Configuration of subunits within crystals of Na, K-ATPase maintained in the frozen-hydrated state

Two-dimensional crystalline sheets of Na, K-ATPase were studied in the vitrified, frozen-hydrated state by electron microscopy and image processing. The technique of correlation averaging was used to determine the projected structure. The projection map shows asymmetry between the pair of "alpha beta" protomers comprising a dimer of Na, K-ATPase molecules. The two protomers differ in overall density as well as in shape. One protomer has an oblong shape, whereas the other with higher density has a head and a hook region. Such an asymmetry has not been reported by other laboratories. This asymmetry may either be due to the coexistence of two different conformations of the enzyme in the dimeric form or due to the simultaneous existence of two molecular species of Na, K-ATPase.     

Rat Brain α-Mannosidase: Purification, Properties, and Interaction with Its Antibodies

Abstract: α - d -Mannosidase (EC 3.2.1.24.) was purified to homogeneity from adult rat brain. The enzyme, of apparent molecular weight 397,000, appears to be formed of subunits of molecular weight 120,000 made of two protomers (62,000) bound by disulfide bridges. Isoelectric focusing gives two bands, of pi 5.40 and 5.15. Both isoenzymes seem to have the same pH curve (a small peak of activity at pH 4.5 and a maximum of activity around pH 6.0). These two isoenzymes are immunologically related.     

Intrinsic asymmetry of oligomer transitions and biomolecular evolution

Structural transitions in oligomeric proteins due to ligand binding are important in biomolecular regulatory processes. The transitions may occur on the secondary, tertiary or quarternary structure levels. Detailed consideration of the time sequence of ligand binding to the oligomer shows that there is an intrinsic dynamic asymmetry in all oligomer transitions, even if the initial and the final state are completely symmetric. This asymmetry has important bearing on the evolution and the divergence of the primary structure (amino acid sequence) of oligomeric proteins. It may explain (at least in part) the occurrence of oligomeric proteins with similar but not identical protomers. Certain specific groups of oligomers are shown to be under greater evolutionary pressure for protomer structure divergence. The dynamic asymmetry of oligomer transitions also results in higher complexity in reaction kinetics. Some implications on ribosome structural evolution are discussed.     

Analysis of putative protomer crosstalk in the trimeric transporter BetP: The heterotrimer approach

The homotrimeric, secondary active betaine carrier BetP from Corynebacterium glutamicum is a model system for stress-regulated transport in bacteria. Its activity responds to hyperosmotic stress and it harbors two different functions, transport catalysis (betaine uptake) and stimulus sensing, resp. activity regulation. Structural information from 2D and 3D crystals as well as functional analysis of monomerized BetP suggested the presence of conformational crosstalk between the individual protomers. To study whether the oligomeric state is functionally significant on a mechanistic level we generated heterooligomeric complexes of BetP in which single protomers within the trimer can be addressed. By testing dominant negative effects in a trimer of one active protomer combined with two protomers in which transport and regulation were abolished, we provide experimental evidence for the absence of functionally significant conformational crosstalk between the protomers on the level of both transport and regulation. This is supported by experiments using mutant forms of putative interacting signal donor and acceptor domains of individual BetP protomers. This result has important consequences for oligomeric transport proteins in general and BetP in particular.     

Hereditary heat-labile hexosaminidase B: its implication for recognizing Tay-Sachs genotypes

Two pairs of alleles, at the two loci of hexosaminidase (HEX), were found to segregate in an Arab inbred family: the normal and the mutant Tay-Sachs (TSD) alleles of HEX A, and the normal and a mutant allele of HEX B. Since the mutant HEX B is heat labile, no reliable identification of TSD genotypes can be obtained in its presence, as long as the proportions of HEX A and B are estimated by the routinely used heat-inactivation method. The genotypes may be correctly identified in such cases by separation of the two isoenzymes on ion-exchange chromatography, estimating their individual activities, and calculating the ratio between them. Of the nine genotype combinations possible with these two pairs of alleles, five have been identified in the reported family by this procedure.     

Low-resolution structure of the tetrameric phenylalanyl-tRNA synthetase from Escherichia coli. A neutron small-angle scattering study of hybrids composed of protonated and deuterated protomers

Escherichia coli phenylalanyl-tRNA synthetase is a tetrameric protein composed of two types of protomers. In order to resolve the subunit organization, neutron small-angle scattering experiments have been performed in different contrasts with all types of isotope hybrids that could be obtained by reconstituting the alpha 2 beta 2 enzyme from the protonated and deuterated forms of the alpha and beta subunits. Experiments have been also made with the isolated alpha promoter. A model for the alpha 2 beta 2 tetramer is deduced where the two alpha promoters are elongated ellipsoids (45 x 45 x 160 A3) lying side by side with an angle of about 40 degrees between their long axes and where the two beta subunits are also elongated ellipsoids (31 x 31 x 130 A3) with an angle of 30 degrees between their axes. This model was obtained by assuming that the two pairs of subunits are in contact in an orthogonal manner and by taking advantage of the measured distance between the centers of mass of the alpha 2 and beta 2 pairs (d = 23 +/- 2 A).     

Comparison of malate dehydrogenase isoenzymes in someAllium species by isoelectric focusing

Malate dehydrogenase isoenzymes were studied in tenAllium species and in six cultivars ofA. cepa by isoelectric focusing in polyacrylamide gel with Ampholine pH 3.5–10.0. Using this method better resolution was obtained than by polyacrylamide gel electrophoresis. The number of MDH isoenzymes obtained by isoelectric focusing is from five to ten in the range of pH 3.65 to 6.75. MDH isoenzymes can be used for characterization on the level of species and cultivars (inA. cepa), but its use on the level of sections and subgenera is questionable.     

Crystal structure of the stationary phase survival protein SurE with metal ion and AMP

The stationary phase survival protein SurE is a metal ion-dependent phosphatase distributed among eubacteria, archaea, and eukaryotes. In Escherichia coli, SurE has activities as nucleotidase and exopolyphosphatase, and is thought to be involved in stress response. However, its physiological role and reaction mechanism are unclear. We report here the crystal structures of the tetramer of SurE from Thermus thermophilus HB8 (TtSurE) both alone and crystallized with Mn(2+) and substrate AMP. In the presence of Mn(2+) and AMP, differences between the protomers were observed in the active site and in the loop located near the active site; AMP-bound active sites with the loops in a novel open conformation were found in the two protomers, and AMP-free active sites with the loops in a conventional closed conformation were found in the other two protomers. The two loops in the open conformation are entwined with each other, and this entwining is suggested to be required for enzymatic activity by site-directed mutagenesis. TtSurE exists as an equilibrium mixture of dimer and tetramer in solution. The loop-entwined structure indicates that SurE acts as a tetramer. The structural features and the absence of negative cooperativity imply the half-of-the-sites reactivity mechanism resulting from a pre-existing tendency toward structural asymmetry.     

Dimensional and discrete dental trait asymmetry relationships

Inuit (Eskimos) from the Foxe Basin region of the Northwest Territories, Canada, were studied to ascertain the amount of dimensional and morphological asymmetry in their dentitions. The results indicate that dimensional asymmetry does not appear to be greater on either the maxillary or mandibular teeth. Both types of asymmetry show partial conformity to the model of tooth fields with an increasing amount of asymmetry as one goes distally in each tooth group. The morphological asymmetry exception, the mandibular incisors, follows Dahlberg's "Field Concept." Rank-order correlations between the amount of dimensional asymmetry and morphological asymmetry reveal no detectable patterns. There appear to be no associations between the presence or absence of morphological asymmetry and the size of the tooth. This lack of association might be explained by differences in developmental timing of tooth dimensions and morphological traits; however, such a hypothesis requires experimental testing. In this population and those for which published results are available, it is practically impossible to overcome the "noise" level and test recent hypotheses regarding random dental asymmetry.     

Genetic and environmental influences on bilateral dental asymmetry in Northwest Indian twins

The role of genetic and environmental factors on dental asymmetry (in maximum crown dimensions) was examined using 58 pairs of twins (23 MZ and 35 DZ) from Chandigarh, India. The t'-test for equality of means by zygosity showed only one variable significantly different among 56: this is ascribable to Type 1 error. Heterogeneity of MZ-DZ total variance was observed in 42.9% of traits of the two types (fluctuating and directional) of bilateral asymmetry. In general, MZ twins showed higher total variance than DZ pairs. MZ twins also showed stronger environmental covariance for a majority of the traits. Dental asymmetry measures thus yielded consistently low genetic variance ratios and indicated predominantly complex environmental determinism. Since fluctuating asymmetry is widely believed to be an environmental stress indicator, this data set allows confirmation of methods for detecting unequal environmental influences on the zygosities which bias estimates of genetic variance and heritability.     

Composition of Esterase and Peroxidase Isoenzyme Complex, Zein-2 Protein Fraction, and SDS-Protein Complex of Zea Mays L. × Tripsacum Dactyloides L. Hybrids and Parents

The patterns of esterase and peroxidase isoenzymes, subunits of zein-2 fraction and protomers of SDS-protein complex of Zea mays L. × Tripsacum dactyloides L. hybrids and their parents were compared. The study has been made to detect specific to Tripsacum isoesterases and isoperoxidases, zein subunits and SDS-protein protomers which could be used as markers for introgression of gene loci encoding these proteins from Tripsacum into hybrids of Tripsacum with Zea mays. Isoesterases and isoperoxidases as well protomers of SDS-protein complex specific to Tripsacum were detected in all hybrids analyzed. Zein subunits, specific to Tripsacum were detected in some of the analyzed hybrids which i that introgression frequency of the loci encoding proteins studied was different. Chromosome counts taken on the examined hybrids showed the addition of 9 – 13 Tripsacum chromosomes to maize chromosome complement.     

DARS (Decoys As the Reference State) potentials for protein-protein docking

Decoys As the Reference State (DARS) is a simple and natural approach to the construction of structure-based intermolecular potentials. The idea is generating a large set of docked conformations with good shape complementarity but without accounting for atom types, and using the frequency of interactions extracted from these decoys as the reference state. In principle, the resulting potential is ideal for finding near-native conformations among structures obtained by docking, and can be combined with other energy terms to be used directly in docking calculations. We investigated the performance of various DARS versions for docking enzyme-inhibitor, antigen-antibody, and other type of complexes. For enzyme-inhibitor pairs, DARS provides both excellent discrimination and docking results, even with very small decoy sets. For antigen-antibody complexes, DARS is slightly better than a number of interaction potentials tested, but results are worse than for enzyme-inhibitor complexes. With a few exceptions, the DARS docking results are also good for the other complexes, despite poor discrimination, and we show that the latter is not a correct test for docking accuracy. The analysis of interactions in antigen-antibody pairs reveals that, in constructing pairwise potentials for such complexes, one should account for the asymmetry of hydrophobic patches on the two sides of the interface. Similar asymmetry does occur in the few other complexes with poor DARS docking results.     

A kinetic method for the simultaneous determination of isoenzymes activities in mixture. Application to A2 and A3 horseradish peroxidases

A graphical method for the simultaneous determination of the activity of two isoenzymes in a mixture, is presented. The method is based on the different kinetic behaviour of the isoenzymes to the changes in the substrate concentrations. Having determined the reaction rates for the enzyme mixture at different substrate concentrations, the activity of both isoenzymes can be derived graphically. An algebraic method for two or more isoenzymes is mentioned, as well. The applications of the graphical and the algebraic method to A2 and A3 horseradish isoperoxidases demonstrated that the difference between the actual activities of the two isoperoxidases and those determined by the proposed method was around 5% of the actual activities. The scope of application of this method could be extended to isoenzymes of clinical importance.     

Single-particle tracking: models of directed transport.

Single-particle tracking techniques make it possible to measure motion of individual particles on the cell surface. In these experiments, individual trajectories are observed, so the data analysis must take into account the randomness of individual random walks. Methods of data analysis are discussed for models combining diffusion and directed motion. In the uniform flow model, a tracer simultaneously diffuses and undergoes directed motion. In the conveyor belt model, a tracer binds and unbinds to a uniform conveyor belt moving with constant velocity. If a tracer is bound, it moves at the velocity of the conveyor belt; if it is unbound, it diffuses freely. Trajectories are analyzed using parameters that measure the extent and asymmetry of the trajectory. A method of assessing the usefulness of such parameters is presented, and pitfalls in data analysis are discussed. Joint probability distributions of pairs of extent and asymmetry parameters are obtained for a pure random walk. These distributions can be used to show that a trajectory is not likely to have resulted from a pure random walk.     

A hypothesis concerning the structure of cAMP-and cGMP-dependent protein kinases.

cAMP-and cGMP-dependent protein kinases have been purified. Each enzyme demonstrates high specificity and affinity for the cyclic nucleotide with binding of two moles of nucleotide per holoenzyme and each enzyme is an ATP: phosphotransferase. The holoenzymes have similar molecular weights and demonstrate similar molecular asymmetry. A structural model relating the two enzymes is proposed. cGMP-dependent protein kinase is proposed to be a dimer composed of two identical protomers in isologous association with the chains arranged in anti-parallel fashion. cAMP-dependent protein kinase is proposed to have a similar structure with a dyad axis of symmetry but with a discontinuity in each chain. These structures account for the differing mechanisms of cyclic nucleotide activation of the two enzymes.     

Beyond bilateral symmetry: geometric morphometric methods for any type of symmetry

Background

Studies of symmetric structures have made important contributions to evolutionary biology, for example, by using fluctuating asymmetry as a measure of developmental instability or for investigating the mechanisms of morphological integration. Most analyses of symmetry and asymmetry have focused on organisms or parts with bilateral symmetry. This is not the only type of symmetry in biological shapes, however, because a multitude of other types of symmetry exists in plants and animals. For instance, some organisms have two axes of reflection symmetry (biradial symmetry; e.g. many algae, corals and flowers) or rotational symmetry (e.g. sea urchins and many flowers). So far, there is no general method for the shape analysis of these types of symmetry.

Results

We generalize the morphometric methods currently used for the shape analysis of bilaterally symmetric objects so that they can be used for analyzing any type of symmetry. Our framework uses a mathematical definition of symmetry based on the theory of symmetry groups. This approach can be used to divide shape variation into a component of symmetric variation among individuals and one or more components of asymmetry. We illustrate this approach with data from a colonial coral that has ambiguous symmetry and thus can be analyzed in multiple ways. Our results demonstrate that asymmetric variation predominates in this dataset and that its amount depends on the type of symmetry considered in the analysis.

Conclusions

The framework for analyzing symmetry and asymmetry is suitable for studying structures with any type of symmetry in two or three dimensions. Studies of complex symmetries are promising for many contexts in evolutionary biology, such as fluctuating asymmetry, because these structures can potentially provide more information than structures with bilateral symmetry.