Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.

The local environment of an amino acid in a folded protein determines the acceptability of mutations at that position. In order to characterize and quantify these structural constraints, we have made a comparative analysis of families of homologous proteins. Residues in each structure are classified according to amino acid type, secondary structure, accessibility of the side chain, and existence of hydrogen bonds from the side chains. Analysis of the pattern of observed substitutions as a function of local environment shows that there are distinct patterns, especially for buried polar residues. The substitution data tables are available on diskette with Protein Science. Given the fold of a protein, one is able to predict sequences compatible with the fold (profiles or templates) and potentially to discriminate between a correctly folded and misfolded protein. Conversely, analysis of residue variation across a family of aligned sequences in terms of substitution profiles can allow prediction of secondary structure or tertiary environment.     

X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.

The structures of the oxidized and reduced forms of the rubredoxin from the archaebacterium, Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, have been determined by X-ray crystallography to a resolution of 1.8 A. Crystals of this rubredoxin grow in space group P2(1)2(1)2(1) with room temperature cell dimensions a = 34.6 A, b = 35.5 A, and c = 44.4 A. Initial phases were determined by the method of molecular replacement using the oxidized form of the rubredoxin from the mesophilic eubacterium, Clostridium pasteurianum, as a starting model. The oxidized and reduced models of P. furiosus rubredoxin each contain 414 nonhydrogen protein atoms comprising 53 residues. The model of the oxidized form contains 61 solvent H2O oxygen atoms and has been refined with X-PLOR and TNT to a final R = 0.178 with root mean square (rms) deviations from ideality in bond distances and bond angles of 0.014 A and 2.06 degrees, respectively. The model of the reduced form contains 37 solvent H2O oxygen atoms and has been refined to R = 0.193 with rms deviations from ideality in bond lengths of 0.012 A and in bond angles of 1.95 degrees. The overall structure of P. furiosus rubredoxin is similar to the structures of mesophilic rubredoxins, with the exception of a more extensive hydrogen-bonding network in the beta-sheet region and multiple electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other residues (the amino-terminal nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen group of Phe 29). The influence of these and other features upon the thermostability of the P. furiosus protein is discussed.     

黄淮海平原高产田作物群体结构特征

本文利用实测资料分析了高产田作物群体结构特征。精播高产栽培麦田春季最大蘖数12×10~6/ha,群体最大叶面积指数5.5—6.0,成穗4.5—5.25×10~6/ha。传统高产栽培麦田春季最大蘖数15—18×10~6/ha,群体最大叶面积指数6.0—6.5,成穗6.0—7.5×10~6/ha。小麦营养生长与生殖生长期叶日积比,精播高产栽培麦田是1∶0.89,传统高产栽培麦田为1∶0.73。夏玉米种植密度主要受叶倾角的影响。紧凑型玉米品种的叶倾角大于65°,种植密度7.5—8.25×10~4/ha;平展型玉米品种的叶倾角小于50°,种植密度5.25—6.0×10~4/ha。     

Nonuniform size distribution of nascent globin peptides, evidence for pause localization sites, and a cotranslational protein-folding model

Examination of nascent globin peptides accumulatingin vitro during globin synthesis in rabbit reticulocyte lysates was carried out. A view was supported that nonrandom distribution of codons with different usage frequencies in mRNA may determine the messenger's translation kinetics. Regions of reduced translation of - and -globin polypeptide chains were localized, and the cotranslational protein-folding model suggested previously was substantiated. An active conjunction of synthesis and folding of proteins was proposed as one of the main destinations of a translation nonuniformity.     

Differentiation-related proteins of the broad bean rust fungus Uromyces viciae-fabae,as revealed by high resolution two-dimensional polyacrylamide gel electrophoresis

On artificial polyethylene membranes providing a thigmotropic signal, uredospores of the broad bean rust fungus Uromyces viciae-fabae differentiated a series of infection structures which in nature are necessary to invade the host tissue through the stomata. Within 24 h germ tubes, appressoria, substomatal vesicles, infection hyphae and haustorial mother cells were developed successively. Alterations in protein metabolism during infection structure differentiation of this obligate plant pathogen were analyzed in the absence of the host plant by high resolution two-dimensional polyacrylamide gel electrophoresis (2-DE) and silver staining. The norm pattern representing the 2-DE protein patterns of the whole developmental sequence of infection structures of U. viciae-fabae showed 733 spots. During infection structure differentiation 55 proteins were newly formed, altered in quantity, or disappeared. Major alterations in the protein pattern occurred during uredospore germination and when infection hyphae were formed. Uredospore germination was characterized by a decrease of acidic proteins and an increase mainly of proteins with isoelectric points ranging from weakly acidic to basic.Abbreviations 2-DE two-dimensional polyacrylamide gel electrophoresis - DAPI 4,6-diamino-phenylindol - kDa kilo Dalton - pl isoelectric point - PMSF phenylmethylsulfonyl fluoride - SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis     

Spawning behaviour ofCheimerius nufar in captivity

Synopsis The santerCheimerius nufar is widespread in tropical and subtropical waters of the western Indian Ocean and forms an important component of linefish catches along the east coast of southern Africa. Observations of spawning behaviour in captivity have revealed that spawning occurs during spring over a period of four months. Mating takes place at sunrise and may continue for up to 105 min (mean duration = 60 min). During spawning males become dark with prominent white markings. They become very aggressive and set up territories. Females remain a uniform silvery-pink. Mating occurs between males and females of similar sizes, culminating in egg and sperm release near the surface. Individual fish spawned up to 14 times during a morning. Streaking occurred throughout the season, with a second male joining a spawning pair and releasing gametes simultaneously. Slinger,Chrysoblephus puniceus, a dominant fish on offshore reefs in the same region, interfered with spawning throughout the season and were observed to eat eggs when they were released. The spawning strategy ofC. nufar is similar to protogynous species in several respects, indicating that this functional gonochorist may not conform to current theoretical predictions.     

Marriage system in the Italo-Albanians

The Italo-Albanian ethno-linguistic minority, living in 9 provinces of Southern Italy, has shown an increase of intermarriages with native Italian speaking individuals for the last decades of the 20th century. Marriage data was obtained through direct interviews of families of primary school students (6–13 years old). The information collected consisted of the birth place of parents and grandparents of each informant. The percentage values of intermarriages are about 25 in grandparents and 40 in parents.     

Observations on the relation between phytoplankton diversity and environmental factors in the Vaal River at Balkfontein,South Africa

The relationship between specific environmental factors as independent variables and temporal changes in phytoplankton community structure in the Vaal River (a turbid system) during 1984 was investigated by employing different diversity indices. Temporal changes in community structure reflected temporal changes in certain environmental factors. Phytoplankton diversity, measured with Shannon-Wie H' and Hurlbert PIE indices, was related firstly to discharge and discharge derived variables (such as SO₄, Si, N and P loading) and secondly to turbidity derived variables (such as euphotic zone depth). Discharge appears to be of prime importance in affecting diversity. Observations were made that shed new light on conditions contributing to the development of an August peak (dominated by Stephanodiscus hantzschii fo. tenuis and Micractinium pusillum) in phytoplankton concentration. Increased environmental stress may reduce the number of sensitive species, thus reducing interspecific competition between tolerant species which could then exploit the — for them — more favourable conditions resulting in an increase in their numbers to peak concentrations.     

Response of harpacticoid copepods to habitat structure at a deep-sea site

Given the quiescent physical environment and the low rates of bioturbation in the deep sea, biologically produced structures, such as animals tubes, may play an important role in creating habitat heterogeneity. In San Diego Trough, the cirratulid polychaete Tharyx luticastellus builds and inhabits a robust mud concretion (a mudball). Mudballs are abundant and persist after the worm has died or abandoned them. Our analysis of twelve 6.6-cm-diameter cores from 32° 51.02 N, 117° 46.97 W, taken with the submersible SEA CLIFF, indicate that one of 29 species of harpacticoids common in San Diego Trough is associated with Tharyx mudballs. This species (of the genus Heteropsyllus) responded only to mudballs containing worms, suggesting that any effects of the inanimate structure were not the cause of the association. We could detect no difference in bacterial numbers in sediments between control and occupied-mudball samples. This result suggests that the response does not result from gross differences in food levels near a mudball, but the possibility that there are differences in some preferred food cannot be discounted. An univestigated possibility is that Heteropsyllus responds to occupied mudballs because the worm's presence deters some (presumably small) predator.     

Effect of stereoconfiguration on ripple phases (Pβ′) of dipalmitoylphosphatidylcholine

Mixtures of sn-1 ( ) and sn-3 ( ) enantiomers of fully hydrated dipalmitoylphosphatidylcholine (DPPC) were studied with differential scanning calorimetry and freeze-fracture microscopy. The pretransition temperature of racemic mixtures of DPPC was 1.8 C° below that of either pure sn-1 or sn-3 enantiomers, which had similar pretransition temperatures. The main transition temperature of racemic mixtures was also depressed, but to a lesser extent, 0.8 C°. Freeze-fracture images of liposomes of sn-1, sn-3, and racemic mixtures of DPPC frozen from the P_β′ phase showed well-defined ripples of wavelength 13 nm. Lipid stereoconfiguration had no effect on ripple wavelength, configuration or amplitude, or on the number and nature of surface defects.