Electron microscopic observations on alterations in cultured Plasmodium falciparum and infected erythrocytes after treatment with cyclic AMP in vitro

The fine structure of Plasmodium falciparum treated with cyclic AMP in vitro was studied. Cyclic AMP stimulated the appearance of membranous structures in P. falciparum-infected erythrocytes. Two types of membranous structures originating from the host cell were observed: multilaminate membranous structures and multistranded layer-like membranous structures. The multilaminate structures may play a role in gametocytogenesis and the maturation of the gametocyte. The multilaminate structures were either free in the cytoplasm of infected erythrocytes or present in association with the parasitophorous vacuole membrane surrounding immature gametocytes. These structures may originate from the erythrocyte plasma membrane and the parasitophorous vacuole membrane. Other notable findings in P. falciparum treated with cyclic AMP included the presence of loop-like membrane structures protruding from the plasma membrane of the parasite and termination of some plasma membranes of the parasite in dense granular structures.     

Comparison of X‐ray and NMR structures: Is there a systematic difference in residue contacts between X‐ray‐ and NMR‐resolved protein structures?

We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures of the same protein have more differences than various X-ray structures obtained for the protein, and even more than various NMR structures of the protein. X-ray and NMR structures of 18 of these 78 proteins have obvious large-scale structural differences that seem to reflect a difference of crystal and solution structures. The other 60 pairs of structures have only small-scale differences comparable with differences between various X-ray or various NMR structures of a protein; we have analyzed these structures more attentively. One of the main differences between NMR and X-ray structures concerns the number of contacts per residue: (1) NMR structures presented in PDB have more contacts than X-ray structures at distances below 3.0 A and 4.5-6.5 A, and fewer contacts at distances of 3.0-4.5 A and 6.5-8.0 A; (2) this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for beta-containing proteins than for all-alpha proteins. Another significant difference is that the main-chain hydrogen bonds identified in X-ray and NMR structures often differ. Their correlation is 69% only. However, analogous difference is found for refined and rerefined NMR structures, allowing us to suggest that the observed difference in interresidue contacts of X-ray and NMR structures of the same proteins is due mainly to a difference in mathematical treatment of experimental results.     

藏红花瓣状体的诱导与花柱-柱头状物的定向分化

藏红花 (ＣｒｏｃｕｓｓａｔｉｖｕｓＬ .)又名番红花、西红花 ;藏药中称为苟日苟木。它是鸢尾科草本植物 ,原产于欧洲、地中海地区。我国长期以来把它作为珍贵的中藏药。其药用部位是柱头 ,有效成分主要是藏红花素、藏红花酸、藏红花醛和藏红花苦素。丁葆祖等于 1979年首次从藏红花的球茎获得完整的植株[1 ] 。Ｓａｎｏ等人 1987年在离体条件下 ,诱导花柱 柱头状物再生获得成功[2 ] ,此后国内外不断有相关报道[3～ 7] 。但试验大多集中在由外植体直接或由愈伤组织间接诱导柱头状物 ,且花柱 柱头状物的频率低和数量少。我们试图先由藏红花…     

Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir

Due to the limited distance data available from the experiments, the structures determined by NMR Spectroscopy may not always be as accurate as desired. Further refinement of the structures is often required and sometimes critical. With the increase of high quality protein structures determined and deposited in PDB Data Bank, commonly shared protein conformational properties can be extracted based on the statistical distributions of the properties in the structural database and used to improve the outcomes of the NMR-determined structures. Here we examine the distributions of protein interatomic distances in known protein structures. We show that based on these distributions, a set of mean-force potentials can be defined for proteins and employed to refine the NMR-determined structures. We report the test results on 70 NMR-determined structures and compare the potential energy, the Ramachandran plot, and the ensemble RMSD of the structures refined with and without using the derived mean-force potentials.     

Cuticular structures of the priapulid Halicryptus spinulosus: A scanning electron microscopical study

Summary The surface anatomy and the structures lining the pharynx of Halicryptus spinulosus were examined by scanning electron microscopy (SEM). The structures were compared and contrasted with those reported for other priapulids, particularly those features previously studied with SEM. Buccal papillae and pharyngeal teeth of two types were described. Surface structures observed with SEM were: scalids, abdominal setae, anal papillae, posterior warts and ring papillae. The latter three structures are unique among described priapulids. The anal papillae are composed of several rounded, perhaps pedunculate, structures; the posterior warts are composed of mitriform structures in close association with columnar structures. Both are located in separate depressions in the posterior integument. The ring papillae occur on the annuli close to the posterior end. Halicryptus spinulosus was previously thought to lack these structures.     

Principal components analysis of protein structure ensembles calculated using NMR data

One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated structural variation across the population. PCA analysis has the additional advantage that it highlights regions of proteins which are varying across the population. To apply PCA, protein structures have to be reduced in complexity and this paper describes two different representations of protein structures which achieve this. The calculated structures of a 28 amino acid peptide are used to demonstrate the methods. The two different representations of protein structure are shown to give equivalent results, and correct results are obtained even though the ensemble of structures used as an example contains two different protein conformations. The PCA analysis also correctly identifies the structural differences between the two conformations.     

Potential for assessing quality of protein structure based on contact number prediction

We developed a novel knowledge-based residue environment potential for assessing the quality of protein structures in protein structure prediction. The potential uses the contact number of residues in a protein structure and the absolute contact number of residues predicted from its amino acid sequence using a new prediction method based on a support vector regression (SVR). The contact number of an amino acid residue in a protein structure is defined by the number of residues around a given residue. First, the contact number of each residue is predicted using SVR from an amino acid sequence of a target protein. Then, the potential of the protein structure is calculated from the probability distribution of the native contact numbers corresponding to the predicted ones. The performance of this potential is compared with other score functions using decoy structures to identify both native structure from other structures and near-native structures from nonnative structures. This potential improves not only the ability to identify native structures from other structures but also the ability to discriminate near-native structures from nonnative structures.     

Flexibility observed in high resolution structures of <Emphasis Type="Italic">Streptomyces aureofaciens</Emphasis> ribonucleases determined by diffraction methods

It has been widely accepted to distinguish between static structures determined by diffraction methods and dynamic structures determined by nuclear magnetic resonance (NMR). The dynamics of NMR structures is demonstrated by an ensemble of a number of overlaid structures. This cannot be seen in one structure determined by diffraction methods. However, it is possible to see the flexibility of a protein molecule in a number of structures of the same protein determined by X-ray techniques which is manifested by different conformations of main-chain. Multiple protein structure determination does not provide identical structures as a result of various factors including flexibility. Overlap of structures of a protein determined at atomic resolution with high accuracy shows that the root-mean-square deviations (rmsd) of main-chain atoms exceed several fold the accuracy of the positional parameters of each structure. Overlap of a number of structures of a protein determined by diffraction methods shows a similar distribution as that determined by NMR. These observations are demonstrated using high resolution structures of Streptomyces aureofaciens ribonucleases, their mutants and complexes with ligands.     

Isolation and initial characterization of residual nuclear structures from yeast

Residual nuclear structures have previously been isolated from a wide range of eukaryotic organisms. When nuclei are isolated from Saccharomyces cerevisiae and then treated with 1.95 M NaCl and DNase I, sedimentable residual structures are obtained similar in several respects to structures isolated from organisms previously studied. These yeast residual nuclear structures retain less than 7% of nuclear DNA, less than 17% of nuclear RNA and less than 50% of nuclear proteins. Electron microscopy suggests that these structures are derived from the nuclear interior and are composed of a sparse fibrogranular network. Replicating DNA is preferentially bound to these yeast residual nuclear structures, just as it is to residual nuclear structures from other organisms.     

电镜下几种病毒的异常形态结构

应用电子显微镜技术观察了马传染性贫血病毒、鸡喉头气管炎病毒、禽流感A型病毒,除观察到正常病毒粒子外,还分别发现了一些异常形态结构,诸如马传染性贫血病毒的长杆形粒子、鸡喉头气管炎病毒的微管结构及禽流感A型病毒的丝状体等,这些异常形态结构可能是各该病毒增殖过程中的某一特殊方式。     

Possible mechanisms of the formation of structures in bacterial populations consisting of motile cells

The formation of fixed and moving structures was studied in Escherichia coli populations. The moving and fixed structures were shown to be formed only by bacteria with a taxis system. The moving structures caused an uneven distribution of the substrate concentration. Bacterial growth on agar with the unevenly distributed substrate led to the appearance of fixed structures. Mechanisms responsible for the formation of bacterial structures remain obscure.     

A mathematical framework for protein structure comparison

Comparison of protein structures is important for revealing the evolutionary relationship among proteins, predicting protein functions and predicting protein structures. Many methods have been developed in the past to align two or multiple protein structures. Despite the importance of this problem, rigorous mathematical or statistical frameworks have seldom been pursued for general protein structure comparison. One notable issue in this field is that with many different distances used to measure the similarity between protein structures, none of them are proper distances when protein structures of different sequences are compared. Statistical approaches based on those non-proper distances or similarity scores as random variables are thus not mathematically rigorous. In this work, we develop a mathematical framework for protein structure comparison by treating protein structures as three-dimensional curves. Using an elastic Riemannian metric on spaces of curves, geodesic distance, a proper distance on spaces of curves, can be computed for any two protein structures. In this framework, protein structures can be treated as random variables on the shape manifold, and means and covariance can be computed for populations of protein structures. Furthermore, these moments can be used to build Gaussian-type probability distributions of protein structures for use in hypothesis testing. The covariance of a population of protein structures can reveal the population-specific variations and be helpful in improving structure classification. With curves representing protein structures, the matching is performed using elastic shape analysis of curves, which can effectively model conformational changes and insertions/deletions. We show that our method performs comparably with commonly used methods in protein structure classification on a large manually annotated data set.     

Use of linear regression model to compare RNA secondary structures

With more and more ribonucleic acid (RNA) secondary structures accumulated, the need for comparing different RNA secondary structures often arises in function prediction and evolutionary analysis. Numerous efficient algorithms were developed for comparing different RNA secondary structures, but challenges remain. In this paper, six new models based on the linear regression model were proposed for the comparison of RNA secondary structures. The proposed models were tested on a mixed data, containing six secondary structures from RNase P RNAs, three secondary structures from SSU rRNA and five secondary structures from 16S ribosomal RNAs. The results have shown the effectiveness of the proposed models. Moreover, the time complexity of our models is favorable by comparing with that of the existing methods which solve the similar problem.     

Electron microscopy of membrane-associated folded chromosomes of Escherichia coli

Membrane-associated folded chromosomes were purified from log-phase cultures of Escherichia coli 15 TAU-bar and prepared for electron microscopy by aqueous spreading techniques. A spectrum of structures was observed, ranging from condensed structures with no DNA fibers visible, to extended structures with DNA fibers. In the extended structures, loops of DNA radiated from residual envelope, the loops sometimes appeared super-coiled, and both their number and apparent contour length approximated previous estimates from physical and biochemical data. It is proposed that the structures with free DNA arose from the condensed structures.     

Ribeiroia marini: Surface ultrastructure of redia,cercaria, and adult

Rediae, cercariae, and adults of Ribeiroia marini were examined using a scanning electron microscope to determine the types of tegumental sensory structures and their locations. Sensory structures were observed among numerous tegumental folds in the area immediately surrounding the mouth of the rediae. These sensory structures are similar in appearance, location and fine structure to sensory structures described from the anterior tips of rediae known to be predacious on the sporocysts of Schistosoma mansoni. These uniciliated structures may function as chemoreceptors to aid the redia in migration through snail tissue. Five types of sensory structures bearing one, two, or multiple cilia were distinguishable on the cercariae. These structures were located on and around the oral sucker, dorsal and ventral body surfaces and on the tail. They may be used by the cercariae to locate the intermediate host fish and to find suitable sites within the lateral line scales for encystment. The ventral surface of the adult fluke is covered with spines and shows an absence of sensory structures on the general body surface. Sensory structures were seen in the area surrounding the oral and ventral suckers. The extended cirrus organ has a folded tegument, but lacks spines or sensory structures.     

Solar radiation as a factor in the evolution of scleromorphic leaf anatomy in Proteaceae

Species of the major Southern Hemisphere family, Proteaceae, have many scleromorphic anatomical structures in their leaves. Many of these structures (very thick cuticles and five anatomically distinct structures beneath the epidermis) are associated with the leaf surface exposed to direct light. These structures increase the path through which solar radiation must pass before reaching the mesophyll. In this study, such structures are proposed to protect the mesophyll from excess solar radiation, including photosynthetically active, ultraviolet, and possibly infrared radiation. Scleromorphic structures of the upper leaf surface and nonscleromorphic photoprotective structures (dense trichomes and papillae of the upper surface) occur almost exclusively in open vegetation. Open vegetation species of Proteaceae occur in oligotrophic and/or cold and/or dry places, where protection from light in excess of photosynthetic capacity and damage from ultraviolet light should be most important. Data from 123 species and a supertree constructed from available molecular phylogenies are used to show that the proposed photoprotective structures evolved many times within Proteaceae. In tests of correlated evolution, the proposed photoprotective structures are significantly associated with open vegetation, but not with dry habitats.     

Vibrational analysis of peptides,polypeptides, and proteins. V. Normal vibrations of β-turns

The normal modes have been calculated for β-turns of types I, II, III, I′, II′, and III′. The complete set of frequencies is given for the first three structures; only the amide I, II, and III modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide II modes. The results show that in the amide I region, β-turn frequencies can overlap with those of the α-helix and β-sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide III modes of β-turns are predicted at significantly higher frequencies than those of α-helix and β-sheet structures, and this region therefore provides the best possibility of identifying β-turn structures. Amide V frequencies of β-turns may also be distinctive for such structures.     

A prediction of tertiary structures of peptide by the Monte Carlo simulated annealing method

The Monte Carlo simulated annealing method has been applied to the prediction of three-dimensional structures of enkephalin. The low-energy conformations obtained were classified into a few groups of similar structures, which indicates that our method is effective. New low-energy structures were identified together with previously proposed structures.     

Prediction of the ensembles of RNA secondary structures. Kinetic analysis of self-organization

A new approach to the problem of prediction of secondary structures of RNA, which is based on the kinetic analysis of self-organising molecules is proposed. Structural reconstructions that take place during formation of secondary structures are described in terms of Markov process. A set of states and probability transition were defined. Monte-Carlo methods were used to describe this process. Probability distributions of various secondary structures depending on time are given. Examples of calculations for ensembles of secondary structures of some tRNAs are described. An effective method of steady-state ensemble research, which is based on a quick RESETTING of all possible variance of the secondary structures of RNAs is given. By ascribing to each of these structures the value of probabilities as a function of free energy it was possible to obtain the Boltzmann ensemble of secondary structures.     

mRNA环结构对蛋白质折叠速率的影响

前期的相关研究发现mRNA二级结构中存在对蛋白质折叠速率的重要影响因素.而mRNA二级结构中普遍存在着各种复杂的环结构,这些环结构是否对蛋白质折叠速率也有重要的影响呢?不同的环结构对蛋白质折叠速率的影响是否相同呢?基于此想法,建立了一个包含mRNA内部环、发夹环、膨胀环和多分支环等环结构信息和相应蛋白质折叠速率的数据库.对于数据库中的每一个蛋白质,计算了mRNA二级结构中各种环结构碱基含量、配对碱基含量及单链碱基含量等参量,分析了各参量与相应蛋白质折叠速率的相关性.结果显示,各种环结构碱基含量与蛋白质折叠速率均呈极显著或显著正相关.说明mRNA环结构对蛋白质折叠速率有重要的影响.进一步,把蛋白质按照不同折叠类型或不同二级结构类型分组后,对每一组蛋白质重复上述的分析工作.结果表明,对不同类蛋白质,mRNA的各种环结构对其相应蛋白质折叠速率的影响存在着显著差异.上述研究将为进一步开展有关mRNA和蛋白质折叠速率的研究奠定理论基础.