Electrostatic screening in molecular dynamics simulations.

The screened Coulombic potential has been shown to describe satisfactorily equilibrium properties like pK shifts, the effects of charged groups on redox potentials and binding constants of metal ions. To test how well the screening of the electrostatic potential describes the dynamical trajectory of a macromolecular system, a series of comparative simulations have been carried out on a protein system which explicitly included water molecules and a system in vacuo. For the system without solvent the results of using (i) the standard potential form were compared with results of (ii) the potential where the Coulomb term was modified by the inclusion of a distance dependent dielectric, epsilon (r), to model the screening effect of bulk water, and (iii) standard potential modified by reducing the charge on ionized residue side chains. All molecular dynamics simulations have been carried out on bovine pancreatic trypsin inhibitor. Comparisons between the resulting trajectories, averaged structures, hydrogen bonding patterns and properties such as solvent accessible surface area and radius of gyration are described. The results show that the dynamical behaviour of the protein calculated with a screened electrostatic term compares more favourably with the time-dependent structural changes of the full system with explicitly included water than the standard vacuum simulation.     

Progress toward an explicit mechanistic model for the light-driven pump, bacteriorhodopsin

Recent crystallographic information about the structure of bacteriorhodopsin and some of its photointermediates, together with a large amount of spectroscopic and mutational data, suggest a mechanistic model for how this protein couples light energy to the translocation of protons across the membrane. Now nearing completion, this detailed molecular model will describe the nature of the steric and electrostatic conflicts at the photoisomerized retinal, as well as the means by which it induces proton transfers in the two half-channels leading to the two membrane surfaces, thereby causing unidirectional, uphill transport.     

Candidate molecular mechanisms for establishing cell identity in the developing retina

In the developing nervous system, individual neurons must occupy appropriate positions within circuits. This requires that these neurons recognize and form connections with specific pre- and postsynaptic partners. Cellular recognition is also required for the spacing of cell bodies and the arborization of dendrites, factors that determine the inputs onto a given neuron. These issues are particularly evident in the retina, where different types of neurons are evenly spaced relative to other cells of the same type. This establishes a reiterated columnar circuitry resembling the insect retina. Establishing these mosaic patterns requires that cells of a given type (homotypic cells) be able to sense their neighbors. Therefore, both synaptic specificity and mosaic spacing require cellular identifiers. In synaptic specificity, recognition often occurs between different types of cells in a pre- and postsynaptic pairing. In mosaic spacing, recognition is often occurring between different cells of the same type, orhomotypic self-recognition. Dendritic arborization can require recognition of different neurites of the same cell, or isoneuronal self-recognition. The retina is an extremely amenable system for studying the molecular identifiers that drive these various forms of recognition. The different neuronal types in the retina are well defined, and the genetic tools for marking cell types are increasingly available. In this review we will summarize retinal anatomy and describe cell types in the retina and how they are defined. We will then describe the requirements of a recognition code and discuss newly emerging candidate molecular mechanisms for recognition that may meet these requirements.     

A new electron microscopic technique for establishing the positions of genes: an analysis of the yeast ribosomal RNA coding region.

A new technique has been developed for distinguishing RNA/DNA or DNA/DNA duplex regions from single-stranded DNA in the electron microscope by thickness enhancement of the single-stranded DNA. This enhancement is achieved by reacting the single-stranded DNA with Escherichia coli DNA binding protein and monovalent antibody prepared from anti-E. coli DNA binding protein γ-globulin. A general application of this technique is the mapping of coding regions after hybridization with complementary RNA, which can vary in size from 100 to several thousand nucleotides. As an example, the coding sequences for the four yeast ribosomal RNAs were located in heteroduplex molecules constructed between DNA of a λ-yeast hybrid carrying a single rDNA repeat unit and DNA of λimm434.     

From Norway to Novartis: cyclosporin from Tolypocladium inflatum in an open access bioprospecting regime

The Convention on Biological Diversity (CBD) introduces a new regime of source countries' national sovereignty over genetic resources, in which benefit sharing is a central factor. This article shows how Tolypocladium inflatum was collected in Norway in 1969 within an open access regime implying that there is no benefit sharing with the source country from Novartis' present sales of the derived medicines based on cyclosporin. We estimate source country's loss of benefits in comparison with present norms and expectations concerning bioprospecting. Two percent annual royalties would have been a reasonable claim in this case, and in 1997 this amounted to US$ 24.3 million. Such benefits could, for instance, have been targeted to conservation, scientific capacity building and health care. The study provides an indication of possible gains for source countries – countries with developed as well as developing economies – in a case of the finding of a blockbuster drug. Institutional prerequisites for benefit sharing are discussed, and the emphasis, which often is placed on the role of patents as the cause of lack of source country benefits, is in this case found to be misleading.     

Understanding molecular mechanisms of proteolysis in Alzheimer's disease: Progress toward therapeutic interventions

Amyloid beta peptide (Aβ) is not only a major constituent of extracellular fibrillary pathologies in Alzheimer's disease (AD) brains, but is also physiologically produced and metabolized in neurons. This fact led us to the notion that an age-related decrease in Aβ catabolism may contribute to the molecular pathogenesis of AD, providing a rationale for seeking proteolytic enzymes that degrade Aβ in the brain. Our recent studies have demonstrated that neprilysin is the most potent Aβ-degrading enzyme in vivo. Deficiency of endogenous neprilysin elevates the level of Aβ in brains of neprilysin-knockout mice in a gene dose-dependent manner, and an age-associated decline of neprilysin occurs in several regions of mouse brain. Neuropathological alterations in these same regions have been implicated in cognitive impairments of AD patients at an early stage of the disease. Furthermore, the level of neprilysin mRNA has been found to be significantly and selectively reduced in the hippocampus and temporal cortex of AD patients. A clarification of the role played by decreased neprilysin activity in the pathogenesis of AD has opened up the possibility of neprilysin up-regulation as a novel preventive and therapeutic approach to AD. Since the expression level and activity of neprilysin are likely to be regulated by neuropeptides and their receptors, non-peptidic agonists for these receptors might be effective agents to maintain a sufficient level of Aβ catabolism in brains of the elderly.In addition to Aβ deposits, intraneuronal fibrillary lesions, such as neurofibrillary tangles, are also a pathological hallmark of AD, and the extent of the resultant cytoskeletal disruptions may be dependent upon the activity levels of proteolytic enzymes. Among proteases for which major cytoskeletal components are good substrates, calpains were shown to participate in excitotoxic stress-induced neuritic degeneration in our recent analysis using genetically engineered mice. Moreover, we have found that this pathology can be reduced by controlling the activity of an endogenous calpain inhibitor known as calpastatin, providing a possible approach for the treatment of diverse neurodegenerative disorders, including AD.     

Progress in establishing the rate-limiting features and kinetic mechanism of the glyceraldehyde-3-phosphate dehydrogenase reaction.

Primary hydrogen isotope effects and steady-state kinetics have been used to study the mechanism of glyceraldehyde-3-phosphate (GAP) dehydrogenase at pH 8.6. The isotope effect determined by using GAP-1d was unity and independent of arsenate (used as the acyl acceptor) and NAD+ concentrations when the aldehyde substrate was at saturating concentrations. At low GAP concentrations (apparent V/K conditions), the primary hydrogen isotope effect (H/D) was in the range of 1.40-1.52 and independent of arsenate and NAD+ concentrations. Apparent V/K for NAD+ was independent of GAP concentration, and apparent V/K for GAP was independent of NAD+ concentration. The dependence of apparent V/K for GAP on arsenate concentration was more complex but extrapolated to nonzero V/K at the zero-arsenate intercept. These observations are consistent with the general features of the Segal and Boyer (1953) mechanism for the reaction.     

Nucleotide sequence of the phoM region of Escherichia coli: four open reading frames may constitute an operon.

The phoM gene is one of the positive regulatory genes for the phosphate regulon of Escherichia coli. We analyzed the nucleotide sequence of a 4.7-kilobase chromosomal DNA segment that encompasses the phoM gene and its flanking regions. Four open reading frames (ORFs) were identified in the order ORF1-ORF2-ORF3 (phoM)-ORF4-dye clockwise on the standard E. coli genetic map. Since these ORFs are preceded by a putative promotor sequence upstream of ORF1 and followed by a putative terminator distal to ORF4, they seem to constitute an operon. The 157-amino-acid ORF1 protein contains highly hydrophobic amino acids in the amino-terminal portion, which is a characteristic of a signal peptide. The 229-amino-acid ORF2 protein is highly homologous to the PhoB protein, a positive regulatory protein for the phosphate regulon. The ORF3 (phoM gene) protein contains two stretches of highly hydrophobic residues in the amino-terminal and central regions and, therefore, may be a membrane protein. The 450-amino-acid ORF4 protein contains long hydrophobic regions and is likely to be a membrane protein.     

Cracking the molecular weight barrier: fragment screening of an aminotransferase using an NMR-based functional assay

NMR-based screening of protein targets has become a well established part of the drug discovery process especially with respect to fragments. However, as target size increases the two-dimensional spectra typically used for such screening become more crowded due to the increased number of signals, and the individual signals broaden due to the decreased rotational correlation time of the protein. Here we present an NMR-based functional assay for the branched-chain aminotransferase BCATc, a dimer with a total molecular weight of 88 kDa, which overcomes the limitations of the typical protein-based NMR screening method. BCATc is involved in glutamate production in the brain and is a therapeutic target for neuronal disorders involving a glutamatergic mechanism. Several fragments which inhibit BCATc were discovered using this assay and these may serve as novel cores for the development of potent BCATc inhibitors.     

Lateral diffusion of membrane-spanning and glycosylphosphatidylinositol-linked proteins: toward establishing rules governing the lateral mobility of membrane proteins.

In the plasma membrane of animal cells, many membrane-spanning proteins exhibit lower lateral mobilities than glycosylphosphatidylinositol (GPI)-linked proteins. To determine if the GPI linkage was a major determinant of the high lateral mobility of these proteins, we measured the lateral diffusion of chimeric membrane proteins composed of normally transmembrane proteins that were converted to GPI-linked proteins, or GPI-linked proteins that were converted to membrane-spanning proteins. These studies indicate that GPI linkage contributes only marginally (approximately twofold) to the higher mobility of several GPI-linked proteins. The major determinant of the high mobility of these proteins resides instead in the extracellular domain. We propose that lack of interaction of the extracellular domain of this protein class with other cell surface components allows diffusion that is constrained only by the diffusion of the membrane anchor. In contrast, cell surface interactions of the ectodomain of membrane-spanning proteins exemplified by the vesicular stomatitis virus G glycoprotein reduces their lateral diffusion coefficients by nearly 10-fold with respect to many GPI-linked proteins.     

Genetic and molecular mapping of the Hmt region of mouse.

We have mapped a new region of the mouse major histocompatibility complex (MHC) that contains the nuclear gene, Hmt, for the maternally transmitted antigen, Mta. The Hmt region of chromosome 17 lies between a recombinational breakpoint distal to Tla and another proximal to Tpx-1, thus including Pgk-2. A novel MHC class I gene fragment, R4B2, was cloned and mapped to this region as was another new class I gene, Thy19.4. Both lie proximal to Pgk-2, within the distal inversion in t-haplotypes. The presence of several other MHC class I genes in the Hmt region is predicted from analysis of the recombinants that define the region.     

Progress in the molecular cytogenetics of man

Recombinant DNA technology has contributed greatly to the precision of chromosome analysis in man. Breakpoints of chromosome deletions and rearrangements may be defined on a chromosome map whose landmarks are the loci of DNA sequences rather than Giemsa bands. Flow cytogenetics allows the extent of chromosome duplications and deletions to be measured more precisely than has hitherto been possible. DNA probes can reveal hidden translocations through the application of in situ hybridization, and may be used as markers to determine the parental origin of non-disjunction. It is evident that a study of the pathology of human chromosomes now requires the combined skills of recombinant DNA and cytology.     

Genetic and molecular analysis of the dpy-14 region in Caenorhabditis elegans.

Summary Essential genes have been identified in the 1.5 map unit (m.u.)dpy-14-unc-29 region of chromosome I inCaenorhabditis elegans. Previous work defined nine genes with visible mutant phenotypes and nine genes with lethal mutant phenotypes. In this study, we have identified an additional 28 essential genes with 97 lethal mutations. The mutations were mapped using eleven duplication breakpoints, eight deficiencies and three-factor recombination experiments. Genes required for the early stages of development were common, with 24 of the 37 essential genes having mutant phenotypes arresting at an early larval stage. Most mutants of a gene have the same time of arrest; only four of the 20 essential genes with multiple alleles have alleles with different phenotypes. From the analysis of complementing alleles oflet-389, alleles with the same time-of-arrest phenotype were classified as either hypomorphic or amorphic. Mutants oflet-605, let-534 andunc-37 have both uncoordinated and lethal phenotypes, suggesting that these genes are required for the coordination of movement and for viability. The physical and genetic maps in thedpy-14 region were linked by positioning two N2/BO polymorphisms with respect to duplications in the region, and by localizing the right breakpoint of the deficiencyhDf8 on the physical map. Using cross-species hybridization toC. briggsae, ten regions of homology have been identified, eight of which are known to be coding regions, based on Northern analysis and/or the isolation of cDNA clones.     

Phylogenetic investigation and divergence dating of Poa (Poaceae,tribe Poeae) in the Australasian region

The Australasian region contains a significant proportion of worldwide Poa diversity, but the evolutionary relationships of taxa from this region are incompletely understood. Most Australasian species have been placed in a monophyletic Poa subgenus, Poa supersection Homalopoa section Brizoides clade, but with limited resolution of relationships. In this study, phylogenetic relationships were reconstructed for Australasian Poa, using three plastid (rbcL and matK genes and the rpl32‐trnL intergenic spacer) and two nuclear [internal/external transcribed spacer (ITS/ETS)] markers. Seventy‐five Poa spp. were represented (including 42 Australian, nine New Guinean, nine New Zealand and three Australian/New Zealand species). Maximum parsimony, maximum likelihood and Bayesian inference criteria were applied for phylogenetic reconstruction. Divergence dates were estimated using Bayesian inference, with a relaxed clock applied and rates sampled from an uncorrelated log‐normal distribution. Australasian Poa spp. are placed in three lineages (section Brizoides, section Parodiochloa and the ‘X clade’), each of which is closely related to non‐Australasian taxa or clades. Section Brizoides subsection Australopoa is polyphyletic as currently circumscribed. In Australasia, Poa has diversified within the last 4.3 Mya, with divergence dating results broadly congruent with fossil data that record the appearance of vegetation with a prominent grassland understorey or shrubland/grassland mosaic vegetation dating from the mid‐Pliocene. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 523–552.     

The Netherlands Heart Tissue Bank: Strengthening the cardiovascular research infrastructure with an open access Cardiac Tissue Repository

AimCardiac diseases remain a leading cause of cardiovascular disease (CVD) related hospitalisation and mortality. That is why research to improve our understanding of pathophysiological processes underlying cardiac diseases is of great importance. There is a strong need for healthy and diseased human cardiac tissue and related clinical data to accomplish this, since currently used animal and in vitro disease models do not fully grasp the pathophysiological processes observed in humans. This design paper describes the initiative of the Netherlands Heart Tissue Bank (NHTB) that aims to boost CVD-related research by providing an open-access biobank.MethodsThe NHTB, founded in June 2020, is a non-profit biobank that collects and stores biomaterial (including but not limited to myocardial tissue and blood samples) and clinical data of individuals with and without previously known cardiac diseases. All individuals aged ≥ 18 years living in the Netherlands are eligible for inclusion as a potential future donor. The stored samples and clinical data will be available upon request for cardiovascular researchers.ConclusionTo improve the availability of cardiac tissue for cardiovascular research, the NHTB will include extensive (cardiac) biosamples, medical images, and clinical data of donors with and without a previously known cardiac disease. As such, the NHTB will function as a translational bridge to boost a wide range of cardiac disease-related fundamental and translational studies.