Residue contacts in protein structures and implications for protein folding

The preferential association of amino acid side groups with specific side chain atoms are examined in 44 known protein structures. The resulting association potentials among residue side groups are used to detect structural homology in proteins displaying little or no homology in their primary sequences. Suggestions are also made regarding the nature of the protein folding process. They are based on statistical observations that delineate the extent of short and long range interactions and that display side group bias in association with other side chain atoms on their N-terminal side.     

Molecular dynamics studies of side chain effect on the beta-1,3-D-glucan triple helix in aqueous solution

beta-1,3-D-glucans have been isolated from fungi as right-handed 6(1) triple helices. They are categorized by the side chains bound to the main triple helix through beta-(1-->6)-D-glycosyl linkage. Indeed, since a glucose-based side chain is water soluble, the presence and frequency of glucose-based side chains give rise to significant variation in the physical properties of the glucan family. Curdlan has no side chains and self-assembles to form an water-insoluble triple helical structure, while schizophyllan, which has a 1,6-D-glucose side chain on every third glucose unit along the main chain, is completely water soluble. A thermal fluctuation in the optical rotatory dispersion is observed for the side chain, indicating probable co-operative interaction between the side chains and water molecules. This paper documents molecular dynamics simulations in aqueous solution for three models of the beta-1,3-D-glucan series: curdlan (no side chain), schizophyllan (a beta-(1-->6)-D-glycosyl side-chain at every third position), and a hypothetical triple helix with a side chain at every sixth main-chain glucose unit. A decrease was observed in the helical pitch as the population of the side chain increased. Two types of hydrogen bonding via water molecules, the side chain/main chain and the side chain/side chain hydrogen bonding, play an important role in determination of the triple helix conformation. The formation of a one-dimensional cavity of diameter about 3.5 A was observed in the schizophyllan triple helix, while curdlan showed no such cavity. The side chain/side chain hydrogen bonding in schizophyllan and the hypothetical beta-1,3-D-glucan triple helix could cause the tilt of the main-chain glucose residues to the helix.     

The effect that side dominance has on barbell power symmetry during the hang power clean

The aim of this study was to examine whether ground reaction force (GRF) side differences were transmitted and related to bar end power output asymmetries during hang power clean (HPC) performance and whether progressive loading would intensify this effect. Differences between the dominant (D) and nondominant (ND) side average GRFs (AGRFs) of both feet and average bar end power outputs were recorded simultaneously from 15 recreationally trained male volunteers at 30, 60, and 90% 1RM using 2 force platforms and 3 high-speed digital cameras, quantifying side dominance from perceived handedness (left- or right-side dominance [LRSD]), GRF side dominance (force side dominance [FSD]), and bar end power output side dominance (barbell side dominance [BSD]). With the exception of the LRSD condition, differences between the D and ND side AGRFs were significant (FSD: 1.8-4.3%; BSD: 5.1-6.4%, p < 0.05). Bar end power output side differences were significant for all conditions (LRSD: 1.5-5.4%; FSD: 0.5-3.4%; BSD: 3.9-5.6%, p < 0.05). Progressive loading did not significantly affect GRF side differences or the FSD average bar power side differences. However, during the LRSD and BSD conditions, the 60 and 90% side average bar power side differences were >the 30% equivalents. Average GRF side differences were not related to bar end power output side differences. Because of the consistent side difference of 4-6% investigators and strength and conditioning practitioners should exercise caution when interpreting changes in bar end power output.     

Unilateral luteotropic effect of uterine venous effluent of a gravid uterine horn in sheep.

The involvement of the main uterine vein in the unilateral maintenance of CL was studied in bilaterally ovulating unilaterally pregnant ewes. Ewes were mated at estrus (Day 0) and bilaterally ovulating ewes were randomized into three groups at surgery on Day 5. In all ewes, the uterine horns were separated through the intercornual area and one was ligated and transected near the internal bifurcation to produce a nongravid horn. One group served as controls (five ewes). In the other two groups the main uterine vein on one side was surgically anastomosed (end to side) to the corresponding vein of the opposite side (gravid side to nongravid side in one group--three ewes, and nongravid side to gravid side in the other--three ewes). Necropsies were done on Day 20. Mean CL weight was less, (P less than .01) on the nongravid side in control ewes than on the gravid side in control ewes or for either side in the other two groups. There were no significant differences among mean weights of CL on the gravid side in control ewes and either side in the other two groups. The CL regressed when the ipsilateral uterine vein contained blood from only the nongravid horn whereas the CL was maintained when the ipsilateral uterine vein contained venous blood from a gravid horn, whether or not it also contained blood from a nongravid horn. Results indicate that the uterine venous effluent from a gravid uterine horn in sheep has a luteotropic effect on the ipsilateral CL.     

A Comparative Floristic Study on the Seed Plants of the East Side and the West Side of the Northern Gaoligong Mts . in Northwestern Yunnan,China

The differences in rainfall and temperature between the east and west sides of the northern GaoligongMts. leads to distinct differences in the plant diversity and floristic characteristics between the two sides . Recorded taxa on the east side include 1 475 native species and 192 varieties (or subspecies) belonging to 580 genera in 152 families and for the west side include 1 804 native species and 186 varieties ( or subspecies) belonging to 659 genera in 162 families . Based on the statistics and analysis of families, genera, and species, a comparative floristic study on the seed plants for the east side and the west side of the northern Gaoligong Mts. was carried out. The results are as follows: 1) The present flora on the east and west sides of the northern Gaoligong Mts . have the same floristic origins, but the relative contribution from these different sources has changed through time . The result is that the floristic similarity of families, genera, and species between the east side and the west side has decreased through time; 2) The floristic characteristic of seed plants for the west side has become more greatly influenced by tropical floristic elements than has that of the east side, and the influence by the temperate floristic elements has become less influenced on the west side but greater on the east side; 3) The flora of the west side is more closely linked with that of the eastern Himalayans than is the flora of the east side, and the flora of the east side is more closely linked with the other floras farther to the east. Owing to the obstruct of the Gaoligong Mts. ridge itself, it is seemingly difficult for the species interchange between the two sides of the northern Gaoligong Mts. ; 4) The ecological-geographical environment has made it more conducive to species conservation and the speciation on the west side than on the east side, so the west side is not only a refuge for some ancient floristic elements but also as a cradle of some new species.     

Statistical and conformational analysis of the electron density of protein side chains

Protein side chains make most of the specific contacts between proteins and other molecules, and their conformational properties have been studied for many years. These properties have been analyzed primarily in the form of rotamer libraries, which cluster the observed conformations into groups and provide frequencies and average dihedral angles for these groups. In recent years, these libraries have improved with higher resolution structures and using various criteria such as high thermal factors to eliminate side chains that may be misplaced within the crystallographic model coordinates. Many of these side chains have highly non-rotameric dihedral angles. The origin of side chains with high B-factors and/or with non-rotameric dihedral angles is of interest in the determination of protein structures and in assessing the prediction of side chain conformations. In this paper, using a statistical analysis of the electron density of a large set of proteins, it is shown that: (1) most non-rotameric side chains have low electron density compared to rotameric side chains; (2) up to 15% of chi1 non-rotameric side chains in PDB models can clearly be fit to density at a single rotameric conformation and in some cases multiple rotameric conformations; (3) a further 47% of non-rotameric side chains have highly dispersed electron density, indicating potentially interconverting rotameric conformations; (4) the entropy of these side chains is close to that of side chains annotated as having more than one chi(1) rotamer in the crystallographic model; (5) many rotameric side chains with high entropy clearly show multiple conformations that are not annotated in the crystallographic model. These results indicate that modeling of side chains alternating between rotamers in the electron density is important and needs further improvement, both in structure determination and in structure prediction.     

A major factor in gravitropism in radish hypocotyls is the suppression of growth on the upper side of hypocotyls

The changes in length on the two opposite sides of etiolated radish (Raphanus sativus) hypocotyls prior to, and following gravitropic stimulation, were measured using an infrared-imaging system. It was observed that the growth suppression on the upper side began first at least 10 min after the onset of gravitropic stimulation, and after 30 min the acceleration in growth on the lower side started. The gravitropic curvature was steadily induced from 10 min. When radish hypocotyls were switched from a vertical to horizontal position for different durations and then replaced to the vertical position, the growth suppression on the gravity-stimulated (upper) side was observed in all cases, but the acceleration in growth on the opposite (lower) side appeared only in continuously gravity-stimulated seedlings, although it occurred later than the growth suppression on the upper side. These results suggest that the suppression in growth on the upper side of the hypocotyls is a direct effect of gravitropic stimulation, but not the acceleration on the lower side. When 4-methylthio-3-butenyl isothiocyanate (4-MTBI), which has an inhibitory activity against radish hypocotyl growth, was applied on the one side of radish hypocotyls and then the 4-MTBI-applied side or opposite side was placed in a horizontal position, the former showed greater bending than the control, suggesting that the growth suppression on the upper side is enhanced and maintained with MTBI application there. In the latter case, the seedlings showed less bending than the control, suggesting a decrease in growth on the lower side with MTBI application. All the results suggest that gravitropism of radish hypocotyls may be caused by an increase in growth-inhibiting substance(s) induced with gravitropic stimulation in the upper side, inducing growth inhibition there.     

Minor and trace sterols in marine invertebrates : VI. Occurrence and possible origins of sterols possessing unusually short hydrocarbon side chains

Sterols with biosynthetically unusually short side chains (fewer than eight carbon atoms expected for primary squalene cyclization products) have been identified in the extracts of numerous marine invertebrates. The structures of the short side chain and conventional side chain sterols have been determined for various species of Porifera and Coelenterata. Sterol structures were determined by comparison of their mass spectra and gas chromatographic retention times with those of authentic or synthetic samples. Evidence is presented supporting the natural occurrence of these compounds in the tissues of the marine invertebrates as opposed to formation by degradative processes during sample handling or laboratory work-up. The short side chain sterols were found to possess predominantly the androst-5-en-3β-ol nucleus with C-17 alkyl side chains ranging from zero to six carbon atoms. Concentrations of short side chain sterols range from trace levels to over 5% of the sterol mixture in various species. The possible origins of these short side chain sterols are evaluated in the light of current knowledge of sterol function, biosynthesis, dealkylation, microbial degradation, and autoxidation. Known sterol autoxidations are reviewed, and possible singlet oxygen and free radical mechanisms of sterol side chain autoxidation (at physiological temperatures) which may lead to sterols with shortened hydrocarbon side chain are suggested. The possible autoxidative generation of short side chain sterols from known marine sterols by the suggested mechanisms is evaluated through application of the REACT computer program. Predicted short side chains are tabulated for each parent marine sterol side chain and then compared with the compositions of the actual sterols found in the marine extracts examined. The possible natural environmental or in vivo autoxidative formation of the short side chain marine sterols is supported by these evaluations.     

Cells scaffold complex for Intervertebral disc Anulus Fibrosus tissue engineering: in vitro culture and product analysis

The study was designed to investigate feasibility of tissue culture in vitro utilizing static culture method. Annulus fibrosus cells obtained from spine of rabbits were cultured. Results showed that fibrous tissue infiltration could be detected in shallow layer. With extended time, tissue infiltration depth increased, but there were still a large amount of holes in central part. Fibrous tissue infiltration was detected in the control side products and inner infiltration wasn't obvious. Hydroxyproline content of the control side products gradually increased with extended culture time. Hydroxyproline content of the control side products in the third and fourth month was significantly higher than that in the first month, but lower than those of the experimental side products and normal annulus fibrosus cells. DNA content of the control side products in the third and fourth month was significantly increased compared to the first month. DNA content of the control side products at each phase point was significantly lower than that of the experimental side and normal annulus fibrosus cells. Furthermore, there was lower expression levels of the type I, II collagen mRNA and protein in the experimental side scaffolds compared to the control side product. This study demonstrates the successful formation of Intervertebral disc Anulus Fibrosus in vitro by static culture method.     

Role of xyloglucan in gravitropic bending of azuki bean epicotyl

The mechanism of the gravitropic bending was studied in azuki bean epicotyls. The cell wall extensibility of the lower side became higher than that of the upper side in the epicotyl bending upward. The contents of matrix polysaccharides of the cell wall (pectin and xyloglucan in hemicellulose-II) in the lower side became smaller than those in the upper side. The molecular mass of xyloglucans in the lower side decreased. After an epicotyl was fixed to a metal rod to prevent the bending, gravistimulation was applied. Fundamentally the same results were obtained with respect to rheological and chemical characteristics of the cell wall as those of epicotyls showing gravitropic bending. The present results suggested that the initial gravitropic bending was caused by the increase in extensibility of the lower side and the decrease in extensibility of the upper side via the change of the cell wall matrix, especially xyloglucans.     

The higher resistance to chilling stress in adaxial side of <Emphasis Type="Italic">Rumex</Emphasis> K-1 leaves is accompanied with higher photochemical and non-photochemical quenching

Responses of two sides of Rumex K-1 leaves to chilling stress (5 °C, photon flux density of 100 μmol m⁻² s⁻¹) were studied by using gas exchange, chlorophyll (Chl) fluorescence, and spectrum reflectance techniques. The Chl and carotenoid contents in the two sides were not affected by chilling treatment, and both were higher in the adaxial side. The maximum quantum yield of photosystem (PS) 2 and fraction of functional PS1 in the abaxial side decreased more markedly than those in the adaxial side during the chilling treatment, indicating that the abaxial side was damaged more significantly than the adaxial side. Before chilling, there were no obvious differences in actual photochemical efficiency of PS2, photosynthesis, and photorespiration between two sides of the leaves. Under chilling stress, the actual photochemical efficiency of PS2, photosynthesis, and photorespiration all declined more significantly in the abaxial side, which was partly attributed to lower carboxylation efficiency in the abaxial side than that in the adaxial side. Non-photochemical quenching was higher in the adaxial side, though the de-epoxidation of xanthophyll cycle pigments’ pool on basis of Chl was higher in the abaxial side. Both the slower decrease in the photochemical quenching and the higher non-photochemical quenching may account for the higher resistance to chilling stress in the adaxial side of Rumex K-1 leaves.     

Analysis of interactions of buried polar side chains in beta-proteins

It was shown in qualitative and quantitative analyses of polar side chains inaccessible for water molecules as well as their interactions in 100 globular beta-structural proteins that completely buried polar side chains are widespread in beta-proteins, their vast majority being involved in "side chain-side chain" or "side chain-main chain" interactions. The analysis of the occurrence of different "side chain-partner" pairs permitted us to demonstrate that such interactions are selective. The results were compared with similar data obtained previously for alpha-helical proteins.     

Analysis of Interactions of Buried Polar Side Chains in β-Proteins

Qualitative and quantitative analysis of polar side chains inaccessible to water molecules, as well as their interactions in 100 globular β-sheet proteins, was performed. It was shown that completely buried polar side chains are widespread in β-proteins, with their vast majority being involved in side chain-side chain or side chain-main chain interactions. An analysis of frequency of occurrence of different side chain-partner pairs demonstrated that these interactions are selective. The results were compared with similar data obtained earlier for α-helical proteins.     

Cell death of olfactory receptor neurons in a rat with nasosinusitis infected artificially with Staphylococcus

Nasosinusitis is a common cause of acquired hyposmia or anosmia. To study the apoptotic death of olfactory receptor neurons in nasosinusitis, we made an inflammation model in rat infected with STAPHYLOCOCCUS: The histochemical changes in olfactory epithelium were examined using antibodies against protein gene product 9.5 (PGP 9.5), single-strand DNA (ssDNA), Bcl-2 and Bax that might be involved in the apoptosis of olfactory receptor neurons. The thickness of olfactory epithelium and the number of ssDNA-labeled cells were evaluated in each post-treatment group and the results were analyzed by two-way analysis of variance (ANOVA) and post hoc tests. Hematoxylin-eosin staining showed that a severe inflammatory reaction had occurred on the infected side of the nasal cavity and sinus, but not on the non-infected side. However, apoptosis of olfactory receptor neurons occurred on both sides; the apoptosis on the non-infected side started later and behaved like a shadow curve similarly to the infected side. Repeated measures ANOVA showed significant differences of both the thickness of olfactory epithelium (P < 0.0001) and the number of ssDNA-labeled cells (P = 0.0339) in the epithelium between the infected side and non-infected side comparing treatment, time and their interactions. Bcl-2 and Bax were detected only on the infected side in the early stages. Thus, nasosinusitis induced the apoptosis of olfactory receptor neurons. However, the apoptosis occurred not only on the infected side, but also on the non-infected side with no significant inflammation. The Bcl-2/Bax family seems to play an important role in the apoptosis induced by infection, but not in the apoptosis on the non-infected side. The results suggest that mechanisms of apoptosis of olfactory receptor neurons on the infected side may differ from those on the non-infected side.     

Transformations of the axial complex of ophiuroids as a result of shifting of the madreporite to the oral side

In comparison with Asteroidea, the axial complex of ophiuroids has some important features, which are the result of shifting of the madreporite from the aboral side to the oral side. In contrast to Asteroidea, the stone canal of ophiuroids connects with the water ring from the outside, not from the inside. In Ophiuroidea, the somatocoelomic perihaemal coelom is closer to the mouth than the axocoelomic ring. The water ring of ophiuroids is shifted to the oral side relative to the perihaemal coelomic rings. The genital coelom and gastric haemal ring are located on the outer side of the axial complex, whereas in Asteroidea, they are located on the inner side. The pericardial part of the axial organ is situated on the oral side. The interradial sections of the genital coelom and genital haemal ring are descended to the oral side. Our hypothesis considers that the ancestors of ophiuroids turned the aboral side of the animal to the substratum. It caused shifting of the madreporite to the oral side and closing of the anus.     

Molecular dynamics simulation on structural conformation of conjugated polymer-functionalised films for optimal fluorescent performance

The sensitive structure-related fluorescent properties of p-phenyleneethynylene (PPE)-functionalised fluorescent films with side chains and without side chains in different chemical environments are studied by molecular dynamics simulations. The calculations demonstrate that the structural change plays a crucial role in the fluorescent performance of PPE films, in which a major contribution is from the conformation of side chains. The PPE molecules with sides chains immobilised on SiO₂ substrate prefer to aggregate together in a dry state, but are more likely to stay in a monomolecular state in THF solvent. To an optimal concentration of the solvent molecules, the side chains are even perpendicular to the backbones of the molecules. The aggregation and separation of the PPE molecules with side chains are found to be controlled by the contraction and extension of the side chains connected to PPE. The van der Waals' force between the side chains is mainly responsible for these changes, which leads to a spreading out of the side chains in the presence of THF. All the results from the simulation studies can successfully explain the experimental observations.     

Side effects of atypical antipsychotics: a brief overview

This paper reviews the available evidence concerning the side effects of atypical antipsychotics, including weight gain, type II diabetes mellitus, hyperlipidemia, QTc interval prolongation, myocarditis, sexual side effects, extrapyramidal side effects and cataract. Some recommendations about how to prevent and manage these side effects are also provided. It is concluded that atypical antipsychotics do not represent a homogeneous class, and that differences in side effects should be taken into account by clinicians when choosing an antipsychotic for an individual patient.     

建湖县城区2008—2011年轮状病毒减毒活疫苗接种副反应监测分析

目的了解轮状病毒活疫苗接种后副反应发生的情况,为该疫苗安全接种提供依据。方法对2008—2011年间每年的6月1日到8月31日在建湖县城区免疫规划门诊接种的婴幼儿登记数据进行分析。结果接种5 139人,报告副反应114人,报告率2.218%。报告发生率,一般副反应109例,发生率为2.121%;异常副反应5例,发生率为0.097%。结论接种轮状病毒活疫苗异常副反应发生率低,接种疫苗安全。     

The relationship between the structure of plastoquinone derivatives and their biological activity in Photosystem II of spinach chloroplasts

The relationship between the structure of reconstituted plastoquinone derivatives and their ability to recover the Hill reaction was investigated by extraction and reconstitution of lyophilized chloroplasts from spinach, followed by monitoring DCIP photoreduction at 600 nm. The results show that: It is not essential that the plastoquinone side chain be an isoprenoid or a phytol; the activity increases with increasing length of the side chain up to 13–15 carbon atoms; for chains longer than 15 carbon atoms, the activity is practically constant. Lipophilic groups (such as -Br) in the side chain increased the activity, hydrophilic groups (such as -OH) decreased the activity. Conjugated double bonds in the side chain decreased the activity greatly, but non-conjugated double bonds had almost no effect on the activity, indicating a requirement of flexibility of the side chain. The activity is decreased in the order of PQ, UbiQ and MQ, showing a large effect of the ring structure.Abbreviations DCIP 2,6-dichlorophenolindophenol - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea - Q_A primary electron acceptor in PS II reaction centers - Q_B secondary electron acceptor in PS II reaction centers - PQ _n plastoquinones with an isoprenoid side chain (n, number of the isoprenoid units in the side chain) - PQ-n synthetic plastoquinones with alkyl side chain (n, number of the carbon atoms in the alkyl side chain) - PQ-n synthetic plastoquinones with a double bond in the alkyl side chain - UQ _n ubiquinones with an isoprenoid side chain (n, number of the isoprenoid units in the side chain) - UQ-n synthetic ubiquinones with alkyl side chain (n, number of the carbon atoms in the akyl side chain) - MQ-n 2-alkyl-1,4-naphthoquinone (n, number of the carbon atoms in the alkyl side chain)     

The apical nutations of pea seedlings in relationship to growth regulators

The apical hook curvatures of pea seedlings are associated with a higher level of endogenous auxin on the lower (ventral) side of the curvature in comparison with the upper (dorsal) side. For this reason this curvature may be reversed by applying IAA to the dorsal side of the hook. On the other hand the analyses did not reveal any differences in the content of endogenous gibberellin between the dorsal and ventral side of the hook. Endogenous gibberellin if applied either to the dorsal or to the ventral side of the hook curvature closes the hook. Exogenous cytokinin benzyladenine closes the curvature only if applied to the ventral side of the hook, but it opens it if applied to the dorsal one.