Lowest Energy (lowest + energy)

Distribution by Scientific Domains

Terms modified by Lowest Energy

  • lowest energy conformation
  • lowest energy conformer
  • lowest energy structure

  • Selected Abstracts

    Prey protein influences growth and decoration building in the orb web spider Argiope keyserlingi

    Abstract. 1. Protein is important for a foraging animal to consume, as it promotes growth and enhances survival, particularly in web-building spiders, which need to invest considerable protein into web building and may trade-off growth for web investment. 2. The influence of dietary protein uptake on growth and web investment was tested in the orb web spider Argiope keyserlingi, by feeding them flies reared on three different media: (1) high protein, (2) low protein, and (3) standard (control) media. There was a negative correlation between protein and energy content of the flies across treatments; flies reared on the high protein media had the highest protein, but lowest energy, while flies reared on the low protein media had the lowest protein but highest energy. 3. It was found that silk investment and web architecture in A. keyserlingi was not affected by diet. Growth and decoration building were both enhanced when spiders were fed a high protein diet. 4. It was concluded that protein intake, rather than energy, influenced both growth and decoration building because: (1) protein intake enhances growth in other animals, (2) protein is essential for silk synthesis, especially aciniform silk, and (3) protein is a limiting factor actively sought by foraging animals in natural environments. [source]

    The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

    Ivelin Georgiev
    Abstract One of the main challenges for protein redesign is the efficient evaluation of a combinatorial number of candidate structures. The modeling of protein flexibility, typically by using a rotamer library of commonly-observed low-energy side-chain conformations, further increases the complexity of the redesign problem. A dominant algorithm for protein redesign is dead-end elimination (DEE), which prunes the majority of candidate conformations by eliminating rigid rotamers that provably are not part of the global minimum energy conformation (GMEC). The identified GMEC consists of rigid rotamers (i.e., rotamers that have not been energy-minimized) and is thus referred to as the rigid-GMEC. As a postprocessing step, the conformations that survive DEE may be energy-minimized. When energy minimization is performed after pruning with DEE, the combined protein design process becomes heuristic, and is no longer provably accurate: a conformation that is pruned using rigid-rotamer energies may subsequently minimize to a lower energy than the rigid-GMEC. That is, the rigid-GMEC and the conformation with the lowest energy among all energy-minimized conformations (the minimized-GMEC) are likely to be different. While the traditional DEE algorithm succeeds in not pruning rotamers that are part of the rigid-GMEC, it makes no guarantees regarding the identification of the minimized-GMEC. In this paper we derive a novel, provable, and efficient DEE-like algorithm, called minimized-DEE (MinDEE), that guarantees that rotamers belonging to the minimized-GMEC will not be pruned, while still pruning a combinatorial number of conformations. We show that MinDEE is useful not only in identifying the minimized-GMEC, but also as a filter in an ensemble-based scoring and search algorithm for protein redesign that exploits energy-minimized conformations. We compare our results both to our previous computational predictions of protein designs and to biological activity assays of predicted protein mutants. Our provable and efficient minimized-DEE algorithm is applicable in protein redesign, protein-ligand binding prediction, and computer-aided drug design. 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source]

    SODOCK: Swarm optimization for highly flexible protein,ligand docking

    Hung-Ming Chen
    Abstract Protein,ligand docking can be formulated as a parameter optimization problem associated with an accurate scoring function, which aims to identify the translation, orientation, and conformation of a docked ligand with the lowest energy. The parameter optimization problem for highly flexible ligands with many rotatable bonds is more difficult than that for less flexible ligands using genetic algorithm (GA)-based approaches, due to the large numbers of parameters and high correlations among these parameters. This investigation presents a novel optimization algorithm SODOCK based on particle swarm optimization (PSO) for solving flexible protein,ligand docking problems. To improve efficiency and robustness of PSO, an efficient local search strategy is incorporated into SODOCK. The implementation of SODOCK adopts the environment and energy function of AutoDock 3.05. Computer simulation results reveal that SODOCK is superior to the Lamarckian genetic algorithm (LGA) of AutoDock, in terms of convergence performance, robustness, and obtained energy, especially for highly flexible ligands. The results also reveal that PSO is more suitable than the conventional GA in dealing with flexible docking problems with high correlations among parameters. This investigation also compared SODOCK with four state-of-the-art docking methods, namely GOLD 1.2, DOCK 4.0, FlexX 1.8, and LGA of AutoDock 3.05. SODOCK obtained the smallest RMSD in 19 of 37 cases. The average 2.29 of the 37 RMSD values of SODOCK was better than those of other docking programs, which were all above 3.0 . 2006 Wiley Periodicals, Inc. J Comput Chem 28: 612,623, 2007 [source]

    Computational analyses of singlet,singlet and singlet,triplet transitions in mononuclear gold-capped carbon-rich conjugated complexes

    Zexing Cao
    Abstract Density functional theory and CASSCF calculations have been used to determine equilibrium geometries and vibrational frequencies of metal-capped one-dimensional ,-conjugated complexes (H3P)Au(CC)n(Ph) (n = 1,6), (H3P)Au(CCC6H4)(CCPh), and H3PAu(CCC6H4)CCAuPH3 in their ground states and selected low-lying ,,* excited states. Vertical excitation energies for spin-allowed singlet,singlet and spin-forbidden singlet,triplet transitions determined by the time-dependent density functional theory show good agreement with available experimental observations. Calculations indicate that the lowest energy 3(,,*) excited state is unlikely populated by the direct electronic excitation, while the low-lying singlet and triplet states, slightly higher in energy than the lowest triplet state, are easily accessible by the excitation light used in experiments. A series of radiationless transitions among related excited states yield the lowest 3(,,*) state, which has enough long lifetimes to exhibit its photochemical reactivities. 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1214,1221, 2005 [source]

    Ab initio crystal structure predictions for flexible hydrogen-bonded molecules.

    Part III.
    Abstract In crystal structure predictions possible structures are usually ranked according to static energy. Here, this criterion has been replaced by the free energy at any temperature. The effects of harmonic lattice vibrations were found by standard lattice-dynamical calculations, including a rough estimate of the effects of thermal expansion. The procedure was tested on glycol and glycerol, for which accurate static energies had been obtained previously (Part II of this series). It was found that entropy and zero-point energy give the largest contribution to free energy differences between hypothetical crystal structures, adding up to about 3 kJ/mol for the structures with lowest energy. The temperature-dependent contribution to the energy and the effects of thermal expansion showed less variation among the structures. The overall accuracy in relative energies was estimated to be a few kJ/mol. The experimental crystal structure for glycol corresponded to the global free energy minimum, whereas for glycerol it ranked second at 1 kJ/mol. 2001 John Wiley & Sons, Inc. J Comput Chem 22: 816,826, 2001 [source]

    The sequence TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase displays structural ambivalence and interconverts between ,-helical and ,-hairpin conformations mediated by collapsed conformational states

    Sunita Patel
    Abstract The peptide TGAAKAVALVL from glyceraldehyde-3-phosphate dehydrogenase adopts a helical conformation in the crystal structure and is a site for two hydrated helical segments, which are thought to be helical folding intermediates. Overlapping sequences of four to five residues from the peptide, sample both helical and strand conformations in known protein structures, which are dissimilar to glyceraldehyde-3-phosphate dehydrogenase suggesting that the peptide may have a structural ambivalence. Molecular dynamics simulations of the peptide sequence performed for a total simulation time of 1.2 s, starting from the various initial conformations using GROMOS96 force field under NVT conditions, show that the peptide samples a large number of conformational forms with transitions from ,-helix to ,-hairpin and vice versa. The peptide, therefore, displays a structural ambivalence. The mechanism from ,-helix to ,-hairpin transition and vice versa reveals that the compact bends and turns conformational forms mediate such conformational transitions. These compact structures including helices and hairpins have similar hydrophobic radius of gyration (Rgh) values suggesting that similar hydrophobic interactions govern these conformational forms. The distribution of conformational energies is Gaussian with helix sampling lowest energy followed by the hairpins and coil. The lowest potential energy of the full helix may enable the peptide to take up helical conformation in the crystal structure of the glyceraldehyde-3-phosphate dehydrogenase, even though the peptide has a preference for hairpin too. The relevance of folding and unfolding events observed in our simulations to hydrophobic collapse model of protein folding are discussed. Copyright 2007 European Peptide Society and John Wiley & Sons, Ltd. [source]

    Shape transition of medium-sized neutral silicon clusters

    A. Sieck
    Abstract Addressing the shape transition of silicon clusters, indicated by mobility experiments on silicon cluster cations with 24 to 30 atoms, we investigate the structure of low energy neutral silicon clusters with 25, 29, and 35 atoms within a density-functional based tight-binding approach. Since there is strong evidence for several nearly degenerate low-energy isomers for clusters of this size, we perform an extensive, but limited global search with Simulated Annealing and statistically analyze for each cluster size the 100 clusters with the lowest energy. We find different dominant shapes in the set of low energy clusters for each size. For neutral silicon clusters with 25 atoms, both prolate and spherical structures with low cohesive energies exist. For clusters containing 29 or 35 atoms, the low-energy isomers exhibit a spherical shape. For each cluster size several stable isomers with similar shapes, and hence similar mobilities, but different bonding patterns exist. The most stable 25 atom cluster resulting from our global search has the lowest energy within DFT-GGA known so far. Finally, we investigate the transition to diamond-like bonding patterns expected for larger silicon clusters. Clusters with up to 239 atoms resemble amorphous silicon rather than the diamond structure and contain several highly coordinated atoms. ( 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

    Ab initio and density functional theory studies of the structure, gas-phase acidity and aromaticity of tetraselenosquaric acid

    Li-Xin Zhou
    Abstract Results of ab initio self-consistent-field (SCF) and density functional theory (DFT) calculations of the gas-phase structure, acidity (free energy of deprotonation, ,G*) and aromaticity of tetraselenosquaric acid (3, 4-diselenyl-3-cyclobutene-1,2-diselenone, H2 C4 Se4)are reported. The global minimum found on the potential energy surface of tetraselenosquaric acid presents a planar conformation. The ZZ isomer was found to have the lowest energy among the three planar conformers and the ZZ and ZE isomers are very dose in energy. The optimized geometric parameters exhibit a bond length equalization relative to reference compounds, cyclobutanediselenone, and cyclobutanediselenol. The computed aromatic stabilization energy (ASE) by homodesmotic reaction is -77.4 (MP2(fu)/6,311+G** /RHF/6 - 311 + G** ) and - 54.8 kJ/mol (B3LYP/6 - 311 + G** //B3LYP/6 -311 + G**). The aromaticity of tetraselenosquaric acid is indicated by the calculated diamagnetic susceptibility exaltation (A) -19.13 (CSGT(IGAIM)-RHF/6,311 + G**// RHF/6,311 + G** and -32.91 (4,10,6 m,3/mol)(CSGT(I-GAIM)-B3LYP/6 - 311 + G* * //B3LYP/6 - 311 + G**). Thus, tetraselenosquaric acid fulfils the geometric, energetic and magnetic criteria of aromaticity. The calculated gas-phase acidity is ,G1*(298k) = 1257.7 and ,G*2 (298k) = 1617.1 kJ/mol. Hence, tetraselenosquaric acid is the strongest acid among the three squaric acids (3, 4-dihydroxy-3-cyclobutene-1, 2-dione, H2 C4 3,4-dithiohydroxy-3-cyclobutene-1,2-dithione, H2C4 S4, 3, 4-diselenyl-3-cyclobutene-1,2-diselenone, H2C4Se4). [source]