PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Models, Structural”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 865 records · Page 48Linked to original sources
PubMed2000

Structural models for carcinoembryonic antigen and its complex with the single-chain Fv antibody molecule MFE23.

MFE23 is a single chain Fv antibody that has a high affinity for carcinoembryonic antigen (CEA). A full homology model for CEA based on V-type, I-type and C2-type immunoglobulin folds, 28 oligosaccharides and the interdomain angle of CD2 was validated using solution scattering data. The superimposition of the intermolecular contacts observed in our recent crystal structure of MFE23 with the N-terminal domain of CEA permitted the MFE23-CEA complex to be modelled. Good surface and electrostatic complementarity and carbohydrate-unhindered access of MFE23 with the indentation between the first two CEA domains was observed. The model is supported by biochemical data and provides insight on the high affinity of MFE23 for CEA.

Amino Acid Sequence↗
PubMed2001

Molecular modeling, structure--activity relationships and functional antagonism studies of 4-hydroxy-1-methyl-4-(4-methylphenyl)-3-piperidyl 4-methylphenyl ketones as a novel class of dopamine transporter inhibitors.

We previously disclosed the discovery of 4-hydroxy-1-methyl-4-(4-methylphenyl)-3-piperidyl 4-methylphenyl ketone (3) as a novel class of dopamine transporter (DAT) inhibitors and showed that (+/-)-3 has a significant functional antagonism against cocaine in vitro. Our previous preliminary structure-activity relationship study led to identification of a more potent DAT inhibitor [(+/-)-4] but this compound failed to show any significant functional antagonism. To search for more potent analogues than 3 but still displaying significant functional antagonism, further SARs, molecular modeling studies and in vitro pharmacological evaluation of this novel class of DAT inhibitors were performed. Sixteen new analogues were synthesized in racemic form and evaluated as DAT inhibitors. It was found that seven new analogues are reasonably potent DAT inhibitors with K(i) values of 0.041--0.30 and 0.052--0.16 microM in [(3)H]mazindol binding and inhibition of DA reuptake. Chiral isomers of several potent DAT inhibitors were obtained through chiral HPLC separation and evaluated as inhibitors at all the three monoamine transporter sites. In general, the (-)-isomer is more active than the (+)-isomer in inhibition of DA reuptake and all the (-)-isomers are selective inhibitors at the DAT site. Evaluation of cocaine's effect on dopamine uptake in the presence and absence of (+)-3 and (-)-3 showed that (-)-3 is responsible for the functional antagonism obtained with the original lead (+/-)-3. Out of the new compounds synthesized, analogue (+/-)-20, which is 8- and 3-fold more potent than (+/-)-3 in binding and inhibition of DA reuptake, appeared to have improved functional antagonism as compared to (+/-)-3.

Animals↗
PubMed1978

A hierarchically-structured model of information processing in neural networks.

In order to describe the information processing mechanisms of a neural system a basic building block (sub-network), consisting of a group of interacting neural elements, is introduced. By interconnecting such units to give an integrated structure, a hierarchically-organised processing chain is formed. The properties of such a system are shown to provide a logical description of information processing which links high level events with underlying neural mechanisms.

Brain↗
PubMed1995

Paratope characterization by structural modelling of two anti-cortisol single-chain variable fragments produced in E. coli.

Two monoclonal antibodies (mAbs), 5A4 and 6D6, directed against cortisol, have been obtained; 6D6 is used in an assay kit for cortisol. The antibodies also recognize other, structurally related steroids present in the sample assayed. To improve the specificity of the assay, we aimed to minimize the recognition of non-cortisol steroids by the two anti-cortisol mAbs. Our strategy consisted in constructing an efficient expression vector in E. coli which produced the single-chain variable fragment (scFv) of the mAbs in the periplasmic space. We demonstrated that temperature and inducer concentration of the bacterial culture influenced dramatically the yield of active scFv. From the nucleotide sequence we constructed a three-dimensional model of the two variable fragments in order to understand why related steroids are, or are not recognized by the antibody. For both antibodies, we have identified chemical groups which are probably involved in the binding of the steroid haptens and the antibodies. The hydrophobic pocket formed by the antibody comprises two or three tryptophan residues which can interact with the steroid nucleus by stacking. The serine at position 35 of the heavy chain is buried in the back of the pocket and can form a hydrogen bond with the 20-keto group of the cortisol. The stacking interactions and the hydrogen bond orient the steroid in the pocket. This reactivity of the binding site is sustained by the analysis of the cross-reactions of related steroids with the mAbs.

Amino Acid Sequence↗
PubMed1984

New structural model for mixed-chain phosphatidylcholine bilayers.

Multilamellar suspensions of a mixed-chain saturated phosphatidylcholine with 18 carbon atoms in the sn-1 chain and 10 carbon atoms in the sn-2 chain have been analyzed by X-ray diffraction techniques. The structural parameters for this lipid in the gel state are quite different than usual phosphatidylcholine bilayer phases. A symmetric and sharp wide-angle reflection at 4.11 A indicates that the hydrocarbon chains in hydrated C(18):C(10)PC bilayers are more tightly packed than in usual gel-state phosphatidylcholine bilayers and that there is no hydrocarbon chain tilt. The lipid thickness is about 12 A smaller than would be expected in a normal bilayer phase, and the area per molecule is 3 times the area per hydrocarbon chain. In addition, the bilayer thickness increases upon melting to the liquid-crystalline state, whereas normal bilayer phases decrease in thickness upon melting. On the basis of these data, we propose a new lipid packing model for gel-state C(18):C(10)PC bilayers in which the long C(18) chain spans the entire width of the hydrocarbon region of the bilayer and the short C(10) chain aligns or abuts with the C(10) chain from the apposing molecule. This model is novel in that there are three hydrocarbon chains per head group at the lipid-water interface. Calculations show that this phase is energetically favorable for mixed-chain lipids provided the long acyl chain is nearly twice the length of the shorter chain. In the liquid-crystalline state C(18):C(10)PC forms a normal fluid bilayer, with two chains per head group.(ABSTRACT TRUNCATED AT 250 WORDS)

Chemical Phenomena↗
PubMed2003

A structural model for actin-induced nucleotide release in myosin.

Myosins are molecular motor proteins that harness the chemical energy stored in ATP to produce directed force along actin filaments. Complex communication pathways link the catalytic nucleotide-binding region, the structures responsible for force amplification and the actin-binding domain of myosin. We have crystallized the nucleotide-free motor domain of myosin II in a new conformation in which switch I and switch II, conserved loop structures involved in nucleotide binding, have moved away from the nucleotide-binding pocket. These movements are linked to rearrangements of the actin-binding region, which illuminate a previously unobserved communication pathway between the nucleotide-binding pocket and the actin-binding region, explain the reciprocal relationship between actin and nucleotide affinity and suggest a new mechanism for product release in myosin family motors.

Actins↗
PubMed1985

On the possibility of reduction of dissipative structure models to a simple form.

A multicomponent reaction-diffusion system containing two different space scales (contrasting system) is considered. It is shown that if the system answers several conditions enumerated, it can be reduced to a bicomponent system which describes a dissipative structure either of a peak or of a step type. While in the first case the original and the final systems are equivalent only in the neighbourhood of zero, in the second case the equivalence is more general as the solution of these systems does not leave the region for which the procedure of reduction was developed.

Biometry↗
PubMed2002

Decision support system for overall welfare assessment in pregnant sows A: model structure and weighting procedure.

The problem of how to objectively assess the overall welfare status of animals under farming conditions has contributed to an ongoing debate that has hampered actual decision making on animal welfare. For this reason we constructed a model based on the assumed hierarchical organization of the animals' needs for overall welfare assessment in the case of pregnant sows. This model is implemented in a computer-based decision support system that takes a description of a housing and management system as input and produces a welfare score as output. A formalized procedure was used to construct the model for welfare assessment in pregnant sows on the basis of available scientific knowledge. This SOWEL (from SOw WELfare) model contains 37 attributes that describe the welfare-relevant properties of housing and management systems. In the decision support system these attributes are linked to scientific statements and a list of needs to provide a scientific basis for welfare assessment. Weighting factors that represent the relative importance of the attributes are derived from the scientific statements about the various welfare performance criteria that have been measured by scientists. The welfare score is calculated as the weighted average score. All information in the decision support system is stored in tables in a relational database such that newly available knowledge and insights can be incorporated to refine the model. The model has been developed in line with several existing models but it differs from these models in that it is the first to provide a formalized procedure to explicate the reasoning steps involved in welfare assessment based on available scientific knowledge.

Animal Husbandry↗
PubMed1993

Divalent cation competition with [3H]saxitoxin binding to tetrodotoxin-resistant and -sensitive sodium channels. A two-site structural model of ion/toxin interaction.

Monovalent and divalent cations competitively displace tetrodotoxin and saxitoxin (STX) from their binding sites on nerve and skeletal muscle Na channels. Recent studies of cloned cardiac (toxin-resistant) and brain (toxin-sensitive) Na channels suggest important structural differences in their toxin and divalent cation binding sites. We used a partially purified preparation of sheep cardiac Na channels to compare monovalent and divalent cation competition and pH dependence of binding of [3H]STX between these toxin-resistant channels and toxin-sensitive channels in membranes prepared from rat brain. The effects of several chemical modifiers of amino acid groups were also compared. Toxin competition curves for Na+ in heart and Cd2+ in brain yielded similar KD values to measurements of equilibrium binding curves. The monovalent cation sequence for effectiveness of [3H]STX competition is the same for cardiac and brain Na channels, with similar KI values for each ion and slopes of -1. The effectiveness sequence corresponds to unhydrated ion radii. For seven divalent cations tested (Ca2+, Mg2+, Mn2+, Co2+, Ni2+, Cd2+, and Zn2+) the sequence for [3H]STX competition was also similar. However, whereas all ions displaced [3H]STX from cardiac Na channels at lower concentrations, Cd2+ and Zn2+ did so at much lower concentrations. In addition, and by way of explication, the divalent ion competition curves for both brain and cardiac channels (except for Cd2+ and Zn2+ in heart and Zn2+ in brain) had slopes of less than -1, consistent with more than one interaction site. Two-site curves had statistically better fits than one-site curves. The derived values of KI for the higher affinity sites were similar between the channel types, but the lower affinity KI's were larger for heart. On the other hand, the slopes of competition curves for Cd2+ and Zn2+ were close to -1, as if the cardiac Na channel had one dominant site of interaction or more than one site with similar values for KI. pH titration of [3H]STX binding to cardiac channels showed a pKa of 5.5 and a slope of 0.6-0.9, compared with a pKa of 5.1 and slope of 1 for brain channels. Tetramethyloxonium (TMO) treatment abolished [3H]STX binding to cardiac and brain channels and STX protected channels, but the TMO effect was less dramatic for cardiac channels. Trinitrobenzene sulfonate preferentially abolished [3H]STX binding to brain channels by action at an STX protected site.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2003

Molecular dynamics studies of alanine racemase: a structural model for drug design.

Alanine racemase (AlaR) is a bacterial enzyme that catalyzes the interconversion of L- and D-alanine, which is an essential constituent of the peptidoglycan layer of the bacterial cell wall and requires pyridoxal 5'-phosphate (PLP) as a cofactor. The enzyme is universal to bacteria, including mycobacteria, making it an attractive target for drug design. To investigate the effects of flexibility on the binding modes of the substrate and an inhibitor and to analyze how the active site is affected by the presence of the substrate versus inhibitor, a molecular dynamics simulation on the full AlaR dimer from Bacillus stearothermophilus (pdb code: 1SFT) with a D-alanine molecule in one active site and the noncovalent inhibitor, propionate, in the second site has been carried out. Within the time scale of the simulation, we show that the active site becomes more stabilized in the presence of substrate versus inhibitor. The results of this simulation are in agreement with the proposed mechanism of alanine racemase reaction in which the substrate carboxyl group directly participates in the catalysis by acting cooperatively with Tyr 265' and Lys 39. A structural water molecule in contact with both substrate and inhibitor (i.e., in both active sites) and bridging residues in both active sites was identified. It shows a remarkably low mobility and does not exchange with bulk water. This water molecule can be taken into account for the design of specific AlaR inhibitors by either utilizing it as a bridging group or displacing it with an inhibitor atom. The results presented here provide insights into the dynamics of the alanine racemase in the presence of substrate/inhibitor, which will be used for the rational design of novel inhibitors.

Alanine↗
PubMed1985

A model for signal transmission in an ear having hair cells with free-standing stereocilia. I. Empirical basis for model structure.

No adequate theory for the signal-transmission properties of the peripheral auditory system exists for any vertebrate ear. Because the mammalian ear seems to pose conceptual and technical problems that complicate the development of an adequate theory, it is worthwhile to investigate simpler ears. The ear of the alligator lizard is simpler than mammalian ears in several respects: the motion of the basilar membrane is approximately independent of longitudinal position and is approximately linearly related to the sound pressure at the tympanic membrane; in a large region of the cochlea the hair cells have free-standing stereocilia that are not in contact with a tectorial membrane; the receptor potential of these hair cells is related to the sound pressure at the tympanic membrane in a relatively simple manner; the cochlear-nerve fiber responses from this region do not exhibit two-tone rate suppression. Also, the relative accessibility of this ear has enabled measurement of several response variables: tympanic-membrane volume velocity, extracolumella velocity, basilar-membrane velocity, hair-cell stereociliary displacement, hair-cell receptor potentials, and cochlear-nerve-fiber discharges. A model is developed to represent these results in terms of underlying anatomical structures and physiological mechanisms.(ABSTRACT TRUNCATED AT 250 WORDS)

Air Pressure↗
PubMed2006

Biogenesis of caveolae: a structural model for caveolin-induced domain formation.

Caveolae are striking morphological features of the plasma membrane of mammalian cells. Caveolins, the major proteins of caveolae, play a crucial role in the formation of these invaginations of the plasma membrane; however, the precise mechanisms involved are only just starting to be unravelled. Recent studies suggest that caveolae are stable structures first generated in the Golgi complex. Their formation and exit from the Golgi complex is associated with caveolin oligomerisation, acquisition of detergent insolubility, and association with cholesterol. Modelling of caveolin-membrane interactions together with in vitro studies of caveolin peptides are providing new insights into how caveolin-lipid interactions could generate the unique architecture of the caveolar domain.

Animals↗
PubMed1994

Design and chemical synthesis of a neoprotein structural model for the cytoplasmic domain of a multisubunit cell-surface receptor: integrin alpha IIb beta 3 (platelet GPIIb-IIIa).

Integrins are a class of heterodimeric cell adhesion receptors involved in cell migration, cell anchorage, and cell-cell interactions. The cytoplasmic domains of integrins are of key importance in these activities. We have designed and chemically synthesized a 126 amino acid model protein (MP-1) containing both cytoplasmic tails of the platelet-derived integrin alpha IIb beta 3 covalently linked via a helical coiled coil. The coiled-coil tertiary structure was incorporated to mimic the membrane-spanning domain of the integrin and to act as a topological constraint fixing the two cytoplasmic tails in a parallel arrangement. This molecule, which contains two C-termini, was constructed by chemical dovetailing. The bromoacetylated and cysteinyl peptide synthons were unambiguously ligated through the formation of a thioether linkage. Ultraviolet circular dichroism (CD) spectroscopy has been performed on MP-1 and related compounds, confirming that a helical coiled coil is present within the MP-1 molecule. Significantly, the helicity apparently extends beyond the predicted amphiphilic region of MP-1. Fluorescence measurements suggest that a defined tertiary structure has formed by the association of the two cytoplasmic domains. We conclude that this is a practical design strategy for the study of the cytoplasmic domain of multisubunit cell-surface receptors.

Amino Acid Sequence↗
PubMed2006

A structural model for chorismate synthase from Mycobacterium tuberculosis in complex with coenzyme and substrate.

The enzymes of the shikimate pathway constitute an excellent target for the design of new antibacterial agents; chorismate synthase (CS) catalyzes the last step of this pathway. The prediction of Mycobacterium tuberculosis (MTB) CS three-dimensional structure and the geometric docking of the coenzyme FMN and the substrate EPSP were performed using the crystal structure of CS from Streptococcus pneumoniae as template. Energy minimization of the whole complex showed, as expected, that most of the template interactions are preserved in the MTB structure, except for HIS11, ARG139 and GLN255. However, novel interactions involving ARG111, GLY113 and SER317 were also observed.

Amino Acid Sequence↗
PubMed2005

A structural model of the vacuolar ATPase from transmission electron microscopy.

Vacuolar ATPases (V-ATPases) are large, membrane bound, multisubunit protein complexes which function as ATP hydrolysis driven proton pumps. V-ATPases and related enzymes are found in the endomembrane system of eukaryotic organsims, the plasma membrane of specialized cells in higher eukaryotes, and the plasma membrane of prokaryotes. The proton pumping action of the vacuolar ATPase is involved in a variety of vital intra- and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release. This review summarizes recent progress in the structure determination of the vacuolar ATPase focusing on studies by transmission electron microscopy. A model of the subunit architecture of the vacuolar ATPase is presented which is based on the electron microscopic images and the available information from genetic, biochemical and biophysical experiments.

Animals↗
PubMed1995

Drastic reduction in antimicrobial activity by replacement of Orn residues with Lys in cyclized amphiphilic beta-structural model peptides.

Recent investigation have indicated that cyclic dodeca- and tetradecapeptides, cyclo(-Leu-Orn-Leu-Orn-D-Phe-Pro)2 (Orn-DLL-12) and cyclo(-Leu-Orn-Leu-Orn-Leu-D-Phe-Pro)2 (Orn-DLL-14), which are designed on the basis of a cyclic beta-structural antibiotic, gramicidin S (GS), inhibit the growth of Gram-positive and -negative bacteria with high potency [Ando, S., Nishikawa, H., Takiguchi, H., Lee, S. & Sugihara, G. (1993) Biochim. Biophys. Acta 1147, 42-49]. In this study we designed and synthesized two analogs, Lys-DLL-12 and Lys-DLL-14, in which four Orn residues in Orn-DLL-12 and Orn-DLL-14 were replaced by Lys residues, respectively, and investigated their interactions with model membranes in terms of CD and dye-leakage experiments, antimicrobial activity and lytic activity for human erythrocytes. Both peptides newly designed showed no antimicrobial activity and no lytic activity of erythrocytes. The present CD study showed that the presence of neutral liposomes and of acidic liposomes of natural or synthetic phospholipids results in no remarkable conformational difference between Orn-DLL-12/-14. The leakage experiment showed a clear relation between the antimicrobial activity and the leakage ability in acidic synthetic phospholipid liposomes but no correlation in acidic natural ones. The difference in hydrophobic and hydrophilic balance between Orn-DLL-12/14 and Lys-DLL-12/14 (derived from the increasing hydrophobicity due to an increase of four methylene units by the substitution of Lys for Orn) may be one of the important factors in the drastic decrease in activity.

Amino Acid Sequence↗
PubMed1991

Crystal, solution, and molecular modeling structural properties and muscarinic antagonist activity of azaprophen.

The structure of azaprophen, which was originally assigned by 1H NMR analysis, was confirmed by X-ray crystallography. A comparison of 13C NMR isotropic chemical shift data for azaprophen in the solid state and in CDCl3 and DMSO-d6 solution was used to correlate solution and solid-state conformation as determined by the X-ray data. The data suggested that the solid-state and solution conformation of azaprophen were similar. The observed solid-state structure was also compared to low-energy conformations identified by molecular-mechanics calculations. A comparison of azaprophen and atropine radioligand binding in guinea pig ileum, rat heart, rat brain, and in CHO cells expressing transfected m1 and m3 receptors was conducted. Azaprophen is more active than atropine in all preparations except the m3 receptor expressed in CHO cells. However, like atropine, it does not provide major discrimination among the muscarinic receptor subtypes.

Animals↗