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PubMed1984

Bovine leukemia virus (BLV)--a structural model based on chemical crosslinking studies.

Nearest neighbor relationships between lipid and protein as well as between high-molecular-weight viral RNA and protein were investigated in bovine leukemia virus (BLV) particles using chemical crosslinking reagents. Separation of dimethyl suberimidate (DMS) induced lipid-protein complexes by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the phosphoprotein pp 15 is linked to the lipid bilayer of the virus. By use of diepoxybutan (DEB) as crosslinking reagent p 12 and again pp 15 were found to be linked to the viral RNA. Based on these results and our previous data describing the spatial relationships of major structural proteins within BLV particles, a structural model of BLV is proposed.

Animals↗
PubMed1994

Self-management of cystic fibrosis: a structural model for educational and behavioral variables.

One hundred and ninety-nine patients and their primary caregivers at two metropolitan cystic fibrosis centers participated in a clinical trial to evaluate the effectiveness of a health education program designed to help improve self-management skills for the care of CF. The baseline data from the study was used to test a structural model that hypothesized the relationship between educational, behavioral, and health status variables. Controlling for the effects of all other variables, including demographic, self-efficacy (confidence in being able to perform a behavior) was the most important educational factor predicting self-management behavior for monitoring and treating respiratory problems. Knowledge about the management of CF was only related to the ability of caretakers to apply coping skills to problems associated with CF. The more caretakers reported performing monitoring behaviors the more likely they were to report performing self-management treatment behaviors. The findings suggest that educational interventions that focus on increased knowledge alone are not likely to be effective in improving self-management behavior for CF. Based on the structural model analyses, it is recommended that educational programs for CF patients and families address increased self-efficacy and improved monitoring skills to influence the improvement of self-management treatment for CF.

Adaptation, Psychological↗
PubMed2003

Structural modeling of the Lhca4 Subunit of LHCI-730 peripheral antenna in photosystem I based on similarity with LHCII.

Peripheral chlorophyll a/b binding antenna of photosystem I (LHCI) from green algae and higher plants binds specific low energy absorbing chlorophylls (red pigments) that give rise to a unique red-shifted emission. A three-dimensional structural model of the Lhca4 polypeptide from the LHCI from higher plants was constructed on the basis of comparative sequence analysis, secondary structure prediction, and homology modeling using LHCII as a template. The obtained model of Lhca4 helps to visualize protein ligands to nine chlorophylls (Chls) and three potential His residues to extra Chls. Central domain of the Lhca4 comprising the first (A) and the third (C) transmembrane (TM) helices that binds 6 Chl molecules and two carotenoids is conserved structurally, whereas the interface between the first and the second TM helices and the outer surface of the second TM helix differ significantly among the LHCI and LHCII polypeptides. The model of Lhca4 predicts a histidine residue in the second TM helix, a potential binding site for extra Chl in close proximity to Chls a5 and b5 (labeling by Kühlbrandt). The interpigment interactions in the formed pigment cluster are suggested to cause a red spectral shift in absorption and emission. Modeling of the LHCI-730 heterodimer based on the model structures of Lhca1 and Lhca4 allowed us to suggest potential sites of pigment-pigment interactions that might be formed upon heterodimerization or docking of the LHCI dimers to the surface of PSI.

Amino Acid Sequence↗
PubMed2004

Solution structure of Eucommia antifungal peptide: a novel structural model distinct with a five-disulfide motif.

The three-dimensional structure in aqueous solution of Eucommia antifungal peptide 2 (EAFP2) from Eucommia ulmoides Oliv was determined using (1)H NMR spectroscopy. EAFP2 is a newly discovered 41-residue peptide distinct with a five-disulfide cross-linked motif. This peptide exhibits chitin-binding activity and inhibitory effects on the growth of cell wall chitin-containing fungi and chitin-free fungi. The structure was calculated by using torsion angle dynamic simulated annealing with a total of 614 distance restraints and 16 dihedral restraints derived from NOESY and DQF-COSY spectra, respectively. The five disulfide bonds were assigned from preliminary structures using a statistical analysis of intercystinyl distances. The solution structure of EAFP2 is presented as an ensemble of 20 conformers with a backbone RMS deviation of 0.65 (+/-0.13) A for the well-defined Cys3-Cys39 segment. The tertiary structure of EAFP2 represents the first five-disulfide cross-linked structural model of the plant antifungal peptide. EAFP2 adopts a compact global fold composed of a 3(10) helix (Cys3-Arg6), an alpha-helix (Gly26-Cys30), and a three-strand antiparallel beta-sheet (Cys16-Ser18, Tyr22-Gly24, and Arg36-Cys37). The tertiary structure of EAFP2 shows a chitin-binding domain (residues 11-30) with a hydrophobic face and a characteristic sector formed by the N-terminal 10 residues and the C-terminal segment cross-linked through the unique disulfide bond Cys7-Cys37, which brings all four positively charged residues (Arg6, Arg9, Arg36, and Arg40) onto a cationic face. On the basis of such a structural feature, the possible structural basis for the functional properties of EAFP2 is discussed.

Amino Acid Sequence↗
PubMed2004

Molecular docking and 3D QSAR studies on 1-amino-2-phenyl-4-(piperidin-1-yl)-butanes based on the structural modeling of human CCR5 receptor.

In the present study, we have used an approach combining protein structure modeling, molecular dynamics (MD) simulation, automated docking, and 3D QSAR analyses to investigate the detailed interactions of CCR5 with their antagonists. Homology modeling and MD simulation were used to build the 3D model of CCR5 receptor based on the high-resolution X-ray structure of bovine rhodopsin. A series of 64 CCR5 antagonists, 1-amino-2-phenyl-4-(piperidin-1-yl)-butanes, were docked into the putative binding site of the 3D model of CCR5 using the docking method, and the probable interaction model between CCR5 and the antagonists were obtained. The predicted binding affinities of the antagonists to CCR5 correlate well with the antagonist activities, and the interaction model could be used to explain many mutagenesis results. All these indicate that the 3D model of antagonist-CCR5 interaction is reliable. Based on the binding conformations and their alignment inside the binding pocket of CCR5, three-dimensional structure-activity relationship (3D QSAR) analyses were performed on these antagonists using comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) methods. Both CoMFA and CoMSIA provide statistically valid models with good correlation and predictive power. The q(2)(r(cross)(2)) values are 0.568 and 0.587 for CoMFA and CoMSIA, respectively. The predictive ability of these models was validated by six compounds that were not included in the training set. Mapping these models back to the topology of the active site of CCR5 leads to a better understanding of antagonist-CCR5 interaction. These results suggest that the 3D model of CCR5 can be used in structure-based drug design and the 3D QSAR models provide clear guidelines and accurate activity predictions for novel antagonist design.

Binding Sites↗
PubMed2000

Long-term memory for spatial and temporal mental models includes construction processes and model structure.

There is a strong case that people construct and manipulate mental models in working memory but relatively little evidence that mental models are preserved in long-term memory. Instead people may remember an episodic construction trace: a record of the operations used to construct a mental model (Payne, 1993). Experiment 1 investigated memory for determinate spatial descriptions (which describe a single configuration of objects) and indeterminate spatial descriptions (which describe two equally plausible configurations). Recognition performance was impaired when the overlap between the episodic construction trace of a description at learning and at test was disrupted by reordering the sentences within a description. Participants were better at remembering the gist of determinate descriptions than that of indeterminate descriptions. For indeterminate descriptions, provided differences in gist recognition were controlled, participants showed better memory for the original description. Experiment 2 showed a similar pattern of results with temporal descriptions. A third experiment manipulated the similarity between foils in the recognition test and the original descriptions to provide further evidence for both episodic construction trace and remembered mental models. In combination, these results favour a hybrid account of memory for mental models, which includes information about both construction processes and model structure.

Adult↗
PubMed1996

Structural model of the anti-snake-toxin antibody, M alpha 2,3.

We present results of structural modeling of the variable fragment of M alpha 2,3, an antibody capable of neutralizing all short snake toxins. Three different methods were used to model the hypervariable loops: the conformational search algorithm CONGEN (Bruccoleri and Karplus, Biopolymers 26:137-168, 1987), high-temperature molecular dynamics (Bruccoleri and Karplus, Biopolymers 29:1847-1862, 1990), and a combined knowledge-based and energy-based algorithm (Martin et al., Proc. Natl. Acad. Sci. USA 86:9268-9272, 1989). Ninety plausible conformations were generated and were clustered into 13 classes. The clustering results indicate that there was little overlap of the conformational space explored by the different methods. Canonical loop structures were found by all methods for two of the loops, in agreement with previously established empirical modeling criteria. Nine of the 13 classes of structure were rejected on the ground of their lacking common features of antibody combining-site structure. The remaining four models were refined using restrained molecular dynamics. It was found that interconversion between the four resulting structures is possible with no significant energy barriers, suggesting that they are in thermodynamic equilibrium at 300 K. Features of the combining-site structure likely to be particularly important for antigen binding are discussed.

Algorithms↗
PubMed2004

Molecular insights into NRTI inhibition and mitochondrial toxicity revealed from a structural model of the human mitochondrial DNA polymerase.

NRTI-based therapy used to treat AIDS can cause mitochondrial toxicity resulting from the incorporation of NRTIs into mitochondrial DNA by DNA polymerase gamma (pol gamma). Pol gamma has poor discrimination against many of the currently used NRTIs resulting in aborted DNA synthesis and subsequent depletion of mtDNA. Pol gamma readily incorporates ddCTP, ddITP and D4T-TP with an efficiency similar to the incorporation of normal nucleotides, whereas AZT-TP, CBV-TP, 3TC-TP and PMPApp act as moderate inhibitors to DNA synthesis. We have sought a structural explanation for the unique selection for NRTIs by the human pol gamma. A structural model of the human pol gamma was developed to ascertain the role of active site amino acids. One residue in particular, Y951 in motif B, is primarily responsible for the selection of dideoxynucleotides and D4T-TP. Our structural model of the human pol gamma should assist in rational design of antiviral nucleoside analogs with higher specificity for HIV-RT and minimal selection and incorporation into mitochondrial DNA.

Journal Article↗
PubMed2006

Structural model for the mannose receptor family uncovered by electron microscopy of Endo180 and the mannose receptor.

The mannose receptor family comprises four members in mammals, Endo180 (CD280), DEC-205 (CD205), phospholipase A(2) receptor (PLA(2)R) and the mannose receptor (MR, CD206), whose extracellular portion contains a similar domain arrangement: an N-terminal cysteine-rich domain (CysR) followed by a single fibronectin type II domain (FNII) and 8-10 C-type lectin-like domains (CTLDs). These proteins mediate diverse functions ranging from extracellular matrix turnover through collagen uptake to homeostasis and immunity based on sugar recognition. Endo180 and the MR are multivalent transmembrane receptors capable of interacting with multiple ligands; in both receptors FNII recognizes collagens, and a single CTLD retains lectin activity (CTLD2 in Endo180 and CTLD4 in MR). It is expected that the overall conformation of these multivalent molecules would deeply influence their function as the availability of their binding sites could be altered under different conditions. However, conflicting reports have been published on the three-dimensional arrangement of these receptors. Here, we have used single particle electron microscopy to elucidate the three-dimensional organization of the MR and Endo180. Strikingly, we have found that both receptors display distinct three-dimensional structures, which are, however, conceptually very similar: a bent and compact conformation built upon interactions of the CysR domain and the lone functional CTLD. Biochemical and electron microscopy experiments indicate that, under a low pH mimicking the endosomal environment, both MR and Endo180 experience large conformational changes. We propose a structural model for the mannose receptor family where at least two conformations exist that may serve to regulate differences in ligand selectivity.

Hydrogen-Ion Concentration↗
PubMed2002

Algebraic direct methods for few-atoms structure models.

As a basis for direct-methods phasing at very low resolution for macromolecular crystal structures, normalized structure-factor algebra is presented for few-atoms structure models with N = 1, 2, 3, em leader equal atoms or polyatomic globs per unit cell. Main results include: [see text]. Triplet discriminant Delta(hk) and triplet weight W(hk) parameters, a approximately 4.0 and b approximately 3.0, respectively, were determined empirically in numerical error analyses. Tests with phases calculated for few-atoms 'super-glob' models of the protein apo-D-glyceraldehyde-3-phosphate dehydrogenase (approximately 10000 non-H atoms) showed that low-resolution phases from the new few-atoms tangent formula were much better than conventional tangent formula phases for N = 2 and 3; phases from the two formulae were essentially the same for N > or = 4.

Crystallization↗
PubMed2000

The general relation between tissue response to x-radiation (alpha/beta-values) and the relative biological effectiveness (RBE) of protons: prediction by the Katz track-structure model.

PURPOSE: Experimental data suggest that the relative biological effectiveness (RBE) of protons compared to x-rays may be determined by the alpha/beta-ratio of the x-ray survival curve. The data are referring to the centre of a spread-out Bragg peak (SOBP) formed to deliver a homogeneous dose to the tumour by modulating the proton energy. In an effort to explore the basis for this observation, calculations were performed to investigate the response of different biological targets through a range of proton energies and doses. MATERIALS AND METHODS: To describe the x-ray survival curve, the parameters of the linear-quadratic equation, alpha and beta, as well as those of the multi-target/single-hit equation, n and D0, were considered. These parameters were varied to investigate the RBE using the Katz track-structure model. Known cell line characterizations, as well as different hypothetical cells assuming different alpha/beta-ratios but similar target size parameters in the framework of the track-structure theory, were considered. RESULTS: The RBE was found to increase with increasing alpha/beta when the parameter n was varied, but to decrease with increasing alpha/beta when D0 was varied. This held when all other radiosensitivity parameters were assumed to stay constant. Thus, the RBE cannot be predicted by the alpha/beta-ratio alone. CONCLUSIONS: Although there is no direct correlation between the proton RBE and the parameters describing the x-ray survival curve, the track-structure model predicts a tendency for late-responding tissues (low alpha/beta) to have higher RBE values than early-responding tissues (high alpha/beta). These calculations reinforce the experimental findings, but also strongly suggest that there are circumstances in which the tendency for RBE to increase with increasing alpha/beta does not occur, or even could be reversed.

Dose-Response Relationship, Radiation↗
PubMed1995

A secondary-structure model for the self-cleaving region of Neurospora VS RNA.

Neurospora VS RNA performs an RNA-mediated self-cleavage reaction whose products contain 2',3'-cyclic phosphate and 5'-hydroxyl termini. This reaction is similar to those of hammerhead, hairpin, and hepatitis delta virus ribozymes; however, VS RNA is not similar in sequence to these other self-cleaving motifs. Here we propose a model for the secondary structure of the self-cleaving region of VS RNA, supported by site-directed mutagenesis and chemical modification structure probing data. The secondary structure of VS RNA is distinct from those of the other naturally occurring RNA self-cleaving domains. In addition to a unique secondary structure, several Mg-dependent interactions occur during the folding of VS RNA into its active tertiary conformation.

Cloning, Molecular↗
PubMed2001

Derivation of a structural model for the c-myc IRES.

We have derived a secondary structure model for the c-myc internal ribosome entry segment (IRES) by using information from chemical probing of the c-myc IRES RNA to constrain structure prediction programs. Our data suggest that the IRES is modular in nature, and can be divided into two structural domains linked by a long unstructured region. Both domains are required for full IRES function. Domain 1 is a complex element that contains a GNNRA apical loop and an overlapping double pseudoknot motif that is topologically unique amongst published RNA structures. Domain 2, the smaller of the two, contains an apical AUUU loop. We have located the ribosome landing site and have shown that ribosomes enter in a 16 nt region downstream of the pseudoknots in a situation similar to that observed in several viral IRESs. To test the structure, several key regions of the IRES were mutated and, interestingly, it appears that some of the structural elements that we have identified function to repress c-myc IRES function. This has profound implications for de-regulation of c-myc expression by mutations occurring in the IRES.

Base Sequence↗
PubMed2005

Proton diffusion determination and dual structure model for nickel hydroxide based on potential step measurements on single spherical beads.

Potential step measurement is carried out on single beads of spherical nickel hydroxide to determine the proton diffusion coefficient (D) and concentration of the effective proton vacancies (C). The semi-infinite diffusion equation for the initial stage and the finite diffusion equation for the long-term of the current response to potential step are used for deducing the D and C values. The diffusion coefficients deduced from short and long-term current responses are in the order of magnitude 10(-7) and 10(-10) cm2 s(-1), respectively. The sum of the effective proton vacancy concentrations associated with the two D values comes out to be equal within experimental error to the effective proton vacancy concentration converted from the released electricity during discharge. A dual structure model is proposed to interpret the above-mentioned findings, featuring densely packed grains within which proton diffusion is slow and an inter-grain matrix where proton diffusion is fast. With this model the huge difference (about 6 orders of magnitude) in D values reported in the literature as well as the controversy of the dependence of diffusion coefficient on the state of charge can be largely rationalized. This dual structure model is supported by SEM and AFM observations.

Journal Article↗
PubMed2004

Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.

The protein CNOT4 possesses an N-terminal RING finger domain that acts as an E3 ubiquitin ligase and specifically interacts with UbcH5B, a ubiquitin-conjugating enzyme. The structure of the CNOT4 RING domain has been solved and the amino acids important for the binding to UbcH5B have been mapped. Here, the residues of UbcH5B important for the binding to CNOT4 RING domain were identified by NMR chemical shift perturbation experiments, and these data were used to generate structural models of the complex with the program HADDOCK. Together with the NMR data, additional biochemical data were included in a second docking, and comparisons of the resulting model with the structure of the c-Cbl/UbcH7 complex reveal some significant differences, notably at specific residues, and give structural insights into the E2/E3 specificity.

Amino Acid Sequence↗
PubMed1999

A structural modeling analysis of anxiety and depression in patients undergoing coronary artery bypass graft surgery: a model generating approach.

The present study is a longitudinal study designed to explore structural relationships between anxiety, depression, personality, and background factors (e.g., gender, age, and complicated medical characteristics) in patients undergoing coronary artery bypass graft (CABG) surgery. At two timepoints before and two after CABG, 217 patients completed self-report questionnaires. To explore structural relationships, the structural equation modeling (SEM) method was applied. Using the model-generating approach, a model was developed, providing a good fit. The structural relationships revealed, in particular, the key position of neuroticism, which was related to both pre- and postoperative anxiety and depression. Relationships between anxiety and depression over time, both intra- and interrelationships, were relatively weak. Relationships between anxiety and depression at the same points in time were relatively strong, with preoperative depression leading to preoperative anxiety, and postoperative anxiety leading to postoperative depression. To provide a useful framework for development of intervention strategies, further research is needed to evaluate the plausibility of the final structural model.

Adult↗
PubMed2001

Syntheses and structures of M(L)(X)BPh4 complexes (M = Co(II), Zn(II); L = cis-1,3,5-tris[3-(2-furyl)prop-2-enylideneamino]cyclohexane, X = OAc, NO3) n: structural models of the active site of carbonic anhydrase.

The metal coordination geometries in the structures of the zinc(II) and cobalt(II) complexes of the ligand cis-1,3,5-tris[3-(2-furyl)prop-2-enylideneamino]cyclohexane (fr-protach) and with the anions nitrate and acetate are structural models for the active site of carbonic anhydrase. The acetate structures show a striking structural correlation with the metal coordination environments in the known bicarbonate forms of the enzyme. Such structures provide a basis for understanding the marked effect of different metal substitution on the catalytic rate of the enzyme.

Acetates↗