Substrate specificity and affinity of a protein modulated by bound water molecules

Water molecules influence molecular interactions in all biological systems, yet it is extremely difficult to understand their effects in precise atomic detail. Here we present evidence, based on highly refined atomic structures of the complexes of the L-arabinose-binding protein with L-arabinose, D-fucose and D-galactose, that bound water molecules, coupled with localized conformational changes, can govern substrate specificity and affinity. The atoms common to the three sugars are identically positioned in the binding site and the same nine strong hydrogen bonds are formed in all three complexes. Two hydrogen-bonded water molecules in the site contribute further to tight binding of L-arabinose but create an unfavourable interaction with the methyl group of D-fucose. Equally tight binding of D-galactose is attained by the replacement of one of the hydrogen-bonded water molecules by its--CH2OH group, coordinated with localized structural changes which include a shift and redirection of the hydrogen-bonding interactions of the other water molecule. These observations illustrate how ordered water molecules can contribute directly to the properties of proteins by influencing their interaction with ligands.     

A fusion protein required for vesicle-mediated transport in both mammalian cells and yeast

A protein sensitive to N-ethylmaleimide catalyses the fusion of transport vesicles with Golgi cisternae in a mammalian cell-free system. By cloning and sequencing its gene from Chinese hamster ovary cells and by use of in vitro assays, we show that this fusion protein is equivalent to the SEC18 gene product of the yeast Saccharomyces cerevisiae, known to be essential for vesicle-mediated transport from the endoplasmic reticulum to the Golgi apparatus. The mechanism of vesicular fusion is thus highly conserved, both between species and at different stages of transport.     

Variation in Lewsia kelloggii (Portulacaceae) with description of a new species endemic to Idaho

Lewisia kelloggii has been understood as a rare plant with a disjunct range in California and Idaho. Examination of herbarium specimens and analysis of isozymes in 6 Idaho and 7 California populations revealed consistent differences between plants of the 2 states. Fixed differences in alleles at 2 loci (AAT2 and PGI1) distinguished Idaho from California plants. Genetic identities based on isozymes between Idaho and California populations averaged 0.58, lower than the average for congeneric plant species. Idaho plants were smaller than most California plants, but California plants were variable. The most consistent morphological difference between Idaho and California specimens was the difference in the number of glands on the margins of bracts and sepals. Idaho plants had 0 (-5) pink glands on each margin of these organs, all on teeth near the tips. In California plants these organs had 12-25 glands on each margin, the distal ones elevated on teeth and the proximal ones sessile. We recognize the Idaho plants as a new species, L. sacajaweana , and retain the name L. kelloggii for the California populations.     

Attributes associated with probability of infestation by the pi?on ips, Ips confusus (Coleoptera: Scolytidae), in pi?on pine, Pinus edulis

We examined attributes of pi?on pine ( Pinus edulis ) associated with the probability of infestation by pi?on ips ( Ips confuses ) in an outbreak in the Coconino National Forest, Arizona. We used data collected from 87 plots, 59 infested and 28 uninfested, and a logistic regression approach to estimate the probability of infestation based on plot and tree-level attributes. Pi?on pine stand density index was a good predictor of the likelihood of infestation by pi?on ips at the plot level, and a cross-validation analysis confirmed that the model correctly classified 82% of the cases. Diameter at root collar and pi?on dwarf mistletoe infestation level were good predictors of individual tree infestation, and a cross-validation analysis indicated that the model correctly classified 72% of the cases. Results suggest that the occurrence of pi?on ips infestations may be related to stress factors associated with increased stocking and pi?on dwarf mistletoe infestations.     

Vegetation characteristics of mountainous northeastern Nevada sagebrush community types

Vegetation characteristics of 15 sagebrush community types identified on the Humboldt National Forest, northeastern Nevada, are described. A total of 218 plant species were found over the 372 relatively undisturbed rangeland communities sampled. The dominant plant families encountered were the Asteraceae (45 taxa), Poaceae (32 taxa), Scrophulariaceae (14 taxa), and the Fabaceae (12 taxa). Average annual dry weight production of the community types ranged from about 400 kg/ha/yr on types with Artemisia nova as the dominant sagebrush species to 1,200 kg/ha/yr on some A. tridentata ssp. vaseyana community types. A general increase in species richness and vegetation plus litter ground cover was observed within community types as the dominant sagebrush species changed from A. nova to A. arbuscula to A. longiloba to A. tridentata spp. tridentata to A. tridentata ssp. vaseyana . Major differences in plant species production and constancy exist between the sagebrush community types studied.     

The nuclear envelope: emerging roles in development and disease

The chromosomes of eukaryotic cells are separated from the cytoplasm by the nuclear envelope. The nuclear envelope includes two riveted membranes, plus embedded pore complexes that mediate nuclear import and export. In this sense, the nuclear envelope is truly a border zone. However, the envelope also links directly to chromosomes, and anchors two major infrastructures--the nuclear lamina and Tpr filaments--to the nuclear perimeter. Proteins of the nuclear envelope mediate a variety of fundamental activities, including DNA replication, gene expression and silencing, chromatin organization, cell division, apoptosis, sperm nuclear remodeling, the behavior of pronuclei, cell fate determination, nuclear migration and cell polarity. Furthermore, mutations in nuclear lamins and lamin-binding proteins cause tissue-specific inherited diseases. This special issue of Cell and Molecular Life Sciences is devoted to recent major advances in the characterization of nuclear envelope proteins and their roles. We offer here an overview of the topics covered in this issue of CMLS, and also discuss the emerging recognition that the nuclear envelope is an organelle critical for a wide range of genetic and developmental activity in multicellular organisms.     

Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas

To identify somatic mutations in pediatric diffuse intrinsic pontine glioma (DIPG), we performed whole-genome sequencing of DNA from seven DIPGs and matched germline tissue and targeted sequencing of an additional 43 DIPGs and 36 non-brainstem pediatric glioblastomas (non-BS-PGs). We found that 78% of DIPGs and 22% of non-BS-PGs contained a mutation in H3F3A, encoding histone H3.3, or in the related HIST1H3B, encoding histone H3.1, that caused a p.Lys27Met amino acid substitution in each protein. An additional 14% of non-BS-PGs had somatic mutations in H3F3A causing a p.Gly34Arg alteration.