Homology modeling of histidine-containing phosphocarrier protein and eosinophil-derived neurotoxin: Construction of models and comparison with experiment

Homology modeling methods have been used to construct models of two proteins—the histidine-containing phosphocarrier protein (HPr) from Mycoplasma capricolum and human eosinophil-derived neurotoxin (EDN). Comparison of the models with the subsequently determined X-ray crystal structures indicates that the core regions of both proteins are reasonably well reproduced, although the template structures are closer to the X-ray structures in these regions—possible enhancements are discussed. The conformations of most of the side chains in the core of HPr are well reproduced in the modeled structure. As expected, the conformations of surface side chains in this protein differ significantly from the X-ray structure. The loop regions of EDN were incorrectly modeled—reasons for this and possible enhancements are discussed. © 1995 Wiley-Liss, Inc.     

Atomic and residue hydrophilicity in the context of folded protein structures

Water-protein interactions drive protein folding, stabilize the folded structure, and influence molecular recognition and catalysis. We analyzed the closest protein contacts of 10,837 water molecules in crystallographic structures to define a specific hydrophilicity scale reflecting specific rather than bulk solvent interactions. The tendencies of different atom and residue types to be the nearest protein neighbors of bound water molecules correlated with other hydrophobicity scales, verified the relevance of crystallographically determined water positions, and provided a direct experimental measure of water affinity in the context of the folded protein. This specific hydrophilicity was highly correlated with hydrogen-bonding capacity, and correlated better with experimental than computationally derived measures of partitioning between aqueous and organic phases. Atoms with related chemistry clustered with respect to the number of bound water molecules. Neutral and negatively charged oxygen atoms were the most hydrophilic, followed by positively-charged then neutral nitrogen atoms, followed by carbon and sulfur atoms. Agreement between observed side-chain specific hydrophilicity values and values derived from the atomic hydrophilicity scale showed that hydrophilicity values can be synthesized for different functional groups, such as unusual side or main chains, discontinuous epitopes, and drug molecules. Two methods of atomic hydrophilicity analysis provided a measure of complementarity in the interfaces of trypsin:pancreatic trypsin inhibitor and HIV protease:U-75875 inhibitor complexes. © 1995 Wiley-Liss, Inc.     

The SEA module: a new extracellular domain associated with O-glycosylation.

Using a variety of homology search methods and multiple alignments, a new extracellular module was identified in (1) agrin, (2) enterokinase, (3) a 63-kDa sea urchin sperm protein, (4) perlecan, (5) the breast cancer marker MUCI (episialin), (6) the cell surface antigen 114/A10, and (7/8) two functionally uncharacterized, probably extracellular, Caenorhabditis elegans proteins. Despite the functional diversity of these adhesive proteins, a common denominator seems to be their existence in heavily glycosylated environments. In addition, the better characterized proteins mentioned above contain all O-glycosidic-linked carbohydrates such as heparan sulfate that contribute considerably to their molecular masses. The common module might regulate or assist binding to neighboring carbohydrate moieties.     

The distribution of alpha-helix propensity along the polypeptide chain is not conserved in proteins from the same family.

We address the question of whether the distribution of secondary structure propensities of the residues along the polypeptide chain (denominated here as secondary structure profiles) is conserved in proteins throughout evolution, for the particular case of alpha-helices. We have analyzed by CD the conformation of peptides corresponding to the five alpha-helices of two alpha/beta parallel proteins (ComA and Ara). The large alpha-helical population of peptide ComA-4 detected by CD in aqueous solution has been confirmed by NMR. These proteins are members of the CheY and P21-ras families, respectively, which have been studied previously in the same way (Muñoz V, Jiménez MA, Rico M, Serrano L, 1995, J Mol Biol 245:275-296). Comparison of the helical content of equivalent peptides reveals that protein alpha-helix propensity profiles are not conserved. Some equivalent peptides show very different helical populations in solution and this is especially evident in very divergent proteins (ComA and CheY). However, all the peptides analyzed so far adopted an important population of helical conformations in the presence of 30% trifluoroethanol, indicating that there could be a conserved minimal requirement for helical propensity.     

Mating type differentiation in tetrahymena thermophila: Characterization of the delayed refeeding effect and its implications concerning intranuclear coordination

Mating type determination in Tetrahymena thermophila involves developmentally programmed, heritable alterations of the macronucleus, localized to the mtd locus. This determination can be predictably controlled by the environmental conditions during macronuclear development, eg, temperature and time of refeeding. In this article we have further characterized the effects of delayed refeeding on mating type determination, as revealed by the frequency of mating types among the progeny of a cross. Our results show that 1) the magnitude of this starvation effect decreases with temperature of conjugation and becomes undetectable at 18°C; 2) starvation during the interval 14 to 22 hr (after conjugation is induced at 30°C) is a necessary and sufficient condition for the induction of starvation effects; 3) relative mating type frequencies vary monotonically with nutrient concentration present during this critical period; and 4) sister macronuclei, developing under starvation conditions in the same cytoplasm, differentiate majority mating types characteristic of early or late refeeding; sister macronuclei show no apparent correlation with each other. On the basis of our observations on early and late refed cells, we propose that the composition of the newly developed macronucleus is the outcome of two key events: 1) mating type determination at the mtd locus and 2) differential molecular cloning of generally one or two autonomously replicating fragments (ARFs) of the macronuclear DNA bearing the mtd locus.     

Theoretical studies on the modes of binding of some of the derivatives of d-mannose to concanavalin A

The possible modes of binding for $\text{methyl}\text{-α-}\text{d}\text{-mannopyranoside}$, $\text{methyl}\text{-β-}\text{d}\text{-mannopyranoside}$, $\text{2-O-}\text{methyl}\text{-α-}\text{d}\text{-mannopyranoside}$, $\text{methyl-2-O-methyl}\text{-α-}\text{d}\text{-mannopyranoside}$ and $\text{methyl}\text{-α-}\text{d}\text{-N-}\text{acetylmannosamine}$ to concanavalin A have been investigated using theoretical methods. All these sugars, except $\text{methyl}\text{-α-}\text{d}\text{-N-}\text{acetylmannosamine}$, reach the active site of concanavalin A with a highly restricted number of binding orientations. Present investigations suggest that the failure of $\text{methyl}\text{-α-}\text{d}\text{-N-}\text{acetylmannosamine}$ to bind to concanavalin A is not so much due to steric factors as to repulsive electrostatic interactions. $\text{Methyl}\text{-2-O-}\text{methyl}\text{-α-}\text{d}\text{-mannopyranoside}$ can bind to concanavalin A in one mode whereas the other sugars can bind in more than one mode. The high potency of $\text{methyl}\text{-α-}\text{d}\text{-mannopyranoside}$ over $\text{methyl}\text{-β-}\text{d}\text{-mannopyranoside}$ is mainly due to the possibility of hydrophobic interactions of the α-methoxy group with Leu(99) or Tyr(100) and also due to the possibility of formation of better and more hydrogen bonds with the protein. A comparison of these data with those for the d-glucopyranosides suggests that the change of the hydroxyl at the C-2 atom from equatorial to axial orientation increases the stereochemically allowed region as well as the possible binding modes. From these studies it is also suggested that the overall shape of the oligosaccharides rather than the terminal or internal mannose alone affects the binding potency of saccharides to concanavalin A.     

Theoretical studies on the modes of binding of some of the derivatives of d-mannose to concanavalin A

The possible modes of binding for methyl-α-d-mannopyranoside, methyl-β-d-mannopyranoside, 2-O-methyl-α-d-mannopyranoside, methyl-2-O-methyl-α-d-mannopyranoside and methyl-α-d-N-acetylmannosamine to concanavalin A have been investigated using theoretical methods. All these sugars, except methyl-α-d-N-acetylmannosamine, reach the active site of concanavalin A with a highly restricted number of binding orientations. Present investigations suggest that the failure of methyl-α-d-N-acetylmannosamine to bind to concanavalin A is not so much due to steric factors as to repulsive electrostatic interactions. Methyl-2-O-methyl-α-d-mannopyranoside can bind to concanavalin A in one mode whereas the other sugars can bind in more than one mode. The high potency of methyl-α-d-mannopyranoside over methyl-β-d-mannopyranoside is mainly due to the possibility of hydrophobic interactions of the α-methoxy group with Leu(99) or Tyr(100) and also due to the possibility of formation of better and more hydrogen bonds with the protein. A comparison of these data with those for the d-glucopyranosides suggests that the change of the hydroxyl at the C-2 atom from equatorial to axial orientation increases the stereochemically allowed region as well as the possible binding modes. From these studies it is also suggested that the overall shape of the oligosaccharides rather than the terminal or internal mannose alone affects the binding potency of saccharides to concanavalin A.     

Cartilage type IX collagen is cross-linked by hydroxypyridinium residues

Type IX collagen, a recently discovered, unusual protein of cartilage, has a segmented triple-helical structure containing interchain disulfides. Its polymeric form and function are unknown. When prepared by pepsin from bovine articular cartilage, type IX collagen was found to contain a high concentration of hydroxypyridinium cross-links, similar to that in type II collagen. Fluorescence spectroscopy located the hydroxylysyl pyridinoline and lysyl pyridinoline cross-linking residues exclusively in the high-molecular-weight collagen fraction, from which they were recovered predominantly in a single CNBr-derived peptide. The results point to a structural role for type IX collagen in cartilage matrix, possibly as an adhesion material to type II collagen fibrils.     

Life history studies of the predaceous mite Phytoseius hawaiiensis

Phytoseius hawaiiensis (Acari: Phytoseiidae) had relatively long periods of preoviposition, oviposition and postoviposition (4.6, 46.9 and 52.0 days, respectively, at 24 °C), and a relatively low fecundity (31.4 eggs per female), compared to other phytoseiid species. The most favorable food tested was all stages of Oligonychus punicae (Hirst), but various other species of mite prey as well as pollen also promoted oviposition. Extreme variation was observed in hatching time of the eggs, from 10 min (rare) to over 4 days (common). Occasionally, females apparently retain their eggs until just before larvae hatch, as eggs containing developed larvae were observed inside some females. Results of experiments suggested that unsuitable substrate (e.g. for oviposition) is a factor which induces longer egg retention prior to oviposition.

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Résumé Chez Phytoseius hawaiiensis, les durées des périodes précédant la ponte, correspondant à la ponte et succédant à la ponte, sont relativement longues; respectivement 4, 6; 31, 4 et 52 jours à 24 °C; dans ces conditions, la fécondité est relativement basse: 31, 4 oeufs par femelle. Oligonychus punicae (aux différents stades) a constitué le meilleur aliment essayé, mais diverses autres espèces d'acariens ainsi que le pollen induisent la ponte. La date d'éclosion des oeufs a présenté une très grande variabilité, de 10 min (rare) à plus de 4 jours (fréquent). Souvent, les femelles semblent retenir leurs oeufs jusqu'au moment précédant l'éclosion des larves, car des oeufs contenant des larves développées on été observés dans quelques femelles. Les résultats des expériences ont suggére qu'un substrat défavorable (pour la ponte) induit une plus longue rétention de la ponte.

     

The biology and energetics of the potato aphid Macrosiphum euphorbiae, living in galls of the apple aphids Dysaphis devecta and Aphis pomi

A non-gall-forming aphid, Macrosiphum euphorbiae, was reared within the galls of Dysaphis devecta and Aphis pomi which had been induced in apple seedlings. Similar aphids were also reared on ungalled seedling leaves of a similar age and also on mature leaves and in old galls.There is a weak positive linear relationship between lipid content and pre-reproductive adult dry weight, but aphids living on young galled or ungalled plant tissue have 30% lipid compared to 11% for aphids living on old plant tissue. Adult aphids gradually decline in weight, losing between 24% and 38% of their pre-reproductive biomass before death. The energy content of this loss subsidieses reproduction. Reproduction of aphids feeding in old galls or on mature leaves was negligible, but on younger tissues average fecundity was 31, there being little difference between aphids living on galled and ungalled tissue. There is no simple relationship between pre-reproductive adult embryo content and fecundity.The principal factor mediating honeydew production was aphid size and this factor overrides any variation caused by different feeding sites. Honeydew production averaged 0.43 mg during a life of 30 days. Aphids successfully completing their life cycle have a life-time energy consumption of 30.58 joules of which 18% is lost as heat during respiration (R), 30% is contained in honeydew (F+U), 1% is contained in exuviae (Pe). Larval growth accounts for 17% (Pg), and adult reproduction for 34% (Pr).The P/C ratio for M. euphorbiae is 53% and is broadly comparable with aphids living on herbaceous plants.

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Résumé Un puceron ne formant pas de galles, Macrosiphum euphorbiae, a été élevé dans des galles de Dysaphis devecta et Aphis pomi formées sur semis de pommiers. D'autres M. euphorbiae ont été élevés sur feuilles sans galles du même âge provenent de semis identiques, sur feuilles mûres et sur vieilles galles.Il y a une faible relation positive linéaire entre la teneur en lipides et le poids sec des adultes avant la reproduction, mais les pucerons élevés sur tissus végétaux jeunes avec ou sans galles contiennent 30% de lipides contre 11% pour ceux élevés sur tissus âgés. Le poids des pucerons adultes diminue progressivement, la perte avant la mort se situant entre 24 et 38% de la biomasse avant la reproduction. Le contenu énergétique de ces pertes alimente la reproduction. La reproduction de pucerons consommant les vieilles galles ou les feuilles mûres était négligeable, mais sur jeunes tissus la fécondité moyenne était de 31-avec peu de différences entre pucerons sur galles ou feuilles-. Il n'y a pas de corrélation simple entre le contenu en embryon des adultes avant la reproduction et la fécondité.Le principal paramètre conditionnant la production de miellat est la taille du puceron; ce paramètre surpasse toute variation provoquée par les divers lieux d'alimentation. La production moyenne de miellat est de 0,43-mg pendant une vie de 30 jours. Les pucerons accomplissant leur cycle avec succès utilisent pendant leur vie 30,58 joules, dont 18% sont dissipés sous forme de chaleur pendant la respiration (R); le contenu du miellat (F+U) correspond à 30%, et 1% est contenu dans l'exuvie (Pe). La croissance larvaire (Pg) utilise 17%, et l'activité reproductrice des adultes (Pr) 34% de l'énergie. Le rapport P/C-53% pour M. euphorbiae-est globalement comparable à celui des pucerons vivant sur plantes herbacées.