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Distance Constraints (distance + constraint)
Selected AbstractsRestoring prairie pothole wetlands: does the species pool concept offer decision-making guidance for re-vegetation?APPLIED VEGETATION SCIENCE, Issue 2 2006Susan M. Galatowitsch Anon. (2004) Abstract Question: Do regional species pools, landscape isolation or on-site constraints cause plants from different guilds to vary in their ability to colonize restored wetlands? Location: Iowa, Minnesota, and South Dakota, USA. Methods: Floristic surveys of 41 restored wetlands were made three and 12 years after reflooding to determine changes in local species pools for eight plant guilds. The effect of landscape isolation on colonization efficiency was evaluated for each guild by plotting local species pools against distance to nearby natural wetlands, and the relative importance of dispersal vs. on-site constraints in limiting colonization was explored by comparing the local species pools of restored and natural wetlands within the region. Results: Of the 517 wetland plant taxa occurring in the region, 50% have established within 12 years. The proportion of the regional species pool represented in local species pools differed among guilds, with sedge-meadow perennials, emergent perennials and floating/submersed aquatics least represented (33-36%) and annual guilds most represented (74-94%). Colonization-to-extinction ratios suggest that floating/submersed aquatics have already reached a species equilibrium while sedge-meadow and emergent perennials are still accumulating species. Increasing distance to nearest wetlands decreased the proportion of the regional species pool present in local pools for all guilds except native annuals and woody plants. The maximum proportion predicted, assuming no distance constraint, was comparable to the lowest-diversity natural wetlands for most perennial guilds, and also lower than what was achieved in a planted, weeded restoration. Conclusions: A biotic constraints seem to limit the colonization of floating/submersed aquatics into natural or restored wetlands, whereas all other guilds are potentially constrained by dispersal or biotic factors (i.e. competition from invasive species). Using species pools to evaluate restoration progress revealed that immigration potential varies considerably among guilds, that local species richness does not necessarily correspond to immigration limitations, and that some guilds (e.g. sedge-meadow perennials) will likely benefit more than others from being planted at restoration sites. [source] Maximum likelihood constrained deconvolution.CONCEPTS IN MAGNETIC RESONANCE, Issue 2 2003II: Application to experimental two-, three-dimensional NMR spectra Abstract The maximum likelihood method (MLM) and related protocols were applied to the experimental 2-D nuclear Overhauser effect (NOE) spectrum of a 24-nucleotide RNA hairpin loop molecule. The output becomes more valuable when diagonal symmeterization is followed by MLM. This symmeterized maximum likelihood (SML) protocol restores the original spectral information with high fidelity by accurately partitioning components from overlapped peaks and provides substantial improvements in line shape and spectral resolution, in particular in the F1 dimension. These advantages lead to a simpler interpretation of the resonance frequencies, intensities, multiplet fine structure, and J -coupling values from a heavily overlapped peak region. This promises a more effective tool for peak picking, assignment, and integration. Also, application of MLM and related protocols to the 2-D NOE proton spectrum of a 24-mer RNA dramatically increases the number of NOE-based distance constraints that can be used for determination of its 3-D molecular structure. By application of 3-D MLM to a simple 3-D spectrum, the spectral resolution and signal-to-noise (S/N) ratio was greatly improved by effective line sharpening and reduction of cross-talk between planes. © 2003 Wiley Periodicals, Inc. Concepts Magn Reson 18A: 146,156, 2003 [source] Development of redundant rigidity theory for formation controlINTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL, Issue 13 2009Changbin Yu Abstract Multiagent formation control may proceed by ensuring that designated pairs of agents maintain a specified distance between each other, in order that the overall shape of the formation can be preserved while it translates or rotates. A minimally rigid formation is one in which loss of any one such constraint or link means that individual agent motions can occur, which do not preserve the shape of the formation. Recognizing that real-world formations may suffer link loss and even agent loss, this paper presents a systematic approach to defining a measure for redundant or nonminimal rigidity, which is the property that formation shape will still be preserved in the face of loss of a certain designated number of distance constraints or formation agents. Most of the results are concerned with advancing a deterministic measure, but this paper also indicates circumstances under which a statistical measure may be relevant. For illustration, the paper analyses a number of standard formations to establish their levels of redundancy. Copyright © 2008 John Wiley & Sons, Ltd. [source] Polyhedral studies for minimum-span graph labelling with integer distance constraintsINTERNATIONAL TRANSACTIONS IN OPERATIONAL RESEARCH, Issue 2 2007Vicky Mak Abstract This paper studies the polytope of the minimum-span graph labelling problems with integer distance constraints (DC-MSGL). We first introduce a few classes of new valid inequalities for the DC-MSGL defined on general graphs and briefly discuss the separation problems of some of these inequalities. These are the initial steps of a branch-and-cut algorithm for solving the DC-MSGL. Following that, we present our polyhedral results on the dimension of the DC-MSGL polytope, and that some of the inequalities are facet defining, under reasonable conditions, for the polytope of the DC-MSGL on triangular graphs. [source] Highly Ordered Interstitial Water Observed in Bone by Nuclear Magnetic Resonance,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 4 2005Erin E Wilson Abstract NMR was used to study the nanostructure of bone tissue. Distance measurements show that the first water layer at the surface of the mineral in cortical bone is structured. This water may serve to couple the mineral to the organic matrix and may play a role in deformation. Introduction: The unique mechanical characteristics of bone tissue have not yet been satisfactorily connected to the exact molecular architecture of this complex composite material. Recently developed solid-state nuclear magnetic resonance (NMR) techniques are applied here to the mineral component to provide new structural distance constraints at the subnanometer scale. Materials and Methods: NMR dipolar couplings between structural protons (OH, and H2O) and phosphorus (PO4) or carbon (CO3) were measured using the 2D Lee-Goldburg Cross-Polarization under Magic-Angle Spinning (2D LG-CPMAS) pulse sequence, which simultaneously suppresses the much stronger proton-proton dipolar interactions. The NMR dipolar couplings measured provide accurate distances between atoms, e.g., OH and PO4 in apatites. Excised and powdered femoral cortical bone was used for these experiments. Synthetic carbonate (,2-4 wt%)-substituted hydroxyapatite was also studied for structural comparison. Results: In synthetic apatite, the hydroxide ions are strongly hydrogen bonded to adjacent carbonate or phosphate ions, with hydrogen bond (O-H) distances of ,1.96 Å observed. The bone tissue sample, in contrast, shows little evidence of ordered hydroxide. Instead, a very ordered (structural) layer of water molecules is identified, which hydrates the small bioapatite crystallites through very close arrangements. Water protons are ,2.3-2.55 Å from surface phosphorus atoms. Conclusions: In synthetic carbonated apatite, strong hydrogen bonds were observed between the hydroxide ions and structural phosphate and carbonate units in the apatite crystal lattice. These hydrogen bonding interactions may contribute to the long-range stability of this mineral structure. The biological apatite in cortical bone tissue shows evidence of hydrogen bonding with an ordered surface water layer at the faces of the mineral particles. This structural water layer has been inferred, but direct spectroscopic evidence of this interstitial water is given here. An ordered structural water layer sandwiched between the mineral and the organic collagen fibers may affect the biomechanical properties of this complex composite material. [source] Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3DJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 8 2010Daniele Fabris Abstract Chemical probing represents a very versatile alternative for studying the structure and dynamics of substrates that are intractable by established high-resolution techniques. The implementation of MS-based strategies for the characterization of probing products has not only extended the range of applicability to virtually all types of biopolymers but has also paved the way for the introduction of new reagents that would not have been viable with traditional analytical platforms. As the availability of probing data is steadily increasing on the wings of the development of dedicated interpretation aids, powerful computational approaches have been explored to enable the effective utilization of such information to generate valid molecular models. This combination of factors has contributed to making the possibility of obtaining actual 3D structures by MS-based technologies (MS3D) a reality. Although approaches for achieving structure determination of unknown targets or assessing the dynamics of known structures may share similar reagents and development trajectories, they clearly involve distinctive experimental strategies, analytical concerns and interpretation paradigms. This Perspective offers a commentary on methods aimed at obtaining distance constraints for the modeling of full-fledged structures while highlighting common elements, salient distinctions and complementary capabilities exhibited by methods used in dynamics studies. We discuss critical factors to be addressed for completing effective structural determinations and expose possible pitfalls of chemical methods. We survey programs developed for facilitating the interpretation of experimental data and discuss possible computational strategies for translating sparse spatial constraints into all-atom models. Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological systems. Copyright © 2010 John Wiley & Sons, Ltd. [source] The role of segment 32,47 of cholecystokinin receptor type A in CCK8 binding: synthesis, nuclear magnetic resonance, circular dichroism and fluorescence studiesJOURNAL OF PEPTIDE SCIENCE, Issue 3 2003Stefania De Luca Abstract The segment 32,47 of the N -terminal extracellular domain of the type A cholecystokinin receptor, CCKA -R(32,47), was synthesized and structurally characterized in a membrane mimicking environment by CD, NMR and molecular dynamics calculations. The region of CCKA -R(32,47) encompassing residues 39,46 adopted a well-defined secondary structure in the presence of DPC micelles, whereas the conformation of the N -terminal region (segment 32,37) could not be uniquely defined by the NOE derived distance constraints because of local flexibility. The conformation of the binding domain of CCKA -R(32,47) was different from that found for the intact N -terminal receptor tail, CCKA -R(1,47). To assess whether CCKA -R(32,47) was still able to bind the nonsulfated cholecystokinin C -terminal octapeptide, CCK8, a series of titrations was carried out in SDS and DPC micelles, and the binding interaction was followed by fluorescence spectroscopy. These titrations gave no evidence for complex formation, whereas a high binding affinity was found between CCKA -R(1,47) and CCK8. The different affinities for the ligand shown by CCKA -R(32,47) and CCKA -R(1,47) were paralleled by different interaction modes between the receptor segments and the micelles. The interaction of CCKA -R(32,47) with DPC micelles was much weaker than that of CCKA -R(1,47), because the former receptor segment lacks proper stabilizing contacts with the micelle surface. In the case of SDS micelles CCKA -R(32,47) was found to form non-micellar adducts with the detergent that prevented the onset of a functionally significant interaction between the receptor segment and the micelle. It is concluded that tertiary structure interactions brought about by the 1,31 segment play a key role in the stabilization of the membrane bound, biologically active conformation of the N -terminal extracellular tail of the CCKA receptor. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] Are Complex A and the Orphan stream related?MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY: LETTERS (ELECTRONIC), Issue 1 2007Shoko Jin ABSTRACT We consider the possibility that the Galactic neutral hydrogen stream Complex A and the stellar Orphan stream are related, and use this hypothesis to determine possible distances to Complex A and the Orphan stream, and line-of-sight velocities for the latter. The method presented uses our current knowledge of the projected positions of the streams, as well as line-of-sight velocities for Complex A, and we show that a solution exists in which the two streams share the same orbit. If Complex A and the Orphan stream are on this orbit, our calculations suggest the Orphan stream to be at an average distance of 9 kpc, with heliocentric radial velocities of approximately ,95 km s,1. Complex A would be ahead of the Orphan stream in the same wrap of the orbit, with an average distance of 4 kpc, which is consistent with the distance constraints determined through interstellar absorption line techniques. [source] On labeling the vertices of products of complete graphs with distance constraintsNAVAL RESEARCH LOGISTICS: AN INTERNATIONAL JOURNAL, Issue 2 2005D.J. Erwin Variations of Hale's channel assignment problem, the L(j, k)-labeling problem and the radio labeling problem require the assignment of integers to the vertices of a graph G subject to various distance constraints. The ,j,k -number of G and the radio number of G are respectively the minimum span among all L(j, k)-labelings, and the minimum span plus 1 of all radio labelings of G (defined in the Introduction). In this paper, we establish the ,j,k -number of ,K for pairwise relatively prime integers t1 < t2 < , < tq, t1 , 2. We also show the existence of an infinite class of graphs G with radio number |V(G)| for any diameter d(G). © 2003 Wiley Periodicals, Inc. Naval Research Logistics, 2005 [source] Enhancement of bound-state residual dipolar couplings: Conformational analysis of lactose bound to Galectin-3PROTEIN SCIENCE, Issue 7 2006Tiandi Zhuang Abstract Residual dipolar couplings (RDCs) have proven to be a valuable NMR tool that can provide long-range constraints for molecular structure determination. The constraints are orientational in nature and are, thus, highly complementary to conventional distance constraints from NOE data. This complementarity would seem to extend to the study of the geometry of ligands bound to proteins. However, unlike transferred NOEs, where collection, even with a large excess of free ligand, results in measurements dominated by bound contributions, RDCs of exchanging ligands can be dominated by free-state contributions. Here we present a strategy for enhancement of RDCs from bound states that is based on specifically enhancing the alignment of the protein to which a ligand will bind. The protein is modified by addition of a hydrophobic alkyl tail that anchors it to the bicelles that are a part of the ordering medium needed for RDC measurement. As an illustration, we have added a propyl chain to the C terminus of the carbohydrate recognition domain of the protein, Galectin-3, and report enhanced RDCs that prove consistent with known bound-ligand geometries for this protein. [source] A helix-turn motif in the C-terminal domain of histone H1PROTEIN SCIENCE, Issue 4 2000Roger Vila Abstract The structural study of peptides belonging to the terminal domains of histone H1 can be considered as a step toward the understanding of the function of H1 in chromatin. The conformational properties of the peptide Ac-EPKRSVAFKKT KKEVKKVATPKK (CH-1), which belongs to the C-terminal domain of histone Hl° (residues 99,121) and is adjacent to the central globular domain of the protein, were examined by means of 1H-NMR and circular dichroism. In aqueous solution, CH-1 behaved as a mainly unstructured peptide, although turn-like conformations in rapid equilibrium with the unfolded state could be present. Addition of trifluoroethanol resulted in a substantial increase of the helical content. The helical limits, as indicated by (i, i + 3) nuclear Overhauser effect (NOE) cross correlations and significant up-field conformational shifts of the C, protons, span from Pro100 to Val 116, with Glu99 and Ala117 as N- and C-caps. A structure calculation performed on the basis of distance constraints derived from NOE cross peaks in 90% trifluoroethanol confirmed the helical structure of this region. The helical region has a marked amphipathic character, due to the location of all positively charged residues on one face of the helix and all the hydrophobic residues on the opposite face. The peptide has a TPKK motif at the C-terminus, following the ,-helical region. The observed NOE connectivities suggest that the TPKK sequence adopts a type (I) ,-turn conformation, a ,-turn conformation or a combination of both, in fast equilibrium with unfolded states. Sequences of the kind (S/T)P(K/R)(K/R) have been proposed as DNA binding motifs. The CH-1 peptide, thus, combines a positively charged amphipathic helix and a turn as potential DNA-binding motifs. [source] Rigidity and persistence for ensuring shape maintenance of multi-agent meta-formations,ASIAN JOURNAL OF CONTROL, Issue 2 2008Julien M. Hendrickx Abstract This paper treats the problem of merging formations, where the underlying model of a formation is graphical. We first analyze the rigidity and persistence of meta-formations, which are formations obtained by connecting several rigid or persistent formations. Persistence is a generalization to directed graphs of the undirected notion of rigidity. In the context of moving autonomous agent formations, persistence characterizes the efficacy of a directed structure of unilateral distance constraints seeking to preserve a formation shape. We derive then, for agents evolving in a two- or three-dimensional space, the conditions under which a set of persistent formations can be merged into a persistent meta-formation, and give the minimal number of interconnections needed for such a merging. We also give conditions for a meta-formation obtained by merging several persistent formations to be persistent. Copyright © 2008 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society [source] Self-Assembled Amphotericin,B Is Probably Surrounded by Ergosterol: Bimolecular Interactions as Evidenced by Solid-State NMR and CD SpectraCHEMISTRY - A EUROPEAN JOURNAL, Issue 4 2008Yusuke Kasai Dr. Abstract Amphotericin,B (AmB) is thought to exert its pharmacological effects by forming a barrel-stave assembly with ergosterol in fungal membranes. To examine the interaction between AmB and ergosterol (Erg) or cholesterol (Cho), 13C- and 19F-labelled covalent conjugates were prepared as reported previously (N. Matsumori et,al. Chem. Biol.2004, 11, 673,679). The CD spectra of the conjugates in a membrane-bound form suggested that the distance between the heptaene moieties of the ergosterol conjugates AmB,C2,(6-F)Erg 2 and AmB,C2,Erg 3 is similar to that of AmB in ergosterol-containing membranes, but significantly larger than that of AmB in nonsterol or cholesterol-containing membranes. These observations suggest that, as is the case with ergosterol-containing membranes, the conjugated sterol moiety prevents the close contact between the heptaene moieties within the membrane that would reduce channel conductivity of the AmB assemblies. To further investigate this bimolecular interaction, we recorded the solid-state NMR spectra of conjugates 2 and AmB,C2,(6-F)Cho 4, which are composed of uniformly 13C-labelled AmB and 6-fluorinated ergosterol or cholesterol; the conjugates were expected to facilitate the estimation of distances between the fluorine and carbon atoms. By using rotor-synchronous double resonance (rotational echo double resonance of X cluster; RDX) experiments, we deduced the distance between the fluorine atom and its nearest carbon atom in the heptaene moiety of 2 to be less than 8.6,Å. This indicates that the B,ring of ergosterol comes close to the AmB polyene moiety. A conformational search of the AmB,ergosterol conjugate by using distance constraints derived from the RDX results suggested that ergosterol molecules possibly surround the AmB assembly, which is in contrast with the conventional image in which ergosterol is inserted into AmB molecules. [source] Solution Structure of , -Am2766: A Highly Hydrophobic , -Conotoxin from Conus amadis That Inhibits Inactivation of Neuronal Voltage-Gated Sodium ChannelsCHEMISTRY & BIODIVERSITY, Issue 4 2005Siddhartha The three-dimensional (3D) NMR solution structure (MeOH) of the highly hydrophobic , -conotoxin , -Am2766 from the molluscivorous snail Conus amadis has been determined. Fifteen converged structures were obtained on the basis of 262 distance constraints, 25 torsion-angle constraints, and ten constraints based on disulfide linkages and H-bonds. The root-mean-square deviations (rmsd) about the averaged coordinates of the backbone (N, C,, C) and (all) heavy atoms were 0.62±0.20 and 1.12±0.23,Å, respectively. The structures determined are of good stereochemical quality, as evidenced by the high percentage (100%) of backbone dihedral angles that occupy favorable and additionally allowed regions of the Ramachandran map. The structure of , -Am2766 consists of a triple-stranded antiparallel , -sheet, and of four turns. The three disulfides form the classical ,inhibitory cysteine knot' motif. So far, only one tertiary structure of a , -conotoxin has been reported; thus, the tertiary structure of , -Am2766 is the second such example. Another Conus peptide, Am2735 from C. amadis, has also been purified and sequenced. Am2735 shares 96% sequence identity with , -Am2766. Unlike , -Am2766, Am2735 does not inhibit the fast inactivation of Na+ currents in rat brain Nav1.2 Na+ channels at concentrations up to 200,nM. [source] | ||||||||||||||||