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Topological Features (topological + feature)
Selected AbstractsUnfolding the fold of cyclic cysteine-rich peptidesPROTEIN SCIENCE, Issue 3 2008Amarda Shehu Abstract We propose a method to extensively characterize the native state ensemble of cyclic cysteine-rich peptides. The method uses minimal information, namely, amino acid sequence and cyclization, as a topological feature that characterizes the native state. The method does not assume a specific disulfide bond pairing for cysteines and allows the possibility of unpaired cysteines. A detailed view of the conformational space relevant for the native state is obtained through a hierarchic multi-resolution exploration. A crucial feature of the exploration is a geometric approach that efficiently generates a large number of distinct cyclic conformations independently of one another. A spatial and energetic analysis of the generated conformations associates a free-energy landscape to the explored conformational space. Application to three long cyclic peptides of different folds shows that the conformational ensembles and cysteine arrangements associated with free energy minima are fully consistent with available experimental data. The results provide a detailed analysis of the native state features of cyclic peptides that can be further tested in experiment. [source] Intramolecular interactions and intramolecular hydrogen bonding in conformers of gaseous glycineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2001L. F. Pacios Abstract Ab initio calculations at the MP2/6-311++G** level of theory led recently to the identification of 13 stable conformers of gaseous glycine with relative energies within 11 kcal/mol. The stability of every structure depends on subtle intramolecular effects arising from conformational changes. These intramolecular interactions are examined with the tools provided by the Atoms In Molecules (AIM) theory, which allows obtaining a wealth of quantum mechanics information from the molecular electron density ,(r). The analysis of the topological features of ,(r) on one side and the atomic properties integrated in the basins defined by the gradient vector field of the density on the other side makes possible to explore the different intramolecular effects in every conformer. The existence of intramolecular hydrogen bonds on some conformers is demonstrated, while the presence of other stabilizing interactions arising from favorable conformations is shown to explain the stability of other structures in the potential energy surface of glycine. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 702,716, 2001 [source] Lipid trafficking to the outer membrane of Gram-negative bacteriaMOLECULAR MICROBIOLOGY, Issue 3 2006William T. Doerrler Summary The envelope of Gram-negative bacteria is composed of two distinct lipid membranes: an inner membrane and outer membrane. The outer membrane is an asymmetric bilayer with an inner leaflet of phospholipids and an outer leaflet of lipopolysaccharide. Most of the steps of lipid synthesis occur within the cytoplasmic compartment of the cell. Lipids must then be transported across the inner membrane and delivered to the outer membrane. These topological features combined with the ability to apply the tools of biochemistry and genetics make the Gram-negative envelope a fascinating model for the study of lipid trafficking. In addition, as lipopolysaccharide is essential for growth of most strains and is a potent inducer of the mammalian innate immune response via activation of Toll-like receptors, Gram-negative lipid transport is also a promising target for the development of novel antibacterial and anti-inflammatory compounds. This review focuses on recent developments in our understanding of lipid transport across the inner membrane and to the outer membrane of Gram-negative bacteria. [source] Stability and coexistence in a lawn community: mathematical prediction of stability using a community matrix with parameters derived from competition experimentsOIKOS, Issue 2 2000Stephen H. Roxburgh Community matrix theory has been proposed as a means of predicting whether a particular set of species will form a stable mixture. However, the approach has rarely been used with data from real communities. Using plant competition experiments, we use community matrix theory to predict the stability and competitive structuring of a lawn community. Seven species from the lawn, including the six most abundant, were grown in boxes, in conditions very similar to those on the lawn. They were grown alone (monocultures), and in all possible pairs. The species formed a transitive hierarchy of competitive ability, with most pairs of species showing asymmetric competition. Relative competitive ability (competitive effect) was positively correlated with published estimates of the maximum relative growth rate (RGRmax) for the same species. A seven-species community matrix predicted the mixture of species to be unstable. Simulations revealed two topological features of this community matrix. First, the matrix was closer to the stability/instability boundary than predicted from a range of null (random) models, suggesting that the lawn may be close to stability. Second, the tendencies of the lawn species to compete asymmetrically, and to be arranged in competitive hierarchies, were found to be positively associated with stability, and hence may be contributing factors to the near-stability seen in the matrix. The limitations of using competition experiments for constructing community matrices are discussed. [source] The ankyrin repeat as molecular architecture for protein recognitionPROTEIN SCIENCE, Issue 6 2004Leila K. Mosavi Abstract The ankyrin repeat is one of the most frequently observed amino acid motifs in protein databases. This protein,protein interaction module is involved in a diverse set of cellular functions, and consequently, defects in ankyrin repeat proteins have been found in a number of human diseases. Recent biophysical, crystallographic, and NMR studies have been used to measure the stability and define the various topological features of this motif in an effort to understand the structural basis of ankyrin repeat-mediated protein,protein interactions. Characterization of the folding and assembly pathways suggests that ankyrin repeat domains generally undergo a two-state folding transition despite their modular structure. Also, the large number of available sequences has allowed the ankyrin repeat to be used as a template for consensus-based protein design. Such projects have been successful in revealing positions responsible for structure and function in the ankyrin repeat as well as creating a potential universal scaffold for molecular recognition. [source] Charge density distribution in aminomethylphosphonic acidACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2010Janicki The experimental charge density distribution in aminomethylphosphonic acid has been determined from X-ray diffraction and its topological features have been analyzed. The results have shown that the P,O bonds are highly polarized, moreover the P,OH bond is weaker than the bonds to unprotonated O atoms. These facts have been confirmed by theoretical density functional theory (DFT) calculations, which have shown that the single, strongly polarized bonds within the phosphonate group are modified by hyperconjugation effects. [source] Description of protein,DNA complexes in terms of electron-density topological featuresACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2003Andy Becue This paper presents a computer-modelling approach for the generation of low-resolution representations of two protein,DNA complexes, NF-,B and HIF-1. The representation is obtained by topological analysis of electron-density maps at 2.85,Å crystallographic resolution, which leads to a set containing a limited number of critical points (CP). Analyses of the structure and properties of the CP graphs (density at peak position, volume and ellipticity), as well as comparisons with other reduced representations, are performed in order to assess the usefulness of such representations in molecular-docking applications at medium resolution. [source] | |||||||||||||