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PubMed1996

T cell immune responses to haptens. Structural models for allergic and autoimmune reactions.

Protein-reactive chemicals, metal salts and drugs, commonly classified as immunological haptens, are major environmental noxes targeted at the immune system of vertebrates. They may not only interfere with this defense system by toxicity alone, but more often by evoking hapten-specific immune responses resulting in allergic and eventually autoimmune responses. Here, we review recent developments in the analysis of the structural basis of hapten recognition, particularly by T lymphocytes, which represent central elements in cell-mediated, as well as in IgE dependent, allergies. A break-through in this field was the finding that T cells detect haptens as structural entities, attached covalently or by complexation to self-peptides anchored in binding grooves of major histocompatibility antigens (MHC-proteins). Synthetic hapten-peptide conjugates were shown to induce hapten-specific contact sensitivity in mice, opening new routes for studying hapten-induced immune disorders.

Amino Acid Sequence↗
PubMed1995

Cognitive structural models: the perception of risk and prevention in coronary heart disease.

This paper examines the relationship between causal models and the assessment of actions in a naturalistic domain. Two studies used a novel network diagram technique to elicit individual causal models of the factors affecting the risk of coronary heart disease. The same individuals also rated the effectiveness of different preventive actions. In their diagrams, individuals depicted the causal interrelationships between various factors and estimated the strength of the connecting paths. Total path strength accounted for two-thirds of the variance in ratings of preventive actions. A number of methodological issues were also explored, which supported the utility of the technique. Consensual models allowed a ready comparison between groups of subjects and showed the importance of distinguishing the presence of paths from the strengths of those paths. The studies support the value of the technique in analysing individual differences in the way people represent complex causal structures; various extensions and applications are also proposed.

Cognition↗
PubMed1995

Predictive study of the conformation of the cytotoxic protein alpha-sarcin: a structural model to explain alpha-sarcin-membrane interaction.

Alpha-sarcin is a cytotoxic protein composed of a single polypeptide chain. This protein shows a significant degree of amino acid sequence similarity with a group of several phylogenetically related fungal ribonucleases. The leading member of such a group is ribonuclease T1. Three proteins of this group, ribonucleases T1, Ms and F1, are well known in terms of their crystal structures. These data have been used to propose a conformation for alpha-sarcin. The secondary structure of the cytotoxin would contain one alpha-helix segment as well as around six beta-strands and 14 beta-turns. The folding of these structural motifs is proposed by comparison with the three-dimensional structure of the three proteins from the ribonuclease T1 subfamily. The four longest beta-strands of alpha-sarcin would define an antiparallel beta-sheet structure resulting in a highly hydrophobic domain. The predicted folding for alpha-sarcin is discussed in terms of the ability of this protein to electrostatically and hydrophobically interact with phospholipid vesicles. The proposed conformation would explain how a highly polar protein, such as alpha-sarcin, can produce membrane destabilization resulting in protein translocation across lipid bilayers.

Amino Acid Sequence↗
PubMed1995

The sensitivity of probabilistic risk assessment results to alternative model structures: a case study of municipal waste incineration.

In this analysis, human health risk due to exposure to municipal waste incinerator emissions is assessed as an example of the application of probabilistic techniques (e.g., Monte Carlo or Latin Hypercube simulations). Incinerator risk assessments are characterized by the dominance of indirect exposure, thus this analysis focuses on exposure via the ingestion of locally grown foods. In addition, since exposure to 2,3,7,8-TCDD drives most incinerator risk assessments, this compound is the subject of the illustrative calculations. An important part of probabilistic risk assessment is determining the relative influence of the input parameters on the magnitude of the variance in the output distribution. This constitutes an important step toward prioritizing data needs for additional research. However, under various possible model forms reflecting incompletely understood aspects of contaminant transport, differences may be observed in estimates of risk, variance in risk, and the relative contributions of individual uncertain and variable inputs to the variance. In this analysis, a sequential structural decomposition of the relationships between the input variables is used to partition the variance in the output (i.e., risk) to identify the most influential contributors to overall variance among them. For comparison, the partitioning of variance is repeated, using techniques of multivariate regression. In summary, this study considers the degree to which results of a probabilistic assessment are contingent on critical model assumptions about the representation of deposition velocity. Specifically, this analysis assesses the impact on the results of uncertainty about the best model of the vapor/particle partitioning behavior of semi-volatile airborne pollutants.

Air Pollution↗
PubMed2005

Structural models of psychopathy.

Psychopathy traditionally is defined by a cluster of inferred personality traits and socially deviant behaviors. The accepted standard for the reliable and valid assessment of psychopathy is the Psychopathy Checklist-Revised (PCL-R). Because of its importance in basic and applied research, and in the mental health and criminal justice systems, the PCL-R has been subjected to intense scrutiny by researchers and clinicians. In this article we discuss issues surrounding its structural properties and those of its derivatives. Using factor analysis, item response theory, and multidimensional scaling, we propose that the PCL-R and its derivatives are underpinned by at least four correlated factors: Interpersonal, Affective, Lifestyle, and Antisocial. We argue that attempts to characterize antisocial behaviors as merely "downstream" manifestations of more central traits are inconsistent with the structural properties of the PCL-R and with evidence that the development of traits and actions are interactive and reciprocal. We also report new evidence that psychopathy and its factors are dimensional in nature, perhaps extreme variants of normal personality traits and behaviors.

Affect↗
PubMed1998

A function-structure model for NGF-activated TRK.

Mechanisms regulating transit of receptor tyrosine kinases (RTKs) from inactive to active states are incompletely described, but require autophosphorylation of tyrosine(s) within a kinase domain 'activation loop'. Here, we employ functional biological assays with mutated TRK receptors to assess a 'switch' model for RTK activation. In this model: (i) ligand binding stimulates activation loop tyrosine phosphorylation; (ii) these phosphotyrosines form specific charge pairs with nearby basic residues; and (iii) the charge pairs stabilize a functionally active conformation in which the activation loop is restrained from blocking access to the kinase catalytic core. Our findings both support this model and identify residues that form specific charge pairs with each of the three TRK activation loop phosphotyrosines.

3T3 Cells↗
PubMed2006

Structural model of the BCL-w-BID peptide complex and its interactions with phospholipid micelles.

A peptide corresponding to the BH3 region of the proapoptotic protein, BID, could be bound in the cleft of the antiapoptotic protein, BCL-w. This binding induced major conformational rearrangements in both the peptide and protein components of the complex and led to the displacement and unfolding of the BCL-w C-terminal alpha-helix. The structure of BCL-w with a bound BID-BH3 peptide was determined using NMR spectroscopy and molecular docking. These studies confirmed that a region of 16 residues of the BID-BH3 peptide is responsible for its strong binding to BCL-w and BCL-x(L). The interactions of BCL-w and the BID-BH3 peptide complex with dodecylphosphocholine micelles were characterized and showed that the conformational change of BCL-w upon lipid binding occurred at the same time as the release and unfolding of the BH3 peptide.

Animals↗
PubMed1983

Electron-microscopical approach to a structural model of intima collagen.

Intima collagen was studied by electron microscopy (rotary shadowing and negative staining) and by analytical ultracentrifugation. It was found that the monomeric unit (Mr 170 000) consists of a 105 nm-long triple helix terminated by a small globular domain (Mr about 30 000) at one end and a large globular domain (Mr about 40 000) at the other end. The monomer was produced by selective reduction of interchain disulphide bridges. Before reduction, dimers, tetramers and larger filamentous structures were found. Dimers are lateral staggered aggregates of two monomers aligned in an anti-parallel fashion. This gives rise to an inner 75 nm-long region of two slightly intertwisted triple helices flanked by the large globular domains. The outer triple-helical segments (length 30 nm) with the small globular domains at their ends emerge at both sides of this structure. Interchain disulphide bridges are probably located in the vicinity of the large domains. Only the outer segments could be degraded by bacterial collagenase. In tetramers the outer segments of two dimers are covalently linked, forming a scissors-like structure. In the fibrous forms several tetramers are assembled end-to-end with an overlap between the outer segments. The molecular masses and sedimentation coefficients were calculated for these various forms from the electron-microscopically observed dimensions and agreed with results obtained by ultracentrifugation. The unique structure of intima collagen suggests that it originates from a microfibrillar component and that it can be considered a unique collagenous protein, for which we propose the designation type VI collagen.

Chemical Phenomena↗
PubMedDate not supplied

MAP: an iterative experimental design methodology for the optimization of catalytic search space structure modeling.

One of the main problems in high-throughput research for materials is still the design of experiments. At early stages of discovery programs, purely exploratory methodologies coupled with fast screening tools should be employed. This should lead to opportunities to find unexpected catalytic results and identify the "groups" of catalyst outputs, providing well-defined boundaries for future optimizations. However, very few new papers deal with strategies that guide exploratory studies. Mostly, traditional designs, homogeneous covering, or simple random samplings are exploited. Typical catalytic output distributions exhibit unbalanced datasets for which an efficient learning is hardly carried out, and interesting but rare classes are usually unrecognized. Here is suggested a new iterative algorithm for the characterization of the search space structure, working independently of learning processes. It enhances recognition rates by transferring catalysts to be screened from "performance-stable" space zones to "unsteady" ones which necessitate more experiments to be well-modeled. The evaluation of new algorithm attempts through benchmarks is compulsory due to the lack of past proofs about their efficiency. The method is detailed and thoroughly tested with mathematical functions exhibiting different levels of complexity. The strategy is not only empirically evaluated, the effect or efficiency of sampling on future Machine Learning performances is also quantified. The minimum sample size required by the algorithm for being statistically discriminated from simple random sampling is investigated.

Algorithms↗
PubMed2002

Kinetic studies and structural models of the association of E. coli sigma(70) RNA polymerase with the lambdaP(R) promoter: large scale conformational changes in forming the kinetically significant intermediates.

The kinetics of interaction of Esigma(70) RNA polymerase (R) with the lambdaP(R) promoter (P) were investigated by filter binding over a broad range of temperatures (7.3-42 degrees C) and concentrations of RNA polymerase (1-123 nM) in large excess over promoter DNA. Under all conditions examined, the kinetics of formation of competitor-resistant complexes (I(2), RP(o)) are single-exponential with first order rate constant beta(CR). Interpretation of the polymerase concentration dependence of beta(CR) in terms of the three step mechanism of open complex formation yields the equilibrium constant K(1) for formation of the first kinetically significant intermediate (I(1)) and the forward rate constant (k(2)) for the conformational change converting I(1) to the second kinetically significant intermediate I(2): R + P-->(K(1))<--I(1)(k(2))-->I(2). Use of rapid quench mixing allows K(1) and k(2) to be individually determined over the entire temperature range investigated, previously not possible at this promoter using manual mixing. Given the large (>60 bp) interface formed in I(1), its relatively small binding constant K(1) at 37 degrees C at this [salt] (approximately 6 x 10(6) M(-1)) strongly argues that binding free energy is used to drive large-scale structural changes in polymerase and/or promoter DNA or other coupled processes. Evidence for coupling of protein folding is provided by the large and negative activation heat capacity of k(a)[DeltaC(o,++)(a)= -1.5(+/-0.2)kcal K(-1)], now shown to originate directly from formation of I(1) [DeltaC(o)(1)= -1.4(+/-0.3)kcal K(-1)] rather than from the formation of I(2) as previously proposed. The isomerization I(1)-->I(2) exhibits relatively slow kinetics and has a very large temperature-independent Arrhenius activation energy [E(act)(2)= 34(+/-2)kcal]. This kinetic signature suggests that formation of the transition state (I(1)-I(2)++ involves large conformational changes dominated by changes in the exposure of polar and/or charged surface to water. Structural and biochemical data lead to the following hypotheses to interpret these results. We propose that formation of I(1) involves coupled folding of unstructured regions of polymerase (beta, beta' and sigma(70)) and bending of promoter DNA (in the -10 region). We propose that interactions with region 2 of sigma(70) and possibly domain 1 of beta induce a kink at the -11/-12 base pairs of the lambdaP(R) promoter which places the downstream DNA (-5 to +20) in the jaws of the beta and beta' subunits of polymerase in I(1). These early interactions of beta and beta' with the DNA downstream of position -5 trigger jaw closing (with coupled folding) and subsequent steps of DNA opening.

Bacteriophage lambda↗
PubMed2004

A functional-structural model to understand cardiac autonomic nervous system (ANS) dysregulation in affective illness and to elucidate the ANS effects of antidepressive treatment.

Numerous studies provide evidence that major depression (MD) is associated with certain disorders of cardiac autonomic nervous system (ANS) function, in particular, with an autonomic neurocardiac imbalance characterized by a low cardiovagal modulation, a raised sympathetic nerve activity and a high resting heart rate. We assume that such MD-associated cardiac ANS disorders are mainly caused by functional-structural abnormalities within the central autonomic network (CAN), in particular, by well-defined abnormalities of hypothalamic structures in MD. In view of the well-known association between an autonomic neurocardiac imbalance and the risk for cardiac arrhythmias, we assume that MD-associated cardiac ANS disorders are at least partly responsible for the high cardiovascular mortality risk in MD. It is, however, still unclear whether antidepressive treatment will lower the risk for cardiovascular complications in MD. There is convincing evidence that a successful antidepressive treatment with electroconvulsive therapy, cognitive behavioral therapy, or pharmacotherapy with primarily non-antimuscarinergic antidepressants can improve an initially disturbed cardiac ANS function in MD. These studies correspond well to our findings that treatment with both, nefazodone or reboxetine, can induce a reduction of central sympathetic nerve activity and an increase of the initially lowered cardiovagal modulation depending on the improvement of depressive symptoms after treatment. Since both effects occured obviously independent from the primarily serotonergic or noradrenergic action of the antidepressants, our findings suggest the existence of a generally supraordinate and uniform mechanism underlying the ANS effects of antidepressive treatment with drugs inhibiting serotonin- or noradrenaline reuptake.

Antidepressive Agents↗
PubMed2006

Supramolecular self-organization of "Janus-like" diblock codendrimers: synthesis, thermal behavior, and phase structure modeling.

We report on the design and synthesis of three series of segmented amphiphilic block codendrimers, and on their self-organizing behavior in liquid-crystalline mesophases. Connecting two prefunctionalized monodendrons, each differing in their chemical constitution and generation number, yielded these diblock supermolecules. One wedge of the codendrimer was made hydrophobic, and is based on a branched poly(benzyl ether) monodendron functionalized at the periphery by lipophilic aliphatic fragments (also known as Percec dendrons). The other segment was made hydrophilic by the grafting of hydroxyl-containing moieties onto the focal functions of the former dendrons. Both types of dendrons were prepared independently by convergent methods and then joined in the ultimate stage of the synthetic procedure by cross-coupling reactions. In this way, the proportion of the dendritic blocks was varied independently to allow control of the hydrophilic/hydrophobic balance (HHB), the hydrogen-bonding ability, and consequently the capacity to tune the mesomorphic properties of the resulting "superamphiphiles" was anticipated. Essentially all the dendritic compounds display a thermotropic mesomorphism directly at or near room temperature as determined by using X-ray diffraction, polarized optical microscopy, and differential scanning calorimetry. The nature and the supramolecular organization of the mesophases, namely columnar and cubic phases, are correlated to the size of the respective block monodendrons and the chemical structures of the dendromesogens. The molecular organization within the cubic phases can be geometrically described and well understood by the space-filling polyhedron model.

Journal Article↗
PubMed2003

A computationally derived structural model of doxorubicin interacting with oligomeric polyalkylcyanoacrylate in nanoparticles.

We report a molecular simulation study of doxorubicin interacting within a frame of n-butyl polycyanoacrylate, one of the most commonly encountered polymers in the production of nanoparticles. Emphasis is put on the tetrameric, hexameric and octameric oligomers (PACA's). Log P was calculated for all interacting species. Molecular dynamics along with energy minimization processes (molecular mechanics MM2, semi-empirical quantum mechanics PM3) were employed to probe the conformational behavior of doxorubicin and polyalkylcyanoacrylate both as isolated species and interacting with each other. A docked structure of protonated doxorubicin with two octamers of n-butyl polycyanoacrylate is described. Among the main stability factors of the assembly was the charge-dipole interaction representing a stabilizing contribution of -33 kcal/mol. The mechanism of aggregation and desegregation (doxorubicin release) can be summarized as follows: oligomeric PACA's are lipophilic entities that scavenge amphiphilic doxorubicin already during the polymerization process by extraction of the protonated species from the aqueous environment to the increasingly lipophilic phase of the growing PACA's. The establishment of hydrogen bonds between the ammonium N-H function and the cyano groups is noteworthy. The cohesion in PACA nanoparticle comes therefore from a blend of dipole-charge interaction, H bonds, and hydrophobic forces,

Cyanoacrylates↗
PubMed1999

Structural model for the organization of the transmembrane spans of the human red-cell anion exchanger (band 3; AE1).

We have examined the functional co-assembly of non-complementary pairs of N- and C-terminal polypeptide fragments of the anion transport domain (b3mem) of human red-cell band 3. cDNA clones encoding non-contiguous pairs of fragments with one transmembrane (TM) region omitted, or overlapping pairs of fragments with between one and ten TM regions duplicated, were co-expressed in Xenopus oocytes and a cell-free translation system. Stilbene disulphonate-sensitive chloride uptake assays in oocytes revealed that the omission of any single TM region of b3mem except spans 6 and 7 caused a complete loss of functional expression. In contrast, co-expressed pairs of fragments overlapping a single TM region 5, 6, 7, 8, 9-10 or 11-12 retained a high level of functionality, whereas fragments overlapping the clusters of TM regions 2-5, 4-5, 5-8 and 8-10 also mediated some stilbene disulphonate-sensitive uptake. The co-assembly of N- or C-terminal fragments with intact band 3, b3mem or other fragments was examined by co-immunoprecipitation in non-denaturing detergent solutions by using monoclonal antibodies against the termini of b3mem. All the fragments, except for TM spans 13-14, co-immunoprecipitated with b3mem. The medium-sized N-terminal fragments comprising spans 1-6, 1-7 or 1-8 co-immunoprecipitated particularly strongly with the C-terminal fragments containing spans 8-14 or 9-14. The fragments comprising spans 1-4 or 1-12 co-immunoprecipitated less extensively than the other N-terminal fragments with either b3mem or C-terminal fragments. There is sufficient flexibility in the structure of b3mem to allow the inclusion of at least one duplicated TM span without a loss of function. We propose a working model for the organization of TM spans of dimeric band 3 based on current evidence.

Animals↗
PubMed1982

The amino acid sequence of chicken muscle desmin provides a common structural model for intermediate filament proteins.

The complete amino acid sequence of muscle desmin reported here is the first for an intermediate filament protein. Alignment with partial data available for vimentin, glial fibrillary acid protein, neurofilament 68 K, two wool alpha-keratins, and a recently described DNA clone covering 90% of an epidermal keratin shows that all seven proteins have extensive homologies and therefore form a complex multigene family, the intermediate filament proteins. The hard alpha-keratins of wool appear to be a special subset of epithelial keratins. The sequence information reveals, as the dominant structural principle, a rod-like middle domain arising from several alpha-helical segments able to form interchain coiled-coil elements. The proposed helices are separated by short spacers, which like the two terminal domains seem built from non-alpha-helical material. Attention is drawn to the sometimes very striking sequence homologies along the rod and the high sequence variability in the terminal domains. Finally, chemical cross-linking experiments performed on the isolated desmin rod show that intermediate filament structure seems not to be based on triple-stranded coiled-coils as currently thought, but rather reflects protofilament units built as a dimer of normal interchain double-stranded coiled-coils.

Amino Acid Sequence↗
PubMed2001

Stereocontrol of intramolecular Diels-Alder reactions: synthetic studies and transition structure modeling with c5-substituted 1,3,8-nonatrienes and nonadienynes.

An investigation into the endo/exo selectivity and pi-diastereofacial selectivity of ester-tethered intramolecular Diels-Alder reactions is reported. High levels of exo selectivity are realized with terminally substituted dienophiles, and high lk pi-diastereofacial selectivities are induced by the presence of a bulky dioxolanyl substituent at the allylic position of the tether. Precursors 19S, 20S, and 21S, readily prepared from glucose, provide densely functionalized bicyclic lactones of predictable stereochemistry in high yields in enantiomerically pure form upon thermolysis at 110 degrees C. B3LYP/6-31G(d) theory provides good descriptions of transition structures for these reactions and allows an understanding of the formation of the major cycloadducts.

Journal Article↗