Theoretical conformational analysis of the opioid δ antagonist H-Tyr-Tic-Phe-OH and the μ agonist H-Tyr-D-Tic-Phe-NH2

A molecular mechanics study (grid search and energy minimization) of the highly δ receptor-selective δ opioid antagonist H-Tyr-Tic-Phe-OH (TIP; Tic: tetrahydroisoquinoline-3-car-boxylic acid) resulted in four low energy conformers with energies within 2 kcal/mol of that of the lowest energy structure. These four conformers contain trans peptide bonds only and represent compact structures showing various patterns of aromatic ring stacking. The centrally located Tic residue imposes several conformational constraints on the N-terminal dipeptide segment; however, the results of molecular dynamics simulations indicated that this tripeptide still shows some structural flexibility, particularly at the Phe³ residue. Analogous studies performed with the structurally related μ receptor-selective μ agonist H-Tyr-D -Tic-Phe-NH₂ resulted in low energy structures that were also compact but showed patterns of ring stacking different from those obtained with TIP. Superim-position of low energy conformers of TIP and H-Tyr-D -Tic-Phe-NH₂ revealed that the Phe³ residues of the L -Tic- and the D -Tic peptide were always located on opposite sides of the plane defined by the Tic residue, thus providing an explanation for the distinct activity profiles of the two compounds in structural terms. Attempts to demonstrate spatial overlap between the pharmacophoric moieties of low energy conformers of TIP and the nonpeptide δ antagonist naltrindole were made by superimposing either the Tyr¹ and Tic² aromatic rings and the N-terminal amino group or the Tyr¹ and Phe³ aromatic rings and the N-terminal amino group of the peptide with the corresponding aromatic rings and nitrogen atom in the alkaloid structure. In each case a low energy structure of TIP was found that showed good spatial overlap of all three specified pharmacophoric groups. These two conformers may represent candidate structures for the δ receptor-bound conformation of TIP. © 1994 John Wiley & Sons, Inc.     

Pharmacological and genetic activation of cAMP synthesis disrupts cholesterol utilization in Mycobacterium tuberculosis

There is a growing appreciation for the idea that bacterial utilization of host-derived lipids, including cholesterol, supports Mycobacterium tuberculosis (Mtb) pathogenesis. This has generated interest in identifying novel antibiotics that can disrupt cholesterol utilization by Mtb in vivo. Here we identify a novel small molecule agonist (V-59) of the Mtb adenylyl cyclase Rv1625c, which stimulates 3’, 5’-cyclic adenosine monophosphate (cAMP) synthesis and inhibits cholesterol utilization by Mtb. Similarly, using a complementary genetic approach that induces bacterial cAMP synthesis independent of Rv1625c, we demonstrate that inducing cAMP synthesis is sufficient to inhibit cholesterol utilization in Mtb. Although the physiological roles of individual adenylyl cyclase enzymes in Mtb are largely unknown, here we demonstrate that the transmembrane region of Rv1625c is required during cholesterol metabolism. Finally, the pharmacokinetic properties of Rv1625c agonists have been optimized, producing an orally-available Rv1625c agonist that impairs Mtb pathogenesis in infected mice. Collectively, this work demonstrates a role for Rv1625c and cAMP signaling in controlling cholesterol metabolism in Mtb and establishes that cAMP signaling can be pharmacologically manipulated for the development of new antibiotic strategies.     

Mechanistic Basis for Type 2 Long QT Syndrome Caused by KCNH2 Mutations that Disrupt Conserved Arginine Residues in the Voltage Sensor

KCNH2 encodes the Kv11.1 channel, which conducts the rapidly activating delayed rectifier K⁺ current (I _Kr) in the heart. KCNH2 mutations cause type 2 long QT syndrome (LQT2), which increases the risk for life-threatening ventricular arrhythmias. LQT2 mutations are predicted to prolong the cardiac action potential (AP) by reducing I _Kr during repolarization. Kv11.1 contains several conserved basic amino acids in the fourth transmembrane segment (S4) of the voltage sensor that are important for normal channel trafficking and gating. This study sought to determine the mechanism(s) by which LQT2 mutations at conserved arginine residues in S4 (R531Q, R531W or R534L) alter Kv11.1 function. Western blot analyses of HEK293 cells transiently expressing R531Q, R531W or R534L suggested that only R534L inhibited Kv11.1 trafficking. Voltage-clamping experiments showed that R531Q or R531W dramatically altered Kv11.1 current (I _Kv11.1) activation, inactivation, recovery from inactivation and deactivation. Coexpression of wild type (to mimic the patients’ genotypes) mostly corrected the changes in I _Kv11.1 activation and inactivation, but deactivation kinetics were still faster. Computational simulations using a human ventricular AP model showed that accelerating deactivation rates was sufficient to prolong the AP, but these effects were minimal compared to simply reducing I _Kr. These are the first data to demonstrate that coexpressing wild type can correct activation and inactivation dysfunction caused by mutations at a critical voltage-sensing residue in Kv11.1. We conclude that some Kv11.1 mutations might accelerate deactivation to cause LQT2 but that the ventricular AP duration is much more sensitive to mutations that decrease I _Kr. This likely explains why most LQT2 mutations are nonsense or trafficking-deficient.     

Thermal habitat use and growth in young-of-the-year Arctic charr from proximal fluvial and lacustrine populations in Labrador,Canada

Predicted increases in temperature associated with climate change are expected to have consequences for fish, in particular for Arctic charr, Salvelinus alpinus, a cold-adapted fish species. Despite differences in predicted hydroecological responses to climate change in fluvial and lacustrine environments, little is known of whether fluvial and lacustrine Arctic charr populations may respond differently to increasing temperatures. In order to compare growth and thermal habitat use between habitat types, otolith-inferred average water temperatures estimated from whole otoliths and fork lengths at capture were measured for young-of-the-year (YOY) Arctic charr obtained from two proximal fluvial and lacustrine sites in Labrador, Canada. Otolith-inferred average experienced water temperatures were not significantly correlated with air temperatures at both sites, suggestive of behavioural thermoregulation by YOY. The majority of Kogluktokoluk Brook (fluvial) YOY were found using water temperatures consistent with laboratory determined preferred temperatures for juvenile Arctic charr, whereas most Tom's Pond (lacustrine) YOY were found using temperatures ranging between preferred temperatures and optimal temperatures for growth. There was no consistent difference between mean water temperatures used between YOY from the two sites. Otolith-inferred average experienced water temperatures were only correlated to fork lengths in Tom's Pond YOY. The lack of correlation in Kogluktokoluk Brook YOY is argued to reflect resource partitioning occurring as a result of territoriality known to occur among stream salmonids. The limited range of temperatures used by fluvial YOY in this study, particularly the lack of cooler temperatures, also suggests that fluvial YOY may face barriers to thermal refugia, and as a result may be particularly vulnerable to climate change.     

Evolution of the Genetic Code by Incorporation of Amino Acids that Improved or Changed Protein Function

Fifty years have passed since the genetic code was deciphered, but how the genetic code came into being has not been satisfactorily addressed. It is now widely accepted that the earliest genetic code did not encode all 20 amino acids found in the universal genetic code as some amino acids have complex biosynthetic pathways and likely were not available from the environment. Therefore, the genetic code evolved as pathways for synthesis of new amino acids became available. One hypothesis proposes that early in the evolution of the genetic code four amino acids—valine, alanine, aspartic acid, and glycine—were coded by GNC codons (N = any base) with the remaining codons being nonsense codons. The other sixteen amino acids were subsequently added to the genetic code by changing nonsense codons into sense codons for these amino acids. Improvement in protein function is presumed to be the driving force behind the evolution of the code, but how improved function was achieved by adding amino acids has not been examined. Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used. The improved or altered protein function afforded by the changes in amino acid function provided the selective advantage underlying the expansion of the genetic code. Analysis of amino acid properties and functions explains why amino acids are found in their respective positions in the genetic code.     

Phylogeny,host association and biogeographical patterns in the diverse millipede‐parasitoid genus Myriophora Brown (Diptera: Phoridae)

Myriophora is the most species‐rich group of parasitoids that attack toxic, chemically defended millipedes in the superorder Juliformia and order Polydesmida—a resource that few insect predators and parasitoids are able to exploit. Worldwide, there are an estimated 200 species of Myriophora, with the majority of the diversity centred in the Neotropical region. The phylogeny of Myriophora is unknown, biogeographical patterns are not documented, and known host associations have not been assessed in a phylogenetic context. We provide the first phylogenetic study of the genus from a data set composed of 52 taxa primarily from the Neotropical region including 10 outgroups, 40 morphological characters, and molecular data from three mitochondrial (16S, COI and ND1) and one nuclear marker (AK). We find that Myriophora dispersed from the New World to the Old World in a single event before subsequently spreading to the Afrotropical region. The ancestral hosts reconstructed for Myriophora are the benzoquinone‐producing Juliformia, and this association has been retained in the Old World clade. In the Neotropical region, Myriophora that are associated with cyanide‐producing polydesmidan millipedes are confined to a single clade that shows remarkably little genetic variation between clearly morphologically diagnosable species.     

Cl− channels in basolateral renal medullary memnbranes: III. Determinants of single-channel activity

Summary We evaluated the effects of vawrying aqueous Cl^– concentrations, and of the arginyl- and lysyl-specific reagent phenylglyoxal (PGO), on the properties of Cl^– channels fused from basolaterally enriched renal medullary vesicles into planar lipid bilayers. The major channel properties studied were the anion selectivity sequence, anionic requirements for, channel activity. and the efects of varying Cl^– concentrations and/or PGO on the relation between holding voltageV _H -mV) and open-time probability (P _o).Reducingcis Cl^– concentrations, in the range 50–320mm, produced a linear reduction in fractional open time (P _v) with a half-maximal reduction inP _o atcis Cl^–170mM. Channel activity was sustained by equimolar replacement ofcis Cl^– with F^–, but not with impermeant isethionate. Fortrans solutions, the relation between Cl^– concentration andP ₀ at 10mm Cl^–. Reducingcis Cl^– had no effect on the gating charge (Z) for channel opening, but altered significantly the voltage-independent, energy (G) for channel opening.Phenylglyoxal (PGO) reducedZ and altered G for Cl^– channel activity when added tocis, but nottrans solutions, Furthermore, in the presence ofcis PGO, reducing thecis Cl^– concentration had no effect onZ but altered G. Thus we propose thatcis PGO and,cis Cl^– concentrations affect separate sites determining channel activity at the extracellular faces of, these Cl^– channels.     

New solution method for equations of reaction and mass transfer in biocatalyst particles

Summary For numerical solution of the reaction-mass transfer equations for immobilised biocatalysts it may be better to start integration at the particle surface and proceed inwards: calculations are targetted on the region to which practically interesting changes are often confined (because concentrations are effectively zero in the interior); and during iterative solution wrong initial estimates may be rejected after detecting anomalies early in the integration.Symbols C_b substrate concentration in bulk (mol m^–3) - c dimensionless substrate concentration (C/C_b) (-) - D_e effective diffusion coefficient (m²s^–1) - Da Damkohler number (V.r_o ²/D_e.K_s) (-) - K_s substrate concentration kinetic coefficient (mol m^–3) - k_e external mass transfer coefficient (ms^–1) - r_o bead radius (m) - Sh Sherwood number (k_e.r_o/D_e) (-) - V maximum rate per unit volume in beads (mol m^–3s^–1) - x dimensionless distance from bead centre (r/r_o) (-) - dimensionless kinetic coefficient (K_s/C_b) (-) - _o effectiveness factor (-)     

The structuring role of free-floating versus submerged plants in a subtropical shallow lake

In shallow temperate lakes many ecological processes depend on submerged macrophytes. In subtropical and tropical lakes, free-floating macrophytes may be equally or more important. We tested the hypothesis that different macrophyte growth forms would be linked with different bottom-up and top-down mechanisms in out-competing phytoplankton. We compared experimentally the effects of submerged and free-floating plants on water chemistry, phytoplankton biomass, zooplankton and fish community structure in a shallow hypertrophic lake (Lake Rodó, 34°55S 56°10W, Uruguay). Except for the retention of suspended solids, we found no other significant bottom-up process connected with either Eichhornia crassipes or Potamogeton pectinatus. Free-floating plants had a lower abundance of medium-sized zooplankton than any other microhabitat and submerged plants were apparently preferred by microcrustaceans. Fish showed a differential habitat use according to species, size-class and feeding habits. Dominant omnivore-planktivores, particularly the smallest size classes, preferred submerged plants. In contrast, omnivore-piscivores were significantly associated with free-floating plants. The density of omnivorous-planktivorous fish, by size class, significantly explained the distribution of medium-sized zooplankton, the high number of size 0 fish being the main factor. The abiotic environment and the structure of the zooplankton community explained little of the fish distribution pattern. Our results suggest that bottom-up effects of free-floating plants are weak when cover is low or intermediate. Top-down effects are complex, as effects on zooplankton and fish communities seem contradictory. The low piscivores:planktivores ratio in all microhabitats suggests, however, that cascading effects on phytoplankton through free-floating plant impacts on piscivorous fish are unlikely to be strong.