be involved.     

OPA1 (dys)functions

Mitochondrial morphology varies according to cell type and cellular context from an interconnected filamentous network to isolated dots. This morphological plasticity depends on mitochondrial dynamics, a balance between antagonistic forces of fission and fusion. DRP1 and FIS1 control mitochondrial outer membrane fission and Mitofusins its fusion. This review focuses on OPA1, one of the few known actors of inner membrane dynamics, whose mutations provoke an optic neuropathy. Since its first identification in 2000 the characterization of the functions of OPA1 has made rapid progress thus providing numerous clues to unravel the pathogenetic mechanisms of ADOA-1.