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Intermediate States (intermediate + states)
Selected AbstractsTactics-Based Behavioural Planning for Goal-Driven Rigid Body ControlCOMPUTER GRAPHICS FORUM, Issue 8 2009Stefan Zickler Computer Graphics [I.3.7]: Animation-Artificial Intelligence; [I.2.8]: Plan execution, formation, and generation; Computer Graphics [I.3.5]: Physically based modelling Abstract Controlling rigid body dynamic simulations can pose a difficult challenge when constraints exist on the bodies' goal states and the sequence of intermediate states in the resulting animation. Manually adjusting individual rigid body control actions (forces and torques) can become a very labour-intensive and non-trivial task, especially if the domain includes a large number of bodies or if it requires complicated chains of inter-body collisions to achieve the desired goal state. Furthermore, there are some interactive applications that rely on rigid body models where no control guidance by a human animator can be offered at runtime, such as video games. In this work, we present techniques to automatically generate intelligent control actions for rigid body simulations. We introduce sampling-based motion planning methods that allow us to model goal-driven behaviour through the use of non-deterministic,Tactics,that consist of intelligent, sampling-based control-blocks, called,Skills. We introduce and compare two variations of a Tactics-driven planning algorithm, namely behavioural Kinodynamic Rapidly Exploring Random Trees (BK-RRT) and Behavioural Kinodynamic Balanced Growth Trees (BK-BGT). We show how our planner can be applied to automatically compute the control sequences for challenging physics-based domains and that is scalable to solve control problems involving several hundred interacting bodies, each carrying unique goal constraints. [source] Conformational heterogeneity of transmembrane residues after the Schiff base reprotonation of bacteriorhodopsinFEBS JOURNAL, Issue 9 200515N CPMAS NMR of D85N/T170C membranes bR, N-like and O-like intermediate states of [15N]methionine-labelled wild type and D85N/T170C bacteriorhodopsin were accumulated in native membranes by controlling the pH of the preparations. 15N cross polarization and magic angle sample spinning (CPMAS) NMR spectroscopy allowed resolution of seven out of nine resonances in the bR-state. It was possible to assign some of the observed resonances by using 13C/15N rotational echo double resonance (REDOR) NMR and Mn2+ quenching as well as D2O exchange, which helps to identify conformational changes after the bacteriorhodopsin Schiff base reprotonation. The significant differences in chemical shifts and linewidths detected for some of the resonances in N- and O-like samples indicate changes in conformation, structural heterogeneity or altered molecular dynamics in parts of the protein. [source] Solvothermal Synthesis, Cathodoluminescence, and Field-Emission Properties of Pure and N-Doped ZnO NanobulletsADVANCED FUNCTIONAL MATERIALS, Issue 1 2009Ujjal K. Gautam Abstract Homogenous crystallization in solution, in the absence of external influences, is expected to lead to growth that is symmetric at least in two opposite facets. Such was not the case when we attempted to synthesize ZnO nanostructures by employing a solvothermal technique. The reaction product, instead, consisted of bullet-shaped tiny single crystals with an abrupt hexagonal base and a sharp tip. A careful analysis of the product and the intermediate states of the synthesis reveals that one of the reaction intermediates with sheet-like morphology acts as a self-sacrificing template and induces such unexpected and novel growth. The synthesis was further extended to dope the nanobullets with nitrogen as previous studies showed this can induce p-type behavior in ZnO, which is technologically complementary to the naturally occurring n-type ZnO. Herein, a soft-chemical approach is used for the first time for this purpose, which is otherwise accomplished with high-temperature techniques. Cathodoluminesce (CL) investigations reveal stable optical behavior within a pure nanobullet. On the other hand, the CL spectra derived from the surfaces and the cores of the doped samples are different, pointing at a N-rich core. Finally, even though N-doped ZnO is known to have high electrical conductivity, the study now demonstrates that the field-emission properties of ZnO can also be greatly enhanced by means of N doping. [source] Experimental and theoretical studies on some new pyrrol-2,3-diones formationHETEROATOM CHEMISTRY, Issue 1 2004Ismail Yildirim 4-Benzoyl-5-phenyl-2,3-furandione (1) reacts with asymmetric disubstituted urea derivatives like 1,1-dimethylurea (2a) and 1,1-diethylurea (2b) by the elimination of a H2O molecule to give the 4-benzoyl-1-(N,N -dialkylcarbamyl)-5-phenyl-2,3-pyrroldiones 3a and 3b. The structures of 3a,b were determined by the 13C NMR, 1H NMR, IR spectroscopic data and elemental analyses. The electronic structures of the reactants, their transition states, intermediate states, and final products of the reactions were investigated on the basis of AM1 and ab initio (DFT) methods. © 2003 Wiley Periodicals, Inc. Heteroatom Chem 15:9,14, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.10204 [source] Theory of chemical bonds in metalloenzymes.INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2008Abstract A first principle investigation has been carried out for intermediate states of the catalytic cycle of a cytochrome P450. To elucidate the whole catalytic cycle of P450, the electronic and geometrical structures are investigated not only at each ground state but also at low-lying energy levels. Using the natural orbital analysis, the nature of chemical bonds and magnetic interactions are investigated. The ground state of the Compound 1 (cpd1) is calculated to be a doublet state, which is generated by the antiferromagnetic coupling between a triplet Fe(IV)O moiety and a doublet ligand radical. We found that an excited doublet state of the cpd1 is composed of a singlet Fe(IV)O and a doublet ligand radical. This excited state lies 20.8 kcal mol,1 above the ground spin state, which is a non-negligible energy level as compared with the activation energy barrier of ,E# = 26.6 kcal mol,1. The reaction path of the ground state of cpd1 is investigated on the basis of the model reaction: 3O(3p) + CH4. The computational results suggest that the reactions of P450 at the ground and excited states proceed through abstraction (3O-model) and insertion (1O-model) mechanisms, respectively. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Development of the force field parameters for phosphoimidazole and phosphohistidineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2004Yuri A. Kosinsky Abstract Phosphorylation of histidine-containing proteins is a key step in the mechanism of many phosphate transfer enzymes (kinases, phosphatases) and is the first stage in a wide variety of signal transduction cascades in bacteria, yeast, higher plants, and mammals. Studies of structural and dynamical aspects of such enzymes in the phosphorylated intermediate states are important for understanding the intimate molecular mechanisms of their functioning. Such information may be obtained via molecular dynamics and/or docking simulations, but in this case appropriate force field parameters for phosphohistidine should be explicitly defined. In the present article we describe development of the GROMOS96 force field parameters for phosphoimidazole molecule,a realistic model of the phosphohistidine side chain. The parameterization is based on the results of ab initio quantum chemical calculations with subsequent refinement and testing using molecular mechanics and molecular dynamics simulations. The set of force constants and equilibrium geometry is employed to derive force field for the phosphohistidine moiety. Resulting parameters and topology are incorporated into the molecular modeling package GROMACS and used in molecular dynamics simulations of a phosphohistidine-containing protein in explicit solvent. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 1313,1321, 2004 [source] Structural and ligand-binding properties of serum albumin species interacting with a biomembrane interfaceJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2007Takamitsu Kosa Abstract In the process of drug development, preclinical testing using experimental animals is an important aspect, for verification of the efficacy and safety of a drug. Serum albumin is a major binding protein for endogenous and exogenous ligands and regulates their distribution in various tissues. In this study, the structural and drug-binding properties of albumins on a biomembrane surface were investigated using reverse micelles as a model membrane. In reverse micelles, the secondary structures of all albumins were found, to varying degrees, to be intermediate between the native and denatured states. The tertiary structures of human and bovine albumin were similar to those of the native and intermediate states, respectively, whereas those of the dog, rabbit, and rat were in a denatured state. Thus, bovine albumin is an appropriate model for studying structural changes in human albumin in a membrane-water phase. Binding studies also showed the presence of species difference in the change in binding capacity of albumins during their interaction with reverse micelles. Among the albumins, rat albumin appears to be a good model for the protein-mediated drug uptake of human albumin in a biomembrane environment. These findings are significant in terms of the appropriate extrapolation of pharmacokinetics and pharmacodynamics data in various animals to humans. © 2007 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 96: 3117,3124, 2007 [source] Indole ring orientations of Trp189 in the ground and M intermediate states of bacteriorhodopsin as studied by polarized UV resonance Raman spectroscopy,JOURNAL OF RAMAN SPECTROSCOPY, Issue 1-3 2006Kazuhiro Asakawa Abstract Polarized resonance Raman spectroscopy provides a means for orientation analysis of proteins in aligned samples. Previously, we developed a Raman linear intensity difference (RLID) method to determine the orientations of aromatic amino acid side chains in flow-oriented or membrane-bound proteins. In this study, we have applied the RLID method to Trp189 in bacteriorhodopsin (BR), a transmembrane protein that acts as a light-driven proton pump. Among the eight Trp residues in BR, the Raman spectrum of Trp189 has been extracted by subtracting the spectrum of the Trp189 , Phe mutant from that of wild-type BR. By examining the 251.3-nm-exited polarized resonance Raman intensities of two indole ring vibrations of Trp189, the directions of the La and Bb transition moments have been determined with respect the membrane normal in the light-adapted ground state (BR568) and a photo-excited intermediate (M). Comparison of the orientations of the Trp189 indole ring derived from the La and Bb inclination angles has shown that the indole ring slightly but significantly reorients toward the ionone ring of the retinal chromophore in the M intermediate. The reorientation of Trp189 is consistent with the previous observation that helix F, on which Trp189 is located, undergoes an outward tilt and the hydrophobic interaction of Trp189 increases in the M intermediate. The RLID method combined with 251.3 nm excitation and point mutation is useful for detecting even a small reorientation of a targeted Trp residue. Copyright © 2006 John Wiley & Sons, Ltd. [source] The Ordovician Trilobite Carolinites, A Test Case for Microevolution in A Macrofossil LineagePALAEONTOLOGY, Issue 2 2002Tim McCormick We use geometric morphometrics to test a claim that the Ordovician trilobite Carolinites exhibits gradualistic evolution. We follow a previously proposed definition of gradualism, and define the criteria an ideal microevolutionary case study should satisfy. We consider the Lower,Middle Ordovician succession at Ibex, western Utah to meet these criteria. We discovered examples of: (1) morphometric characters which fluctuate with little or no net change; (2) characters which show abrupt ,step' change; (3) characters which show transitional change through intermediate states. Examples belonging to (2) and (3) exhibit reversals. The transitional characters were tested against a null hypothesis of symmetrical random walk. The tests indicated that they were not changing under sustained directional selection. Two alternative interpretations are possible. (1) The characters are responding to random causes (genetic drift or rapidly fluctuating selection pressures) or to causes that interact in so complex a way that they appear random. This observation may be applicable to most claimed cases of gradualistic evolution in the literature. (2) Sampling was at too poor a resolution to allow meaningful testing against the random walk. If so, then this situation is likely to apply in most evolutionary case studies involving Palaeozoic macrofossils. [source] Unusual binding interactions in PDZ domain crystal structures help explain binding mechanismsPROTEIN SCIENCE, Issue 4 2010Jonathan M. Elkins Abstract PDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domain's "binding groove". We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here allow comparison with canonical binding for the PDLIM PDZ domain family. Although influenced by crystal packing arrangements, the structures nevertheless show that changes in the positions of PDZ domain side-chains and the ,B helix allow noncanonical binding interactions. These interactions may be indicative of intermediate states between unbound and fully bound PDZ domain and target protein. The noncanonical "perpendicular" binding observed potentially represents the general form of a kinetic intermediate. Comparison with canonical binding suggests that the rearrangement during binding involves both the PDZ domain and its ligand. [source] Cofactor effects on the protein folding reaction: Acceleration of ,-lactalbumin refolding by metal ionsPROTEIN SCIENCE, Issue 4 2006Natalia A. Bushmarina Abstract About 30% of proteins require cofactors for their proper folding. The effects of cofactors on the folding reaction have been investigated with ,-lactalbumin as a model protein and metal ions as cofactors. Metal ions accelerate the refolding of ,-lactalbumin by lessening the energy barrier between the molten globule state and the transition state, mainly by decreasing the difference of entropy between the two states. These effects are linked to metal ion binding to the protein in the native state. Hence, relationships between the metal affinities for the intermediate states and those for the native state are observed. Some residual specificity for the calcium ion is still observed in the molten globule state, this specificity getting closer in the transition state to that of the native state. The comparison between kinetic and steady-state data in association with the , value method indicates the binding of the metal ions on the unfolded state of ,-lactalbumin. Altogether, these results provide insight into cofactor effects on protein folding. They also suggest new possibilities to investigate the presence of residual native structures in the unfolded state of protein and the effects of such structures on the protein folding reaction and on protein stability. [source] The X-ray structure determination of bovine carbonmonoxy hemoglobin at 2.1 Å resoultion and its relationship to the quaternary structures of other hemoglobin crystal formsPROTEIN SCIENCE, Issue 6 2001Martin K. Safo Abstract Crystallographic studies of the intermediate states between unliganded and fully liganded hemoglobin (Hb) have revealed a large range of subtle but functionally important structural differences. Only one T state has been reported, whereas three other quaternary states (the R state, B state, and R2 or Y state) for liganded Hb have been characterized; other studies have defined liganded Hbs that are intermediate between the T and R states. The high-salt crystal structure of bovine carbonmonoxy (CO bovine) Hb has been determined at a resolution of 2.1 Å and is described here. A detailed comparison with other crystallographically solved Hb forms (T, R, R2 or Y) shows that the quaternary structure of CO bovine Hb closely resembles R state Hb. However, our analysis of these structures has identified several important differences between CO bovine Hb and R state Hb. Compared with the R state structures, the ,-subunit N-terminal region has shifted closer to the central water cavity in CO bovine Hb. In addition, both the ,- and ,-subunits in CO bovine Hb have more constrained heme environments that appear to be intermediate between the T and R states. Moreover, the distal pocket of the ,-subunit heme in CO bovine Hb shows significantly closer interaction between the bound CO ligand and the Hb distal residues Val 63(E11) and His 63(E7). The constrained heme groups and the increased steric contact involving the CO ligand and the distal heme residues relative to human Hb may explain in part the low intrinsic oxygen affinity of bovine Hb. [source] Denaturant sensitive regions in creatine kinase identified by hydrogen/deuterium exchangeRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 11 2005Hortense Mazon The GdmHCl-induced unfolding of creatine kinase (CK) has been studied by hydrogen/deuterium (H/D) exchange combined with mass spectrometry. MM-CK unfolded for various periods in different denaturant concentrations was pulsed-labeled with deuterium to identify different conformational intermediate states. For all denaturation times or GdmHCl concentrations, we observed variable proportions of only two species. The low-mass envelope of isotope peaks corresponds to a species that has gained about 10 deuteriums more than native CK, and the high-mass envelope to a completely deuterated species. To localize precisely the unfolded regions in the states highly populated during denaturation, the protein was digested with two proteases (pepsin and type XIII protease) after H/D exchange and rapid quenching of the reaction. The two sets of fragments obtained were analyzed by liquid chromatography coupled to mass spectrometry to determine the deuterium level in each fragment. Bimodal distributions of deuterium were found for most peptides, indicating that these regions were either folded or unfolded. This behavior is consistent with cooperative, localized unfolding. However, we observed a monomodal distribution of deuterium in two regions (1,12 and 162,186). We conclude that the increment of mass observed in the low-mass species of the intact protein (+10,Da) has its origin in these two segments. These regions, which are very sensitive to low GdmHCl concentrations, are involved in the monomer,monomer interface of CK and their perturbation is likely to weaken the dimeric structure. At higher denaturant concentration, this would induce dissociation of the dimer. Copyright © 2005 John Wiley & Sons, Ltd. [source] Temperature-dependent macromolecular X-ray crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2010Martin Weik X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100,K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15,K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography. [source] Energetic aspects of locked nucleic acids quadruplex association and dissociationBIOPOLYMERS, Issue 6 2006Luigi Petraccone Abstract The design of modified nucleic acid aptamers is improved by considering thermodynamics and kinetics of their association/dissociation processes. Locked Nucleic Acids (LNA) is a promising class of nucleic acid analogs. In this work the thermodynamic and kinetic properties of a LNA quadruplex formed by the TGGGT sequence, containing only conformationally restricted LNA residues, are reported and compared to those of 2,-OMe-RNA (O-RNA) and DNA quadruplexes. The thermodynamic analysis indicates that the sugar-modified quadruplexes (LNA and O-RNA) are stabilized by entropic effects. The kinetic analysis shows that LNA and O-RNA quadruplexes are characterized by a slower dissociation and a faster association with respect to DNA quadruplex. Interestingly, the LNA quadruplex formation process shows a second-order kinetics with respect to single strand concentration and has a negative activation energy. To explain these data, a mechanism for tetramer formation with two intermediate states was proposed. © 2006 Wiley Periodicals, Inc. Biopolymers 83: 584,594, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Ligand-Exchange Processes on Solvated Zinc Cations: Water Exchange on [Zn(H2O)4(L)]2+,2,H2O (L=Heterocyclic Ligand)CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2010Basam Abstract The water-exchange mechanisms of [Zn(H2O)4(L)]2+,2,H2O (L=imidazole, pyrazole, 1,2,4-triazole, pyridine, 4-cyanopyridine, 4-aminopyridine, 2-azaphosphole, 2-azafuran, 2-azathiophene, and 2-azaselenophene) have been investigated by DFT calculations (RB3LYP/6-311+G**). The results support limiting associative reaction pathways that involve the formation of six-coordinate intermediates [Zn(H2O)5(L)]2+,H2O. The basicity of the coordinated heterocyclic ligands shows a good correlation with the activation barriers, structural parameters, and stability of the transition and intermediate states. [source] Pathways for the Non-CO-Involved Oxidation of Methanol on Pt(111)CHEMPHYSCHEM, Issue 14 2008Wang Gao Dr. Abstract The non-CO-involved oxidation of methanol (NCOIOM) on a Pt(111) surface is investigated by using density functional theory. Relative energy diagrams for the NCOIOM are established in which the reaction mechanisms for a catalytic cycle,including the associated barriers, the reactive energies, the intermediates, and the transient states,are shown. The results indicate that the reaction proceeds via the kinetically favored pathways: A) HCOH,HC(OH)2,HCOOH,HCOO- [-COOH],CO2 and B) CHO,HCOOH,HCOO- [-COOH],CO2, with OH playing a key role in the entire process. The vibrational frequencies of the intermediate states derived from the calculations are in agreement with the experimental measurements. [source] Photochemical Z,E Isomerization of a Hemithioindigo/Hemistilbene ,-Amino AcidCHEMPHYSCHEM, Issue 11 2007Thorben Cordes Abstract The molecule HTI, which combines hemithioindigo and hemistilbene molecular parts, allows reversible switching between two isomeric states. Photochromic behaviour of the HTI molecule is observed by irradiation with UV/Vis light. The photochemical reaction, a Z/E isomerization around the central double bond connecting the two molecular parts, is investigated by transient absorption and emission spectroscopy. For a special HTI molecule, namely, an ,-amino acid, the Z,E isomerization process occurs on a timescale of 30 ps. In the course of the reaction fast processes on the 1,10 ps timescale are observed which point to motions of the molecule on the potential-energy surface of the excited state. The combination of transient absorption experiments in the visible spectral range with time-resolved fluorescence and infrared measurements reveal a photochemical pathway with three intermediate states. Together with a theoretical modelling procedure the experiments point to a sequential reaction scheme and give indications of the nature of the involved intermediates. [source] Studies on the Refolding of Egg White Lysozyme Denatured by Urea Using "Phase Diagram" Method of FluorescenceCHINESE JOURNAL OF CHEMISTRY, Issue 12 2007Liu-Jiao BIAN Abstract The refolding of reduced and non-reducing egg white lysozymes in a urea solution was studied by a "phase diagram" method of fluorescence. The result showed that in the refolding of the reduced egg white lysozyme, an intermediate state of an egg white lysozyme exists at the urea concentrations in a final renaturation solution being about 4.5 mol/L, their refolding follows a three-state model; while in the refolding of the non-reducing egg white lysozyme, two intermediate states exist at the urea concentrations being separately 4.0 and 2.5 mol/L, and their refolding follows a four-state model. Through the comparison between the unfolding and refolding of an egg white lysozyme in the urea solution, it was found that both of the refolding of reduced and non-reducing egg white lysozyme molecules was irreversible to their unfolding in the urea solution. Finally, a suggested refolding was separately presented for the reduced and non-reducing egg white lysozymes in the urea solution. [source] BML revisited: Statistical physics, computer simulation, and probability,COMPLEXITY, Issue 2 2006Raissa M. D'Souza Abstract Statistical physics, computer simulation, and discrete mathematics are intimately related through the study of shared lattice models. These models lie at the foundation of all three fields, are studied extensively, and can be highly influential. Yet new computational and mathematical tools may challenge even well-established beliefs. Consider the BML model, which is a paradigm for modeling self-organized patterns of traffic flow and first-order jamming transitions. Recent findings, on the existence of intermediate states, bring into question the standard understanding of the jamming transition. We review the results and show that the onset of full-jamming can be considerably delayed based on the geometry of the system. We also introduce an asynchronous version of BML, which lacks the self-organizing properties of BML, has none of the puzzling intermediate states, but has a sharp, discontinuous, transition to full jamming. We believe this asynchronous version will be more amenable to rigorous mathematical analysis than standard BML. We discuss additional models, such as bootstrap percolation, the honey-comb dimer model and the rotor-router, all of which exemplify the interplay between the three fields, while also providing cautionary tales. Finally, we synthesize implications for how results from one field may relate to the other, and also implications specific to computer implementations. © 2006 Wiley Periodicals, Inc. Complexity, 12, 30,39, 2006 [source] | |||||||||||||||||||