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At least 613 records · Page 34Linked to original sources
PubMed2000

The bicyclomycin sensitivities of 38 bicyclomycin-resistant mutants of transcription termination protein rho and the location of their mutations support a structural model of rho based on the F(1) ATPase.

A total of 38 bicyclomycin-resistant mutants of Escherichia coli transcription termination protein Rho have been isolated. The locations of their mutations identify the ATP-binding region as the functional domain inhibited by bicyclomycin. Strains containing the S266C, S266A and L208R Rho mutations are very resistant to bicyclomycin in vivo. In a similar way, the mutant Rho proteins containing these mutations are very resistant to bicyclomycin in vitro. These data suggest that Ser266 and Leu208 might make direct contact with the antibiotic. These two residues are close to each other in the tertiary structure of a model of Rho based on the alpha and beta subunits of the F(1) ATPase, supporting the validity of the model. The strain containing the G337S Rho mutation also has high bicyclomycin resistance, and the proximity of L208, S266 and G337 in the quaternary structure of the Rho model has enabled a candidate bicyclomycin-binding pocket to be delineated. As a whole, the bicyclomycin sensitivities of the mutants are consistent with the locations of their respective mutations in the model of Rho based on the F(1) ATPase, therefore supporting the emerging consensus model of Rho structure.

Adenosine Triphosphate↗
PubMed1997

Meta-analyses of age-cognition relations in adulthood: estimates of linear and nonlinear age effects and structural models.

A meta-analysis was conducted on 91 studies to derive a correlation matrix for adult age, speed of processing, primary-working memory, episodic memory, reasoning, and spatial ability. Structural equation modeling with a single latent common cognitive factor showed that all cognitive measures shared substantial portions of age-related variance. A mediational model revealed that speed of processing and primary-working memory appear to be important mediators of age-related differences in the other measures. However, not all of the age-related influences were mediated. An examination of quadratic age effects and correlational patterns for subsamples under and over 50 years of age revealed that (a) negative age-cognition relations were significant for the 18- to 50-year-old sample and (b) the age-related decline accelerated significantly over the adult life span for variables assessing speed, reasoning, and episodic memory.

Adult↗
PubMed1987

A structural model for molded thermoplastic ankle-foot orthoses.

The structural response of a posterior leaf spring, ankle-foot orthosis (AFO) was studied both experimentally and with a simple theoretical model. The theoretical model, which was compared with other analytical solutions and experimental data, predicted the bending and twisting of the AFO due to unit loads. The simple theoretical model utilized beam equations and small deflection theory. Excellent agreement between test and predicted values was achieved, indicating that the simple theoretical model, which was relatively easy to implement computationally, could serve as the major component of a computer-aided design program.

Ankle↗
PubMed1995

The development of an age structured model for schistosomiasis transmission dynamics and control and its validation for Schistosoma mansoni.

Mathematical models are potentially useful tools to aid in the design of control programmes for parasitic diseases. In this paper, a fully age structured epidemiological model of human schistosomiasis is developed and parameterized, and used to predict trends in infection prevalence, intensity and prevalence of heavy infections over age and time during several rounds of mass and age targeted treatment. The model is validated against data from a Schistosoma mansoni control programme in Kenya.

Adolescent↗
PubMed1998

Structural modeling of the complex between an acetylcholine receptor-mimicking antibody and its snake toxin antigen.

The antibody M alpha2-3 neutralizes the functional, acetylcholine receptor binding activity of its antigen, neurotoxin alpha, and exhibits several other properties in common with the receptor itself. We present here the results of calculations examining the three-dimensional structure of the toxin alpha:M alpha2-3 complex. The antigen structure, determined by nuclear magnetic resonance spectroscopy, was docked to models of the variable fragment of the antibody combining site by using a method based on surface complementarity and maximization of buried surface area while taking into account the possibility of conformational change on complexation. Extensive experimental information on the location of the functional epitope was incorporated into the analysis and used to screen candidate geometries of the complex resulting from the modeling. Eight plausible structures that are in accord with the experimental data were derived. Common structural features of the models are discussed, and residues of the antibody-combining site that are expected to play important roles in complexation are identified. In particular, three epitope residues that, according to mutagenesis experiments, make particularly strong contributions to the binding, interact excentrically and do not make contact with the central loops of the combining site, L3 and H3.

Animals↗
PubMed2006

Structural modelling of the human drug-metabolizing cytochromes P450.

The structural and functional aspects of cytochrome P450 (CYP) enzymes are reviewed in the light of current developments in X-ray crystallography and other physical evidence, together with recent findings on the regulation of, and polymorphisms in, the human drug-metabolizing CYPs. It is emphasized that the crystal structures of eukaryotic CYPs are particuarly useful for constructing homology models of the human enzymes associated with drug metabolism, and that these models can aid in the high-throughput screening of novel compounds destined for human exposure.

Animals↗
PubMed2006

Synthesis of zinc, copper, nickel, cobalt, and iron complexes using tris(pyrazolyl)methane sulfonate ligands: a structural model for N,N,O binding in metalloenzymes.

Ligands of intermediate steric bulk were designed to mimic metalloenzymes with histidine and carboxlyate binding sites. The reaction between tris(3-isopropylpyrazolyl)methane and butyllithium followed by SO3NMe3 in THF yielded the new ligand lithium tris(3-isopropylpyrazolyl)methane sulfonate (LiTpmsiPr). Various metal salts reacted with LiTpmsiPr to give the octahedral complexes M(TpmsiPr)2 (M = Zn, Cu, Ni, Co, Fe) in which each ligand has N,N,O binding to the metal. In the reaction between LiTpmsiPr and ZnCl2, in addition to the major product Zn(TpmsiPr)2, [LiTpmsiPrZnCl2].2THF was also formed as a minor product with a tetrahedral zinc atom coordinated to either N,N,Cl,Cl in the solid phase or N,N,N,Cl in acetonitrile solution. Although TpmsiPr is coordinatively flexible and can act as a bipodal or tripodal ligand, it appears to favor the formation of octahedral L2M complexes.

Binding Sites↗
PubMed2004

Structural modelling of optical and electrochemical properties of 4-aminodiphenylamines - optoelectronic studies on a polyaniline repeating unit.

Amino-diphenylanilines and their planarized and twisted model compounds have been investigated by steady state and time-resolved absorption and emission, as well as by spectroelectrochemistry. These polyaniline model compounds show that the observation of excited states with full charge separation is linked to molecular twisting where the diaminobenzene is the donor and the phenyl group the acceptor. The observable charge transfer fluorescence shows the characteristic features of twisted intramolecular charge transfer (TICT) excited states, i.e. forbidden emissive properties and strong solvatochromic red shift. The transient absorption spectrum of the TICT state matches the ground state absorption spectrum of the electrochemically produced radical cation of the molecule. This is the first example where excited-state properties of the neutral and ground state properties of the radical cation are directly linked.

Aniline Compounds↗
PubMed1985

Structural model for the trialkyltin binding site on cat hemoglobin.

The binding site for trialkyltin complexes on the alpha- chain of cat oxyhemoglobins is proposed to involve the SG and NE2 atoms of Cys-13 and His-113 respectively. On deoxygenation, the conformation of this region changes substantially, allowing complexation only through the ND1 nitrogen atom of His-113, a much less favorable interaction. Thus the model presented explains the preferential binding of trialkyltin complexes to R-state cat hemoglobin and suggests the type of interaction that is likely to occur between these compounds and a variety of less well-characterized enzymes to produce the metabolic effects that trialkyltin complexes are known to produce in vivo.

Animals↗
PubMed2004

Recall and recognition in mild hypoxia: using covariance structural modeling to test competing theories of explicit memory.

To test theories of explicit memory in amnesia, we examined the effect of hypoxia on memory performance in a group of 56 survivors of sudden cardiac arrest. Structural equation modeling revealed that a single-factor explanation of recall and recognition was insufficient to account for performance, thus contradicting single-process models of explicit memory. A dual-process model of recall in which two processes (e.g., declarative memory and controlled search) contribute to recall performance, whereas only one process (e.g., declarative memory) underlies recognition performance, also failed to explain the results adequately. In contrast, a dual-process model of recognition provided an acceptable account of the data. In this model, two processes--recollection and familiarity--underlie recognition memory, whereas only the recollection process contributes to free recall. The best-fitting model was one in which hypoxia and aging led to deficits in recollection, but left familiarity unaffected. Moreover, a controlled search process was correlated with recollection, but was not associated with familiarity or the severity of hypoxia. The results support models of explicit memory in which recollection depends on the hippocampus and frontal lobes, whereas familiarity-based recognition relies on other brain regions.

Aged↗
PubMed2003

Relationship between structural modeling and hyperelastic material behavior: application to CNS white matter.

Recent measurements of the material properties of brain tissue allow an examination of the underlying microstructural basis in both physiological and pathophysiological conditions. The purpose of this study is to develop a mathematical relationship between microstructurally based models of the central nervous system (CNS) white matter and equivalent hyperelastic material models. For simplicity, time dependent material behavior is not included in this formulation. The microstructural representation is used to formulate structural property relationships for highly oriented white matter, and is mathematically compared to one isotropic and two anisotropic hyperelastic formulations. For the anisotropic characterizations, the population of axons in the white matter is assumed to align along one preferred direction of the material, yielding a transversely isotropic formulation. Relatively simple strain-energy functions incorporating material anisotropy provide sufficient flexibility to model the nonlinear behavior predicted from structurally based models, although the tangential stiffness of the hyperelastic approaches does not follow completely the behavior of the structurally based formulations. This analysis is an initial step towards linking microstructural aspects of the tissue to material models commonly used for large deformations, and may be an important step in relating predicted tissue deformation to the deformation and stress of cellular and subcellular structures.

Animals↗
PubMed1998

Structural model of the HIV-1 Tat(46-58)-TAR complex.

The trans-activator protein (Tat) of human immunodeficiency virus type 1 (HIV-1) binds to an uridine-rich bulge of an RNA target (TAR; trans-activation responsive element) predominantly via its basic sequence domain. The structure of the Tat(46-58)-TAR complex has been determined by a novel modeling approach relying on structural information about one crucial arginine residue and crosslink data. The strategy described here solely uses this experimental data without additional "modeling" assumptions about the structure of the complex in order to avoid human bias. Model building was performed in a fashion similar to structure calculations from nuclear magnetic resonance (NMR)-spectroscopic data using restrained molecular dynamics. The resulting set of structures of Tat(46-58) in its complex with TAR reveals that all models have converged to a common fold, showing a backbone root mean square deviation (RMSD) of 1.36A. Analysis of the calculated structures suggests that HIV-I Tat forms a hairpin loop in its complex with TAR that shares striking similarity to the hairpin formed by the structure of the bovine immunodeficiency virus Tat protein after TAR binding as determined by NMR studies. The outlined approach is not limited to the Tat-TAR complex modeling, but is also applicable to all molecular complexes with sufficient biochemical and biophysical data available.

Amino Acid Sequence↗
PubMed1995

Structural model of the phospholamban ion channel complex in phospholipid membranes.

Phospholamban is a 52 amino acid residue membrane protein involved with the regulation of calcium levels across sarcoplasmic reticulum membranes in cardiac muscle cells. The N-terminal 30 amino acid residues of the protein are largely hydrophilic and include two sites whose phosphorylation is thought to dissociate an inhibitory complex between phospholamban and Ca2+ ATPase. The C-terminal 22 amino acid residues are largely hydrophobic, anchor the protein in the membrane and are responsible for Ca2+ selective ion conductance. Specific interactions between the transmembrane domains stabilize a pentameric protein complex. We have obtained circular dichroism (CD), transmission Fourier transform infrared (FTIR) and attenuated total reflection Fourier transform infrared (ATR-FTIR) spectra of the full-length protein and have compared these results to those from a 28 residue peptide that includes the transmembrane domain. Both proteins reconstituted into phospholipid membranes are largely alpha-helical by CD and FTIR. Polarized ATR-FTIR measurements show that both the cytosolic and transmembrane helices are oriented perpendicular to the membrane plane with a tilt of 28 (+/- 6) degrees with respect to the membrane normal. This tilt angle is in close agreement to that calculated from a model for the transmembrane domain of phospholamban suggested by mutagenesis and molecular modeling. Phosphorylation does not significantly change the secondary structure or orientation of the protein. The pentameric complex is modeled as a left-handed coiled-coil of five long helices (40 (+/- 3) residues) that extend across the membrane from the lumenal carboxy terminus to the phosphorylation site in the cytoplasm. The helix bundle forms a perpendicular ion pore that may begin at a distance (17 to 29 A) from the membrane surface. Based on the above, we propose a mechanism by which phospholamban regulates Ca2+ levels across membranes that takes into account both its selective ion conductance and inhibitory association with the Ca2+ pump.

Amino Acid Sequence↗
PubMed1987

Proton NMR studies of the biologically active 1-34 fragment of bovine parathyroid hormone: examination of a structural model.

Proton NMR spectra of the biologically active 1-34 fragment of bovine parathyroid hormone (bPTH) were studied as a function of pH over the range of pH 4 to 10, in buffer and in 6 M guanidine DC1. One of the histidine C-2 peaks titrated normally, with a pKa value of 6.8, but the other two histidines in this peptide had pKa values of 6.3. Denatured PTH showed only one histidine C-2 peak with a pKa of 6.7. An aliphatic peak identified as due to either a methionine or a glutamine residue also shifted with pH, and the pKa for this shift was 6.3. Finally, small but significant upfield shifts in the methyl and methylene resonances were observed as a function of pH, and when compared to the denatured peptide. These results indicate that the N-terminal domain of native PTH has considerable structure in solution, and are consistent with a theoretical model for the folding of this peptide.

Animals↗
PubMed2006

Structural model reveals key interactions in the assembly of the pregnane X receptor/corepressor complex.

The human pregnane X receptor (PXR), also known as steroid and xenobiotic receptor, is a member of the orphan nuclear receptors and mediates the mammalian xenobiotic response with broad specificity and implications for drug clearance. The mouse pregnane X receptor is highly similar to the human ortholog in structure but with subtle species differentiation in the ligand binding domain (LBD). The C-terminal helix named alphaAF or AF-2 helix in other nuclear receptors is responsible for transcription activation by recruiting coactivators through conformational change. In the absence of ligands, PXR can also repress gene expression by interacting with transcriptional corepressors, such as the silencing mediator for retinoid and thyroid hormone receptor (SMRT). We first constructed homology models of the complete LBD with two SMRT nuclear receptor (NR)-interacting domains (ID1 and ID2), respectively. We then performed energy minimization and molecular dynamics simulations on these systems to study the specific interactions between the interacting domains and LBD. Further experimental results supported and validated the observed preference of SMRT toward ID2 over ID1. Our modeling results revealed the key interactions that account for the binding preference. Here, we propose structural models of the PXR-LBD/SMRT-ID1 and PXR-LBD/SMRT-ID2 complexes to understand their molecular interactions and potential inhibitory mechanism.

Amino Acid Sequence↗