Role of the tyrosine corner motif in the stability of neocarzinostatin

Although the immunoglobulin-like beta-sandwich fold has no specifically conserved function, some common structural features have been observed, in particular a structural motif, the tyrosine corner. Such a motif was described in neocarzinostatin (NCS), a bacterial protein the structure of which is very similar to that of the immunoglobulin domain. Compared with the other beta-sheet proteins, the NCS 'tyrosine corner' presents non-standard structural features. To investigate the role of this motif in the NCS structure and stability, we studied the properties of a mutant where the H bond interaction had been eliminated by replacing the tyrosine with a phenylalanine. This mutation costs 4.0 kcal/mol showing that the NCS 'tyrosine corner' is involved in protein stability as in the other Greek key proteins. This destabilization is accompanied by remote structural effects, including modification of the binding properties, suggesting an increase in the internal flexibility of the protein. With a view to using this protein for drug targeting, these results along with those obtained previously allow us to define clearly the limitations of the modifications that can be performed on this scaffold.     

The structural changes in the ribosome during the elongation cycle

The plenty of data about structural changes in the ribosome during its functioning has been accumulated. The most interesting information on such changes was obtained by cryo-EM of various ribosomal complexes with the ligands and by combination of rRNA site-directed mutagenesis with the analysis of structural changes in ribosome by chemical modification technique (chemical probing). The most studied structural transformations of the ribosome interacting with tRNAs and elongation factors are considered in this review. The structural rearrangements are discussed in the context of interactions between the functional centers of the ribosome. We also describe the system of tertiary contacts between the rRNA helices and proteins which forms the universal structure in the ribosome. We pay attention that by means of such system the allosteric conformational signal can be transmitted between the functional centers. Besides the discussion of different biochemical data in the scope of structural data we also consider the hypothesis that the position of GTPase associated center (GAC) in the ribosome regulates the binding of elongation factors.     

Evolutionary diversification of the flowers in angiosperms

Angiosperms and their flowers have greatly diversified into an overwhelming array of forms in the past 135 million years. Diversification was shaped by changes in climate and the biological environment (vegetation, interaction with other organisms) and by internal structural constraints and potentials. This review focuses on the development and structural diversity of flowers and structural constraints. It traces floral diversification in the different organs and organ complexes (perianth, androecium, gynoecium) through the major clades of extant angiosperms. The continuously improved results of molecular phylogenetics provide the framework for this endeavor, which is necessary for the understanding of the biology of the angiosperms and their flowers. Diversification appears to work with innovations and modifications of form. Many structural innovations originated in several clades and in special cases could become key innovations, which likely were hot spots of diversification. Synorganization between organs was an important process to reach new structural levels, from which new diversifications originated. Complexity of synorganization reached peaks in Orchidaceae and Apocynaceae with the independent evolution of pollinaria. Such a review throughout the major clades of angiosperms also shows how superficial and fragmentary our knowledge on floral structure in many clades is. Fresh studies and a multidisciplinary approach are needed.     

Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes

A detailed comparison of the structures of aspartate aminotransferase, alanine race-mase, the beta subunit of tryptophan synthase, D-amino acid aminotransferase and glycogen phosphorylase has revealed more extensive structural similarities among pyridoxal phosphate (PLP)-binding domains in these enzymes than was observed previously. These similarities consist of seven common structural segments of the polypeptide chain, which form an extensive common structural organization of the backbone chain responsible for the appropriate disposition of key residues, some from the aligned fragments and some from variable loops joined to these fragments, interacting with PLPs in these enzymes. This common structural organization contains an analogous hydrophobic minicore formed from four amino acid side chains present in the two most conserved structural elements. In addition, equivalent alpha-beta-alpha-beta supersecondary structures are formed by these seven fragments in three of the five structures: alanine racemase, tryptophan synthase and glycogen phosphorylase. Despite these similarities, it is generally accepted that these proteins do not share a common heritage, but have arisen on five separate occasions. The common and contiguous alpha-beta-alpha-beta structure accounts for only 28 residues and all five enzymes differ greatly in both the orientation of the PLP pyridoxal rings and their contacts with residues close to the common structural elements.     

Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome

The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically. We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination (NAHR) mediated by low-copy repeats (LCRs). Combined evidence from four human sperm methylome maps, human genome evolution, structural polymorphisms in the human population, and previous genomic and disease studies consistently points to a strong association of germline hypomethylation and genomic instability. Specifically, methylation deserts, the ~1% fraction of the human genome with the lowest methylation in the germline, show a tenfold enrichment for structural rearrangements that occurred in the human genome since the branching of chimpanzee and are highly enriched for fast-evolving loci that regulate tissue-specific gene expression. Analysis of copy number variants (CNVs) from 400 human samples identified using a custom-designed array comparative genomic hybridization (aCGH) chip, combined with publicly available structural variation data, indicates that association of structural mutability with germline hypomethylation is comparable in magnitude to the association of structural mutability with LCR-mediated NAHR. Moreover, rare CNVs occurring in the genomes of individuals diagnosed with schizophrenia, bipolar disorder, and developmental delay and de novo CNVs occurring in those diagnosed with autism are significantly more concentrated within hypomethylated regions. These findings suggest a new connection between the epigenome, selective mutability, evolution, and human disease.     

Differential algebra methods for the study of the structural identifiability of rational function state-space models in the biosciences

In this paper methods from differential algebra are used to study the structural identifiability of biological and pharmacokinetics models expressed in state-space form and with a structure given by rational functions. The focus is on the examples presented and on the application of efficient, automatic methods to test for structural identifiability for various input-output experiments. Differential algebra methods are coupled with Gr?bner bases, Lie derivatives and the Taylor series expansion in order to obtain efficient algorithms. In particular, an upper bound on the number of derivatives needed for the Taylor series approach for a structural identifiability analysis of rational function models is given.     

Amplitude-temporal parameters of the evoked potentials of the visual and motor areas in the visual perception and mental representation of an image

Amplitude-temporal analysis was carried out of the EP components of the visual and motor areas elicited by neutral (diffuse light) and structural (checker board pattern) stimuli in different situations, defined by instruction. Interserial comparisons showed that at any instruction, the latency of the first EP component of the motor areas is reduced; as a result it can appear here simultaneously with the EP of the visual areas. At the instruction involving the subject in the process of active change of perception, activation of the right hemisphere, including the motor area, is manifest by EP parameters, while the right occipital area is activated in response to the structural stimulus, and the left one--in response to the neutral stimulus. At complication of the stimulus or instruction, the period is prolonged when the latency of EP components of the motor area is shorter than the latency of the isopolar components of the visual area--from 120 to 150 ms in response to the neutral stimuli and the neutral with their counting; from 90 to 150 ms in response to the structural stimuli; from 80 to 210 ms in response to the neutral stimuli with mental representation of the structural one.     

Junctions in the central nervous system of the cat

Summary The leptomeningeal tissue of the choroid plexuses and of the brain surfaces have been studied by means of the freeze-etching technique. The pia-arachnoid membrane and the subdural neurothel represent the morphological barrier between the extracerebral tissue and the cerebrospinal compartment. The freeze-etch findings indicate that the arachnoid and neurothelial cells are coupled by extensive zonulae occludentes which seem to represent the structural basis of the barrier mechanism provided by these cell layers. Furthermore, it became evident that gap junctions of considerable structural heterogeneity occur on the pial and arachnoid cells of the interstitial choroidal compartment and of the free brain surfaces. The structural heterogeneity of the nexuses is taken as an indication of the plasticity of the leptomeningeal tissue. The different morphological characteristics of the nexal formations are discussed with respect to their probable functional meaning.This investigation was supported by the Deutsche Forschungsgemeinschaft SFB 114 (Bionach).     

Structural changes in the ribosome during the elongation cycle

Ample data on structural changes that arise in the ribosome during translation have been accumulated. The most interesting information on such changes has been obtained by cryoelectron microscopy of ribosome complexes with various ligands and by rRNA site-directed mutagenesis combined with a structural analysis of the ribosome by a chemical modification technique (chemical probing). The review considers the best-known structural changes that arise in the translating ribosome upon its interactions with tRNA and the elongation factors. The changes are discussed in the context of interactions between the functional centers of the ribosome. A universal system of rRNA helices and proteins is described in detail. The system integrates the functional centers of the ribosome and allows transduction of allosteric conformational signals. Biochemical data are considered in terms of the structures and interactions of ribosomal elements, and a hypothesis is advanced that the position of the GTPase-associated center in the ribosome regulates the binding of the elongation factors.     

Single amino acid substitutions in the Ca2+-binding site of recoverin.II.The unusual behavior of the protein upon the binding of calcium ions

The structural properties of myristoylated forms of recombinant recoverin of the wild type and of its mutants with damaged second and/or third Ca(2+)-binding sites were studied by fluorimetry and circular dichroism. The interaction of wild-type recoverin with calcium ions was shown to induce unusual structural rearrangements in its molecule. In particular, protein binding with Ca2+ ions results in an increase in the mobility of the environment of Trp residues, in higher hydrophobicity, and in elevated thermal stability (its thermal transition shifts by 15 degrees C to higher temperatures) but has almost no effect on its secondary structure. Similar structural changes induced by Ca2+ are also characteristic of the -EF2 mutant of recoverin whose second Ca(2+)-binding site is modified and cannot bind calcium ions. The structural properties of the -EF3 and -EF2,3 mutants (whose third or simultaneously second and third Ca(2+)-binding sites, respectively, are modified and damaged) are practically indifferent to calcium ions.     

Importance of conserved residues for the conformation of the T-loop in tRNAs

The conformation of the T-loop of yeast tRNA(Asp) was studied by structural mapping techniques using chemical and enzymatic probes and by three-dimensional graphics modeling with the known crystallographic structures of tRNAs as references. The structural importance of C61 (conserved in the T-stem of all tRNAs) for the loop conformation was directly checked by ethylnitrosourea phosphate alkylation, either on the 3'-half tRNAAsp molecule or on a variant in which C61 was replaced by U61. The reactivity of P60 against ethylnitrosourea alkylation in the variant emphasizes the role of the hydrogen bond between this phosphate and position N4 of C61 for stabilizing the conformation of the T-loop. Experiments on several tRNA variants, containing C61 but altered in the sequence or in the length of the T-loop, indicate that other structural features help to stabilize the hydrogen bond network around P60. Evidence is presented that the reverse Hoogsteen base pair T54-A58 contributes to this stabilization by maintaining the hydrogen bonding between the 2'OH of ribose 58 and P60. Using graphics modeling and based on the chemical data. T-loops of several variants were constructed. It appears that both the constant length of the T-loop and the presence of psi 55 are crucial for the correct interaction between the T- and D-loops. The conclusion of this study is that the T-loop in tRNA possesses an intrinsic conformation (mainly governed by the constant residues) existing primarily without the structural context of the entire tRNA molecule.     

On the efficiency of energy migration from the chlorosome to the main bacteriochlorophyll in green bacteria

It is shown that the results provided in a number of publications based on structural characteristics of chlorosomes of green bacteria are in explicit contradiction with their kinetic and energy characteristics. The data on chlorosome structure and composition give no explanation as to how the additional electronic excitations generated by light in its dominating pigment C750 feed the main photosystem. To reveal the contradictions, the structural and spectral data on the chlorosome are analyzed using the theory of inductive resonance developed by Förster.     

Phytostructural characterization of several vegetation types in northern Portugal. II. The structural expressivity and the resistance of the vegetation

Abstract

The encouraging results obtained in a previous work induced the authors to pursue here the characterization of the structure of the vegetation in northern Portugal, using the phytostructural methodology proposed earlier by the authors. With this objective, eight different types of vegetal communities, representative of the apparent states of the successional process present in this area, and representing the diversity of plant community types in the same area, were selected. The phytostructural method was elaborated on the basis of three types of structural basic matrices regarding diversity, abundance and cover. The data obtained were collected in a contingency matrix, which was then treated by means of a statistical multivariate analysis. Three structural tendencies emerged from this analysis. With the aim of studying their stability, the results are discussed in terms of resistance and resilience, according to the Highest Expressive Amplitude (HEA) concept, and by considering the intra- and inter-community structural dynamics as structural parameters. The data obtained suggest structural situations with different degrees of non-equilibrium that reflect resistance to environmental factors. The resistance of the vegetation is correlated with the apparent functional connectivity detected for the communities analysed.     

Dimethylaminochalcone, an indicator of the structural changes in the cellular envelop of E. coli under the action of Ca2+ cations and tris buffer]

An attempt was made to detect possible structural changes in E. coli cell envelope induced by Ca2+ treatment with the help of an uncharged fluorescent probe 4-dimethylaminochalcon (DMC). The effects of the treatment with tris buffer (0.01 M) at 0 degrees C and other agents (Mg2+ and EDTA) were also studied for the purpose of comparison. It is shown that Ca2+ treatment of E. coli cells results in structural changes in the cell envelope surface, whick differ from those induced by tris-buffer at 0 degrees C, Mg2+ and EDTA. DMC can be used successfully as a suitable probe for monitoring structural changes in biomembranes.     

On the efficiency of energy migration from chlorosoma to the main bacteriochlorophyll in green bacteria

It is shown that the results provided in a variety of publications, which deal with structural characterization of green bacteria chlorosoma, are in explicit contradiction with kinetic and energy characteristics of microorganisms studied. The data on chlorosoma structure and composition represent no explanation as to how the additional quantity of electronic excitations generated by light in its dominating pigment C750 feeds the main photosystem.. In order to reveal the contradictions, the structural and spectral data on chlorosoma are analyzed in cooperation with the theory of inductive resonance developed by T. Ferster.     

Spin-labeling studies of the conformational changes in the vicinity of D36, D38, T46, and E161 of bacteriorhodopsin during the photocycle.

Electron paramagnetic resonance (EPR) spectroscopy of site-directed spin-labeled bacteriorhodopsin mutants is used to study structural changes during the photocycle. After exchange of the native amino acids D36 and D38 in the A-B loop, E161 in the E-F loop, and T46 in the putative proton channel by cysteines, these positions were modified by a methanethiosulfonate spin label. Time-resolved EPR spectroscopy reveals spectral changes during the photocycle for the mutants with spin labels attached to C36, C161, and C46. A comparison of the transient spectral amplitudes with simulated EPR difference spectra shows that the detected signals are due to changes in the spin label mobility and not to possible polarity changes in the vicinity of the attached spin label. The kinetic analysis of the EPR and the visible data with a global fitting procedure exhibits a structural rearrangement near position 161 in the E-F loop in the M state. The environmental changes at positions 36 and 46, however, occur during the M-to-N transition. All structural changes reverse with the recovery of the BR ground state. No structural changes are detected with a spin label attached to C38.     

Extension of the Limits of the Xdh Structural Element in DROSOPHILA MELANOGASTER

Experiments expanding the array of mutants affecting the xanthine dehydrogenase (XDH) structural element in Drosophila melanogaster are described. These include rosy eye color mutants which exhibit interallelic complementation, and mutants with normal eye color but lowered levels of XDH. Evidence is presented which argues that these are structural alterations in the enzyme. Recombination experiments were performed using these mutants as well as some electrophoretic variants. The two ends of the rosy locus are marked with mutant sites which are clearly structural in nature; the XDH structural element and the rosy null mutant map are completely concordant. A possible procedure to recover control element mutants is described.     

Assessment of the probabilities for evolutionary structural changes in protein folds

MOTIVATION: The evolution of protein sequences can be described by a stepwise process, where each step involves changes of a few amino acids. In a similar manner, the evolution of protein folds can be at least partially described by an analogous process, where each step involves comparatively simple changes affecting few secondary structure elements. A number of such evolution steps, justified by biologically confirmed examples, have previously been proposed by other researchers. However, unlike the situation with sequences, as far as we know there have been no attempts to estimate the comparative probabilities for different kinds of such structural changes. RESULTS: We have tried to assess the comparative probabilities for a number of known structural changes, and to relate the probabilities of such changes with the distance between protein sequences. We have formalized these structural changes using a topological representation of structures (TOPS), and have developed an algorithm for measuring structural distances that involve few evolutionary steps. The probabilities of structural changes then were estimated on the basis of all-against-all comparisons of the sequence and structure of protein domains from the CATH-95 representative set. The results obtained are reasonably consistent for a number of different data subsets and permit the identification of several 'most popular' types of evolutionary changes in protein structure. The results also suggest that alterations in protein structure are more likely to occur when the sequence similarity is >10% (the average similarity being approximately 6% for the data sets employed in this study), and that the distribution of probabilities of structural changes is fairly uniform within the interval of 15-50% sequence similarity. AVAILABILITY: The algorithms have been implemented on the Windows operating system in C++ and using the Borland Visual Component Library. The source code is available on request from the first author. The data sets used for this study (representative sets of protein domains, matrices of sequence similarities and structural distances) are available on http://bioinf.mii.lu.lv/epsrc_project/struct_ev.html.     

Universally increased mRNA stability downstream of the translation initiation site in eukaryotes and prokaryotes

Local secondary structures in coding sequences have important functions across various translational processes. To date, however, the local structures and their functions in the early stage of translation elongation remain poorly understood. Here, we surveyed the structural stability in the first 180 nucleotides of the coding sequence of 27 species using computational method. We found that the structural stability in the 30–80 nucleotide interval was significantly higher than that in other regions in eukaryotes and most prokaryotes. No significant correlation between local translation efficiency and structural stability was observed, suggesting that this structural region has undergone selection pressure directly to maintain high stability. Furthermore, ribosome was blocked by this region, providing an opportunity for co-translational regulation. Remarkably, in eukaryotes, we found that mRNAs with higher structural stability in the 30–80 nucleotide interval tended to encode the secreted proteins. Overall, our results revealed a previously unappreciated correlation between structural stability and protein localization.