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Computational Predictions (computational + prediction)
Selected AbstractsComputational prediction of fatigue crack paths in ship structural detailsFATIGUE & FRACTURE OF ENGINEERING MATERIALS AND STRUCTURES, Issue 1-2 2005Y. SUMI ABSTRACT The characteristics of fatigue crack propagation and the remaining life assessment of ship structures are investigated focusing attention on a curved crack path due to the effects of welds, complicated stress distributions at three-dimensional structural joints and structural redundancy. An advanced numerical simulation method is demonstrated for the remaining life assessment for curved crack propagation. The simulation method is based on a step-by-step finite-element analysis. The crack path is predicted by the perturbation method with the local symmetry criterion, which gives a higher order approximation of the crack path, while the finite-element re-zoning is carried out by an improved paving method. Fatigue crack paths in the welded structural details of the transverse girder of a ship structure are investigated by experiments and simulation. The present method may offer an efficient simulation-based tool for the design of critical details, which prevents the failure of the plates forming a compartment boundary. [source] Enzymatic control of anhydrobiosis-related accumulation of trehalose in the sleeping chironomid, Polypedilum vanderplankiFEBS JOURNAL, Issue 20 2010Kanako Mitsumasu Larvae of an anhydrobiotic insect, Polypedilum vanderplanki, accumulate very large amounts of trehalose as a compatible solute on desiccation, but the molecular mechanisms underlying this accumulation are unclear. We therefore isolated the genes coding for trehalose metabolism enzymes, i.e. trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) for the synthesis step, and trehalase (TREH) for the degradation step. Although computational prediction indicated that the alternative splicing variants (PvTps,/,) obtained encoded probable functional motifs consisting of a typical consensus domain of TPS and a conserved sequence of TPP, PvTps, did not exert activity as TPP, but only as TPS. Instead, a distinct gene (PvTpp) obtained expressed TPP activity. Previous reports have suggested that insect TPS is, exceptionally, a bifunctional enzyme governing both TPS and TPP. In this article, we propose that TPS and TPP activities in insects can be attributed to discrete genes. The translated product of the TREH ortholog (PvTreh) certainly degraded trehalose to glucose. Trehalose was synthesized abundantly, consistent with increased activities of TPS and TPP and suppressed TREH activity. These results show that trehalose accumulation observed during anhydrobiosis induction in desiccating larvae can be attributed to the activation of the trehalose synthetic pathway and to the depression of trehalose hydrolysis. [source] Computer-aided NMR assay for detecting natively folded structural domains,PROTEIN SCIENCE, Issue 4 2006Takayuki Hondoh Abstract Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of proteins into structural domains that form stable native structures. However, protein dissection essentially remains an empirical and often a tedious process. Here, we describe a simple strategy for rapidly identifying structural domains and assessing their structures. This approach combines the computational prediction of sequence regions corresponding to putative domains with an experimental assessment of their structures and stabilities by NMR and biochemical methods. We tested this approach with nine putative domains predicted from a set of 108 Thermus thermophilus HB8 sequences using PASS, a domain prediction program we previously reported. To facilitate the experimental assessment of the domain structures, we developed a generic 6-hour His-tag-based purification protocol, which enables the sample quality evaluation of a putative structural domain in a single day. As a result, we observed that half of the predicted structural domains were indeed natively folded, as judged by their HSQC spectra. Furthermore, two of the natively folded domains were novel, without related sequences classified in the Pfam and SMART databases, which is a significant result with regard to the ability of structural genomics projects to uniformly cover the protein fold space. [source] Mechanism of the Nucleophilic Substitution of Acyl Electrophiles using Lithium OrganocupratesADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 7-8 2008Naohiko Yoshikai Abstract The mechanism of nucleophilic substitution reaction at an sp2 carbon center of a thioester or an acid chloride with a lithium organocuprate reagent has been investigated. Density functional calculations indicated that the thioester undergoes oxidative addition of the CS bond to the copper(I) atom through a three-centered transition state to afford an organocopper(III) intermediate, which gives the product through reductive elimination of the alkyl and the acyl groups. On the other hand, the acid chloride loses a chloride anion very easily when it interacts with the cuprate, because the chloride anion is captured by a lithium(I) cation rather than a copper(I) atom. 13C kinetic isotope effect (KIE) experiments showed excellent agreement with computational predictions for the thioester reaction, but suggested that the nucleophilic displacement transition state of the acid chloride occurs much more advanced than the calculations predict. [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 ensemblesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2008Ivelin 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] The characterization of fluidization behavior using a novel multichamber microscale fluid bedJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 3 2004Eetu Räsänen Abstract In the preformulation stage, there is a special need to determine the process behavior of materials with smaller amounts of samples. The purpose of this study was to assemble a novel automated multichamber microscale fluid bed module with a process air control unit for the characterization of fluidization behavior in variable conditions. The results were evaluated on the basis of two common computational methods, the minimum fluidization velocity, and the Geldart classification. The materials studied were different particle sizes of glass beads, microcrystalline cellulose, and silicified microcrystalline cellulose. During processing, the different characteristic fluidization phases (e.g., plugging, bubbling, slugging, and turbulent fluidization) of the materials were observed by the pressure difference over the bed. When the moisture content of the process air was increased, the amount of free charge carriers increased and the fine glass beads fluidized on the limited range of velocity. The silicification was demonstrated to improve the fluidization behavior with two different particle sizes of cellulose powders. Due to the interparticle (e.g., electrostatic) forces of the fine solids, the utilization of the computational predictions was restricted. The presented setup is a novel approach for studying process behavior with only a few grams of materials. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93: 780,791, 2004 [source] Systematizing the generation of missing metabolic knowledgeBIOTECHNOLOGY & BIOENGINEERING, Issue 3 2010Jeffrey D. Orth Abstract Genome-scale metabolic network reconstructions are built from all of the known metabolic reactions and genes in a target organism. However, since our knowledge of any organism is incomplete, these network reconstructions contain gaps. Reactions may be missing, resulting in dead-ends in pathways, while unknown gene products may catalyze known reactions. New computational methods that analyze data, such as growth phenotypes or gene essentiality, in the context of genome-scale metabolic networks, have been developed to predict these missing reactions or genes likely to fill these knowledge gaps. A growing number of experimental studies are appearing that address these computational predictions, leading to discovery of new metabolic capabilities in the target organism. Gap-filling methods can thus be used to improve metabolic network models while simultaneously leading to discovery of new metabolic gene functions. Biotechnol. Bioeng. 2010;107: 403,412. © 2010 Wiley Periodicals, Inc. [source] Early Structural Evolution of Native Cytochrome c after Solvent RemovalCHEMBIOCHEM, Issue 15 2008Michal Z. Steinberg Abstract Electrospray ionization transfers thermally labile biomolecules, such as proteins, from solution into the gas phase, where they can be studied by mass spectrometry. Covalent bonds are generally preserved during and after the phase transition, but it is less clear to what extent noncovalent interactions are affected by the new gaseous environment. Here, we present atomic-level computational data on the structural rearrangement of native cytochrome c immediately after solvent removal. The first structural changes after desolvation occur surprisingly early, on a timescale of picoseconds. For the time segment of up to 4.2 ns investigated here, we observed no significant breaking of native noncovalent bonds; instead, we found formation of new noncovalent bonds. This generally involves charged residues on the protein surface, resulting in transiently stabilized intermediate structures with a global fold that is essentially the same as that in solution. Comparison with data from native electron capture dissociation experiments corroborates both its mechanistic postulations and our computational predictions, and suggests that global structural changes take place on a millisecond timescale not covered by our simulations. [source] Synthesis, Structures, and Physical Properties of Benzo[k]fluoranthene-Based Linear Acenes,CHEMISTRY - A EUROPEAN JOURNAL, Issue 20 2010Yun-Hua Kung Abstract This work describes the syntheses, crystal structures, photophysical properties, and electro-chemical analyses of benzo[k]fluoranthene-based linear acenes, together with ab initio density functional theory computations on them. The molecules were prepared in generally moderate to good yields through Pd-catalyzed cycloadditions between 1,8-diethynylnaphthalene derivatives and aryl iodides. This protocol is simpler and more efficient than conventional methods. The scope and limitations of this reaction were examined. The structures of compounds 4,hb, 15,ac, 17,ab, 19,ac, and 24,je were determined by X-ray analysis; they are either bent or twisted, rather than planar. The photophysical and electrochemical properties of these cycloadducts were also investigated and compared with computational predictions based on density functional theory. [source] | ||||||||||