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At least 1,063 records · Page 59Linked to original sources
PubMed2005

Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations.

Considering the large number of putative Ras effector proteins, it is highly desirable to develop computational methods to be able to identify true Ras binding molecules. Based on a limited sequence homology among members of the Ras association (RA) and Ras binding (RB) sub-domain families of the ubiquitin super-family, we have built structural homology models of Ras proteins in complex with different RA and RB domains, using the FOLD-X software. A critical step in our approach is to use different templates of Ras complexes, in order to account for the structural variation among the RA and RB domains. The homology models are validated by predicting the effect of mutating hot spot residues in the interface, and residues important for the specificity of interaction with different Ras proteins. The FOLD-X calculated energies of the best-modelled complexes are in good agreement with previously published experimental data and with new data reported here. Based on these results, we can establish energy thresholds above, or below which, we can predict with 96% confidence that a RA/RB domain will or will not interact with Ras. This study shows the importance of in depth structural analysis, high quality force-fields and modelling for correct prediction. Our work opens the possibility of genome-wide prediction for this protein family and for others, where there is enough structural information.

Amino Acid Sequence↗
PubMed2000

A rapid screening system to determine drug affinities for the intestinal dipeptide transporter 2: affinities of ACE inhibitors.

PURPOSE: To assess the affinities of a series of ACE inhibitors for the di/tri/oligopeptide transport system (DTS) using a rapid in vitro system. METHODS: Monolayers of Caco-2 cells were cultured in plastic wells for 7-9 days and the uptake of Gly-[3H]L-Pro was used as an affinity probe. Gly-[3H]L-Pro (50 nM), together with excess L-Pro (10 mM), to suppress uptake of any [3H]L-Pro produced by degradation of the probe, was incubated with the test compound (usually 1 mM) at pH 6 for 3-mins. The uptake of radiolabel was determined by liquid scintillation counting. RESULTS: A 2-dimensional six-domain model of the transporter based on the structure of a phosphinate ACE inhibitor (SQ-29852) was constructed to facilitate interpretation of the competitor affinities. The SQ-29852 molecule was divided into six binding domains (A-F) based on functional groups within these regions and the effects of structural variation in four of these domains (A, C-E) were explored. A series of dipeptide-like compounds varying within specific domains were selected from a large number of commercially available ACE inhibitors and SQ-29852 analogues. Domain A had a preference for an uncharged group, with bulky hydrophobic groups reducing affinity. Domain C exhibited a preference for a positive charge over a neutral function, with the space this functional group occupies contributing to affinity. Domain D favoured lipophilic residues and domain E retained activity when the carboxylic acid was esterified. CONCLUSION: The test system is able to reveal structure-activity relationships of peptidomimetic agents and may well serve as a design tool to optimise affinity for the DTS.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1975

Conformational studies on parvalbumins by circular dichroism.

Structural variations of two parvalbumins, Whiting III and Pike III, in various denaturing conditions, have been studied by circular dichroism. CD signals are depressed from 4 urea. For Pike III, acidic pH, sodium dodecyl sulfate or complete removal of Ca2+ show little effect in the far ultraviolet region but rather strong effects in the near ultraviolet. For Whiting III similar results are obtained at acidic pH. Carboxymethylated Whiting III (0.15 Ca2+/mol) shows, on the contrary, decreased CD signals in the far and in the near ultraviolet spectra. Addition of Ca2+ fully restores the native CD spectra in both proteins. Ca2+ binding produces structural modifications which are found to vary according to parvalbumin and which seem in any case different from those described for troponin C.

Animals↗
PubMed1988

Genomic structure and sequence variation of a 3.3-kb repeat DNA element of the kangaroo rat, Dipodomys ordii.

The genomic structure and sequence variation of a 3.3-kb repeat DNA element, representing 5% of the genome of the kangaroo rat Dipodomys ordii, has been investigated. Most of the repeats are arranged in tandem arrays of 50 kb or more. Thirteen randomly selected genomic clones have been mapped with twelve restriction enzymes. The frequency of sequence divergence in the genomic clones is 0.5%. The clone maps and the genomic structure studies have permitted the characterization of a number of variant members of the 3.3-kb repeat family. The genomic organization of the repeat resembles that for repeated DNAs found in large tandem arrays or satellites.

Animals↗
PubMed1991

Molecular genetics of human erythrocyte MiIII and MiVI glycophorins. Use of a pseudoexon in construction of two delta-alpha-delta hybrid genes resulting in antigenic diversification.

Human glycophorins alpha and delta (or A and B) specify the MNSs blood group antigens; they exhibit considerable structural variation among populations. We show that two variant phenotypes of Miltenberger class III and VI are encoded by similar hybrid glycophorin genes in a delta-alpha-delta arrangement. Restriction mapping identified altered fragments unique to the MiIII and MiVI genes. Genomic sequences spanning exons 2 to 4 of the two genes were obtained by allele-specific polymerase chain reaction. Restriction analysis and direct sequencing of the amplified DNA revealed that MiIII and MiVI genes are identical to the delta gene except that, in both, an internal segment of the delta gene has been replaced by its homologous counterpart of the alpha gene, resulting in a delta-alpha-delta hybrid structure. In the process of hybrid formation a portion of alpha exon 3 and intron 3, that carries a functional 5' splicing signal, has been fused to an exon-like sequence in the delta gene that retains a 3' but lacks a 5' splicing signal. These rearrangements created a composite exon resulting in the expression of the ordinarily unexpressed delta gene sequence and conferred the hybrid proteins with new antigenic specificities. The expression of this sequence in MiIII glycophorin is directly demonstrated by protein sequencing. MiIII and MiVI genes differ in the location of upstream (delta-alpha) and downstream (alpha-delta) breakpoints and in the length of sequence replacement. The delta-alpha breakpoints of the two genes occur at different locations within a 35-base pair sequence of exon 3 that is clustered with multiple inverted repeats, whereas the alpha-delta breakpoints reside downstream in two dissimilar blocks of sequences of intron 3. The minimal length of the delta gene sequence that has been replaced by the alpha gene is 55 base pairs in the MiIII gene and 131 base pairs in the MiVI gene. Such segmental DNA transfers may have proceeded unidirectionally through the mechanisms of gene conversion.

Amino Acid Sequence↗
PubMed2004

Crystal structure of human bisphosphoglycerate mutase.

Bisphosphoglycerate mutase is a trifunctional enzyme of which the main function is to synthesize 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. The gene coding for bisphosphoglycerate mutase from the human cDNA library was cloned and expressed in Escherichia coli. The protein crystals were obtained and diffract to 2.5 A and produced the first crystal structure of bisphosphoglycerate mutase. The model was refined to a crystallographic R-factor of 0.200 and R(free) of 0.266 with excellent stereochemistry. The enzyme remains a dimer in the crystal. The overall structure of the enzyme resembles that of the cofactor-dependent phosphoglycerate mutase except the regions of 13-21, 98-117, 127-151, and the C-terminal tail. The conformational changes in the backbone and the side chains of some residues reveal the structural basis for the different activities between phosphoglycerate mutase and bisphosphoglycerate mutase. The bisphosphoglycerate mutase-specific residue Gly-14 may cause the most important conformational changes, which makes the side chain of Glu-13 orient toward the active site. The positions of Glu-13 and Phe-22 prevent 2,3-bisphosphoglycerate from binding in the way proposed previously. In addition, the side chain of Glu-13 would affect the Glu-89 protonation ability responsible for the low mutase activity. Other structural variations, which could be connected with functional differences, are also discussed.

Amino Acid Sequence↗
PubMed2003

Motions and structural variability within toxins: implication for their use as scaffolds for protein engineering.

Animal toxins are small proteins built on the basis of a few disulfide bonded frameworks. Because of their high variability in sequence and biologic function, these proteins are now used as templates for protein engineering. Here we report the extensive characterization of the structure and dynamics of two toxin folds, the "three-finger" fold and the short alpha/beta scorpion fold found in snake and scorpion venoms, respectively. These two folds have a very different architecture; the short alpha/beta scorpion fold is highly compact, whereas the "three-finger" fold is a beta structure presenting large flexible loops. First, the crystal structure of the snake toxin alpha was solved at 1.8-A resolution. Then, long molecular dynamics simulations (10 ns) in water boxes of the snake toxin alpha and the scorpion charybdotoxin were performed, starting either from the crystal or the solution structure. For both proteins, the crystal structure is stabilized by more hydrogen bonds than the solution structure, and the trajectory starting from the X-ray structure is more stable than the trajectory started from the NMR structure. The trajectories started from the X-ray structure are in agreement with the experimental NMR and X-ray data about the protein dynamics. Both proteins exhibit fast motions with an amplitude correlated to their secondary structure. In contrast, slower motions are essentially only observed in toxin alpha. The regions submitted to rare motions during the simulations are those that exhibit millisecond time-scale motions. Lastly, the structural variations within each fold family are described. The localization and the amplitude of these variations suggest that the regions presenting large-scale motions should be those tolerant to large insertions or deletions.

Amino Acid Sequence↗
PubMed1989

A multivariate approach to saccharide quantitative structure-activity relationships exemplified by two series of 9-hydroxyellipticine glycosides.

Multivariate saccharide quantitative structure-activity relationships (QSARs) have been developed for two series of 9-hydroxyellipticine glycosides. In order to describe the structural variation of the glycoside moieties, thirteen chromatographic variables were used. Eleven D-glycosides and seven L-glycosides were used in separate QSARs to model 9-hydroxyellipticine glycoside antitumour activity against L 1210 leukemia. The multivariate partial least squares (PLS) method was used to establish the QSARs.

Animals↗
PubMed1986

Aminoglycoside antibiotics. 7. Dihydrostreptomycin analogues.

Dihydrostreptomycin analogues with structural variations in their guanidino groups were prepared. The analogue with a methyl group on the guanidine at C-1 was nearly as active as dihydrostreptomycin against bacteria. However, the 2-imidazolin-2-ylamino substituent at C-1 eliminated activity. No analogue with a substituent on the C-3 guanidino group was active.

Dihydrostreptomycin Sulfate↗
PubMed1984

[Biochemical studies on tienocarbine and related compounds].

Tienocarbine (1,9-dimethyl-7,8,9,10-tetrahydrothieno[3,2-e] pyrido[4,3-b] indole lactate) in oral doses of 10 mg X kg-1 lowers dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA) in the striata of rats without influencing contents of biogenic amines; this points to a reduced dopamine (DA) turnover. This effect is still present after 28 days of daily application. At the same time the serotonin (5-HT) turnover is not influenced. Tienocarbine displaces 3H-DA and 3H-spiperone from their specific binding sites in the nucleus caudatus of calf brain. Structural variation results in preponderance of either dopamineagonistic (turnover lowered) or antagonistic (turnover increased) properties of the molecules. The whole class of compounds therefore can be considered as mixed dopamine agonists-antagonists.

3,4-Dihydroxyphenylacetic Acid↗
PubMed1983

Molecular and functional changes in spectrin from patients with hereditary pyropoikilocytosis.

The structural and functional properties of spectrin from normal and hereditary pyropoikilocytosis (HPP) donors from the two unrelated families were studied. The structural domains of the spectrin molecule were generated by mild tryptic digestion and analyzed by two-dimensional electrophoresis (isoelectric focusing; sodium dodecyl sulfate-polyacrylamide gel electrophoresis). The alpha I-T80 peptide (Mr 80,000) is not detectable in two related HPP donors; instead, two new peptides (Mr 50,000 and 21,000) are generated and have been identified as fragments of the normal alpha I-T80. A third sibling has reduced levels of both the normal alpha I-T80 and the two new peptides. A similar analysis of spectrin from another HPP family indicates that their spectrins contain reduced amounts of the alpha I-T80 and the 50,000 and 21,000 fragments of the alpha I domain. The HPP donor also has other structural variations in the alpha I, alpha II, and alpha III domains. The alpha I-T80 domain of normal spectrin has been shown to be an important site for spectrin oligomerization (J. Morrow and V.T. Marchesi. 1981. J. Cell Biol. 88: 463-468), and in vitro assays indicate that HPP spectrin has an impaired ability to oligomerize. Ghost membranes from HPP donors are also more fragile than membranes from normal erythrocytes when measured by ektacytometry. In both the oligomerization and fragility assays, the degree of impairment is correlated with the amount of normal alpha I-T80 present in the spectrin molecule. We believe that a structural alteration in the alpha I-T80 domain perturbs normal in vivo oligomerization of spectrin, producing a marked decrease in erythrocyte stability.

Adult↗
PubMed2003

Monoamine oxidase A inhibitory potency and flavin perturbation are influenced by different aspects of pirlindole inhibitor structure.

Reversible inhibitors of monoamine oxidase A (MAO A) are used as antidepressants. The influence of inhibitors such as pirlindole (pyrazinocarbazole) on the redox co-factor (flavin adenine dinucleotide, FAD) is a key factor in the inhibition. The kinetic, spectral, and thermodynamic changes induced by four closely related pirlindole analogues have been determined to investigate their interaction with the FAD in the active site of MAO A. For a model of flavin-inhibitor stacking, more favourable association would be expected between lumiflavin and the flatter analogues with a double bond at N3, and indeed lower K(i) values were found. However, the spectral changes induced by inhibitor binding to MAO A were 45% less for inhibitors with a double bond. Both in the absence and presence of the double bond, compounds with cyclohexyl at C8 induced 85% larger decrease in absorbance at 500nm than did those with a methyl substituent. In contrast, the K(i) values for the cyclohexyl compounds were lower, indicating greater affinity despite the lower perturbation of the flavin spectrum. All inhibitors stabilised the semiquinone of the FAD when MAO A was titrated with dithionite and prevented further reduction. These results indicate that the active site of MAO A is far more sensitive to structural variation than would be predicted by the simple flavin stacking model. Further, the independent changes in inhibitory potency and flavin perturbation preclude direct interaction with the flavin as a mode of binding and indicate that inhibitor-protein interactions must be important for inhibition.

Binding Sites↗
PubMed2003

Dual wavelength parametric test of two-state models for circular dichroism spectra of helical polypeptides: anomalous dichroic properties of alanine-rich peptides.

A two-state helix-coil model underlies all calculations of fractional helicities FH from CD spectra of helical polypeptides. The presence of an isodichroic point near 203 nm is widely assumed to validate this model, but is shown here to provide inadequate validation for alanine-rich peptides. A parametric correlation with constant slope B between CD ellipticities at a pair of wavelengths is introduced as a more rigorous two-state test. Correlations of temperature-dependent [theta](222) vs [theta](208) values are reported for a variety of peptides. Constant slopes B are observed for literature CD data obtained from fragments of helical proteins and dimeric helical coiled coils, but parametric correlations of CD data for alanine-rich peptides consistently exhibit anomalous concave upward curvature, characterized by local slopes that are linearly temperature dependent. Low-temperature CD studies together with parametric correlations at a series of wavelengths demonstrate that the curvature anomaly is maximal at 222 nm and localized in the 215-230 nm wavelength region. Precedented structural variation of the phi, psi dihedral angles of the alpha-helix is suggested as a possible explanation. For the important case of alanine-rich peptides, experiments are proposed that may yield temperature corrections for [theta](222) and permit reliable calculations of FH from [theta](222) values.

Alanine↗
PubMed2004

Cytotoxic sterols and saponins from the starfish Certonardoa semiregularis.

Eleven new polyhydroxysterols (1-11) and eight new saponins (12-19) were isolated from the brine shrimp active fraction of the starfish Certonardoa semiregularis. The structures were determined on the basis of spectral analysis and chemical derivatization. The structural variations of these compounds are due to the hydroxylation pattern of the sterol nucleus, the functionalization of the side chain, or the nature and location of the saccharide moiety. These compounds displayed considerable cytotoxicity against a small panel of human solid tumor cell lines.

Animals↗
PubMedDate not supplied

Poly(glycoamidoamine)s for gene delivery. structural effects on cellular internalization, buffering capacity, and gene expression.

The study of polymeric nucleic acid delivery vehicles has recently grown because of their promise for many biomedical applications. In an effort to understand how the chemical traits of polymers affect the biological mechanisms of nucleic acid delivery, we have calculated the buffering capacity in the physiological pH range of a series of 10 poly(glycoamidoamine)s with systematic structural variations in the amine stoichiometry (from 1 to 4), carbohydrate moiety (d-glucarate or l-tartarate), and amine spacer (ethylene or butylene) within their repeat units. In addition, we have compared the buffering capacity of these polymeric vectors to their polyplex (polymer-DNA complex) stability, cellular internalization, and gene expression profiles to understand the parameters that are important for increasing gene delivery efficiency. The results indicate that the buffering capacity is not always the primary characteristic that determines the gene delivery efficiency for all the poly(glycoamidoamine)s. We have found that the buffering capacity may affect the gene delivery efficiency only when analogous structures containing the same number of amines but different carbohydrates are compared. We reveal that the cellular internalization is the key step in the gene delivery process with systems containing different amine stoichiometry. Also, increasing the number of methylene groups between the secondary amines increases toxicity to a large degree. This systematic and heuristic approach of studying the correlations between structural variables and gene delivery efficiency will facilitate the development of effective synthetic vectors for specific nucleic acid delivery applications.

Amides↗
PubMedDate not supplied

Prediction of inhibition of the sodium ion-proton antiporter by benzoylguanidine derivatives from molecular structure.

The use of quantitative structure-activity relationships to predict IC50 values of 113 potential Na+/H+ antiporter inhibitors is reported. Multiple linear regression and computational neural networks (CNNs) are used to develop models using a set of information-rich descriptors. The descriptors encode information about topology, geometry, electronics, and combination hybrids. A five-descriptor CNN model with root-mean-square (rms) errors of 0.278 log units for the training set and 0.377 log units for the prediction set was developed. Examination of data set subclasses showed that systematic structural variations were also well-encoded resulting in 100% accuracy of prediction trends. An experiment involving a committee of five CNNs was also performed to examine the effect of network output averaging. This showed improved results decreasing the training and cross-validation set rms error to 0.228 log units and the prediction set rms error to 0.296 log units.

Animals↗
PubMed2005

Overproduction of alpha chains provides a proton-insensitive component to the bluefish hemoglobin system.

Expression of alpha and beta chains and their post-translational assembly into alpha(2)beta(2) tetramers is fundamental to the formation and function of most vertebrate hemoglobins. There is a strong evolutionary bias that favors expression of equal amounts of the two types of chains, because cooperativity, pH sensitivity, and anionic control of function occurs only for the alpha(2)beta(2) tetramers. Remarkably, an over-production of alpha chains, as in the pathological condition known as beta thalassemia in humans, is adaptive rather than pathological in the bluefish hemoglobin system. The thalassemia of the bluefish is a novel means of providing for oxygen uptake and delivery when low pH conditions incapacitate the highly pH-sensitive Root effect hemoglobins of the fish. Although fish often have pH-insensitive along with highly pH-sensitive hemoglobins, having pH-insensitive alpha chain monomers in circulation is an unusual structural variation. The role of bluefish alpha chains in oxygen transport is enabled by their remarkably lower oxygen affinity relative to human alpha chains. This is the first reported case of a thalassemic condition that is maintained in a species as an adaptive advantage.

Adaptation, Physiological↗
PubMed2004

A set of homology models of pore loop domain of six eukaryotic voltage-gated potassium channels Kv1.1-Kv1.6.

Homology models of the pore loop domain of six eukaryotic potassium channels, Kv1.1-Kv1.6, were generated based on the crystallographic structure of KcsA. The results of amino acid sequence alignment indicate that these Kv channels are composed of two structurally and functionally independent domains: the N-terminal 'voltage sensor' domain and the C-terminal 'pore loop' domain. The homology models reveal that the pore loop domains of these Kv channels exhibit similar folds to those of KcsA. The structural features and specific packing of aromatic residues around the selectivity filter of these Kv channels are nearly identical to those of KcsA, whereas most of the structural variations occur in the turret as well as in the inner and outer helices. The distribution of polar and nonpolar side chains on the surfaces of the KcsA and Kv channels reveals that they exhibit a segregation of side chains common to most integral membrane proteins. As the hydrogen bond between Glu71 and Asp80 in KcsA plays an important role in stabilizing the channel, the substituted Val residue in the Kv family corresponding to Glu71 of KcsA stabilizes the channel by making hydrophobic contact with Tyr residue from the signature sequence of the selectivity filter. The homology models of these Kv channels provide particularly attractive subjects for further structure-based studies.

Amino Acid Sequence↗