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Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth.

Advances in determination of polymer structure and in preservation of structure for electron microscopy provide the best view to date of how polysaccharides and structural proteins are organized into plant cell walls. The walls that form and partition dividing cells are modified chemically and structurally from the walls expanding to provide a cell with its functional form. In grasses, the chemical structure of the wall differs from that of all other flowering plant species that have been examined. Nevertheless, both types of wall must conform to the same physical laws. Cell expansion occurs via strictly regulated reorientation of each of the wall's components that first permits the wall to stretch in specific directions and then lock into final shape. This review integrates information on the chemical structure of individual polymers with data obtained from new techniques used to probe the arrangement of the polymers within the walls of individual cells. We provide structural models of two distinct types of walls in flowering plants consistent with the physical properties of the wall and its components.

Carbohydrate Sequence↗

The effect of population structure on the adaptive radiation of microbial populations evolving in spatially structured environments.

Spatial structure is thought to be an important factor influencing the emergence and maintenance of genetic diversity. Previous studies have demonstrated that environmental heterogeneity, provided by spatial structure, leads to adaptive radiation of populations. In the present study, we investigate not only the impact of environmental heterogeneity on adaptive radiation, but also of population fragmentation and niche construction. Replicate populations founded by a single genotype of Escherichia coli were allowed to evolve for 900 generations by serial transfer in either a homogeneous environment, or a spatially structured environment that was either kept intact or destroyed with each daily transfer. Only populations evolving in the structured environment with intact population structure diversified: clones are significantly divergent in sugar catabolism, and show frequency-dependent fitness interactions indicative of stable coexistence. These findings demonstrate an important role for population fragmentation, a consequence of population structure in spatially structured environments, on the diversification of populations.

Adaptation, Physiological↗

X-ray crystallographic structures of gramicidin and their relation to the Streptomyces lividans potassium channel structure.

Gramicidin has been used extensively as a model system for structure/function studies of ion channels. Long before crystals of other ion channel proteins were produced, crystals of gramicidin had been prepared, even though it was many years before the first forms of those crystals were solved. There now exist a large number of crystal structures of both uncomplexed and ion-complexed forms of gramicidin crystallized from organic solvents. In all these crystals, the molecules are double helices, although they differ in helical pitch, handedness and side chain orientations, depending on the conditions used for crystallization. Since many of these structures have been discussed in detail in a recent review (Wallace 1998), this chapter concentrates on recently reported structures and how they relate to previously described X-ray and NMR structures. It also discusses how the crystal structure of a K+ complex of gramicidin relates to the recently solved structure of a K+ complex of the potassium channel from Streptomyces lividans and argues that this demonstrates that gramicidin is indeed a good model structure for biological ion channels, despite the presence of D-amino acids in its sequence.

Anti-Bacterial Agents↗

Structural proteomics: methods in deriving protein structural information and issues in data management.

Structural proteomics is an emerging paradigm that is gaining importance in the post-genomic era as a valuable discipline to process the protein target information being deciphered. The field plays a crucial role in assigning function to sequenced proteins, defining pathways in which the targets are involved, and understanding structure-function relationships of the protein targets. A key component of this research sector is accessing the three-dimensional structures of protein targets by both experimental and theoretical methods. This then leads to the question of how to store, retrieve, and manipulate vast amounts of sequence (1-D) and structural (3-D) information in a relational format so that extensive data analysis can be achieved. We at SBI have addressed both of these fundamental requirements of structural proteomics. We have developed an extensive collection of three-dimensional protein structures from sequence data and have implemented a relational architecture for data management. In this article we will discuss our approaches to structural proteomics and the tools that life science researchers can use in their discovery efforts.

Computational Biology↗

Cap structure of U3 small nucleolar RNA in animal and plant cells is different. gamma-Monomethyl phosphate cap structure in plant RNA.

U3 small nucleolar RNA (snoRNA) is an abundant small RNA involved in the processing of pre-ribosomal RNA of eukaryotic cells. U3 snoRNA has been previously characterized from several sources, including human, rat, mouse, frog, fruit fly, dinoflagellates, slime mold, and yeast; in all these organisms, U3 snoRNA contains trimethylguanosine cap structure. In all instances where investigated, the trimethylguanosine-capped snRNAs including U3 snoRNA, are synthesized by RNA polymerase II. However, in higher plants, the U3 snoRNA is synthesized by RNA polymerase III and contains a cap structure different from trimethylguanosine (Kiss, T., and Solymosy, F. (1990) Nucleic Acids Res. 18, 1941-1949; Marshallsay, C., Kiss, T., and Filipowicz, W. (1990) Nucleic Acids Res. 18, 3451-3458; Kiss, T., Marshallsay, C., and Filipowicz, W. (1991) Cell 65, 517-526). In this study, we present evidence that cowpea and, most likely, tomato plant U3 snoRNA contains a methyl-pppA cap structure. These data show that the same U3 snoRNA contains different cap structures in different species and suggest that the kind of cap structure that an uridylic acid-rich small nuclear RNA contains is dependent on the RNA polymerase responsible for its synthesis. In vitro synthesized plant U3 snoRNA, with pppA or pppG as its 5' end, was converted to methyl-pppA/G cap structure in vitro when incubated with extracts prepared from wheat germ or HeLa cells. These data show that the capping machinery is conserved in organisms as evolutionarily distant as plants and mammals. Nucleotides 1-45 of tomato U3 snoRNA, which are capable of forming a stem-loop structure, are sufficient to direct the methyl cap formation in vitro.

Animals↗

[Stratum-structure of the spinal nerves in the understanding of body structure].

The main methodology employed in the progressive gross anatomy of today's Japan is typological anatomy (typologische Anatomie) as introduced by Seiho Nishi (1943; 1950; 1961). This typological methodology is sufficient to suggest the existence of a certain constancy between muscle phylogeny and innervation in spite of the classic theory of nerve-muscle specificity having been discredited. On the basis of findings obtained from the many recent Japanese studies including the author's study on the cervical plexus (Kida, 1987), it has been noted that the stratum-structure of the spinal nerves may be an important key for the phylogenetic understanding of animal body structure (Kida, 1988). 1) The stratum-structure of the spinal nerves was initially observed only in the limb plexus by Fürbringer (Schwalbe, 1981). At that time, it was accepted as the longitudinal strata corresponding to the portion occupied by nerve fibers to the flexors or the extensors (Bolk, 1902). This theory was effective for the systematic understanding of limb structure. 2) The stratum-structure of the spinal nerves was at first considered to be related to the concept of nerve-muscle specificity. After the review of Straus (1946) on the concept of nerve-muscle specificity, this concept was disproved and has since been generally regarded as a theory of the past, therefore stratum-structure is now treated independently of that concept. 3) However, recent Japanese studies have modified and progressed beyond the concept of the stratum-structure of the spinal nerves.(ABSTRACT TRUNCATED AT 250 WORDS)

Humans↗

Predicted structures of apolipoprotein II mRNA constrained by nuclease and dimethyl sulfate reactivity: stable secondary structures occur predominantly in local domains via intraexonic base pairing.

Analyses of apolipoprotein II mRNA with chemical and enzymatic probes showed that double- and single-stranded regions were distributed uniformly along the mRNA except for a large (72 nucleotides) single-stranded region containing the translation stop codon. Secondary structure models constrained by the experimental data were made by varying the distance (along the mRNA) over which base pairing was allowed. Four prominent secondary structures were seen with restrictions of 165, 330, or 659 nucleotides suggesting that such structures from via local interactions over distances of 50-120 nucleotides. Predicted long range interactions involve only 2-3 base pairs while local interactions involve helices of 4-10 base pairs. Predicted helices of greater than or equal to 4 base pairs occur primarily within exons, raising the possibility that prominent secondary structures in mRNAs may be largely due to intraexonic base pairing. Tests of single- and double-stranded domains by oligonucleotide-directed RNase H cleavage and primer extension were in accord with the structure model and with nuclease and chemical modification data. The model predicting base pairing between the coding and the 3' noncoding regions was tested by RNase H cleavage followed by oligo(dT)-cellulose chromatography to separate 5' and 3' mRNA fragments. Most (82%) of the 5' fragment remained associated with the 3' noncoding region in a structure with a tm = 50 degrees C in 0.2 M Na+ suggesting that this stem could be stable in vivo. This stem may be stable in the isolated mRNA, but would likely occur transiently in polyribosomal apolipoprotein II mRNA due to ribosome transit through the 5' side of the stem. Alternate structures may occur in this region during ribosome transit and play a role in translation termination or in determining the susceptibility of the mRNA to degradation.

Animals↗

Nature and biosynthesis of structural matrix protein in melanosomes: melanosomal structural protein as differentiation antigen for neoplastic melanocytes.

Two major classes of protein, i.e., structural matrix and enzymic, exist in the melanosome. In normal melanocytes, synthesis of these two components is under a strict genetic control with regulatory steps associated with transcription and translation coded with appropriate pigment genes. In abnormal neoplastic melanocytes, they become markedly aberrant. The aberrant melanogenesis can be typically manifested by an abnormality in fine structure of the melanosome. The fine structural heterogeneity of the melanosome can often be diagnostic to certain forms of malignant melanoma and dysplastic melanocytic nevus. This study brings about the importance of the structural matrix protein for the expression of fine structural heterogeneity in the melanosome by developing the 2 monoclonal antibodies, MoAb HMSA-1 and HMSA-2. The 2 MoAbs recognized the cytoplasmic antigen on paraffin embedded sections, which under immunoelectron microscopy and cell fractionation studies, were found to be localization the melanosome and smooth ER, but not Golgi complex and coated vesicles as seen in the tyrosinase studies. It is indicated (a) that the sites of the synthesis for the melanosomal protein and tyrosinase are different, (b) that the melanosomal structural protein is accumulated in the dilated vacuole of smooth ER from which the stage I melanosome is synthesized, (c) that the synthesis of melanosomal protein becomes markedly aberrant and directly reflects the abnormal fine structure of the melanosome and (d) the heterogeneity in synthesis of melanosomal protein as expressed by MoAb HMSA-1 and HMSA-2 is a useful adjunct for immunohistopathological differentiation of malignant melanoma cells from benign nevoid cells and normal melanocytes.

Antigens, Differentiation↗

Borderline personality organization, structural diagnosis and the structural interview. A pilot study of interview analysis.

Kernberg has related the level of integration of the personality to the level of integration (and "structuring") of internalized object relations. He has designated three levels of personality organization: neurotic, borderline, and psychotic, and has developed a specially focused clinical interview designed to reveal intrapsychic structural characteristics--a "structural interview"--as a diagnostic instrument to differentiate the three types of personality organization. This study presents a method of analysis of the structural interview. Interviews of ten hospitalized psychiatric patients were studied to determine whether indicators could be retrieved from the typescripts of the interviews consonant with the diagnoses made by clinicians utilizing Kernberg's structural theory. Results indicate that scores generated from the typescripts are consistent with the hypothesis that the interviews did contain the indicators called for by structural theory and differentiate borderline from psychotic structures better than chance. In addition, this method of analysis of contingencies of interaction in the interview may have broader application to the study of psychotherapy and psychoanalysis.

Adult↗

[Investigation of the structure of magnesium and lithium salts of T2 phage DNA by the method of x-ray diffraction. The possible mechanisms of the participation of cations in the structural transformation of double-stranded DNA].

The secondary structure of DNA is known to be largely determined by the kind of counterion bound to it. We have used the X-ray diffraction method to study the structure of magnesium and lithium salts of T2 phage DNA in oriented fibres. The structural behaviour of this glucosylated DNA in the form of magnesium and lithium salts was shown to be identical to the behaviour of the same salts of "normal" calf thymus DNA throughout the studied range of relative humidities (44-95%). However these two DNAs in the form of sodium salt are known to behave quite differently. One can presume that Mg2+ and Li+ influence the structural behaviour of double-stranded DNA so effectively as to be able to "ignore" the fact that T2 phage DNA contains glucoside residues. The results of this work and the already known facts concerning the structure of DNA in the form of various cation salts (in solution and in "solid" fibres) indicate that the structural behaviour of double-stranded DNA is mainly determined by the cation located in the region of the narrow groove of the double helix. If cations are graded according to the efficiency of their influence on the structural behaviour of DNA in fibres, the scale will coincide with that of their DNA-binding strength in water solution, that is: Mg2+ greater than Li+ greater than Na+ greater than K+ greater than Rb+. A qualitative consideration of electrostatic interaction between the cations and the negatively charged DNA strands leads one to suppose that this interaction must obstruct the transition of individual DNA molecules from the B-form to the A-form. Aggregation of self-aggregation of DNA molecules is presumed necessary to enable them to adopt the A-conformation.

Cations, Monovalent↗

[Structure and structural disorder].

One of the central tasks of psychodynamic diagnosis, next to determining intrapsychic conflicts, central relational patterns, and subjective forms of experiencing is assessing the psychic structure or the structural disorder. This article develops the structure term from object relationship theoretical, ego-psychological, and self-psychological concepts of psychoanalysis. This "Structure of the self in the relationship to others" thus obtained is described with six structural criteria (self-perception, self-control, defence, object perception, communication, attachment). In order to be able to distinguish the extent and the quality of structural disorders four structure levels of integration based on psychoanalytic experience in the out-patient and the in-patient setting are differentiated. A basis for an operationalization is then made; it is made in the system OPD (Operationalized Psychodynamic Diagnostics). First studies regarding practicalibility and reliability are promising.

Communication↗

Probabilistic structure calculations: a three-dimensional tRNA structure from sequence correlation data.

Algorithms based on probability theory can address issues of uncertainty directly through their representational framework and their theory for data combination. In this paper, we discuss the advantages of probabilistic formulations for molecular-structure calculations, describe one implementation of such a formulation, and show its performance on a data set derived from analysis of the statistical correlations within a set of aligned transfer RNA sequences. By assigning reasonable physical interpretations to certain statistical correlations, we are able to calculate three-dimensional structures for tRNA from a random starting structure. The constraints that we use are associated with different variances, and so their effects are not uniform, and must be reconciled by a probabilistic algorithm to yield the most likely structure. As might be predicted, the uncertainty in the position for each base is a function of both the number and strength of the constraints, and is reflected in the variances in atomic position calculated by the algorithm. For example, the hinge region in the tRNA is shown to be the most uncertain. In addition, the algorithm retains information about positional covariation that is useful for understanding the relationships between different parts of the structure. These experiments also demonstrate that we can define a single-sphere representation for each base that is useful for nucleic acid structural calculations in the same way that alpha-carbon representations are useful for protein structural calculations.

Algorithms↗

Crystal structure of rat transthyretin at 2.5 A resolution: first report on a unique tetrameric structure.

The first observation of a unique tetrameric molecular structure of transthyretin from rat (rTTR, prealbumin) is reported. The structure has been determined by X-ray diffraction using molecular replacement and the structure of human transthyretin (hTTR) as a starting model. Crystals of native rat transthyretin are tetragonal, space group P4(3)2(1)2, and have four independent monomers in the asymmetric unit of the crystal lattice. Data were collected to 2.5 A resolution and the structure has been refined to R = 18.9% for 13584 data points between 8-2.5 A resolution. Like hTTR, the rat protein is also a 54000 Da tetramer with four identical polypeptide chains of 127 amino-acid residues. Of the 22 amino-acid residues which are different in the human and rat TTR sequences, none are in the thyroxine binding domain. Analysis of these data reveal that the tertiary structure of rTTR is similar to that of hTTR with only small differences in the flexible loop regions on the surface of the protein. As a result of local changes in flexible loop regions near residues 30-41, 60-65 and 102-104, the structure of rTTR monomers is more compact than that of the corresponding hTTR monomers. The loop between residues 30-41 is bound closer to the monomer core in the former as compared with the latter structure and there is a wider opening of the space formed between these loops at two adjacent monomeric subunits. These conformational changes do not affect the interfaces between the monomeric subunits and are not transmitted to the thyroxine binding site so that its topology remains not altered.

Amino Acid Sequence↗

Statistical correlation between protein secondary structure and messenger RNA stem-loop structure.

A new integrated sequence-structure database, called IADE (Integrated ASTRAL-DSSP-EMBL), incorporating matching mRNA sequence, amino acid sequence, and protein secondary structural data, is constructed. It includes 648 protein domains. Based on the IADE database, we studied the relation between RNA stem-loop frequencies and protein secondary structure. It was found that the alpha-helices and beta-strands on proteins tend to be preferably "coded" by mRNA stem region, while the coils on proteins tend to be preferably "coded" by mRNA loop region. These tendencies are more obvious if we observe the structural words (SWs). An SW is defined by a four-amino-acid-fragment that shows the pronounced secondary structural (alpha-helix or beta-strand) propensity. It is demonstrated that the deduced correlation between protein and mRNA structure can hardly be explained as the stochastic fluctuation effect.

Databases as Topic↗

Protein structure prediction using a combination of sequence-based alignment, constrained energy minimization, and structural alignment.

We present a novel approach to protein structure prediction in which fold recognition techniques are combined with ab initio folding methods. Based on the predicted secondary structure, one of two different protocols is followed. For mostly alpha proteins, global optimization and sampling of a statistical energy function is used to generate many low-energy structures; these structures are then screened against a fold library. Any structural matches are then selected for further refinement. For proteins predicted to have significant beta-content, sequence and secondary structure-based alignment is used to identify candidate templates; spatial constraints are then extracted from these templates and used, along with the statistical energy function, in the global sampling and optimization program. Successes and failures of both protocols are discussed.

Algorithms↗

A novel computer modeling approach to the structures of small bioactive peptides: the structure of gonadotropin releasing hormone.

A novel computer modeling approach suitable for the structure analysis of small bioactive peptides has been developed. This approach involves identification of conformational patterns in protein structure data bank based on the sequence homology with the bioactive peptide. The models built on the basis of this homology and having common conformational patterns are analyzed under the structural constraints derived from the activity data of various synthetic analogs of the peptide. Application of this procedure to the gonadotropin-releasing hormone (GnRH) resulted in a library of possible structures for GnRH, 9 among which shared a common beta-turn. Further analysis of the structures containing the beta-turn motif, in the context of the structure-activity data, led to a model for the active conformation of GnRH. The topology of the putative receptor binding site of the hormone is defined by a contiguous surface formed through an appropriate juxtaposition of the N-terminal pGlu1, the guanidyl group of Arg8, aromatic side chain of Trp3, and the Gly10-NH2 at the C-terminal end.

Amino Acid Sequence↗

Structure of phaseolin at 2.2 A resolution. Implications for a common vicilin/legumin structure and the genetic engineering of seed storage proteins.

The refinement to 2.2 A resolution of the three-dimensional structure of the seed storage protein phaseolin from the French bean (Phaseolus vulgaris) via an alternative crystal form is described. The refined structure reveals details of the molecule hitherto unobserved and in particular we identify the structural role of conserved residues within the broader 7 S (vicilin) family of seed storage proteins. On this basis we are able to postulate a canonical model for the structure of the 7 S proteins. This model in turn provides a means for interpreting the structure of the 11 S (legumin) family of seed storage proteins, for which no X-ray diffraction data are available. The 11 S proteins are shown to bear a much closer relationship to the 7 S proteins than was previously recognized. The canonical model of the 7 S protein structure also provides a basis for proposing engineered mutations of these proteins with the goal of enhancing nutritional and functional properties.

Amino Acid Sequence↗

Nuclear magnetic resonance solution structure of truncated human GRObeta [5-73] and its structural comparison with CXC chemokine family members GROalpha and IL-8.

The three-dimensional structure of a novel four amino acid truncated form of the CXC chemokine GRObeta [5-73] isolated from bone marrow stromal cells with potent hematopoietic and anti-infective activities has been determined by two-dimensional (1)H nuclear magnetic resonance (NMR) spectroscopy in solution. On the basis of 1878 upper distance constraints derived from nuclear Overhauser effects (NOE) and 314 dihedral angle constraints, a group of 20 conformers representing the solution structure of the human GRObeta [5-73] was computed with the program DYANA. At the concentrations used for NMR study, GRObeta [5-73] forms a dimer in solution that is architectured by a six-stranded antiparallel beta-sheet (residues 25 to 29, 39 to 44, 49 to 52) and a pair of helices (residues 58 to 68) with 2-fold symmetry, while the C terminus of the protein is disordered. The average of the pairwise root-mean-square deviations of individual NMR conformers relative to the mean coordinates for the backbone atoms N, C(alpha) and C' of residues 5 to 68 is 0.47 A. Overall, the global fold of GRObeta [5-73] is similar to that of the previously reported NMR structure of GROalpha and the NMR and X-ray structures of interleukin-8. Among these three CXC chemokines, GRObeta [5-73] is most similar in structure to GROalpha. Significant differences between GRObeta [5-73], GROalpha and interleukin-8 are in the N-terminal loop comprising residues 12 to 19. The N-terminal arm containing the conserved ELR motif and the loop of residues 30 to 38 containing the GPH motif are different among these three CXC chemokines. The structural differences in these two regions may be responsible for the specificity of the receptor binding and biological activity of different chemokines.

Amino Acid Motifs↗