A peroxisomal β-oxidative pathway contributes to the formation of C6–C1 aromatic volatiles in poplar

Benzenoids (C₆–C₁ aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C₆–C₃). The biosynthesis of C₆–C₁ aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C₆–C₁ aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.

A three-step peroxisomal β-oxidative pathway mediates the shortening of the propyl side chain of cinnamic acid and contributes to herbivore-induced aromatic volatile formation in poplar.     

Chromosomal unit fibers in Drosophila

Chromosomal unit fibers consisting of long, regular fibers of about 0.40 m diameter were obtained from disintegrated, isolated chromosomes of two Drosophila melanogaster cell lines. In one cell line with an essentially normal karyotype, three clearly defined size classes of 15, 13, and 11 m length were observed corresponding to the three larger chromosomes of Drosophila. In a cell line carrying an additional translocation between the two largest chromosomes a 19 m fiber derived from the translocation chromosome was observed. Direct determinations of the DNA content per m length of Drosophila unit fibers show that DNA is contracted by a factor of about 1400x in agreement with calculations based on the length of the unit fibers and the known DNA content of the individual Drosophila chromosomes. These findings support our previously proposed model for the unit fiber sub-structure of chromosomes as being derived by a hierarchy of coiling with the corresponding contraction ratios being 7 (100 Å string of nucleosomes), 5 to 6 (250–300 Å thick nucleohistone fiber), and about 40 (unit fiber), resulting in a total contraction of DNA in unit fibers in the order of 1400x.     

Der Feinbau der Mikrotubuli in Hefe nach Gefrierätzung

Zusammenfassung Im Zellkern der Bäckerhefe wunden beim Übergang von anaeroben zu aeroben Kulturbedingungen drei verschiedene Sorten vom Mikrotubuli beobachtet. Die Durchmesser der Röhrchen betragen 210, 224 und 250 Å, die Lumina 60, 75 und 105 Å. Der Grundbaustein dieser Mikrotubuli ist ein 80 Å großes, in erster Näherung globuläres Teilchen, in dem höchst wahrscheinlich acht Untereinheiten mit einem Durchmesser von 40 Å enthalten sind. Das Bauprinzip der Mikrotubuli ist eine eingängige Schraube, die von einer Perlenkette der Grundbausteine aufgebaut wird. Die drei verschiedenen Tubuli-Sorten unterscheiden sich darin, daß bei der einen 5, bei der anderen 6 und bei der drittem 7 Perlen (80 Å-Einheiten) pro Umgang der Schraube zu finden sind. Wenn man die 40 Å großen Untereinheiten berücksichtigt, so besteht die Tubulus-Wand aus einer doppelten Lage dieser Teilchen mit 10, 12 oder 14 Einheiten pro Schraubenumgang. Die Übereinstimmung vieler Daten aus der Literatur mit diesem Modell läßt den gleichartigen Aufbau aller Mikrotubuli und Spindelfasern als wahrscheinlich erschieinen.

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Summary Three different classes of microtubules have been detected in the nucleus of yeast cells passing from anaerobiosis to aerobiosis. The diameter of theses structures is 210, 224 and 250 Å respectively, the lumen 60, 75 and 105 Å. The structural unit of all these microtubules is a nearly globular particle having a diameter of 80 Å. This unit most probably contains 8 subunits of a diameter of 40 Å. The 80 Å-units are arranged in a beaded chain which is screwd up to form the tubule. This screw may contain 5, 6 or 7 of the units per turn. Taking into account the subunits, the wall of a tubule would then be constructed of two layers of 40 Å-particles; so we may count 10, 12 or 14 beads per turn of a double threaded screw. This model can be compared with many data about microtubules available in the literature.

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Zu besoniderem Dank verpflichtet bin ich Herrn Dr. C. Robinow für viele anregende Diskussionen, Herrn Dr. Matile für die Ausarbeitung der Kulturbedingunigen, Frl. S. Chicherio für die sachkundige Präparation und Frl. Tür ler für die graphische Ausstattung dieses Berichtes. Diese Arbeit wurde durch einen Kredit das Schweizerischen Nationalfonds unterstützt.     

The difference between protein structures obtained by x-ray analysis and nuclear magnetic resonance

We have analyzed the pairs of protein structures obtained by X-ray diffraction analysis and nuclear magnetic resonance (X-ray and NMR structures) that display no major differences when superimposed on one another (61 pairs). Analyzing atom-to-atom contacts (contact distances 2–8 Å), it has been found that the NMR structures (compared to the X-ray structures) have more contacts at distances below 3.5 Å and above 5.5 Å. In the case of residue-to-residue contacts, the NMR structures have more contacts at distances below 3 Å and between 4.5 and 6.5 Å. At other distances analyzed, the X-ray structures have more contacts. The difference in the numbers of atom-to-atom and residue-to-residue contacts is greater for buried residues inaccessible to water than for surface residues. Another important difference is related to the number of hydrogen bonds in the main chain: this number is greater in the X-ray structures. The coefficient of correlation between the numbers of hydrogen bonds identified in the structures obtained by both methods is only 32%. If a complete set of NMR models of protein structure is considered, the total number of hydrogen bonds proves to be 1.2 times greater than in the X-ray structures, whereas the correlation coefficient increases to only 65%. We have also demon-strated that -helices in the NMR structures are more distorted (compared to the ideal -helix) than those in the X-ray structures.Translated from Molekulyarnaya Biologiya, Vol. 39, No. 1, 2005, pp. 129–138.Original Russian Text Copyright © 2005 by Melnik, Garbuzynskiy, Lobanov, Galzitskaya.     

Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints

To improve tertiary structure predictions of more difficult targets, the next generation of TASSER, TASSER_2.0, has been developed. TASSER_2.0 incorporates more accurate side-chain contact restraint predictions from a new approach, the composite-sequence method, based on consensus restraints generated by an improved threading algorithm, PROSPECTOR_3.5, which uses computationally evolved and wild-type template sequences as input. TASSER_2.0 was tested on a large-scale, benchmark set of 2591 nonhomologous, single domain proteins ≤200 residues that cover the Protein Data Bank at 35% pairwise sequence identity. Compared with the average fraction of accurately predicted side-chain contacts of 0.37 using PROSPECTOR_3.5 with wild-type template sequences, the average accuracy of the composite-sequence method increases to 0.60. The resulting TASSER_2.0 models are closer to their native structures, with an average root mean-square deviation of 4.99 Å compared to the 5.31 Å result of TASSER. Defining a successful prediction as a model with a root mean-square deviation to native <6.5 Å, the success rate of TASSER_2.0 (TASSER) for Medium targets (targets with good templates/poor alignments) is 74.3% (64.7%) and 40.8% (35.5%) for the Hard targets (incorrect templates/alignments). For Easy targets (good templates/alignments), the success rate slightly increases from 86.3% to 88.4%.     

The aggregation behavior of zinc-free insulin studied by small-angle neutron scattering

The aggregation behavior of zinc-free insulin has been studied by small-angle neutron scattering as a function of pH and ionic strength of the solution. The pair distance distribution functions for the 12 samples have been obtained by indirect Fourier transformation. The results show that the diameter of the aggregates is 40 Å at pH 11 and 10 mM NaCl, independent of the protein concentration. The largest diameter of about 120 Å is found for pH 8, 100 mM NaCl, and a protein concentration of 10 mg/ml. Estimates of the pair distance distribution functions, free of inter-particle correlation effects, were obtained by an indirect Fourier transformation, omitting the data at small scattering vectors, which are influenced by these effects. By this procedure the weight-averaged molecular mass and the average radius of gyration were determined. These parameters vary from 1.3 times the monomer mass and 14 Å, to 6.8 times the monomer mass and 31 Å, respectively. The mass distribution between the oligomers was determined by a model based on the crystal structure of zinc-free insulin. The results from this model and the Fourier transformations have been compared to an equilibrium model recently introduced by Kadima et al. (1993). The neutron scattering results agree well with the predictions of this model except that broader mass distributions are suggested by neutron scattering. Correspondence to: J. Skov Pedersen     

Protein filaments-structural components of the phloem exudate

Summary Fine structure and chemical composition of the phloem exudate of Cucurbita maxima and Nicotaiana glauca x suaveolens are investigated. Filamentous structures, several microns in length, are identified as structural components of the exudate by means of negative staining and electron microscopy. Two types of filaments are described: one form measures nearly 40 Å in diameter and shows a beaded appearance with regular spacings of about 50 Å; it is termed elementary filament. The second form has a diameter of about 90 Å and presumably consists of two helically arranged 40 Å subunits.The proteinaceous nature of the filaments is indicated by chemical analysis. The main macromolecular component of the exudate is demonstrated to be protein. Only traces of nucleic acids are detectable, lipids and polysaccharides cannot be found. The identity of the protein filaments with the filamentous structures (slime, P-protein), as revealed in thin sections of mature sieve tubes, is discussed.     

Cutoff variation induces different topological properties: A new discovery of amino acid network within protein

An increasing attention has been dedicated to the characterization of complex networks within the protein world. Before now most investigations about protein structures were only considered where the interactive cutoff distance R_c=5 or 7 Å. It is noteworthy that the length of peptide bond is about 1.5 Å, the length of hydrogen bond is about 3 Å, the range of London-van der Waals force is about 5 Å and the range of hydrophobic effect can reach to 12 Å in protein molecule. Present work reports a study on the topological properties of the amino acid network constructed by different interactions above. The results indicate that the small-world property of amino acid network constructed by the peptide and hydrogen bond, London-van der Waals force and the hydrophobic effect is strong, very strong and relatively weak, respectively. Besides, there exists a precise exponential relation C∝k^−0.5 at R_c=12 Å. It means that the amino acid network constructed by the hydrophobic effect tend to be hierarchical. Functional modules could be the cause for hierarchical modularity architecture in protein structures. This study on amino acid interactive network for different interactions facilitates the identification of binding sites which is strongly linked with protein function, and furthermore provides reasonable understanding of the underlying laws of evolution in genomics and proteomics.     

Amino acid and lipid composition of refringent granules from the ameboid sperm of Ascaris suum (Nematoda)

Summary Transformation of the spermatozoon of Ascaris suum from a spheroidal to an ameboid cell is associated with the formation of a motile pseudopodium and coalescence of the intracellular refringent granules. The pseudopodia of the ameboid spermatozoa contain filaments organized into dense patches, bundles, web-like or lace-like networks, as observed by electron microscopy.The morphology and chemistry of the refringent granules were investigated in subcellular fractions enriched for these structures. Isolated refringent granules were heterogeneous in size measuring from 0.5×0.6 to 2.3×3.5 m. Each granule is surrounded by a 110 Å thick layer. During fusion, the surfaces of the refringent granules form small extensions resembling micropodia. The process of fusion occurs at many sites on a given granule and simultanenous fusion of several granules was commonly observed.Amino acid analyses of the refringent granule proteins (RGP's) indicated: they are rich in aspartic acid or asparagine (48%), leucine (10%), serine (19%) and aromatic amino acids (11%). Gas-liquid chromatographic analyses of alditol acetate derivatives of monosaccharides released by mild acid hydrolysis showed the predominant sugars to be glucose (7.3 g/mg protein), galactose (9.2 g/mg) and N-acetylglucosamine (5.5 g/mg). Lipid analyses indicated a complex mixture of glycerides, ascarosides and waxes, together with a major component that resembled free fatty acid in mobility on TLC.     

Nautilus pompilius hemocyanin: 9 A cryo-EM structure and molecular model reveal the subunit pathway and the interfaces between the 70 functional units

Hemocyanins are giant extracellular oxygen carriers in the hemolymph of many molluscs. Nautilus pompilius (Cephalopoda) hemocyanin is a cylindrical decamer of a 350 kDa polypeptide subunit that in turn is a “pearl-chain” of seven different functional units (FU-a to FU-g). Each globular FU has a binuclear copper centre that reversibly binds one O₂ molecule, and the 70-FU decamer is a highly allosteric protein. Its primary structure and an 11 Å cryo-electron microscopy (cryo-EM) structure have recently been determined, and the crystal structures of two related FU types are available in the databanks. However, in molluscan hemocyanin, the precise subunit pathway within the decamer, the inter-FU interfaces, and the allosteric unit are still obscure, but this knowledge is crucial to understand assembly and allosterism of these proteins. Here we present the cryo-EM structure of Nautilus hemocyanin at 9.1 Å resolution (FSC_1/2-bit criterion), and its molecular model obtained by rigid-body fitting of the individual FUs. In this model we identified the subunit dimer, the subunit pathway, and 15 types of inter-FU interface. Four interface types correspond to the association mode of the two protomers in the published Octopus FU-g crystal. Other interfaces explain previously described morphological structures such as the fenestrated wall (which shows D5 symmetry), the three horizontal wall tiers, the major and minor grooves, the anchor structure and the internal collar (which unexpectedly has C5 symmetry). Moreover, the potential calcium/magnesium and N-glycan binding sites have emerged. Many interfaces have amino acid constellations that might transfer allosteric interaction between FUs. From their topologies we propose that the prime allosteric unit is the oblique segment between major and minor groove, consisting of seven FUs from two different subunits. Thus, the 9 Å structure of Nautilus hemocyanin provides fundamentally new insight into the architecture and function of molluscan hemocyanins.     

Ultrastructural changes in nurse and follicle cells during late stages of oogenesis in Drosophila melanogaster

Summary During stages 11 and 12, follicle cells surrounding the nurse cells produce lysosomes which presumably aid in the breakdown of the nurse cells. Accompanying a DNA reduction in nurse cell nuclei are several characteristic morphological changes including the appearance of intranuclear rod-like structures and nuclear granules about 300 Å in diameter. Similarities between structures seen in Drosophila nurse cell nuclei and those seen in other organisms are discussed.This research was supported by U. S. Public Health Service Grants 5TIGM903-3 and 1-F1-GM-33, 385-01 and National Science Foundation grant GB-7457.     

Liquorkontaktneurone im Nucleus infundibularis

Zusammenfassung Der Nucleus infundibularis verschiedener Reptilien wurde licht- und elektronenmikroskopisch untersucht. Zellen dieses Kernes entsenden Fortsätze durch ein mehrreihiges Ependym in den 3. Ventrikel und bilden dort freie, intraventrikuläre Nervenendigungen (Liquorkontakt-Nervenendigungen, Lkne). Lichtmikroskopisch konnten in der Kerngruppe a) kleine, AChE-negative, toluidinblaue und b) große, AChE-positive, mit Toluidinblau hell erscheinende Nervenzellen unterschieden werden.Die knöpfchenförmigen LKNE weisen Elemente des endoplasmatischen Retikulums, freie Ribosomen, eine wechselnde Anzahl Mitochondrien, einzelne Lysosomen, asymmetrische Zilien (Typ 9+0) mit akzessorischem Basalkörper und Zilienwurzeln auf. Zwei LKNE-Typen sind unterscheidbar: a) LKNE mit granulierten Vesikeln mit einem Durchmesser von 800–1100 Å und b) LKNE mit großen, elektronendichten Granula (Durchmesser 1200–1600 Å).Im Lumen des 3. Ventrikels treten kleinkalibrige Axone auf, die kleine, granulierte Bläschen (Durchmesser 700–900 Å) enthalten und mit den LKNE des Nucleus infundibularis intraventrikuläre Synapsen bilden.Die Perikaryen des Nucleus infundibularis weisen ein reichliches endoplasmatisches Retikulum, zahlreiche Polyribosomen, Neurotubuli und Mitochondrien auf. Ähnlich wie bei den LKNE sind zwei Perikaryenarten zu unterscheiden: a) Perikaryen mit granulierten Vesikeln (Durchmesser 800–1100 Å) und b) solche mit elektronendichten Granula (1200–1700 Å). Außerdem kommen verschiedene Arten axosomatischer und axodendritischer Synapsen vor.Die Funktion der intraventrikulären Nervenendigungen und verschiedenen Synapsenarten in der Kerngruppe wird im Hinblick auf einen Informationsaustausch zwischen dem Liquor cerebrospinalis und dem Nucleus infundibularis diskutiert.

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Liquor contacting neurons in the infundibular nucleus

Summary The infundibular nucleus of various reptiles was studied light and electron microscopically. Cells of this nucleus send processes through a stratified ependyma into the 3rd ventricle where they form free, intraventricular nerve terminals (liquor contacting nerve endings, LCNE). In the nucleus, two kinds of neurons could be distinguished light microscopically: a) small, AChE-negative, toluidine blue neurons, and b) large, AChE-positive cells staining light with toluidine blue.The club shaped LCNE contain elements of the endoplasmic reticulum, free ribosomes, a various amount of mitochondria, and single lysosomes. The terminals bear asymmetrical cilia (type 9+0) supplied with accessory basal bodies and rootlet fibres. Two kinds of LCNE are demonstrable: a) LCNE containing dense-core vesicles with a diameter of about 800–1100 Å, and b) LCNE with large, electron-dense granules (diameter about 1,200–1,600 Å). In the lumen of the 3rd ventricle, there occur small axons that contain small granulated vesicles (diameter about 700–900 Å), and that form intraventricular synapses with the LCNE of the infundibular nucleus.The perikarya of the infundibular nucleus contain an abundant endoplasmic reticulum, numerous polyribosomes, neurotubules and mitochondria. Similarly to the LCNE, two kinds of perikarya can be distinguished: a) perikarya containing granulated vesicles (diameter about 800–1100 Å), and b) perikarya with electron-dense granules (diameter about 1200–1700 Å). Furthermore, different types of axosomatic and axodendritic synapses occur.The function of the intraventricular nerve terminals and the different types of synapses in the nucleus is discussed with regard to an exchange of informations between the cerebrospinal fluid and the infundibular nucleus.

     

Effect of different protocols of caffeine intake on metabolism and endurance performance.

Competitive athletes completed two studies of 2-h steady-state (SS) cycling at 70% peak O(2) uptake followed by 7 kJ/kg time trial (TT) with carbohydrate (CHO) intake before (2 g/kg) and during (6% CHO drink) exercise. In Study A, 12 subjects received either 6 mg/kg caffeine 1 h preexercise (Precaf), 6 x 1 mg/kg caffeine every 20 min throughout SS (Durcaf), 2 x 5 ml/kg Coca-Cola between 100 and 120 min SS and during TT (Coke), or placebo. Improvements in TT were as follows: Precaf, 3.4% (0.2-6.5%, 95% confidence interval); Durcaf, 3.1% (-0.1-6.5%); and Coke, 3.1% (-0.2-6.2%). In Study B, eight subjects received 3 x 5 ml/kg of different cola drinks during the last 40 min of SS and TT: decaffeinated, 6% CHO (control); caffeinated, 6% CHO; decaffeinated, 11% CHO; and caffeinated, 11% CHO (Coke). Coke enhanced TT by 3.3% (0.8-5.9%), with all trials showing 2.2% TT enhancement (0.5-3.8%; P < 0.05) due to caffeine. Overall, 1) 6 mg/kg caffeine enhanced TT performance independent of timing of intake and 2) replacing sports drink with Coca-Cola during the latter stages of exercise was equally effective in enhancing endurance performance, primarily due to low intake of caffeine (approximately 1.5 mg/kg).     

Automated assignment and 3D structure calculations using combinations of 2D homonuclear and 3D heteronuclear NOESY spectra

The NOAH/DIAMOD suite uses feedback filtering and self-correcting distance geometry to generate 3D structures from unassigned NOESY spectra. In this study we determined the minimum set of experiments needed to generate a high quality structure bundle. Different combinations of 3D ¹⁵N-edited, ¹³C-edited HSQC-NOESY and 2D homonuclear ¹H-¹H NOESY spectra of the 77 amino acid protein, myeloid progenitor inhibitory factor-1 (MPIF-1) were used as input for NOAH/DIAMOD calculations. The quality of the assignments of NOESY cross peaks and the accuracy of the automatically generated 3D structures were compared to those obtained with a conventional manual procedure. Combining data from two types of experiments synergistically increased the number of peaks assigned unambiguously in both individual spectra. As a general trend for the accuracy of the structures we observed structural variations in the backbone fold of the final structures of about 2 Å for single spectral data, of 1 Å to 1.5 Å for double spectral data, and of 0.6 Å for triple spectral data sets. The quality of the assignments and 3D structures from the optimal data using all three spectra were similar to those obtained from traditional assignment methods with structural variations within the bundle of 0.6 Å and 1.3 Å for backbone and heavy atoms, respectively. Almost all constraints (97%) of the automatic NOESY cross peak assignments were cross compatible with the structures from the conventional manual assignment procedure, and an even larger proportion (99%) of the manually derived constraints were compatible with the automatically determined 3D structures. The two mean structures determined by both methods differed only by 1.3 Å rmsd for the backbone atoms in the well-defined regions of the protein. Thus NOAD/DIAMOD analysis of spectra from labeled proteins provides a reliable method for high throughput analysis of genomic targets.     

Probing protein fold space with a simplified model

We probe the stability and near-native energy landscape of protein fold space using powerful conformational sampling methods together with simple reduced models and statistical potentials. Fold space is represented by a set of 280 protein domains spanning all topological classes and having a wide range of lengths (33-300 residues) amino acid composition and number of secondary structural elements. The degrees of freedom are taken as the loop torsion angles. This choice preserves the native secondary structure but allows the tertiary structure to change. The proteins are represented by three-point per residue, three-dimensional models with statistical potentials derived from a knowledge-based study of known protein structures. When this space is sampled by a combination of parallel tempering and equi-energy Monte Carlo, we find that the three-point model captures the known stability of protein native structures with stable energy basins that are near-native (all α: 4.77 Å, all β: 2.93 Å, α/β: 3.09 Å, α+β: 4.89 Å on average and within 6 Å for 71.41%, 92.85%, 94.29% and 64.28% for all-α, all-β, α/β and α+β, classes, respectively). Denatured structures also occur and these have interesting structural properties that shed light on the different landscape characteristics of α and β folds. We find that α/β proteins with alternating α and β segments (such as the β-barrel) are more stable than proteins in other fold classes.     

On the involvement of the water-polaron mechanism in energy trapping by reaction centers of purple bacteria

A locus for binding a mobile water molecule was searched for in the immediate vicinity of the special pair in the reaction center. Using the PROTEUS PC-program (a part of the GRASP package) atomic structures of the reaction centers were analyzed in purple bacteria Rhodopseudomonas viridis and Rhodobacter sphaeroides. In both structures the loci for binding mobile water molecules were found at the distance of about 4.5 Å from the middle of the special pair in the reaction center. The reorientation of a hydrogen atom of this water molecule in the electric field of the excited special pair required energy of no less than 40 MeV that corresponded to predictions of the water-polarization model of trapping of electron excitation which was developed by M. V. Fok and one of the authors of this article.     

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes

Conformational transitions between open/closed or free/bound states in proteins possess functional importance. We propose a technique in which the collective modes obtained from an anisotropic network model (ANM) are used in conjunction with a Monte Carlo (MC) simulation approach, to investigate conformational transition pathways and pathway intermediates. The ANM-MC technique is applied to adenylate kinase (AK) and hemoglobin. The iterative method, in which normal modes are continuously updated during the simulation, proves successful in accomplishing the transition between open-closed conformations of AK and tense-relaxed forms of hemoglobin (C^α− root mean square deviations between two end structures of 7.13 Å and 3.55 Å, respectively). Target conformations are reached by root mean-square deviations of 2.27 Å and 1.90 Å for AK and hemoglobin, respectively. The intermediate conformations overlap with crystal structures from the AK family within a 3.0-Å root mean-square deviation. In the case of hemoglobin, the transition of tense-to-relaxed passes through the relaxed state. In both cases, the lowest-frequency modes are effective during transitions. The targeted Monte Carlo approach is used without the application of collective modes. Both the ANM-MC and targeted Monte Carlo techniques can explore sequences of events in transition pathways with an efficient yet realistic conformational search.     

A new interpretation of plasmodesmatal ultrastructure

Summary It is shown that simple, unbranched, plasmodesmata between young xylem ray cells of willow have no direct intercellular continuity apart from the plasmalemma which limits the cytoplasm and lines the plasmodesmatal canal. Each plasmodesma is traversed by a 200 Å diameter tubule (the desmotubule) which has a wall with probably 11 subunits arranged around a central cavity through which runs a 40 Å diameter rod. This rod is connected to the inside of the tubule wall, by fine filaments. At the ends of each plasmodesma the plasmalemma and cell wall are closely appressed to the tubule, thus precluding direct continuity between the cytoplasm of adjacent cells. Through the central part of the plasmodesmata the tubule is separated from the plasmalemma by a 90–100 Å wide gap. Cytoplasmic microtubules in the same tissue have a diameter of approximately 250 Å and a wall probably composed of 13 subunits: both desmotubules and cytoplasmic microtubules therefore have a centre-to-centre subunit spacing of about 47 Å. It is suggested that the desmotubules are not microtubules but may be nuclear spindle fibres which become trapped in the wall during cell plate formation. The endoplasmic reticulum, while closely approaching the plasmodesmata, is not continuous across them. It is thought most unlikely that the endoplasmic reticulum traverses plasmodesmata, as the dimensions of the central tubule — found here as well as by other workers — are smaller than those which would be expected to allow a stable molecular configuration in a unit membrane. The plasmalemma, where it lines the plasmodesmatal canal, appears to have particulate subunits in the outer opaque layers and the presence of these subunits may be attributable to the need for stability in membranes arranged about so small a radius.