The complete set of genes encoding major intrinsic proteins in Arabidopsis provides a framework for a new nomenclature for major intrinsic proteins in plants

Major intrinsic proteins (MIPs) facilitate the passive transport of small polar molecules across membranes. MIPs constitute a very old family of proteins and different forms have been found in all kinds of living organisms, including bacteria, fungi, animals, and plants. In the genomic sequence of Arabidopsis, we have identified 35 different MIP-encoding genes. Based on sequence similarity, these 35 proteins are divided into four different subfamilies: plasma membrane intrinsic proteins, tonoplast intrinsic proteins, NOD26-like intrinsic proteins also called NOD26-like MIPs, and the recently discovered small basic intrinsic proteins. In Arabidopsis, there are 13 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, nine NOD26-like intrinsic proteins, and three small basic intrinsic proteins. The gene structure in general is conserved within each subfamily, although there is a tendency to lose introns. Based on phylogenetic comparisons of maize (Zea mays) and Arabidopsis MIPs (AtMIPs), it is argued that the general intron patterns in the subfamilies were formed before the split of monocotyledons and dicotyledons. Although the gene structure is unique for each subfamily, there is a common pattern in how transmembrane helices are encoded on the exons in three of the subfamilies. The nomenclature for plant MIPs varies widely between different species but also between subfamilies in the same species. Based on the phylogeny of all AtMIPs, a new and more consistent nomenclature is proposed. The complete set of AtMIPs, together with the new nomenclature, will facilitate the isolation, classification, and labeling of plant MIPs from other species.     

Redox-sensitive loops D and E regulate NADP(H) binding in domain III and domain I-domain III interactions in proton-translocating Escherichia coli transhydrogenase.

Membrane-bound transhydrogenases are conformationally driven proton-pumps which couple an inward proton translocation to the reversible reduction of NADP+ by NADH (forward reaction). This reaction is stimulated by an electrochemical proton gradient, Delta p, presumably through an increased release of NADPH. The enzymes have three domains: domain II spans the membrane, while domain I and III are hydrophilic and contain the binding sites for NAD(H) and NADP(H), respectively. Separately expressed domain I and III together catalyze a very slow forward reaction due to tightly bound NADP(H) in domain III. With the aim of examining the mechanistic role(s) of loop D and E in domain III and intact cysteine-free Escherichia coli transhydrogenase by cysteine mutagenesis, the conserved residues beta A398, beta S404, beta I406, beta G408, beta M409 and beta V411 in loop D, and residue beta Y431 in loop E were selected. In addition, the previously made mutants betaD392C and betaT393C in loop D, and beta G430C and beta A432C in loop E, were included. All loop D and E mutants, especially beta I406C and beta G430C, showed increased ratios between the rates of the forward and reverse reactions, thus approaching that of the wild-type enzyme. Determination of values indicated that the former increase was due to a strongly increased dissociation of NADPH caused by an altered conformation of loops D and E. In contrast, the cysteine-free G430C mutant of the intact enzyme showed the same inhibition of both forward and reverse rates. Most domain III mutants also showed a decreased affinity for domain I. The results support an important and regulatory role of loops D and E in the binding of NADP(H) as well as in the interaction between domain I and domain III.     

Measuring and modelling leaf diffusive conductance in juvenile silver birch, <Emphasis Type="Italic">Betula pendula</Emphasis>

Leaf diffusive conductance for water (g_l) and twig xylem pressure (_xt) was measured in juvenile silver birch, Betula pendula, under field conditions in southern Sweden. Data from one site were used to parameterise two different multiplicative models for g_l (dependent data), and measurements from another site were used to validate these models (independent data). In addition, experiments were performed in controlled environments to validate the g_l response functions used in the models. The driving variables in the D-model were photosynthetic photon flux density, air temperature and water vapour pressure deficit of the air (D_a), while the DH-model also included the accumulated hours after sunrise each day with D_a above a certain threshold (H). Both models satisfactorily predicted the variation in g_l in dependent as well as in independent data, and the g_l response functions used were supported by the experiments in controlled environments. The DH-model was more successful in predicting g_l than the D-model by accounting for the observation that g_l was lower at higher H under similar weather conditions. There was a considerable variation in maximum g_l during the season, as well as between the two sites. On relatively warm and dry days _xt rapidly declined during the morning and then stabilized around a constant value until the late afternoon, with the stomatal regulation effectively preventing _xt from decreasing below this value. We suggest that these models could be used to simulate the g_l in juvenile birch if maximum g_l is locally estimated and if the response functions are not extrapolated beyond the climate range for this study.     

SPR for molecular interaction analysis: a review of emerging application areas

PubMed searches identified four emerging application areas for surface plasmon resonance systems. Food analysis, proteomics, immunogenicity and drug discovery. These application areas are reviewed. In connection with the review of drug discovery applications a case study is presented. This study demonstrates the value of combining results from drug-target and ADME predictive assays for compound selection.     

Studies on gangliosides with affinity for Helicobacter pylori: binding to natural and chemically modified structures

Helicobacter pylori, like many other microbes, has the ability to bind to carbohydrate epitopes. Several sugar sequences have been reported as active for the bacterium, including some neutral, sulfated, and sialylated structures. We investigated structural requirements for the sialic acid-dependent binding using a number of natural and chemically modified gangliosides. We have chosen for derivatization studies two kinds of binding-active glycolipids, the simple ganglioside S-3PG (Neu5Ac alpha 3Gal beta 4GlcNAc beta 3Gal beta 4Glc beta 1Cer, sialylparagloboside) and branched polyglycosylceramides (PGCs) of human origin. The modifications included oxidation of the sialic acid glycerol chain, reduction of the carboxyl group, amidation of the carboxyl group, and lactonization. Binding experiments confirmed a preference of H. pylori for 3-linked sialic acid and penultimate 4-linked galactose. As expected, neolacto gangliosides (with Gal beta 4GlcNAc in the core structure) were active in our assays, whereas gangliosides with lacto (Gal beta 3GlcNAc) and ganglio (Gal beta 3GalNAc) carbohydrate chains were not. Negative binding results were also obtained for disialylparagloboside (with terminal NeuAc alpha 8NeuAc) and NeuAc alpha 6-containing glycolipids. Chemical studies revealed dependence of the binding on Neu5Ac and its glycerol and carboxyl side chains. Most of the derivatizations performed on these groups abolished the binding; however, some of the amide forms turned out to be active, and one of them (octadecylamide) was found to be an excellent binder. The combined data from molecular dynamics simulations indicate that the binding-active configuration of the terminal disaccharide of S-3PG is with the sialic acid in the anticlinal conformation, whereas in branched PGCs the same structural element most likely assumes the synclinal presentation.     

Physical activity, skeletal health and fractures in a long term perspective

Exercise during adolescence, especially during the pre-pubertal years, builds a skeleton with a high bone mineral density (BMD) and possibly a larger skeleton with a different skeletal architecture. This would lead to a stronger skeleton more resistant to trauma. These changes could be of biological significance for fracture reduction, if they were maintained into old age where fragility fractures exponentially rise. The Achilles heel of exercise is its cessation. Most BMD benefits achieved by exercise appear to be eroded with cessation of exercise. Reduced exercise intensity after a period of high activity, may maintain some residual BMD benefits into old age. A decreased fracture rate in the population could perhaps be achieved by promoting a physically active life style with lifelong high activity. But what happens if the activity in former athletes is reduced to the same level as in individuals who never exercised? The null hypothesis that exercise has no effect on fracture rates in old age cannot be rejected on the basis of any published, randomised, prospective data. Instead we have to rely on retrospective observational and case control studies, all hypothesis-generating, not hypothesis-testing. Existing data suggest that there could be a reduced fracture risk in former athletes. This notion may be correct, but consistently replicated sampling bias may produce the same observation and any biological explanation for this fracture reduction is unclear. Residual structural skeletal benefits, improved muscle strength, coordination and balance are all traits possibly maintained in former athletes after their active career. These traits may possibly reduce the number of fractures in later life.     

Towards in vivo aorta material identification and stress estimation

This paper addresses the problem of constructing a mechanical model for the abdominal aorta and calibrating its parameters to in vivo measurable data. The aorta is modeled as a pseudoelastic, thick-walled, orthotropic, residually stressed cylindrical tube, subjected to an internal pressure. The model parameters are determined by stating a minimization problem for the model pressure and computing the optimal solution by a minimization algorithm. The data used in this study is in vivo pressure–diameter data for the abdominal aorta of a 24-year-old man. The results show that the axial, circumferential and radial stresses have magnitudes in the span 0 to 180 kPa. Furthermore, the results show that it is possible to determine model parameters directly from in vivo measurable data. In particular, the parameters describing the residual stress distribution can be obtained without interventional procedures.