Secondary structure of histones in solution

The secondary structure of histones H2B and H3 from calf thymus has been quantitatively studied in heavy water solutions in a wide range of histone concentrations, pD, and concentrations of sodium chloride by an infrared spectroscopy method. Also, the interactions between molecules of different histones in equimolar mixtures H2A-H2B, H2A-H3, H2A-H4, H2B-H3, H2B-H4, H3-H4, and H2A-H2B-H3-H4 have been investigated using the same method. For H2B and H3 conditions favourable for aggregation have been shown to induce the formation of pleated sheet structure. When the pD and concentration of NaCl are in a physiological range, the secondary structure of H2B and H3 contains about 15% of alpha-helix, 4% of parallel pleated sheet structure, 14% of antipatallel pleated sheet structure in H2B and 18% in H3. For mixtures in all cases, except H2A-H4, there is an interaction between molecules of different histones followed by a reduction of the antiparallel pleated sheet structure content. The data on the secondary structure of histones in different states (under self-association, in mixtures, in nucleosomes, and in chromatin) have been discussed and it is suggested that: 1) the secondary structure of histones in chromatin is essentially similar to that in the state of self-association; 2) in the core nucleosome particle the quantity of DNA (in nucleotide pairs), and the quantities of alpha-helix and antiparallel pleated sheet structure (in peptide groups) satisfy the relation 1 : 1 : 1.     

棉酚对鱼精DNA作用的量子生物学研究

紫外吸收光谱显示棉酚与DNA相互作用没有共价键形成.也不生成电荷迁移络台物.量子化学计算棉酚与胸腺嘧啶分子中的净电荷分布,发现沿两者结构式粗线上各原子的电荷恰好符号相反(图2).这表示棉酚很可能以共轭平面平行地插入到DNA分子双螺旋结构的碱基片层之间,与其中的胸腺嘧啶碱基以弱相互作用的极性键形成复合物.这种结合是可逆的,不影响DNA的一级结构.     

Far-infrared spectra of sequential copolymers of amino acids with alkyl group side chains

Far-infrared spectra were measured for the sequential copolymers of amino acids with alkyl group side chains. The analysis of the spectra showed that (L -Ala-L -Ala-Gly)_n, (L -Ala-Gly)_n, (L -Ala-Gly-Gly)_n, (L -Val-L -Ala-L -Ala)_n, and (L -Val-L -Ala)_n, have the antiparallel pleated sheet structures and that the backbone conformations of (L -Val-L -Val-L -Ala)_n and (L -Val-L -Val-Gly)_n are the same as that of poly-L -valine. The far-infrared bands characteristic of the antiparallel pleated sheet structure were assigned on the basis of the result of the normal coordinate analysis of poly-L -alanine with this structure. The intersheet and interchain spacings of the sequential copolymers with the antiparallel pleated sheet structure were determined from the x-ray powder-diffraction patterns of these samples.     

Structure of polyglycine I: a comparison of the antiparallel pleated and antiparallel rippled sheets

Packing energy calculations are made for two possible sheet structures of polyglycine I, i.e. the antiparallel pleated and rippled sheets. They indicate that the rippled sheet is the more stable structure and that its calculated lattice parameters are close to those experimentally determined. Furthermore, the results on the packing of pleated sheets of polyglycine improve understanding of the well-known model of silk fibroin structure of Marsh et al. (1955). They also suggest that the sheet structures of l-polypeptides with short side-chains should pack in monoclinic unit cells rather than the orthorhombic ones which are observed. A possible origin of this discrepancy is discussed.     

L-alanyl-L-alanyl-L-alanine: parallel pleated sheet arrangement in unhydrated crystal structure, and comparisons with the antiparallel sheet structure

The tripeptide L-alanyl-L-alanyl-L-alanine has been crystallized from a water/dimethylformamide solution in an unhydrated form, with cell dimensions a = 11.849, b = 10.004, c = 9.862 A, beta = 101.30 degrees, monoclinic space group P21 with 4 molecules per cell (2 independent molecules in the asymmetric unit). The structure was determined by direct methods and refined to a discrepancy index R = 0.057. The tri-L-alanine molecules are packed in a parallel pleated sheet arrangement with unusually long amide nitrogen-carbonyl oxygen contacts within sheets. Comparisons are made with the antiparallel pleated sheet structure of tri-L-alanine hemihydrate, previously crystallized from the same solvent system.     

The pleated sheet: an unusual negative-staining method for transmission electron microscopy of biological macromolecules

A novel method for preparing negatively stained specimens is described which appears to improve the routine resolution of biological structure in direct images obtained by transmission electron microscopy. In the new method, which we term the pleated sheet technique, macromolecules are adsorbed to a carbon film by the Valentine procedure (R. Valentine, B. Shapiro, and E. Stadtman (1968) Biochemistry, 7, 2143-2152), and the film then carefully pleated while in contact with a 1% uranyl formate solution to trap stain within the folds of pleats. A grid is placed on the compressed film, and film plus grid retrieved with a Saran Wrap drum. Subsequent dehydration produces a filmed grid containing negatively stained macromolecules within the folds of pleated regions and positively stained macromolecules in single sheet regions. The effect of sandwiching sample and stain between carbon layers is to produce exceedingly uniform negative staining so that stain contours more accurately and more reproducibly reflect true molecular contours. Electron micrographs of IgG and IgA molecules prepared by these methods are exhibited that permit unambiguous comparison of structure imaged in the electron microscope against known structures solved by single-crystal X-ray diffraction. Correlation is excellent; the smallest resolvable element in micrographs is an immunoglobulin domain, whose molecular weight is 12 000.     

Structure of apoproteins in insect lipophorin

The two polypeptide chains of cockroach and locust lipophorins were separated and their amino acid compositions were determined. Circular dichroic spectra of the lipophorins and apolipophorin from 190 to 250 nm showed a single trough at 218 nm and a peak at 194 nm. Infrared spectra of the lipophorins in D2O showed a strong peak at 1625 cm-1 and a weak shoulder at 1693 cm-1 corresponding to v (pi, 0) and nu (0, pi) of antiparallel pleated sheet. The resonance frequency splitting delta nu = nu (0, pi) -nu (pi, 0) was 68 cm-1, which was larger than that of ordinary globular proteins containing antiparallel pleated sheet. From circular dichroic and infrared spectra it was concluded that lipophorins contained polypeptides rich in antiparallel pleated sheet with longer unbroken extensions than the case for ordinary globular proteins. Partial proteolytic digestion study of lipophorins with trypsin, chymotrypsin, and subtilisin showed that the larger apolipophorin (AL1) was exposed to the surface of the particle and the smaller apolipophorin (AL2) lay protected from the attack of the enzymes. Crosslinked products between AL1 and AL2 were readily obtained when dimethylsuberimidate or dimethyladipimidate was added to the lipophorin solution, without giving lipophorin dimers, suggesting that the two chains were located within 11 A from each other. Such structural features of insect lipoprotein were compared with other insect lipophorins and the human serum low-density lipoprotein (LDL). Similarities between lipophorins and LDL were found in the molecular weight, amino acid compositions, and the secondary structure of major apoproteins.     

Infrared spectra and resonance interaction of amide-I vibration of the antiparallel-chain pleated sheet.

Theoretical treatment of resonance interaction of amide-I vibration has been done in a dipole–dipole approximation on the basis of perturbation theory. A single infinite antiparallel-chain pleated sheet as well as different kinds of its finite fragments have been considered. A good agreement has been obtained between calculated spectral parameters of amide I of the infinite sheet and observed ones in infrared and Raman spectra of synthetic polypeptides and fibrous proteins. A theoretical dependence of the resonance frequency shift of the main component and frequency splitting of two components active in the infrared spectra on the number of polypeptide chains in the finite sheet has been found.     

Molecular conformation of erabutoxin b; atomic coordinates at 2.5 A resolution.

Atomic coordinates determined from a 2.5 Å electron density map are given for erabutoxin b, a sea snake venom postsynaptic neurotoxin. The principal structural features, anti-parallel β pleated sheet, β bulge and β bends are described. The erabutoxin b structure is discussed as structural prototype of this class of homologous curare-mimetic neurotoxins from both land and sea snakes.     

A DFT study of structure and stability of pleated and rippled cross‐β sheets with hydrophobic sidechains

The rippled cross‐β sheet, a topography, in which mirror‐image peptides are arranged with alternating chirality into a periodic two‐dimensional network, is burgeoning as a new design principle for materials and biomedical applications. Experiments by the Schneider, Nilsson, and Raskatov labs have independently shown diverse racemic mixtures of aggregation‐prone peptide of different sizes to favor the rippled over the pleated topography. Yet, systematic ab initio studies are lacking, and the field is yet to develop rules that would enable the design of new rippled cross‐β frameworks from first principles. Here, DFT calculations were performed on a set of model systems, designed to begin understanding the impact that bulky, hydrophobic sidechains have upon the formation of pleated and rippled cross‐β frameworks. It is hoped that this study will help stimulate the development of a predictive, general framework to enable rational design of rippled cross‐β sheets in the future.     

Properties of an aldose reductase from pig lens. Comparative studies of an aldehyde reductase from pig lens

THe characteristic feature of the crystal structure of erabutoxin b, a short neurotoxin from Laticauda semifasciata, and alpha-cobratoxin, a long neurotoxin from Naja naja siamensis, is the presence of a triple-stranded antiparallel pleated beta-sheet structure formed by the central and the third peptide loops. In the present study, we have studied the assignment of slowly exchangeable amide protons of Laticauda semifasciata III from L. semifasciata, using nuclear Overhauser effects (NOE) and spin-decoupling methods. The results show that nearly all of the slowly exchangeable amide protons are to be assigned to the back-bone amide protons, involved in the triple-stranded antiparallel pleated beta-sheet structure, indicating that this sheet is stable in 2H2O solution. In contrast, the amide protons in short neurotoxins are readily exchangeable under the same experimental condition, suggesting that long neurotoxins have a more rigid sheet structure than short ones. This rigidity may come from the hydrophobic and hydrogen bond interaction between the central loop and the tail, which is not present in short neurotoxins. Since the functionally important residues are located on this beta-sheet, the different kinetic properties of the neurotoxins are well correlated with the difference in the rigidity of the beta-sheet.     

Binding of tyrosine, adenosine triphosphate and analogues to crystalline tyrosyl transfer RNA synthetase

Crystalline complexes of tyrosyl tRNA synthetase were prepared with the following substrates and substrate analogues: ATP, AMP, α-β methylene ATP, tyrosine and tyrosinyl adenylate. Using ¹⁴C-labelled ligands, the binding constants for tyrosine and ATP to crystals were shown to be similar to those observed in solution. Two tyrosine molecules were found to bind to the symmetrical dimer in the crystalline enzyme, while only one tyrosine binds with high affinity in solution. Electron density difference maps show that tyrosine and the AMP derivatives all bind at the same site, in a cleft 10 Å deep at one side of the pleated sheet, tyrosine binding over 100 times more strongly. The phosphate groups of AMP and ATP are not unambiguously observed in the difference electron density maps. Tyrosinyl adenylate is clearly delineated in the electron density difference map, with the tyrosyl side-chain occupying the site previously observed. The adenosine group is in a wide cup-like depression outside the pocket, lying between the carboxyl-terminal continuations of strands 3 and 5 of the pleated sheet. The adenine ring is lying against an α-helix. The binding of tyrosinyl adenylate causes no detectable conformational changes of the enzyme.     

Septate junctions in the cephalic epidermis of turbellarians (Bipalium)

Summary In the epidermis of turbellarians septate junctions of the pleated sheet type have been demonstrated in conventional thin sections and freeze fractured preparations. The structure of these junctions entirely agrees with that found in molluscs and arthropods.Financially supported by DFG (Sto 75/3,4; We 380/5)     

The peptide chain of tyrosyl tRNA synthetase: No evidence for a super-secondary structure of four α-helices

A detailed backbone model has been built for 274 residues of tyrosyl tRNA synthetase, based on an X-ray diffraction study. This includes eight helical sections and a six-stranded pleated sheet. The four helices near the carboxyl terminal end are not arranged like the helices of TMV disk protein and hemerythrin, and the structure gives no support to the idea that four antiparallel helices form a common structural unit in proteins.     

A computational study of the aerodynamic performance of a dragonfly wing section in gliding flight

A comprehensive computational fluid-dynamics-based study of a pleated wing section based on the wing of Aeshna cyanea has been performed at ultra-low Reynolds numbers corresponding to the gliding flight of these dragonflies. In addition to the pleated wing, simulations have also been carried out for its smoothed counterpart (called the 'profiled' airfoil) and a flat plate in order to better understand the aerodynamic performance of the pleated wing. The simulations employ a sharp interface Cartesian-grid-based immersed boundary method, and a detailed critical assessment of the computed results was performed giving a high measure of confidence in the fidelity of the current simulations. The simulations demonstrate that the pleated airfoil produces comparable and at times higher lift than the profiled airfoil, with a drag comparable to that of its profiled counterpart. The higher lift and moderate drag associated with the pleated airfoil lead to an aerodynamic performance that is at least equivalent to and sometimes better than the profiled airfoil. The primary cause for the reduction in the overall drag of the pleated airfoil is the negative shear drag produced by the recirculation zones which form within the pleats. The current numerical simulations therefore clearly demonstrate that the pleated wing is an ingenious design of nature, which at times surpasses the aerodynamic performance of a more conventional smooth airfoil as well as that of a flat plate. For this reason, the pleated airfoil is an excellent candidate for a fixed wing micro-aerial vehicle design.     

Strain-based estimation of time-dependent transmural myocardial architecture in the ovine heart

Left ventricular myofibers are connected by an extensive extracellular collagen matrix to form myolaminar sheets. Histological cardiac tissue studies have previously observed a pleated transmural distribution of sheets in the ovine heart, alternating sign of the sheet angle from epicardium to endocardium. The present study investigated temporal variations in myocardial fiber and sheet architecture during the cardiac cycle. End-diastolic histological measurements made at subepicardium, midwall, and subendocardium at an anterior-basal and a lateral-equatorial region of the ovine heart, combined with transmural myocardial Lagrangian strains, showed that the sheet angle but not the fiber angle varied temporally throughout the cardiac cycle. The magnitude of the sheet angle decreased during systole at all transmural depths at the anterior-basal site and at midwall and subendocardium depths at the lateral-equatorial site, making the sheets more parallel to the radial axis. These results support a previously suggested accordion-like wall-thickening mechanism of the myocardial sheets.     

火菇素的溶液二级结构与变性动力学

为了弄清抗肿瘤活性物质火菇素蛋白的二级结构及其活性在保存时自然衰减的规律 ,为临床应用提供依据 ,测定了火菇素的圆二色性并用蛋白质二级结构解析程序分析了火菇素的溶液二级结构 ,研究了火菇素的变性动力学 .火菇素的远紫外圆二色性的研究表明 ,其水溶液在 2 0 8nm处表现为大负峰 ,最大平均残基摩尔椭圆度 [θ]2 0 8=- 6574deg·cm2·dmol-1,在 2 2 3nm处为肩 .经二级结构解析程序计算分析 ,火菇素的二级结构组成为 :α螺旋 1 5.2 % ,平行 β折叠片和 β转角6.1 % ,反平行 β折叠片 32 .7% ,无规卷曲和 γ转角 2 3.4% ,其中二硫键和芳香氨基酸对火菇素圆二色性的贡献占 2 2 .6% .热变性几乎使所有的二级结构都遭到破坏 ,转化为无规卷曲 .利用已建立的火菇素免疫单向琼脂扩散定量检测技术 ,对在 4℃下保存的火菇素进行了长期跟踪检测 ,结果表明 ,在保存过程中火菇素的活性逐步降低 ,同时其二级结构也被破坏 .根据实验结果 ,建立了火菇素变性的一级动力学方程模型 :ct=coe-t/τ,该模型方程能很好地拟合实验结果 .根据模型方程计算的火菇素的寿命为 370 d,半衰期为 2 56d.说明火菇素这种很有应用前景的抗肿瘤药物比较容易长期保存 .     

Unusual denaturation properties of vicilin from Cajanus cajan

Pigeonpea (Cajanus cajan) vicilin (Mr 190 kD) holoprotein contains 2 subunits and the N-terminal amino acid sequence is Gly-Ala-Arg-Val-Asp-Gln-Glu for purified vicilin subunit 1 (Mr 72 kD) and Thr-Thr-Cys-Met-Glu-Ser-Gly for purified vicilin subunit 2 (Mr 57 kD). Circular dichroism spectra of vicilin indicate the occurrence of a predominant beta- pleated sheet structure. The fluorescence studies of vicilin reveal its unusual stability to 8 M urea and 6 M guanidine HCl.     

A clarification of the two types of invertebrate pleated septate junction

It is confirmed that there are two distinct variations of invertebrate septate junction. The first of these, the ‘lower invertebrate pleated septate junction’, is described fully using conventional thin section, lanthanum tracer and freeze-fracture techniques. The second type, the well-known pleated septate junction characteristic of the molluscs and athropods, is renamed the ‘mollusc-arthropod pleated septate junction’, and is described briefly to allow easier comparison between the two variations. As both types have now been studied in a range of invertebrate phyla the results can be used as a basis for discussing their respective phylogenetic positions. The lower invertebrate pleated septate junction occurs in several groups in the minor phyla immediately above the Coelenterata and in the lower phyla of both the deuterostome and proterostome lineages. The mollusc-arthropod pleated septate junction is restricted to the Mollusca and Arthropoda as its name implies.     

Analog of vertebrate anionic sites in blood-brain interface of larval Drosophila

The blood-brain barrier ensures brain function in vertebrates and in some invertebrates by maintaining ionic integrity of the extraneuronal bathing fluid. Recent studies have demonstrated that anionic sites on the luminal surface of vascular endothelial cells collaborate with tight junctions to effect this barrier in vertebrates. We characterize these two analogous barrier factors for the first time on Drosophila larva by an electron-dense tracer and cationic gold labeling. Ionic lanthanum entered into but not through the extracellular channels between perineurial cells. Tracer is ultimately excluded from neurons in the ventral ganglion mainly by an extensive series of (pleated sheet) septate junctions between perineurial cells. Continuous junctions, a variant of the septate junction, were not as efficient as the pleated sheet variety in blocking tracer. An anionic domain now is demonstrated in Drosophila central nervous system through the use of cationic colloidal gold in LR White embedment. Anionic domains are specifically stationed in the neural lamella and not noted in the other cell levels of the blood-brain interface. It is proposed that in the central nervous system of the Drosophila larva the array of septate junctions between perineurial cells is the physical barrier, while the anionic domains in neural lamella are a charge-selective barrier for cations. All of these results are discussed relative to analogous characteristics of the vertebrate blood-brain barrier.