ALBERT

Notes: Abstract The lumens of the endoplasmic reticulum and Golgi apparatus are the subcellular sites where glycosylation, sulfation, and phosphorylation of secretory and membrane-bound proteins, proteoglycans, and lipids occur. Nucleotide sugars, nucleotide sulfate, and ATP are substrates for these reactions. ATP is also used as an energy source in the lumen of the endoplasmic reticulum during protein folding and degradation. The above nucleotide derivatives and ATP must first be translocated across the membrane of the endoplasmic reticulum and/or Golgi apparatus before they can serve as substrates in the above lumenal reactions. Translocation of the above solutes is mediated for highly specific transporters, which are antiporters with the corresponding nucleoside monophosphates as shown by biochemical and genetic approaches. Mutants in mammals, yeast, and protozoa showed that a defect in a specific translocator activity results in selective impairments of the above posttranslational modifications, including loss of virulence of pathogenic protozoa. Several of these transporters have been purified and cloned. Experiments with yeast and mammalian cells demonstrate that these transporters play a regulatory role in the above reactions. Future studies will address the structure of the above proteins, how they are targeted to different organelles, their potential as drug targets, their role during development, and the possible occurrence of specific diseases.

Notes: Abstract Ribonuclease P (RNase P) is the endoribonuclease that generates the mature 5'-ends of tRNA by removal of the 5'-leader elements of precursor-tRNAs. This enzyme has been characterized from representatives of all three domains of life (Archaea, Bacteria, and Eucarya) (1) as well as from mitochondria and chloroplasts. The cellular and mitochondrial RNase Ps are ribonucleoproteins, whereas the most extensively studied chloroplast RNase P (from spinach) is composed solely of protein. Remarkably, the RNA subunit of bacterial RNase P is catalytically active in vitro in the absence of the protein subunit (2). Although RNA-only activity has not been demonstrated for the archaeal, eucaryal, or mitochondrial RNAs, comparative sequence analysis has established that these RNAs are homologous (of common ancestry) to bacterial RNA. RNase P holoenzymes vary greatly in organizational complexity across the phylogenetic domains, primarily because of differences in the RNase P protein subunits: Mitochondrial, archaeal, and eucaryal holoenzymes contain larger, and perhaps more numerous, protein subunits than do the bacterial holoenzymes. However, that the nonbacterial RNase P RNAs retain significant structural similarity to their catalytically active bacterial counterparts indicates that the RNA remains the catalytic center of the enzyme.

Notes: Abstract In the vegetative (mitotic) cycle and during sexual conjugation, yeast cells display polarized growth, giving rise to a bud or to a mating projection, respectively. In both cases one can distinguish three steps in these processes: choice of a growth site, organization of the growth site, and actual growth and morphogenesis. In all three steps, small GTP-binding proteins (G proteins) and their regulators play essential signaling functions. For the choice of a bud site, Bud1, a small G protein, Bud2, a negative regulator of Bud1, and Bud5, an activator, are all required. If any of them is defective, the cell loses its ability to select a proper bud position and buds randomly. In the organization of the bud site or of the site in which a mating projection appears, Cdc42, its activator Cdc24, and its negative regulators play a fundamental role. In the absence of Cdc42 or Cdc24, the actin cytoskeleton does not become organized and budding does not take place. Finally, another small G protein, Rho1, is required for activity of beta(1 3)glucan synthase, the enzyme that catalyzes the synthesis of the major structural component of the yeast cell wall. In all of the above processes, G proteins can work as molecular switches because of their ability to shift between an active GTP-bound state and an inactive GDP-bound state.

Notes: Abstract Replication of the two template strands at eukaryotic cell DNA replication forks is a highly coordinated process that ensures accurate and efficient genome duplication. Biochemical studies, principally of plasmid DNAs containing the Simian Virus 40 origin of DNA replication, and yeast genetic studies have uncovered the fundamental mechanisms of replication fork progression. At least two different DNA polymerases, a single-stranded DNA-binding protein, a clamp-loading complex, and a polymerase clamp combine to replicate DNA. Okazaki fragment synthesis involves a DNA polymerase-switching mechanism, and maturation occurs by the recruitment of specific nucleases, a helicase, and a ligase. The process of DNA replication is also coupled to cell-cycle progression and to DNA repair to maintain genome integrity.

Notes: Abstract Synthetic oligonucleotide analogs have greatly aided our understanding of several biochemical processes. Efficient solid-phase and enzyme-assisted synthetic methods and the availability of modified base analogs have added to the utility of such oligonucleotides. In this review, we discuss the applications of synthetic oligonucleotides that contain backbone, base, and sugar modifications to investigate the mechanism and stereochemical aspects of biochemical reactions. We also discuss interference mapping of nucleic acid-protein interactions; spectroscopic analysis of biochemical reactions and nucleic acid structures; and nucleic acid cross-linking studies. The automation of oligonucleotide synthesis, the development of versatile phosphoramidite reagents, and efficient scale-up have expanded the application of modified oligonucleotides to diverse areas of fundamental and applied biological research. Numerous reports have covered oligonucleotides for which modifications have been made of the phosphodiester backbone, of the purine and pyrimidine heterocyclic bases, and of the sugar moiety; these modifications serve as structural and mechanistic probes. In this chapter, we review the range, scope, and practical utility of such chemically modified oligonucleotides. Because of space limitations, we discuss only those oligonucleotides that contain phosphate and phosphate analogs as internucleotidic linkages.

Notes: Abstract Molecular and genetic characterizations of circadian rhythms in Drosophila indicate that function of an intracellular pacemaker requires the activities of proteins encoded by three genes: period (per), timeless (tim), and doubletime (dbt). RNA from two of these genes, per and tim, is expressed with a circadian rhythm. Heterodimerization of PER and TIM proteins allows nuclear localization and suppression of further RNA synthesis by a PER/TIM complex. These protein interactions promote cyclical gene expression because heterodimers are observed only at high concentrations of, per and tim RNA, separating intervals of RNA accumulation from times of PER/TIM complex activity. Light resets these molecular cycles by eliminating TIM. The product of dbt also regulates accumulation of per and tim RNA, and it may influence action of the PER/TIM complex. The recent discovery of PER homologues in mice and humans suggests that a related mechanism controls mammalian circadian behavioral rhythms.

Notes: Abstract Interferons play key roles in mediating antiviral and antigrowth responses and in modulating immune response. The main signaling pathways are rapid and direct. They involve tyrosine phosphorylation and activation of signal transducers and activators of transcription factors by Janus tyrosine kinases at the cell membrane, followed by release of signal transducers and activators of transcription and their migration to the nucleus, where they induce the expression of the many gene products that determine the responses. Ancillary pathways are also activated by the interferons, but their effects on cell physiology are less clear. The Janus kinases and signal transducers and activators of transcription, and many of the interferon-induced proteins, play important alternative roles in cells, raising interesting questions as to how the responses to the interferons intersect with more general aspects of cellular physiology and how the specificity of cytokine responses is maintained.

Notes: Abstract Spacecraft in low earth orbit exhibit an unusual phenomenon: Surfaces facing the atmospheric wind produce a bright orange glow. This phenomenon was first noticed on the space shuttle but has since been verified as occurring on all spacecraft. The intensity of the glow depends on atmospheric density, on the angle between the velocity vector and the spacecraft surface, and on the temperature of the surface. This review summarizes the observations as well as the current explanation for the glow, namely its being due to NO*2 formed in surface-aided recombination between O and NO. Laboratory measurements and surface studies related to the phenomenon are briefly discussed.

Notes: Abstract Most experimental studies on the dynamics of protein folding have been confined to timescales of 1 ms and longer. Yet it is obvious that many phenomena that are obligatory elements of the folding process occur on much faster timescales. For example, it is also now clear that the formation of secondary and tertiary structures can occur on nanosecond and microsecond times, respectively. Although fast events are essential to, and sometimes dominate, the overall folding process, with a few exceptions their experimental study has become possible only recently with the development of appropriate techniques. This review discusses new approaches that are capable of initiating and monitoring the fast events in protein folding with temporal resolution down to picoseconds. The first important results from those techniques, which have been obtained for the folding of some globular proteins and polypeptide models, are also discussed.

Notes: Abstract The magnitudes, time scales, and underlying mechanisms responsible for broadening the electronic spectra of molecules in liquid solutions and glasses are reviewed. The emphasis is on experimental results from hole-burning, single-molecule, photon echo, and resonance Raman and fluorescence studies. The influence of the time scale of the measurement in distinguishing between homogeneous broadening (electronic dephasing) and inhomogeneous broadening is discussed, and the role of coupling of solvent phonons to the solute's electronic transition is stressed.

Notes: Abstract Proton-coupled electron transfer (PCET) is an important mechanism for charge transfer in a wide variety of systems including biology- and materials-oriented venues. We review several areas where the transfer of an electron and proton is tightly coupled and discuss model systems that can provide an experimental basis for a test of PCET theory. In a PCET reaction, the electron and proton may transfer consecutively (ET/PT) or concertedly (ETPT). The distinction between these processes is formulated, and rate-constant expressions for the two reaction channels are presented. Methods for the evaluation of these rate constants are discussed that are based on dielectric continuum theory. Electron donor hydrogen-bonded-interface electron acceptor systems displaying PCET reactivity are presented, and the rate-constant expressions corresponding to the ETPT and ET/PT channels for several model reaction complexes are evaluated.

Notes: Abstract Human immunodeficiency virus type 1 is a complex retrovirus encoding 15 distinct proteins. Substantial progress has been made toward understanding the function of each protein, and three-dimensional structures of many components, including portions of the RNA genome, have been determined. This review describes the function of each component in the context of the viral life cycle: the Gag and Env structural proteins MA (matrix), CA (capsid), NC (nucleocapsid), p6, SU (surface), and TM (transmembrane); the Pol enzymes PR (protease), RT (reverse transcriptase), and IN (integrase); the gene regulatory proteins Tat and Rev; and the accessory proteins Nef, Vif, Vpr, and Vpu. The review highlights recent biochemical and structural studies that help clarify the mechanisms of viral assembly, infection, and replication.

Notes: Abstract Mammalian AMP-activated protein kinase and yeast SNF1 protein kinase are the central components of kinase cascades that are highly conserved between animals, fungi, and plants. The AMP-activated protein kinase cascade acts as a metabolic sensor or "fuel gauge" that monitors cellular AMP and ATP levels because it is activated by increases in the AMP:ATP ratio. Once activated, the enzyme switches off ATP-consuming anabolic pathways and switches on ATP-producing catabolic pathways, such as fatty acid oxidation. The SNF1 complex in yeast is activated in response to the stress of glucose deprivation. In this case the intracellular signal or signals have not been identified; however, SNF1 activation is associated with depletion of ATP and elevation of AMP. The SNF1 complex acts primarily by inducing expression of genes required for catabolic pathways that generate glucose, probably by triggering phosphorylation of transcription factors. SNF1-related protein kinases in higher plants are likely to be involved in the response of plant cells to environmental and/or nutritional stress.

Notes: Abstract Ribonucleotide reductases provide the building blocks for DNA replication in all living cells. Three different classes of enzymes use protein free radicals to activate the substrate. Aerobic class I enzymes generate a tyrosyl radical with an iron-oxygen center and dioxygen, class II enzymes employ adenosylcobalamin, and the anaerobic class III enzymes generate a glycyl radical from S-adenosylmethionine and an iron-sulfur cluster. The X-ray structure of the class I Escherichia coli enzyme, including forms that bind substrate and allosteric effectors, confirms previous models of catalytic and allosteric mechanisms. This structure suggests considerable mobility of the protein during catalysis and, together with experiments involving site-directed mutants, suggests a mechanism for radical transfer from one subunit to the other. Despite large differences between the classes, common catalytic and allosteric mechanisms, as well as retention of critical residues in the protein sequence, suggest a similar tertiary structure and a common origin during evolution. One puzzling aspect is that some organisms contain the genes for several different reductases.

Notes: Abstract Base flipping is the phenomenon whereby a base in normal B-DNA is swung completely out of the helix into an extrahelical position. It was discovered in 1994 when the first co-crystal structure was reported for a cytosine-5 DNA methyltransferase binding to DNA. Since then it has been shown to occur in many systems where enzymes need access to a DNA base to perform chemistry on it. Many DNA glycosylases that remove abnormal bases from DNA use this mechanism. This review describes systems known to use base flipping as well as many systems where it is likely to occur but has not yet been rigorously demonstrated. The mechanism and evolution of base flipping are also discussed.

Notes: Abstract Active transport between the nucleus and cytoplasm involves primarily three classes of macromolecules: substrates, adaptors, and receptors. Some transport substrates bind directly to an import or an export receptor while others require one or more adaptors to mediate formation of a receptor-substrate complex. Once assembled, these transport complexes are transferred in one direction across the nuclear envelope through aqueous channels that are part of the nuclear pore complexes (NPCs). Dissociation of the transport complex must then take place, and both adaptors and receptors must be recycled through the NPC to allow another round of transport to occur. Directionality of either import or export therefore depends on association between a substrate and its receptor on one side of the nuclear envelope and dissociation on the other. The Ran GTPase is critical in generating this asymmetry. Regulation of nucleocytoplasmic transport generally involves specific inhibition of the formation of a transport complex; however, more global forms of regulation also occur.

Notes: Abstract Phosphatidylinositol, a component of eukaryotic cell membranes, is unique among phospholipids in that its head group can be phosphorylated at multiple free hydroxyls. Several phosphorylated derivatives of phosphatidylinositol, collectively termed phosphoinositides, have been identified in eukaryotic cells from yeast to mammals. Phosphoinositides are involved in the regulation of diverse cellular processes, including proliferation, survival, cytoskeletal organization, vesicle trafficking, glucose transport, and platelet function. The enzymes that phosphorylate phosphatidylinositol and its derivatives are termed phosphoinositide kinases. Recent advances have challenged previous hypotheses about the substrate selectivity of different phosphoinositide kinase families. Here we re-examine the pathways of phosphoinositide synthesis and the enzymes involved.

Notes: Abstract G protein-coupled receptor kinases (GRKs) constitute a family of six mammalian serine/threonine protein kinases that phosphorylate agonist-bound, or activated, G protein-coupled receptors (GPCRs) as their primary substrates. GRK-mediated receptor phosphorylation rapidly initiates profound impairment of receptor signaling, or desensitization. This review focuses on the regulation of GRK activity by a variety of allosteric and other factors: agonist-stimulated GPCRs, betagamma subunits of heterotrimeric GTP-binding proteins, phospholipid cofactors, the calcium-binding proteins calmodulin and recoverin, posttranslational isoprenylation and palmitoylation, autophosphorylation, and protein kinase C-mediated GRK phosphorylation. Studies employing recombinant, purified proteins, cell culture, and transgenic animal models attest to the general importance of GRKs in regulating a vast array of GPCRs both in vitro and in vivo.

Notes: Abstract The proteoglycan superfamily now contains more than 30 full-time molecules that fulfill a variety of biological functions. Proteoglycans act as tissue organizers, influence cell growth and the maturation of specialized tissues, play a role as biological filters and modulate growth-factor activities, regulate collagen fibrillogenesis and skin tensile strength, affect tumor cell growth and invasion, and influence corneal transparency and neurite outgrowth. Additional roles, derived from studies of mutant animals, indicate that certain proteoglycans are essential to life whereas others might be redundant. The review focuses on the most recent genetic and molecular biological studies of the matrix proteoglycans, broadly defined as proteoglycans secreted into the pericellular matrix. Special emphasis is placed on the molecular organization of the protein core, the utilization of protein modules, the gene structure and transcriptional control, and the functional roles of the various proteoglycans. When possible, proteoglycans have been grouped into distinct gene families and subfamilies offering a simplified nomenclature based on their protein core design. The structure-function relationship of some paradigmatic proteoglycans is discussed in depth and novel aspects of their biology are examined.

Notes: Abstract While many aspects of prion disease biology are unorthodox, perhaps the most fundamental paradox is posed by the coexistence of inherited, sporadic, and infectious forms of these diseases. Sensible molecular mechanisms for prion propagation must explain all three forms of prion diseases in a manner that is compatible with the formidable array of experimental data derived from histopathological, biochemical, biophysical, human genetic, and transgenetic studies. In this review, we explore prion disease pathogenesis initially from the perspective of an autosomal dominant inherited disease. Subsequently, we examine how an intrinsically inherited disease could present in sporadic and infectious forms. Finally, we explore the phenomenologic constraints on models of prion replication with a specific emphasis on biophysical studies of prion protein structures.

Notes: Abstract Many roles for sphingolipids have been identified in mammals. Available data suggest that sphingolipids and their intermediates also have diverse roles in Saccharomyces cerevisiae. These roles include signal transduction during the heat stress response, regulation of calcium homeostasis or components in calcium-mediated signaling pathways, regulation of the cell cycle, and functions as components in trafficking of secretory vesicles from the endoplasmic reticulum to the Golgi apparatus and as the lipid moiety in many glycosylphosphatidylinositol-anchored proteins. S. cerevisiae is likely to be the first organism in which all genes involved in sphingolipid metabolism are identified. This information will provide an unprecedented opportunity to determine, for the first time in any organism, how sphingolipid synthesis is regulated. Through the use of both genetic and biochemical techniques, the identification of the complete array of processes regulated by sphingolipid signals is likely to be possible, as is the quantification of the physiological contribution of each.

Notes: Abstract The cell biology of caveolae is a rapidly growing area of biomedical research. Caveolae are known primarily for their ability to transport molecules across endothelial cells, but modern cellular techniques have dramatically extended our view of caveolae. They form a unique endocytic and exocytic compartment at the surface of most cells and are capable of importing molecules and delivering them to specific locations within the cell, exporting molecules to extracellular space, and compartmentalizing a variety of signaling activities. They are not simply an endocytic device with a peculiar membrane shape but constitute an entire membrane system with multiple functions essential for the cell. Specific diseases attack this system: Pathogens have been identified that use it as a means of gaining entrance to the cell. Trying to understand the full range of functions of caveolae challenges our basic instincts about the cell.

Notes: Abstract Cytoplasmic RNA localization is an evolutionarily ancient mechanism for producing cellular asymmetries. This review considers RNA localization in the context of animal development. Both mRNAs and non-protein-coding RNAs are localized in Drosophila, Xenopus, ascidian, zebrafish, and echinoderm oocytes and embryos, as well as in a variety of developing and differentiated polarized cells from yeast to mammals. Mechanisms used to transport and anchor RNAs in the cytoplasm include vectorial transport out of the nucleus, directed cytoplasmic transport in association with the cytoskeleton, and local entrapment at particular cytoplasmic sites. The majority of localized RNAs are targeted to particular cytoplasmic regions by cis-acting RNA elements; in mRNAs these are almost always in the 3'-untranslated region (UTR). A variety of trans-acting factors-many of them RNA-binding proteins-function in localization. Developmental functions of RNA localization have been defined in Xenopus, Drosophila, and Saccharomyces cerevisiae. In Drosophila, localized RNAs program the antero-posterior and dorso-ventral axes of the oocyte and embryo. In Xenopus, localized RNAs may function in mesoderm induction as well as in dorso-ventral axis specification. Localized RNAs also program asymmetric cell fates during Drosophila neurogenesis and yeast budding.

Notes: Abstract In just three years, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability to generate a highly visible, efficiently emitting internal fluorophore is both intrinsically fascinating and tremendously valuable. High-resolution crystal structures of GFP offer unprecedented opportunities to understand and manipulate the relation between protein structure and spectroscopic function. GFP has become well established as a marker of gene expression and protein targeting in intact cells and organisms. Mutagenesis and engineering of GFP into chimeric proteins are opening new vistas in physiological indicators, biosensors, and photochemical memories.

Notes: Abstract The transforming growth factor beta (TGF-beta) family of growth factors control the development and homeostasis of most tissues in metazoan organisms. Work over the past few years has led to the elucidation of a TGF-beta signal transduction network. This network involves receptor serine/threonine kinases at the cell surface and their substrates, the SMAD proteins, which move into the nucleus, where they activate target gene transcription in association with DNA-binding partners. Distinct repertoires of receptors, SMAD proteins, and DNA-binding partners seemingly underlie, in a cell-specific manner, the multifunctional nature of TGF-beta and related factors. Mutations in these pathways are the cause of various forms of human cancer and developmental disorders.

Notes: Abstract The selective degradation of many short-lived proteins in eukaryotic cells is carried out by the ubiquitin system. In this pathway, proteins are targeted for degradation by covalent ligation to ubiquitin, a highly conserved small protein. Ubiquitin-mediated degradation of regulatory proteins plays important roles in the control of numerous processes, including cell-cycle progression, signal transduction, transcriptional regulation, receptor down-regulation, and endocytosis. The ubiquitin system has been implicated in the immune response, development, and programmed cell death. Abnormalities in ubiquitin-mediated processes have been shown to cause pathological conditions, including malignant transformation. In this review we discuss recent information on functions and mechanisms of the ubiquitin system. Since the selectivity of protein degradation is determined mainly at the stage of ligation to ubiquitin, special attention is focused on what we know, and would like to know, about the mode of action of ubiquitin-protein ligation systems and about signals in proteins recognized by these systems.

Notes: Abstract Recent structural and biochemical investigations have come together to allow a better understanding of the mechanism of chaperonin (GroEL, Hsp60)-mediated protein folding, the final step in the accurate expression of genetic information. Major, asymmetric conformational changes in the GroEL double toroid accompany binding of ATP and the cochaperonin GroES. When a nonnative polypeptide, bound to one of the GroEL rings, is encapsulated by GroES to form a cis ternary complex, these changes drive the polypeptide into the sequestered cavity and initiate its folding. ATP hydrolysis in the cis ring primes release of the products, and ATP binding in the trans ring then disrupts the cis complex. This process allows the polypeptide to achieve its final native state, if folding was completed, or to recycle to another chaperonin molecule, if the folding process did not result in a form committed to the native state.

Notes: Abstract Von Willebrand factor (VWF) is a blood glycoprotein that is required for normal hemostasis, and deficiency of VWF, or von Willebrand disease (VWD), is the most common inherited bleeding disorder. VWF mediates the adhesion of platelets to sites of vascular damage by binding to specific platelet membrane glycoproteins and to constituents of exposed connective tissue. These activities appear to be regulated by allosteric mechanisms and possibly by hydrodynamic shear forces. VWF also is a carrier protein for blood clotting factor VIII, and this interaction is required for normal factor VIII survival in the circulation. VWF is assembled from identical =250 kDa subunits into disulfide-linked multimers that may be 〉20,000 kDa. Mutations in VWD can disrupt this complex biosynthetic process at several steps to impair the assembly, intracellular targeting, or secretion of VWF multimers. Other VWD mutations impair the survival of VWF in plasma or the function of specific ligand binding sites. This growing body of information about VWF synthesis, structure, and function has allowed the reclassification of VWD based upon distinct pathophysiologic mechanisms that appear to correlate with clincial symptoms and the response to therapy.

Notes: Abstract The nucleosome, which is the primary building block of chromatin, is not a static structure: It can adopt alternative conformations. Changes in solution conditions or changes in histone acetylation state cause nucleosomes and nucleosomal arrays to behave with altered biophysical properties. Distinct subpopulations of nucleosomes isolated from cells have chromatographic properties and nuclease sensitivity different from those of bulk nucleosomes. Recently, proteins that were initially identified as necessary for transcriptional regulation have been shown to alter nucleosomal structure. These proteins are found in three types of multiprotein complexes that can acetylate nucleosomes, deacetylate nucleosomes, or alter nucleosome structure in an ATP-dependent manner. The direct modification of nucleosome structure by these complexes is likely to play a central role in appropriate regulation of eukaryotic genes.

Notes: Abstract All chemical transformations pass through an unstable structure called the transition state, which is poised between the chemical structures of the substrates and products. The transition states for chemical reactions are proposed to have lifetimes near 10-13 sec, the time for a single bond vibration. No physical or spectroscopic method is available to directly observe the structure of the transition state for enzymatic reactions. Yet transition state structure is central to understanding catalysis, because enzymes function by lowering activation energy. An accepted view of enzymatic catalysis is tight binding to the unstable transition state structure. Transition state mimics bind tightly to enzymes by capturing a fraction of the binding energy for the transition state species. The identification of numerous transition state inhibitors supports the transition state stabilization hypothesis for enzymatic catalysis. Advances in methods for measuring and interpreting kinetic isotope effects and advances in computational chemistry have provided an experimental route to understand transition state structure. Systematic analysis of intrinsic kinetic isotope effects provides geometric and electronic structure for enzyme-bound transition states. This information has been used to compare transition states for chemical and enzymatic reactions; determine whether enzymatic activators alter transition state structure; design transition state inhibitors; and provide the basis for predicting the affinity of enzymatic inhibitors. Enzymatic transition states provide an understanding of catalysis and permit the design of transition state inhibitors. This article reviews transition state theory for enzymatic reactions. Selected examples of enzymatic transition states are compared to the respective transition state inhibitors.

Notes: Abstract To predict the branching between energetically allowed product channels, chemists often rely on statistical transition state theories or exact quantum scattering calculations on a single adiabatic potential energy surface. The potential energy surface gives the energetic barriers to each chemical reaction and allows prediction of the reaction rates. Yet, chemical reactions evolve on a single potential energy surface only if, in simple terms, the electronic wavefunction can evolve from the reactant electronic configuration to the product electronic configuration on a time scale that is fast compared to the nuclear dynamics through the transition state. The experiments reviewed here investigate how the breakdown of the Born-Oppenheimer approximation at a barrier along an adiabatic reaction coordinate can alter the dynamics of and the expected branching between molecular dissociation pathways. The work reviewed focuses on three questions that have come to the forefront with recent theory and experiments: Which classes of chemical reactions evidence dramatic nonadiabatic behavior that influences the branching between energetically allowed reaction pathways? How do the intramolecular distance and orientation between the electronic orbitals involved influence the nonadiabaticity in the reaction? How can the detailed nuclear dynamics mediate the effective nonadiabatic coupling encountered in a chemical reaction?

Notes: Abstract The application of in vitro model systems to evaluate the toxicity of xenobiotics has significantly enhanced our understanding of drug- and chemical-induced target toxicity. From a scientific perspective, there are several reasons for the popularity of in vitro model systems. From the public perspective, in vitro model systems enjoy increasing popularity because their application may allow a reduction in the number of live animals employed in toxicity testing. In this review, we present an overview of the use of in vitro model systems to investigate target organ toxicity of drugs and chemicals, and provide selective examples of these model systems to better understand cutaneous and ocular toxicity and the role of drug metabolism in the hepatotoxicity of selected agents. We conclude by examining the value and use of in vitro model systems in industrial development of new pharmaceutical agents.

Notes: Abstract This paper reviews investigations of homogeneous nucleation in phase transitions in large molecular clusters. The principal techniques brought to bear are electron diffraction analyses of transformations in clusters formed by condensation of vapor in supersonic expansions and computer simulations of spontaneous phase changes in clusters. Results obtained to date are contrasted with those of larger systems and interpreted in terms of nucleation theory. The review also refers to some unresolved aspects of nucleation theory.

Notes: Abstract The detection of explosives, energetic materials, and their associated compounds for security screening, demining, detection of unexploded ordnance, and pollution monitoring is an active area of research. A wide variety of detection methods and an even wider range of physical chemistry issues are involved in this very challenging area. This review focuses on techniques such as optical and mass spectrometry and chromatography for detection of trace amounts of explosives with short response times. We also review techniques for detecting the decomposition fragments of these materials. Molecular data for explosive compounds are reviewed where available.

Notes: Abstract A critical review is presented of results obtained with different computational methods (mainly ab initio) on C60, C70, and specific fullerene derivatives, also in comparison with experimental data. From the discussion of diverse systems, the (often underestimated) complexity of their physical and chemical behavior emerges, and hence the importance of an accurate description and the need for a careful inspection of the experimental data, with which comparison is often intrinsically difficult. The ambition of this review is to help establish a basis not only for a nonsuperficial reading of the existing literature, but also for a constructive approach with computations to the challenge posed by recent promising applications of fullerenes in nanotechnology, optoelectronics, and biology.

Notes: Abstract The multiconfiguration self-consistent field (MCSCF) method offers the most general approach to the computation of chemical reactions and multiple electronic states. This review discusses the design of MCSCF wavefunctions for treating these problems and the interpretation of the resulting orbitals and configurations. In particular, localized orbitals are convenient both for selection of the appropriate active space and for understanding the computed results. The computational procedures for optimizing these wavefunctions and the techniques for recovery of dynamical correlation energy are reviewed.

Notes: Abstract Recent developments in optical studies of single molecules at room temperature are reviewed, with an emphasis on the underlying principles and the potential of single-molecule experiments. Examples of single-molecule studies are given, including photophysics and photochemistry pertinent to single-molecule measurements, spectral fluctuations, Raman spectroscopy, diffusional motions, conformational dynamics, fluorescence resonant energy transfer, exciton dynamics, and enzymatic turnovers. These studies illustrate the information obtainable with the single-molecule approach that is hidden in ensemble-averaged measurements.

Notes: Abstract The imaging and control of self-assembled, physisorbed monolayers have been the subject of numerous scanning tunneling microscopy and atomic force microscopy investigations. The successful interpretation of the structures observed in scanning probe images of molecules self-assembled at liquid-solid and gas-solid interfaces has benefited greatly from recent experimental and theoretical work. These studies are converging on a general tunneling mechanism that accounts for the images of weakly bound, insulating adsorbates. Experiments in which the dynamical behavior of these monolayers has been monitored as a function of time both statically and after the introduction of an external perturbation are described, and novel studies of the selective control of monolayer structure that make use of internal and external electric fields, photons, and solvent coadsorption are reviewed.

Notes: The major research accomplishments of the author are described from the time of his PhD thesis work on the mechanism of cobalt polycythemia to the present day. His early work on the quest for the cell that produces erythropoietin (Epo) to his current work on oxygen sensing and signal transduction pathways involved in erythropoietin gene expression are reported. He describes his main research interest in the mechanism of cobalt polycythemia between 1954 and 1962 and his research on how hormones such as the glucocorticoids function in the regulation of erythropoiesis (1956-1962). His major findings during this period were the discovery that hydrocortisone and corticosterone stimulated erythropoiesis (1958) and that cobalt increased erythropoietin production in the isolated perfused dog kidney (1961). He describes how he was led astray in some of his early studies on the cells in the kidney that produce erythropoietin, because of the less-developed technology available to him at that time; and how in situ hybridization and other molecular biology techniques enabled him to confirm some of the earlier work in mice by other investigators that interstitial cells in the kidney were the site of production of erythropoietin in the primate. His work in the controversial area of the mechanism of the anemia of end-stage renal disease is described in detail, as it pertains to Epo deficiency and suppressed erythroid progenitor cell response to Epo. He also discusses his recent work on signal transduction pathways (hypoxia, nitric oxide, adenosine, and C kinase) in oxygen sensing and Epo gene expression.

Notes: Abstract Progressive deficits in the growth hormone (GH)/insulin-like growth factor I axis may contribute to the acquired biochemical, body composition, and functional changes of normal human aging, but they do not offer a sole, or even a major explanation for these changes. The concept that GH "replacement" would materially benefit the daily function of older men and women finds little support in the results of the controlled clinical trials that have been reported. GH, either as monotherapy or in combination with antiresorptive medication, does not offer a clinically useful improvement in bone mass, and it is difficult to find a rationale for its use in the treatment of osteoporosis. GH may yet prove to be a useful agent for older men and women in the management of other clinical syndromes, such as visceral obesity, but conclusions in this area await compelling evidence. For the time being, potential benefits of GH in older men and women must be viewed with skepticism, and use of this agent outside the context of a clinical trial is not justified.

Notes: Abstract Development of breast cancer in women is dependent on diverse factors, including genetic predisposition, exposure to both exogenous and endogenous chemicals, which can modulate initiation, promotion and progression of this disease, and the timing of exposure to these agents. Several compounds-including 16alpha-hydroxyestrone (16alpha-OHE1), catecholestrogens, and aromatic amines-have been proposed as initiators of mammary carcinogenesis in humans; however, their role as genotoxins is unconfirmed. Lifetime exposure to estrogens has been established as an important risk factor for breast cancer, and it has been suggested that xenoestrogens may directly add to the hormonal risk or indirectly increase risk by decreasing 2-hydroxyestrone (2-OHE1)/16alpha-OHE1 metabolite ratios. Results of recent studies suggest that chemical-induced modulation of 2-OHE1/16alpha-OHE1 metabolite ratios is not predictive of xenoestrogens or mammary carcinogens. Moreover, based on current known dietary intakes of natural and xenoestrogenic/antiestrogenic chemicals, it is unlikely that xenoestrogens contribute significantly to a woman's overall lifetime exposure to estrogens. More information is required on the identities and serum levels of both natural and xenoendocrine active compounds, their concentrations in serum, and the mammary gland and levels of these compounds at critical periods of exposure.

Notes: Abstract Mounting evidence suggests that cognitive dysfunction developing as a result of HIV-1 infection is mediated at least in part by generation of excitotoxins and free radicals in the brain. This syndrome is currently designated HIV-1-associated cognitive/motor complex, was originally termed the AIDS Dementia Complex, and for simplicity, is called AIDS dementia in this review. Recently, brains of patients with AIDS have been shown to manifest neuronal injury and apoptotic-like cell death. How can HIV-1 result in neuronal damage if neurons themselves are only rarely, if ever, infected by the virus? Experiments from several different laboratories have lent support to the existence of HIV- and immune-related toxins in a variety of in vitro and in vivo paradigms. In one recently defined pathway to neuronal injury, HIV-infected macrophages and microglia, or immune-activated macrophages and astrocytes (activated by the shed HIV-1 envelope protein, gp120, or other viral proteins and cytokines), appear to secrete excitants and neurotoxins. These substances may include arachidonic acid, platelet-activating factor, free radicals (NO. and O2.-), glutamate, quinolinate, cysteine, amines, and as yet unidentified factors emanating from stimulated macrophages and reactive astrocytes. A final common pathway for neuronal susceptibility is operative, similar to that observed in stroke and several neurodegenerative diseases. This mechanism involves excessive activation of N-methyl-d-aspartate (NMDA) receptor-operated channels, with resultant excessive influx of Ca2+ and the generation of free radicals, leading to neuronal damage. With the very recent development of clinically tolerated NMDA antagonists, there is hope for future pharmacological intervention.

Notes: Abstract Polyphenolic-glutathione (GSH) conjugates and their metabolites retain the electrophilic and redox properties of the parent polyphenol. Indeed, the reactivity of the thioether metabolites frequently exceeds that of the parent polyphenol. Although the active transport of polyphenolic-GSH conjugates out of the cell in which they are formed will limit their potential toxicity to those cells, once within the circulation they can be transported to tissues that are capable of accumulating these metabolites. There are interesting physiological similarities between the organs that are known to be susceptible to polyphenolic-GSH conjugate-mediated toxicity. In addition, the frequent localization of gamma-glutamyl transpeptidase to cells separating the circulation from a second fluid-filled compartment coincides with tissues that are susceptible either to polyphenolic-GSH conjugate-induced toxicity or to quinone and reactive oxygen species-induced toxicity. Polyphenolic-GSH conjugates therefore contribute to the nephrotoxicity, nephrocarcinogenicity, and neurotoxicity of a variety of polyphenols.

Notes: Abstract Adrenergic receptors are key targets within the autonomic nervous system, regulating a wide variety of physiological processes. The ability to modify adrenergic receptor expression patterns in vivo has added a powerful new tool to the functional analysis of these receptors. Modification of adrenergic receptor gene expression by overexpression, genetic ablation, or site-specific mutation has added new insight to models of receptor coupling behavior, pharmacology, and subtype-specific physiological function. This review highlights some of the recent advances resulting from such genetic approaches to the study of adrenergic receptors.

Notes: Abstract Multiple carboxylesterases (EC 3.1.1.1) play an important role in the hydrolytic biotransformation of a vast number of structurally diverse drugs. These enzymes are major determinants of the pharmacokinetic behavior of most therapeutic agents containing ester or amide bonds. Carboxylesterase activity can be influenced by interactions of a variety of compounds either directly or at the level of enzyme regulation. Since a significant number of drugs are metabolized by carboxylesterase, altering the activity of this enzyme class has important clinical implications. Drug elimination decreases and the incidence of drug-drug interactions increases when two or more drugs compete for hydrolysis by the same carboxylesterase isozyme. Exposure to environmental pollutants or to lipophilic drugs can result in induction of carboxylesterase activity. Therefore, the use of drugs known to increase the microsomal expression of a particular carboxylesterase, and thus to increase associated drug hydrolysis capacity in humans, requires caution. Mammalian carboxylesterases represent a multigene family, the products of which are localized in the endoplasmic reticulum of many tissues. A comparison of the nucleotide and amino acid sequence of the mammalian carboxylesterases shows that all forms expressed in the rat can be assigned to one of three gene subfamilies with structural identities of more than 70% within each subfamily. Considerable confusion exists in the scientific community in regards to a systematic nomenclature and classification of mammalian carboxylesterase. Until recently, adequate sequence information has not been available such that valid links among the mammalian carboxylesterase gene family or evolutionary relationships could be established. However, sufficient basic data are now available to support such a novel classification system.

Notes: Abstract Transmitter receptor diversity often indicates differences in transmitter receptor transduction mechanisms. This is not the case for gamma-aminobutyric acid subtype A (GABAA) receptor subtypes despite the presence of 16 genes to encode the 5 families of native GABAA receptor subtypes. Similar considerations apply to GABAC receptors and GABAB receptors. Both GABAA and GABAB receptors cause hyperpolarization of neuronal membranes and inhibition of neuronal excitability, but their mechanisms differ. GABAB receptors involve an efflux of K+ rather than an influx of Cl-, as in the case of GABAA and GABAC receptors. The stimulation of GABAA receptors can sometimes cause depolarization by Cl- efflux; this efflux is not the result of a transduction mechanism modification, but of Cl--concentration gradient modification. Presumably, GABAA receptor diversity is directly linked to the inhibitory activity of basket cells and other interneuron axons, each innervating several postsynaptic neurons (cortical and hippocampal pyramidal cells for instance). Since the role of this inhibition is to entrain hippocampal and cortical pyramidal neurons into columnary activity, the GABAA receptor diversification may be a mechanism expressed by these postsynaptic neuron populations that uses different GABA potencies to synchronize pyramidal neurons into columnary activity. Thus, GABA potency variability, which emerges from GABAA receptor diversity, plays a unifying role in the intrinsic functional mechanism of laminated structures. GABAA receptor structural differences also play a role in diazepam tolerance, which is a mechanism operative in neuronal circuit adaptation to the extreme amplification of GABA-gated Cl- current intensities. Partial agonists (such as imidazenil), which modestly amplify GABA action at many GABAA receptor subtypes, fail to cause tolerance, dependence, ataxia, or ethanol and barbiturate potentiation. Partial agonists might become a new class of anxiolytic and anticonvulsant drugs that are virtually devoid of the side effects that cause serious concerns in the clinical use of full allosteric positive modulators of GABA action, such as diazepam, alprazolam, triazolam, and others. None of the above can be used as anticonvulsants because of an extremely high tolerance liability. When there is tolerance to diazepam, signs of sensitization to proconvulsive action are exhibited simultaneously. After tolerance, associated changes in GABAA recepter subtype expression are virtually reversed in 72 h. Also, 96 h after termination of long-term diazepam treatment, rats exhibit anxiety and are more sensitive to kainic acid-elicited convulsions. At the same time, these rats have an increase in brain expression of GLuR1, R2, and R3. It is believed that the supersensitivity to kainic acid, convulsions and anxiety, and the increased expression of GLuR1, R2, and R3 may be parts of the mechanism of diazepam dependence.

Notes: Abstract Cytochrome P4503A (CYP3A) is importantly involved in the metabolism of many chemically diverse drugs administered to humans. Moreover, its localization in high amounts both in the small intestinal epithelium and liver makes it a major contributor to presystemic elimination following oral drug administration. Drug interactions involving enzyme inhibition or induction are common following the coadministration of two or more CYP3A substrates. Studies using in vitro preparations are useful in identifying such potential interactions and possibly permitting extrapolation of in vitro findings to the likely in vivo situation. Even if accurate quantitative predictions cannot be made, several classes of drugs can be expected to result in a drug interaction based on clinical experience. In many instances, the extent of such drug interactions is sufficiently pronounced to contraindicate the therapeutic use of the involved drugs.

Notes: Abstract Bisphosphonates (BPs) are pyrophosphate analogs in which the oxygen bridge has been replaced by carbon and diverse carbon side chains have generated a large family of compounds. Several are potent inhibitors of bone destruction (resorption) and are in clinical use for the treatment and prevention of osteoporosis, Paget's disease, hypercalcemia caused by malignancy, tumor metastases in bone, and other bone ailments. Selective action on bone is based on the binding of the BP moiety to the bone mineral. The molecular mode of action of BPs, which may differ from compound to compound, is unknown. However, at the tissue level, all BPs inhibit bone destruction and lead to an increase in bone mineral density by decreasing bone resorption and bone turnover. At the cellular level, the ultimate target of BP action is the osteoclast, the bone resorbing cell. In vitro evidence shows BP inhibition of osteoclast formation, via action on osteoblasts, and there is in vitro and in vivo evidence for BP inhibition of osteoclast activity. There is in vivo and in vitro evidence for increased apoptosis. The relative contribution of these various effects on the therapeutic action of BPs remains to be established. At the molecular level, it is not known if BPs act on a single or multiple targets. Enzymes in the cholesterol biosynthesis pathway and protein tyrosine phosphatases were shown to be inhibited by BPs.

Notes: Abstract Organic cation transporters are critical in drug absorption, targeting, and disposition. It has become increasingly clear that multiple mechanisms are involved in organic cation transport in the key tissues responsible for drug absorption and disposition: the kidney, liver, and intestine. In this review, we discuss current models of transepithelial flux of organic cations in these three tissues. Particular emphasis is placed on the more recent molecular studies that have paved the way for a more complete understanding of the physiological and pharmacological roles of the organic cation transporters. Such information is essential in predicting pharmacokinetics and pharmacodynamics and in the design and development of cationic drugs.

Notes: Abstract It is of great importance to predict in vivo pharmacokinetics in humans based on in vitro data. We summarize recent findings of the quantitative prediction of the hepatic metabolic clearance from in vitro studies using human liver microsomes, hepatocytes, or P450 isozyme recombinant systems. Furthermore, we propose a method to predict pharmacokinetic alterations caused by drug-drug interactions that is based on in vitro metabolic inhibition studies using human liver microsomes or human enzyme expression systems. Although we attempt to avoid the false negative prediction, the inhibitory effect was underestimated in some cases, indicating the possible contribution of the active transport into hepatocytes and/or interactions at the processes other than the hepatic metabolism, such as the metabolism and transport processes during gastrointestinal absorption.

Notes: Abstract Several halogenated alkenes are nephrotoxic in rodents. A mechanism for the organ-specific toxicity of these compounds to the kidney has been elucidated. The mechanism involves hepatic glutathione conjugation to dihaloalkenyl or 1,1-difluoroalkyl glutathione S-conjugates, which are cleaved by gamma-glutamyltransferase and dipeptidases to cysteine S-conjugates. Haloalkene-derived cysteine S-conjugates may have four fates in the organism: (a) They may be substrates for renal cysteine conjugate beta-lyases, which cleave them to form reactive intermediates identified as thioketenes (chloroalkene-derived S-conjugates), thionoacyl halides (fluoroalkene-derived S-conjugates not containing bromide), thiiranes, and thiolactones (fluoroalkene-derived S-conjugates containing bromine); (b) cysteine S-conjugates may be N-acetylated to excretable mercapturic acids; (c) they may undergo transamination or oxidation to the corresponding 3-mercaptopyruvic acid S-conjugate; (d) finally, oxidation of the sulfur atom in halovinyl cysteine S-conjugates and corresponding mercapturic acids forms Michael acceptors and may also represent a bioactivation reaction. The formation of reactive intermediates by cysteine conjugate beta-lyase may play a role in the target-organ toxicity and in the possible renal tumorigenicity of several chlorinated olefins widely used in many chemical processes.

Notes: Abstract Traditional herbal remedies have increased in popularity in Europe and the United States in recent years but have always been important to people living in rural Mexico and to their Mexican American/Chicano descendants in the United States. Mexican American patients will often be ingesting herbal teas at the same time that they are being treated for their ailments with antibiotics or antiinflammatory agents. The plant family Asteraceae (Compositae) has contributed the largest number of plants to this pharmacopoeia; the reasons for the importance of this family include its large number of species in Mexico and its wide array of natural products that are useful in the treatment of the maladies that have afflicted the inhabitants of rural Mexico. These natural products include sesquiterpene lactones, polyacetylenes, alkaloids, monoterpenes, and various phenolics such as flavonoids. In this review, we emphasize the sesquiterpene lactones, a large group of compounds with antiinflammatory properties and the ability to relax smooth muscles and thereby relieve gastrointestinal distress. These compounds also readily form adducts with glutathione or free thiols and can thereby affect the metabolism, activity, and toxicology of a wide array of pharmacological agents.

Notes: Abstract Chemical reaction and optical dynamics in the liquid phase are strongly affected by specific solute-solvent interactions. The dynamical part of this coupling leads to energy fluctuations. The associated energy gap dynamics can be probed by using various nonlinear optical spectroscopies. We discuss various forms of photon echo-time-integrated, time-gated, and heterodyne-detected photon echo-as well as Fourier transform spectral interferometry. It is shown that for solutions of the dye molecule DTTCI, a system-bath correlation function can be acquired that provides a quantitative description of all (non)linear spectroscopic experiments. The deduced correlation function is projected onto the multimode Brownian oscillator model, which allows for a physical interpretation of the multiple-time correlation function and a determination of the spectral density relevant to the solvation process. The following applications of photon echo to condensed phase dynamics are discussed: enhanced vibrational mode suppression, Liouville pathways interference, and dynamical Stokes shift. Recent results of echo-peak shift experiments on the hydrated electron are also presented. The review concludes that photon echo should be useful as a novel tool to explore transition state dynamics.

Notes: Abstract This contribution summarizes the use of plasmon surface polaritons and guided optical waves for the characterization of interfaces and thin organic films. After a short introduction to the theoretical background of evanescent wave optics, examples are given that show how this interfacial "light" can be employed to monitor thin coatings at a solid/air or solid/liquid interface. Examples are given for a very sensitive thickness determination of samples ranging from self-assembled monolayers, to multilayer assemblies prepared by the Langmuir/Blodgett/Kuhn technique or by the alternate polyelectrolyte deposition. These are complemented by the demonstration of the potential of the technique to also monitor time-dependent processes in a kinetic mode. Here, we put an emphasis on the combination set-up of surface plasmon optics with electrochemical techniques, allowing for the on-line characterization of various surface functionalization strategies, e.g. for (bio-) sensor purposes.

Notes: Abstract Laser ablation of in situ metals has recently made it possible to immerse a large number of different metal atoms and ions and small clusters of metal atoms in liquid helium (He) and thus study their absorption and emission spectra in the visible region. Atoms and molecules are readily picked up by large ( 〉= 103 atoms) He droplets, and their spectra are sensitively detected through the use of either beam depletion following absorption or laser-induced fluorescence. Within the past three years, a wide variety of molecules, ranging from OCS to large organic molecules such as amino acids and a number of van der Waals complexes and even large metal clusters, have been embedded in He droplets and studied either in infrared or in the visible region. These results are discussed here in detail, and the evidence for the effect of superfluidity on the spectral features is reviewed.

Notes: Physical chemistry and theoretical chemistry have advanced over the past 50 years from being largely qualitative to having a mature status based firmly on the principles of quantum and statistical mechanics. My interest in the chemical elements and their compounds has prompted me to learn more about the nature of matter through the measurement and interpretation of optical, electric, and magnetic properties of molecules. In addition to holding intrinsic interest, such properties tell us about charge and current distributions and form the basis of electro-optics, magneto-optics, and nonlinear optics. They also help us understand the nature and strength of long-range intermolecular forces, the hydrogen bond, and molecular biology-topics that are apparently forever young.

Notes: Abstract Ordered arrays, or superlattices, of metallic, insulating, or semiconducting quantum dots, represent an exciting new class of materials. These superlattices are often referred to as artificial solids, in which the nanocrystals take the place of atoms in traditional solids, and the packing arrangement of the nanocrystals determines the unit cell parameters of the superstructure. In this review, we discuss various approaches toward assembling nanocrystal superlattices and we discuss their physical properties.

Notes: Abstract A review of recent high-resolution microwave, infrared, and optical spectroscopy experiments demonstrates that remarkable progress has been made in the past 20 years in determining the equilibrium geometries of large polyatomic molecules and their clusters in the gas phase, and how these geometries change when the photon is absorbed. A special focus is on the dynamical information that can be obtained from such studies, particularly of electronically excited states.

Notes: Abstract This review focuses on recent progress in two areas in which computer simulations with explicit solvent are being applied: the thermodynamic decomposition of free energies, and modeling electrostatic effects. The computationally intensive nature of these simulations has been an obstacle to the systematic study of many problems in solvation thermodynamics, such as the decomposition of solvation and ligand binding free energies into component enthalpies and entropies. With the revolution in computer power continuing, these problems are ripe for study but require the judicious choice of algorithms and approximations. We provide a critical evaluation of several numerical approaches to the thermodynamic decomposition of free energies and summarize applications in the current literature. Progress in computer simulations with explicit solvent of charge perturbations in biomolecules was slow in the early 1990s because of the widespread use of truncated Coulomb potentials in these simulations, among other factors. Development of the sophisticated technology described in this review to handle the long-range electrostatic interactions has increased the predictive power of these simulations to the point where comparisons between explicit and continuum solvent models can reveal differences that have their true physical origin in the inherent molecularity of the surrounding medium.

Notes: Abstract Signal transduction is the process by which specific information is transferred from the cell surface to the cytosol and ultimately to the nucleus, leading to changes in gene expression. Since these chains of biochemical and molecular steps control the normal function of each cell, disruption of these processes would have a significant impact on cell physiology. Some of the major signal transduction pathways are briefly reviewed. The interactions of four chemicals (lead, ethanol, polychlorinated biphenyls, and trimethyltin) with different cell signaling systems, particularly the phospholipid hydrolysis/protein kinase C pathway, are discussed. The possible causal relationship of such cellular and molecular interactions with known signs and symptoms of neurotoxicity are highlighted.

Notes: Abstract Cyclooxygenase (COX), first purified in 1976 and cloned in 1988, is the key enzyme in the synthesis of prostaglandins (PGs) from arachidonic acid. In 1991, several laboratories identified a product from a second gene with COX activity and called it COX-2. However, COX-2 was inducible, and the inducing stimuli included pro-inflammatory cytokines and growth factors, implying a role for COX-2 in both inflammation and control of cell growth. The two isoforms of COX are almost identical in structure but have important differences in substrate and inhibitor selectivity and in their intracellular locations. Protective PGs, which preserve the integrity of the stomach lining and maintain normal renal function in a compromised kidney, are synthesized by COX-1. In addition to the induction of COX-2 in inflammatory lesions, it is present constitutively in the brain and spinal cord, where it may be involved in nerve transmission, particularly that for pain and fever. PGs made by COX-2 are also important in ovulation and in the birth process. The discovery of COX-2 has made possible the design of drugs that reduce inflammation without removing the protective PGs in the stomach and kidney made by COX-1. These highly selective COX-2 inhibitors may not only be anti-inflammatory but may also be active in colon cancer and Alzheimer's disease.

Notes: Abstract Marijuana has been in use for over 4000 years as a therapeutic and as a recreational drug. Within the past decade, two cannabinoid receptor types have been identified, their signal transduction characterized, and an endogenous lipid agonist isolated from mammalian tissues. The CB1 cannabinoid receptor is widely distributed in mammalian tissues, with the highest concentrations found in brain neurons. CB1 receptors are coupled to modulation of adenylate cyclase and ion channels. The CB2 receptor is found in cells of the immune system and is coupled to inhibition of adenylate cyclase. Both receptor types selectively bind Delta9-THC, the active principle in marijuana, and anandamide (arachidonylethanolamide), an endogenous cannabimimetic eicosanoid. Progress is being made in the development of novel agonists and antagonists with receptor subtype selectivity, mice with genetic deletion of the cannabinoid receptors, and receptor-specific antibodies, which should help in providing a better understanding of the physiological role of the cannabinoid receptors.

Notes: Abstract Activation of different types of G-protein-linked and ionotropic presynaptic receptors has been shown to regulate neurotransmitter release throughout the central and peripheral nervous systems. In the case of G-protein-linked receptors, three major mechanisms have been suggested: (a) inhibition of Ca channels in the nerve terminal; (b) the activation of presynaptic K channels, resulting in a reduction in the effectiveness of the action potential; and (c) direct modulation of one or more components of the neurotransmitter vesicle release apparatus. In the case of ionotropic presynaptic receptors, inhibition of release may be achieved through depolarization of the terminal and inactivation of Na and Ca channels. Activation of presynaptic ionotropic receptors that are appreciably Ca permeable can also enhance the release of transmitters as a result of their ability to raise [Ca]i in the terminal directly. Many transmitters employ several of these mechanisms, thus allowing considerable flexibility in the presynaptic regulation of transmitter release.

Notes: Abstract G protein-coupled receptors (GPRs) play a key role in controlling hormonal regulation of numerous second-messenger pathways. However, following agonist activation, most GPRs rapidly lose their ability to respond to hormone. For many GPRs, this process, commonly referred to as desensitization, appears to be primarily mediated by two protein families: G protein-coupled receptor kinases (GRKs) and arrestins. GRKs specifically bind to the agonist-occupied receptor, thereby promoting receptor phosphorylation, which in turn leads to arrestin binding. Arrestin binding precludes receptor/G protein interaction leading to functional desensitization. Many GPRs are then removed from the plasma membrane via clathrin-mediated endocytosis. Recent studies have implicated endocytosis in the resensitization of GPRs and have linked both GRKs and arrestins to this process. In this review, we discuss the role of GRKs and arrestins in regulating agonist-specific signaling and trafficking of GPRs.