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PubMed1984

Immunobiologically active lipid A analogs synthesized according to a revised structural model of natural lipid A.

Synthetic lipid A analogs which have two amide-bound and two ester-bound (R)-3-hydroxytetradecanoyl groups at the C-2 and -2' and C-3 and -3' positions of beta(1-6)glucosamine disaccharide mono- or diphosphates showed high activities in most in vitro assays, and the lethality of a diphosphate derivative to galactosamine-treated mice was almost comparable to that of natural lipid A. The pyrogenicity and Shwartzman induction activity of the synthetic analogs, however, were much less than those of natural lipid A.

Adult↗
PubMed1997

Catching With Both Hands: An Evaluation of Neural Cross-Talk and Coordinative Structure Models of Bimanual Coordination.

Kelso, Southard, and Goodman (1979) and Marteniuk and MacKenzie (1980) have each proposed a different theoretical model for bimanual coordination. In the model of Kelso et al., a close temporal relationship between the hands in a bimanual task is predicted, even when each hand is required to move different distances. In Marteniuk and MacKenzie's model, separate motor commands are issued so that each limb will arrive simultaneously at the specified movement endpoint, leading to low temporal associations between limbs. In most previous work on bimanual coordination, manual aiming tasks with differing constraints have been used by subjects in individual studies. In this study, the usefulness of existing models for predicting performance in a real-world catching task in which the required movement pattern was constrained by ball flight characteristics was examined. Eleven university students caught tennis balls with both hands in the following 3 conditions: Condition 1. Ball projected to the right shoulder area (left hand moved a greater distance than the right); Condition 2. Ball projected to center of the chest area, (both hands moved same distance); and Condition 3. Ball projected to left shoulder area (right hand moved a greater distance). Kinematic data (time to peak velocity, movement initiation time) indicating significant cross-correlations between the left and right limbs in all 3 conditions concurred with the data of Kelso et al. (1979) on manual aiming. Timing appeared to be an essential variable coordinating bimanual interceptive actions. Although the limbs moved at different speeds when each was required to move different distances, times to peak velocity showed strong associations, suggesting the presence of a coordinative structure.

bimanual coordination↗
PubMed1999

Alcohol and Aldehyde Adducts of Zinc Thiolates: Structural Modeling of Alcoholdehydrogenase.

Bis(pentafluorothiophenolato)zinc (1) and bis(2,4,6-triisopropylthiophenolato)zinc (2) can be combined with nitrogen-containing derivatives of benzyl alcohol and benzaldehyde to form (N,O-chelate) zinc thiolates. 2-Pyridylmethanol as well as 2-quinolylmethanol (HetMeOH) yield [(HetMeO)Zn(SR)](4) (3, 4) having a cyclo-Zn(4)(&mgr;-O)(4) backbone and only terminal SR. Likewise, thiolate 1 and 2-(dimethylamino)benzyl alcohol form zwitterionic [(dimethylammoniobenzylato)Zn(SR)(2)](2) (5) with bridging alkoxide and terminal thiolate. In contrast, 6-picolylmethanol (PicMeOH) and thiolate 1 result in [(PicMeOH)Zn(SC(6)F(5))(2)] (6) containing zinc in a tetrahedral ZnNS(2)O, environment. Simple aromatic aldehydes form polymeric complexes [(RCHO)Zn(SC(6)F(5))(2)] (7: R = p-tolyl, 8: R = mesityl) with a [Zn-S](infinity) backbone. Chelating aldehydes (CA) yield mononuclear complexes with tetrahedral ZnNS(2)O coordination [(CA)Zn(SC(6)F(5))(2)] (9, CA = pyridine-2-carbaldehyde; 10, CA = 6-methylpyridine-2-carbaldehyde; 11, CA = 6-methoxypyridine-2-carbaldehyde; 12, CA = quinoline-2-carbaldehyde; 13, CA = 2-(dimethylamino)benzaldehyde). In contrast, N-methylimidazole-2-carbaldehyde (ImA) is coordinated twice in tetrahedral [(ImA)(2)Zn(SC(6)F(5))(2)] (14) lacking any Zn-O interactions. Pyridine-2,6-dicarbaldehyde (PDA) forms trigonal bipyramidal [(PDA)Zn(SC(6)F(5))(2)] (15) with ZnNO(2)S(2) ligation. The structures of 3, 4, 6, 8, 10, 11, 13, and 14 were determined crystallographically, and the structures of 5 and 15 were deduced from those of the corresponding ZnBr(2) complexes. The ZnNS(2)O coordination pattern observed for the enzyme has been reproduced to a very good approximation. In complexes 6 and 10, which are almost superimposable, it is realized for both the corresponding alcohol and aldehyde.

Journal Article↗
PubMed1997

Synthesis and Characterization of the Benzoylformato Ferrous Complexes with the Hindered Tris(pyrazolyl)borate Ligand as a Structural Model for Mononuclear Non-Heme Iron Enzymes.

By using a hindered tripodal ligand, hydrotris(3-tert-butyl-5-isopropylpyrazol-1-yl)borate HB(3-tBu-5-iPrpz)(3), a series of monomeric ferrous complexes having acetate, hydroxide, and benzoylformate ligands were synthesized. Reaction of KHB(3-tBu-5-iPrpz)(3) with anhydrous Fe(OAc)(2) yielded acetato complexes Fe(OAc)[HB(3-tBu-5-iPrpz)(3)] (1) and Fe(OAc)[HB(3-tBu-5-iPrpz)(3)](3-iPr-5-tBupzH) (2). A hydroxo complex Fe(OH)[HB(3-tBu-5-iPrpz)(3)] (3) was prepared by the treatment of 1 or 2 with aqueous NaOH. The geometry of Fe(II) in 3 is a slightly distorted tetrahedron as determined by X-ray crystallography. The hydroxo complex 3 reacted with benzoylformic acid to give the benzoylformato complex Fe(O(2)CC(O)Ph)[HB(3-tBu-5-iPrpz)(3)] (4), which showed thermochromism which depended on the coordination geometry of the benzoylformate ligand. The Fe(II) ion in the colorless form of 4 isolated at 4 degrees C is coordinated by a tetrahedral N(3)O(1) ligand donor set including the unidentate benzoylformato ligand. On the other hand, the bluish purple form of 4 isolated at -20 degrees C has a five-coordinate trigonal bipyramidal Fe(II) center. The benzoylformate ligand in this bluish purple form works as a chelate ligand through coordination of the unidentate carboxylate oxygen atom as well as the ketonic oxygen atom. A benzoylformato complex containing an additional pyrazole, Fe(O(2)CC(O)Ph)[HB(3-tBu-5-iPrpz)(3)](3-iPr-5-tBupzH) (5), was obtained by the reaction of 3 with benzoylformic acid in the presence of 3-tert-butyl-5-isopropylpyrazole. The iron atom in 5 is coordinated by an N(4)O(1) ligand donor set with trigonal bipyramidal geometry. A hydrogen-bonding interaction between the carboxylate oxygen atom and the additional pyrazole's NH proton in 5 is suggested from the short distance between O(carboxylate) and N(pyrazole) observed in the X-ray structure and the absence of the nuNH vibration in the IR spectrum.

Journal Article↗
PubMed1997

Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex.

In the reverse transcription initiation complex of the yeast Ty1 retrotransposon, interaction between the template RNA and primer tRNAiMet is not limited to base pairing of the primer binding site (PBS) with ten nucleotides at the 3' end of tRNAiMet, but three regions named boxes O, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Sequence comparison of 33 Ty1 elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved in the region spanning the PBS and the three boxes. Since the domain of the template RNA encodes a portion of protein TyA, we have calculated its amino acid profile and its nucleotide profile to evaluate the role played by nucleotide sequence conservation in the selection for TyA function and in the maintenance of base pairing interactions for the priming function of Ty1 RNA. Our results show that the nucleotide sequence conservation of Ty1 RNA is constrained not only by selection for Ty1 function but also by maintenance of a given nucleotide sequence able to base pair with the tRNAiMet in the primer-template initiation complex.

Amino Acid Sequence↗
PubMed1988

Model structure of a fragment of biological knowledge (cell motility).

The aim of the study is to contribute to a better understanding of some aspects of the structure of biological knowledge and to make clearer to what extent the methods of reasoning may be useful in this field when only qualitative information is available. A fragment of biological knowledge (theory of cell motility) is analysed from the logicomethodological point of view as a coherent system and the possibility of its formal representation is investigated. The analysis is based on distinguishing the main objects and their features (attributes) of which a given piece of knowledge is composed and on the values which these features may display. The features are interconnected by relations (in which various number of arguments appear) and these relations constitute the main (general, higher level) laws of a given fragment of knowledge (theory). Values of attributes are also mutually connected and these relations correspond to the detailed (lower level) laws. A computer system (in which Prolog language was used) enables to perform inference operations of progressive as well as regressive type. The main categories of reasoning procedures are described and illustrated by examples, namely a) search for conclusions which may be confronted with the actual knowledge in order to verify the system as a whole, b) formation of working hypotheses in the process of their empirical verification and explanation of facts and laws. The problem of development and modification of the system is also discussed.

Cell Movement↗
PubMed1996

Vibrational analysis of nucleic acids. IV. Normal modes of the DNA phosphodiester structure modeled by diethyl phosphate.

Raman and ir spectra are reported for diethyl phosphate [(CH3CH2O)2PO2-] and diethyl phosphate isotopomers incorporating carbon-13 at methylene group sites [(CH313CH2O)2PO2-] and deuterium substituents on methyl and methylene carbons [(CH3CD2O)2PO2-, (CD3CH2O)2PO2-, (CD3CD2O)2PO2-]. The vibrational spectra are analyzed to develop a consistent set of assignments for the C-C-O-P(O2-)-O-C-C network, which serves as a model for the nucleic acid phosphodiester backbone. The present study resolves previously conflicting vibrational assignments for the phosphodiester skeleton and provides a firm empirical basis for interpreting conformationally sensitive modes of DNA and RNA. Ab initio vibrational analyses have also been conducted on the above isotopomers of diethyl phosphate in the trans-gauche-gauche-trans conformation, optimized using the 3-21+G* basis set at the restricted Hartree-Fock level. The ab initio calculations are in good agreement with the empirical results, thus strengthening the proposed assignment scheme for Raman and infrared spectra. The present study provides a basis for improvement of empirical force fields utilized in previous normal coordinate analyses of the nucleic acid phosphodiester group.

DNA↗
PubMed2005

Structured model for denitrifier diauxic growth.

We present a model for diauxic growth of denitrifying bacteria in which nitrate reductase synthesis kinetics dominate the overall growth kinetics. The model is based on the assumption of the existence of a nitrate respiration operon, thereby linking the rate of nitrate uptake to the activity of nitrate reductase. We show that this approach can model diauxic growth of Pseudomonas denitrificans by conducting experiments in which nitrate reductase activity was measured during both lag and ensuing exponential growth phases. We consistently observed the pattern of low nitrate reductase enzyme activity during the lag phase, increasing before the onset of growth. By fitting model parameters we were able to successfully match experimental data for growth, nitrate uptake, and enzyme activity level.

Models, Biological↗
PubMed2004

NMR structural model of the interaction of herbicides with the photosynthetic reaction center from Rhodobacter sphaeroides.

The interaction of the herbicides acifluorfen and paraquat with the photosynthetic reaction center from Rhodobacter sphaeroides has been studied by NMR relaxation measurements. Interaction in aqueous solution has been demonstrated by evaluating motional features of the bound form through cross-relaxation terms of protons at fixed distances on the herbicides. Contributions to longitudinal nonselective relaxation rates different from the proton-proton dipolar relaxation were inferred, most probably due to paramagnetic effects originating from the high-spin nonheme Fe(II) ion in the reaction center. Paramagnetic contributions to proton relaxation rates were converted into distance constraints in order to build a model for the interaction. The models place paraquat in the QB site, where most herbicides interact, in agreement with docking calculations, whereas acifluorfen was placed between the metal and the QB site, as also demonstrated by the induced paramagnetic shifts. Acifluorfen could therefore act to break the electron-transfer pathway between the QA and QB sites.

Crystallography, X-Ray↗
PubMed1995

Hard alpha-keratin IF: a structural model lacking a head-to-tail molecular overlap but having hybrid features characteristic of both epidermal keratin and vimentin IF.

In intermediate filaments (IF) both epidermal keratin and vimentin molecules have been shown to have an eight residue head-to-tail overlap between the rod domains of similarly directed molecules. In the case of the epidermal keratins this region has also been shown to have particular structural/functional significance since it represents a hot-spot for mutations in the four keratinopathies characterized to date. While there is good evidence that this head-to-tail overlap is present in IF containing Type III, IV, and V chains, as well as in the epidermal keratin IF (Ib/IIb), there are no data currently available for the hard alpha-keratin IF (Ia/IIa). Using a variety of data derived from X-ray diffraction and crosslinking studies, as well as theoretical modeling, it is now possible to demonstrate that the overlap region is not a feature of hard alpha-keratin IF. Indeed, it is shown that there is a nine residue gap between consecutive parallel molecules in the IF. An explanation for this observation is presented in terms of compensating disulfide bonds that occur both within the IF, and between the IF and the matrix in which the IF are embedded.

Amino Acid Sequence↗
PubMed1993

Measurement error in dietary assessment: an investigation using covariance structure models. Part I.

Repeated measures of diet are analysed in an attempt to discover the measurement error properties of various dietary assessment methods. It is customary in such studies to assume that one reference measurement is 'valid' (without error) but this assumption is not tenable. An alternative approach, widely used in social science, is to model the covariance matrix of the repeated measures. We apply this methodology to assessments of nitrogen intake, which is essentially equivalent to protein intake.

Bias↗