bluuebunny/crossref_metadata_2025 huggingface dataset:
CoA‐Dependent Enzymes, Chemistry of
Authors: Drueckhammer Dale G.
Published: February 2008

Coenzyme A (CoA) and its thioesters play a diverse array of roles in biologic systems. The enzymes that catalyze reactions of CoA are of interest for a variety of reasons, including, but not limited to, their potential as drug targets. The enzymology of CoA biosynthesis is now well understood, and the genes for all of the enzymes involved have been identified. Thioesters are inherently reactive toward acyl transfer reactions and toward reactions involving deprotonation of the α‐carbon, and these are the primary reactivity patterns in enzyme‐catalyzed reactions of CoA thioesters. CoA utilizing enzymes have been widely studied mechanistically and structurally. Analogs of the natural CoA thioester substrates have been widely used in these studies, including thioesters of unnatural or uncommon acyl groups as well as a large number of analogs in which the thioester is replaced with alternative functionality. Recent technical applications of CoA have included the tagging of carrier protein domains and carrier protein fusions with tagged phosphopantetheine derivatives transferred enzymatically from the corresponding tagged CoA derivatives using promiscuous phosphopantetheinyl transferases.
Endocytosis: Receptor‐Mediated
Authors: Peterson Blake R.
Published: February 2008

Specific receptors on the surface of mammalian cells actively internalize cell‐impermeable ligands by the mechanism of receptor‐mediated endocytosis (RME). This process is critical for the acquisition of nutrients, signal transduction, development, neurotransmission, and cellular homeostasis. Binding of ligands to internalizing receptors on the plasma membrane results in clustering of the complex in clathrin‐coated pits or other dynamic membrane regions. Invagination of these regions yields intracellular vesicles that fuse to form membrane‐sealed endosomes. Receptors typically dissociate from ligands in these acidic compartments, which allows the free receptor to cycle back to the cell surface, whereas ligands are often degraded on delivery to lysosomes, which liberates amino acids and other nutrients. By mimicking endogenous ligands, certain protein toxins, viruses, and other pathogens exploit RME to enter the cytoplasm or reach other intracellular destinations. Similarly, artificial delivery systems that mimic ligands or receptors can enhance efficiently the cellular uptake of impermeable molecules, including drugs, proteins, and nucleic acids. Advances in small‐molecule probes, structural biology, and genetic methods are beginning to illuminate the complex mechanisms of this process at the molecular level.
Enzyme Catalysis: Chemical Strategies
Authors: Bugg Timothy D.H.
Published: February 2008

This article will describe the different chemical strategies used by enzymes to achieve rate acceleration in the reactions that they catalyze. The concept of transition state stabilization applies to all types of catalysts. Because enzyme‐catalyzed reactions are contained within an active site of a protein, proximity effects caused by the high effective concentrations of reactive groups are important for enzyme‐catalyzed reactions, and, depending on how solvent‐exposed the active site is, substrate desolvation may be important also. Examples of acid–base catalysis and covalent (nucleophilic) catalysis will be illustrated as well as examples of “strain” or substrate destabilization, which is a type of catalysis observed rarely in chemical catalysis. Some more advanced topics then will be mentioned briefly: the stabilization of reactive intermediates in enzyme active sites and the possible involvement of protein dynamics and hydrogen tunneling in enzyme catalysis.
Enzyme Inhibition
Authors: Silverman Richard B.
Published: February 2008

This article describes various approaches to inhibition of enzyme catalysis. Reversible inhibition includes competitive, uncompetitive, mixed inhibition, noncompetitive inhibition, transition state, and slow tight‐binding inhibition. Irreversible inhibition approaches include affinity labeling and mechanism‐based enzyme inhibition. The kinetics of the various inhibition approaches are summarized, and examples of each type of inhibition are presented.
Epigenetic Modifications
Authors: Huertas Dori , Esteller Manel
Published: February 2008

Epigenetic modifications play a fundamental role in chromatin structure and function. Histone modifications and DNA methylation regulate important biologic processes such as heterochromatin formation, genomic imprinting, X‐chromosome inactivation, and transcriptional activation and silencing. Epigenetic mechanisms are responsible for a considerable part of the phenotype of complex organisms. The understanding of epigenetic modifications in chromatin may offer some clues to solve the mechanisms of cellular identity, tumorigenesis, stem cell plasticity, regeneration, and aging. These processes are of interest in the fields of human biology and human diseases. Here, we describe the principal components involved in epigenetic modifications, such as the enzymes that modify chromatin, the protein domains that recognize modified chromatin, some best‐characterized downstream effectors, and the tools and techniques for studying epigenetics. However, the biological mechanism of the majority of components is still poorly understood, and the analysis of these components is fundamental to our understanding of epigenetics.
Fatty Acid Desaturases, Chemistry of
Authors: Buist Peter H.
Published: February 2008

The mid‐chain dehydrogenation of saturated fatty acyl derivatives is carried out by a large family of O2‐dependent, nonheme diiron‐containing enzymes known as desaturases. Both soluble and membrane‐bound desaturases have been characterized. The mechanism of desaturation is thought to involve the stepwisesynremoval of vicinal hydrogen atoms via a short‐lived carbon‐centered radical intermediate. The most common desaturase inserts a (Z)‐double bond between the C9,10 carbons of a stearoyl thioester; however, many variations of this prototypical reaction have been discovered. Accounting for this diversity in terms of subtle alterations in active‐site architecture constitutes a new frontier for research in this area.
Forward Chemical Genetics
Authors: Chang Young‐Tae
Published: February 2008

With the successful results of the Human Genome Project, we are now faced with the problem of handling numerous gene targets whose functions remain to be studied; this challenge is being undertaken by the field known as functional genomics. Chemical genetics is an emerging new paradigm to attack this challenging problem, of which there are two approaches: forward and reverse. Although reverse chemical genetics uses a “cause‐to‐effect” approach, forward chemical genetics uses an “effect‐to‐cause” approach. As opposed to conventional genetics where gene knock‐outs or overexpression, forward chemical genetics uses a small‐molecule library to produce a novel phenotype that eventually is employed in the elucidation of gene function. Compared with conventional genetics, chemical genetics holds several unique advantages. A successful forward genetic study provides not only knowledge about a novel gene's function, but also it provides a small moleculeON/OFFswitch that can regulate biologic processes. These small molecules will be extremely useful biologic probes as well as potential new drug candidates. Three main components make up forward chemical genetics: 1) chemical toolbox generation, 2) phenotypic screening, and 3) target identification. Although all three components require additional refinement, target identification poses the greatest challenge. Herein, the general concepts of chemical genetics, with a focus on the forward approach, and the technical overviews for each component are described.
Glycan Biosynthesis in Mammals
Authors: Meledeo M. Adam , Yarema Kevin J.
Published: February 2008

Mammalian glycosylation, the process by which a cellular complement of glycans of dazzling complexity is produced, involves a minimum of 1% of the genome (in humans) and is the dominant postsynthetic modification of both proteins and lipids endowing these molecules with an extended range of structure and function. This article provides a brief outline of the metabolic process by which monosaccharides—the raw material for the construction of complex oligosaccharides—are converted into high energy nucleotide sugar “building blocks” that are in turn assembled into four major classes of mammalians carbohydrates: glycoproteins, glycolipids, GPI anchored structures, and polysaccharides. Finally, the article concludes with a brief discussion of modern methods for manipulating glycans in living cells and in animals–using synthetic, molecular biology, and “chemical biology” approaches—as early steps toward developing sugar‐based medicines.
Glycosylation of Proteins in the Golgi Apparatus
Authors: Desko Marguerite M. , Kohler Jennifer J.
Published: February 2008

Oligosaccharides are essential for interactions of cells with their environments. These complex carbohydrates are often found covalently attached to proteins embedded in eukaryotic cell membranes. Protein glycosylation is heterogeneous; this heterogeneity stems from the biosynthesis of these polymers. As proteins destined for secretion or cell‐surface presentation traffic through the endoplasmic reticulum and the Golgi apparatus, they are modified with sugars in a stepwise fashion by enzymes called glycosyltransferases. The differential expression of these enzymes leads to a multiplicity of specific oligosaccharides both among and within cells because not all cells contain all enzymes and because not all substrate proteins will encounter every enzyme. Although myriad oligosaccharides are found attached to proteins, most of these diverse structures can be grouped into several classes of glycans. In this article, we will discuss some of the most common forms of Golgi protein glycosylation: mucin‐typeO‐linked glycosylation,N‐linked glycosylation, and the formation of glycosaminoglycans. In addition, we will briefly consider some less common, but essential, forms of glycosylation.
Glycosyltransferases, Chemistry of
Authors: Weadge Joel T. , Palcic Monica M.
Published: February 2008

Glycosyltransferases (GTs) form glycosidic bonds by catalyzing the transfer of saccharides from a donor to a wide variety of acceptors. The donors used by GTs are sugars conjugated to nucleotides, phosphates, or lipid phosphates; whereas acceptors consist of carbohydrates, proteins, lipids, DNA, and numerous small molecules such as antibiotics, flavonols, steroids, and so on. Together, the products of these reactions comprise the most diverse and abundant class of natural compounds found in nature. Numerous GTs are needed to synthesize these compounds because the formation of each distinct glycosidic linkage requires a different enzyme. The abundance of these enzymes is emphasized by the fact that GTs constitute 1% of the genes in all genomes sequenced. They are ubiquitous in every kingdom of life and in all compartments of the cell. Currently, over 32,000 GT ORFs have been classified into 90 families on the basis of amino acid sequence similarity. The structures for 64 GTs have been determined to date and generally reveal conserved architectures of a GT‐A or GT‐B fold, although other folds have been observed and are predicted. These crystal structures, together with biochemical data, have provided insight into the catalytic mechanism. GTs generally exhibit strict regio/stereospecificity and transfer with either retention or inversion of configuration at the anomeric carbon of the donor sugar. The importance of characterizing the precise activity of these enzymes is exemplified by the many genetic disorders that have been linked to aberrant glycosylation.
LargeG‐Proteins
Authors: Siderovski David P. , Kimple Adam J. , Willard Francis S.
Published: February 2008

Large G‐proteins, also known as heterotrimeric G‐proteins, cycle through inactive (GDP‐bound) and active (GTP‐bound) states, thereby coupling the activation of cell‐surface receptors to the modulation of various second messengers and intracellular effector proteins. High‐resolution structures of the constituent subunits of the heterotrimer (Gα, Gβ, and Gγ) have revealed the determinants involved in heterotrimer assembly and effector protein engagement as well as the mechanism of nucleotide hydrolysis by the Gα subunit and its acceleration by “regulator of G‐protein signaling” (RGS) proteins. Mechanistic details have also been gleaned from studies of G‐protein modulation by pathogen toxins and chemicals such as aluminum tetrafluoride. Recent identification of peptide‐binding “hotspots” on G‐protein subunits should facilitate discovery and design of new chemical entities that can modulate nucleotide cycling and receptor/effector coupling at the level of the G‐protein heterotrimer.
Inositol Polyphosphates
Authors: Resnick Adam C. , Saiardi Adolfo
Published: February 2008

Inositol polyphosphates comprise a large family of water‐soluble molecules derived from the combinatorial phophorylation of the six hydroxyls ofmyo‐inositol. Second messenger roles for inositol polyphosphates in Ca2+mobilization were first identified for what is now the best characterized family member, inositol 1,4,5‐trisphosphate (InsP3). Additional anabolic and catabolic metabolism of InsP3results in the formation of a large, diverse family of higher inositol polyphosphates whose signaling roles and biologic functionality remain largely undefined. However, the recent cloning and identification of the kinases and phosphatases involved in the combinatorial modification of inositol polyphosphates has served to further define and characterize this complex metabolic network and to identify its preeminence in nearly all aspects of cell biology. Conserved from yeast to humans, inositol polyphosphates regulate a wide array of processes, including ion‐channel conductance, membrane dynamics, transcription, nucleic acid metabolism, and protein phosphorylation.
Lipid Domains, Chemistry of
Authors: Epand Richard M.
Published: February 2008

Biological membranes are composed largely of proteins and lipids. A wide range of molecular structures exists among these molecules. It is therefore not surprising that biological membranes are not uniform but rather cluster certain molecules in specific regions or domains. This behavior can be mimicked in model systems comprising a limited number of components to study in more detail the molecular nature of this domain formation. Two types of domains exist that have been more extensively studied. One is a membrane domain enriched in polyanionic lipids, such as phosphatidylinositol diphosphate. Such domains are formed by the presence of proteins with segments containing several cationic amino acid residues. Such proteins have been termed “pipmodulins.” Another kind of domain is formed as a consequence of the nonuniform distribution of cholesterol in the membrane. Caveolae represent one type of cholesterol‐rich domain that is well characterized. Other cholesterol‐rich domains are termed “rafts.” Characterization of rafts in model membranes is well documented, but the nature of cholesterol‐rich domains in biological membranes remains a subject of controversy. Several imaging and fluorescence methods are being employed to further characterize the size and lifetime of small raft domains in biological membranes.
Lipid Homeostasis, Chemistry of
Authors: Black Paul N. , Sealls Whitney , DiRusso Concetta C.
Published: February 2008

Lipid metabolism encompasses a large part of intermediary metabolism and includes highly dynamic processes, which are subject to regulation at transcriptional and enzymatic levels. The maintenance of lipid metabolism or lipid homeostasis is multilayered and includes biosynthesis and degradation, the impact of external stimuli proceeding through signal transduction, the function of lipid‐responsive transcription factors, and lipid trafficking. It also includes the production of bioactive lipids, which have regulatory roles in different lipid metabolic pathways, effect specific transcription factors, and influence a myriad of cellular processes. Lipid metabolism is responsive to external supplies of fatty acids and other precursors required for neutral lipid, glycerol phospholipid, and sphingolipids synthesis. In some cell types, fatty acid composition within membrane lipids must necessarily adapt to changes in temperature to maintain appropriate fluidity essential for biologic activity. Finally, lipids are diverse in both structure and abundance and differ among animals, plants, fungi, and bacteria. This article will focus on the fatty acid metabolism and, to some extent, its relationship to sterol metabolism, which underpins lipid homeostasis. Readers are referred to other articles in this series (see cross‐references below), particularly on steroid and lipid synthesis, chemistry and chemical reactivity of lipids, and lipidomics.
Lipids: Phase Transitions
Authors: Koynova Rumiana , Tenchov Boris
Published: February 2008

Lipids constitute a diverse group of biomolecules of varied biologic roles. Their major function is to serve as building blocks of the biologic membranes. According to the fluid‐mosaic model, the biomembranes are liquid‐crystalline lipid bilayers with embedded proteins. This model includes two references to the lipid phase state—liquid crystallineandbilayer—both of which are of critical importance for the proper membrane functioning. The majority of lipids are amphiphilic compounds, which, similarly to other surfactants, also can form a large variety of other, non‐liquid‐crystalline and nonbilayer phases by transforming into each other via different kinds of phase transitions. In particular, the impressive variety of lipids in the biomembranes includes a large fraction of species that in isolation prefer to adopt curved, hexagonal, or cubic phases rather than the lamellar phase. The physiologic importance of the lipid diversity and mesomorphic behavior stems from the possibility of finely tuning and optimizing the properties of the biomembranes by regulating their lipid composition.
Lipidomics
Authors: Farwanah Hany , Kolter Thomas
Published: February 2008

Lipids are hydrophobic or amphiphilic low‐molecular‐weight substances with a low solubility in water. Glycerophospholipids, sphingolipids, and cholesterol are the building blocks of cellular membranes, and triacylglycerols are the major molecular storage forms of metabolic energy. Various lipids serve as signaling substances either as first or second messengers in signal transduction; as autocrinic, paracrinic, or endocrinic regulators; or are covalently bound to cellular proteins. Several diseases are caused by, or at least associated with, alterations in lipid metabolism, such as inherited disorders of lipid metabolism, atherosclerosis, diabetes, obesity, or Alzheimer's disease.
Lipids: Chemical Diversity
Authors: Guschina Irina A. , Harwood John L.
Published: February 2008

Lipids represent some of the most complex biologic molecules, and their diversity is crucial for their cellular functions. The wide range of chemical and physical properties of different lipids determines a variety of roles for these compounds in biologic processes. According to their structures, lipids can be divided into two main groups: the nonpolar lipids (acylglycerols, sterols, free fatty acids, hydrocarbons, alcohols, wax, and steryl esters) and the polar lipids (phosphoglycerides, glycosylglycerides, and sphingolipids). Triacylglycerols act as energy stores and metabolic fuels. Polar lipids and sterols are important structural components of cell membranes where they may have many diverse functions. Arranged as bilayers, they establish permeability barriers for cells and organelles and provide a microenvironment for membrane‐associated proteins as well as participate directly in metabolism and a multitude of membrane fusion events (1). Waxes as surface coverings are integral to water balance and protect organisms from noxious environmental conditions. In addition to a structural role, lipids serve as important intermediates in cell signaling pathways (e.g., sphingolipids, inositol lipids, phosphatidic acid, lysophospholipids, oxidative products) and play a role in mediating cellular responses to the environment (2). In this article, we will summarize our knowledge on the structural diversity of lipids that provide information on the various lipid classes and the fatty acids that occur naturally.
Metal Homeostasis
Authors: Outten F. Wayne , Twining Benjamin S.
Published: February 2008

Transition metals are a key component of biological systems. Because of their special properties, they are incorporated into proteins functioning in dioxygen transport, electron transfer, redox transformations, and regulatory control. The metals used in biological systems have been selected throughout evolution based on their availability in the environment and their kinetic lability, resulting in preferential use of first‐row transition metals in biology. These essential metals must be obtained from the environment and concentrated within the cell for use in biochemical pathways. Once appropriated, metals must be directed to metalloenzymes or metal storage proteins within the cell. In addition, organisms must be able to distinguish between essential and toxic metals and must have mechanisms for minimizing the toxicity of both essential and toxic metals that are present in excess. Metal homeostasis is broadly defined as the metal uptake, trafficking, efflux, and sensing pathways that allow organisms to maintain an appropriate (often narrow) intracellular concentration range of essential transition metals. This review will introduce several unifying concepts of metal homeostasis with brief illustrative examples for each concept.
Metallo‐Enzymes and Metallo‐Proteins, Chemistry of
Authors: Williams Robert J.P.
Published: February 2008

Metallo‐enzymes and metallo‐proteins are a combination of a metal ion or several metal ions in which the metal ion is strongly held in a protein. Hence, before describing their properties and functions, it is necessary to appreciate which metal ions bind strongly to proteins and exchange slowly. The biological significance of metallo‐enzymes is that they are essential catalysts, especially for the metabolism of small molecules such as H2, CH4, CO, N2, and O2, as well as for long‐range electron transfer. The control of uptake and the synthesis of their proteins rest with feedback in a series of metallo‐proteins.
Metallointercalators as Probes of DNA Recognition and Reactions
Authors: Augustyn Katherine E. , Pierre Valerie C. , K. Barton Jacqueline
Published: February 2008

Here we describe studies of metallointercalators bound to DNA. These octahedral transition metal complexes primarily bind noncovalently by stacking within the DNA helix. Given the rich photophysics and photochemistry of the ruthenium and rhodium complexes we employ, we have used a variety of biophysical studies to characterize their interactions with DNA. X‐ray crystallography has also provided atomic resolution detail as to their binding to the duplex. Complexes have been designed that target DNA with high specificity. We have, for example, designed metal complexes that bind specifically to mismatched sites in the DNA duplex, and these have found application in the detection of single nucleotide polymorphisms and studies of mismatch repair deficiency. The photophysical properties of the metal complexes along with their intercalative stacking have been useful in particular as tools to characterize long‐range charge transport in DNA. Using metallointercalators tethered to the duplex, oxidative damage to DNA from a distance has been demonstrated. The metallointercalators may serve as models for DNA‐binding proteins, not only in binding DNA sites with high specificity, but also in carrying out electron transfer chemistry mediated by the DNA base‐pair stack. Certainly these metallointercalators have proven to be powerful probes of this chemistry.
Metalloregulatory Proteins
Authors: Zamble Deborah B.
Published: February 2008

Metalloregulators are proteins that bind metals and modulate gene expression through direct interactions with DNA or RNA. The genes under this metal‐dependent control encode a variety of proteins involved in the cellular homeostasis of both essential and toxic metals. Metalloregulators are present in all types of organisms, and extensive information exists about their mechanisms, although many unanswered questions remain. The global activities of these metal‐responsive factors require overcoming complex challenges, such as the manner in which the proteins regulate gene expression, the mechanisms of the metal‐dependent protein conformation transformations, and the ability of the proteins to recognize the designated metal(s). An understanding of these key biomolecules draws from disciplines such as cell biology, protein chemistry, and inorganic chemistry and provides molecular insight into one fundamental aspect of life.
Metals in Medicine: Imaging Agents
Authors: Caravan Peter
Published: February 2008

The use of metal ions in diagnostic medicine is widespread. Metal complexes and nanoparticles are used clinically in magnetic resonance imaging, nuclear medicine (gamma scintigraphy and positron emission tomography), and X‐ray imaging. Preclinically, additional advances are being made in these fields through the creative application of metal complexes and metal‐containing nanoparticles. This article briefly describes different clinical imaging modalities and the physico‐chemical properties required for imaging agents. Commercial agents are used to illustrate these properties and to describe the clinical state of the art. Selected examples of exciting preclinical imaging agents that have shown efficacyin vivoalso are described.
AdoMet‐Dependent Methyltransferases, Chemistry of
Authors: Klimasauskas Saulius , Lukinavicius Grazvydas
Published: February 2008

S‐adenosyl‐L‐methionine is a high energy compound and is the major source of methyl groups for a myriad of biologic transmethylation reactions. These highly specific single‐carbon transfers onto diverse nucleophilic centers in biomolecules are catalyzed by methyltransferase enzymes and play important regulatory and structural roles in the cell. Here we discuss the chemical mechanism of the methylation reactions, including structural features of the methylsulfonium center in the cofactor molecule, enzyme‐assisted activation of diverse nucleophilic targets by deprotonation or covalent catalysis, and spatial constraints of the reaction.
Mitochondrial Medicine
Authors: Rodenburg Richard J.T. , Smeitink Jan A.M.
Published: February 2008

Mitochondrial medicine is an emerging field in medicine that focuses on diseases in which the mitochondrial energy generating system plays a central role. These diseases include the “classical” mitochondrial disorders, in which a (genetic) defect in the mitochondrial energy generating system is the primary cause of the disease, but also more common disorders such as Parkinson and cancer, in which mitochondrial energy metabolism plays an important role in the pathogenesis. In this review, we present an overview of the mitochondrial energy generating system, starting at the conversion of pyruvate into acetyl‐CoA by pyruvate dehydrogenase, via the TCA cycle in which reduction equivalents are formed, to the oxidative phosphorylation system, where the reduction equivalents are used to convert ADP into ATP. The mitochondrial energy generating system can be examined by global assays that measure the rate of pyruvate conversion, the rate of oxygen consumption, or the rate of ATP production. In addition, an overview is given of the spectrophotometric assays that are available to measure PDHc, several TCA cycle enzymes, and the enzymes of the oxidative phosphorylation. In the diagnostic analysis of patients suspected to suffer from a mitochondrial disorder, these assays are applied to evaluate the functioning of the mitochondrial energy generating system in muscle biopsies and other types of patient samples. In addition, the results provide clues for further investigations at the molecular genetic level. Thus, the biochemical analysis of patient material is an important step in establishing the diagnosis of a mitochondrial disorder.
Natural Products as Anticancer Agents
Authors: Kingston David G. I. , Newman David J.
Published: February 2008

Natural products have provided some of the most effective drugs for the treatment of cancer, including such well‐known drugs as paclitaxel (Taxol
™
; Bristol‐Myers Squibb) adriamycin, vinblastine, and vincristine. Natural products have also provided many compounds that have led to the discovery of new biochemical mechanisms. This review summarizes the major natural products in clinical use today and introduces several new ones on the cusp of entering clinical practice. The review is organized by mechanism of action, with compounds that interact with proteins discussed first, followed by compounds that interact with RNA or DNA.
Nature: A Model System for Chemists
Authors: Breslow Ronald
Published: February 2008

Chemists have learned to imitate the principles of biologic chemistry in the quest to produce artificial enzymes, artificial receptors, and, ultimately, artificial living cells. The field of natural products chemistry is concerned chiefly with discovering the structures of the molecules produced in living systems as well as the paths by which they are produced. Biomimetic chemistry takes nature as a model and extends what exists in biology into what is possible. This process includes using hydrophobic effects in water to achieve selective reactions and making new amino acids and new nucleotides to generalize the properties of proteins and nucleic acids. Potent new catalysts are based on the chemistry performed by coenzymes using bifunctional acid–base catalysis and the water exclusion achieved by natural enzymes. Exciting new areas include molecular machines, mimics of the chemical senses, and work on the origin on earth of the homochirality observed in biomolecules. The studies using nature as a model have enriched chemistry greatly and furnished interesting insights into biochemistry.
NMR
: Lipids
Authors: Dufourc Erick J.
Published: February 2008

Lipid structure and dynamics are keys factors for cell life. Phospholipids are essential in signalling pathways as they are recognition sites at the membrane surface. Other lipids such as cholesterol and sphingomyelin are crucial molecules in maintaining membrane integrity and are involved in membrane domains (rafts). NMR both with its liquid and solid‐state facets is a very powerful tool for deciphering both the structure and the dynamics of various classes of lipids. Lipids extracted from membranes and dissolved in organic solvents can reveal their molecular structure when observed with multinuclear one‐dimensional or two‐dimensional solution NMR. Multinuclear, wide‐line, solid‐state NMR brings information on the nature of the membrane phase (lamellar, hexagonal, isotropic, etc.), its dynamics (diffusion, fluid/gel, or liquid‐ordered with cholesterol) and the molecular structure of embedded lipids when using the Magic Angle Spinning technique.
NMR: Proteins
Authors: Gronenborn Angela M.
Published: February 2008

Solution NMR methods for determining three‐dimensional, atomic resolution structures and dynamic properties of biologic macromolecules are well established. Currently, an ever‐increasing number of experimentally solved protein NMR structures is available and contributes to our understanding of biology. The development of novel NMR approaches, labeling techniques, and calculational algorithms allows the study of larger and more complex systems. Here I summarize the basic NMR approaches, discuss labeling and assignment strategies, and provide examples for their uses.
Artificial Metalloproteins: Design and Engineering
Authors: Lu Yi , Garner Dewain K. , Zhang Jun‐long
Published: February 2008

Engineering of artificial metalloproteins is an expanding field with potential impacts in many areas from fundamental understanding of protein structure and function to industrial production of specialty chemicals such as chiral drug intermediates. Incorporation of unnatural amino acids and non‐native metal cofactors into proteins is an emerging field in the area of protein design, as it offers the tantalizing prospect of introducing new functionality and provides exquisite probes for and fine‐tuning of native protein properties. Although it is a relatively young field, engineering of non‐native metalloproteins boasts a myriad of techniques for design, construction, and/or expression of the desired artificial protein. Additionally, many groundbreaking studies exist in this field that have enhanced basic scientific understanding of protein function or generated promising artificial enzymes. Discussion of the techniques prominent for incorporation of unnatural amino acids and non‐native cofactors is followed by some of the most interesting applications of these techniques reported to date.
Nucleic Acids: Hydration
Authors: Chalikian Tigran V. , Völker Jens
Published: February 2008

Water is an integral part of DNA structure, and it plays an important role in dictating conformational preferences and binding properties of nucleic acids. Although in recent years a wealth of information on the physical properties of water in the vicinity of nucleic acids has accumulated, our understanding of how water interacts with nucleic acids and how it mediates DNA recognition by small ligands and DNA‐binding proteins remains limited. In this article, we review the current state of DNA hydration research. In particular, we discuss structural, dynamic, and thermodynamic aspects of nucleic acid hydration. We also present an overview of the structural and thermodynamic role of water in modulating protein–DNA recognition and highlight the importance of hydration as a major contributor to the energetics of nucleic acid recognition. We emphasize the need for additional physico‐chemical studies of DNA hydration by experimental and theoretic scientists.
Oxygen‐Activating Enzymes, Chemistry of
Authors: R. Hess Corinna , W. D. Welford Richard , P. Klinman Judith
Published: February 2008

Aerobic organisms derive the energy required for cellular processes from the conversion of dioxygen to water, which highlights the importance of dioxygen chemistry in biologic systems. The biochemistry of dioxygen is far from simple and has been the subject of intense study in a range of chemical and biologic disciplines. The reduction of dioxygen is energetically favorable; however, dioxygen is a ground state triplet, kinetically unreactive with singlet organic molecules. Nature has developed a diverse array of catalysts to overcome this kinetic barrier. These dioxygen‐activating enzymes are divided into two classes: oxygenases and oxidases. Oxygenases incorporate directly at least one atom from dioxygen into the organic products of their reaction. Oxidases couple the reduction of dioxygen with the oxidation of substrate. Typically, enzymes that react with dioxygen contain transition metal ions and/or conjugated organic molecules as cofactors. The reaction with dioxygen is initiated by electron transfer from the cofactor to O2. The subsequent chemistry varies depending on both the nature of the cofactor and the protein scaffold. Here we review the fascinating chemistry of the dioxygen‐activating enzymes and identify some of the common strategies and themes that have emerged from over half a century of research.
Peptide Combinatorial Libraries
Authors: Liu Ruiwu , Lam Kit S.
Published: February 2008

Peptide libraries, which consist of a few thousands to tens of millions of distinct peptides, can be generated combinatorially through biologic or synthetic approaches. The phage‐display peptide library method is simple and economical, and peptides with various natural protein folds can be generated by this approach; but this biologic method generally is limited to peptides that contain only L‐amino acids. Synthetic combinatorial libraries, however, can accommodate D‐amino acids, unnatural amino acids, and even organic moieties, which makes these approaches highly versatile. These synthetic methods include the spatially addressable parallel library method, the combinatorial library method that requires deconvolution, the one‐bead one‐compound (OBOC) combinatorial library method, the self‐assembled peptide nucleic acid (PNA) encoded chemical microarrays, and the synthetic library method that requires chromatography selection. Various methods to screen these combinatorial libraries have been developed. For example, phage‐display peptide libraries can be screened for the ability of phages to bind to unique immobilized target proteins or whole cells, peptide microarrays can be screened for their ability to interact with fluorescent proteins, combinatorial library methods that require deconvolution can be screened by standard solution‐phase assays, and OBOC libraries can be screened by on‐bead binding or functional assays or several solution‐phase cell‐based or biochemical assays. Combinatorial peptide library methods are enabling technologies that have proven to be very useful in basic research and drug discovery.
Photosynthesis: Electron Transfer Chemistry
Authors: van der Est Art
Published: February 2008

In oxygenic photosynthesis, light‐induced electron transfer reactions occur in two photosystems embedded in the thylakoid membrane. These complexes bind many cofactors and are among the handful of membrane proteins for which the X‐ray crystal structures have been determined. The availability of this structural information, in combination with advanced spectroscopic techniques, has allowed the electron transfer reactions to be studied in detail. This work has revealed the pathways, rates, and yields of the electron transfer reactions but has also raised several intriguing questions about how these properties are governed by the protein–cofactor interactions. In this article, a brief overview of the main features of these very complex reactions is given, along with a summary of some techniques used to study them. A short survey of some recent advances in our understanding of the chemistry of electron transfer in photosynthesis is given.
Polyketide Biosynthesis: Polyethers
Authors: Hill Alison M.
Published: February 2008

This review covers the biosynthesis of terrestrial and marine polyethers and discusses their biologic properties and the molecular genetics and enzymology of the proteins responsible for their formation. The biosynthesis of monensin, nanchangmycin, nonactin, and the marine polyether ladders are discussed in detail. Novel enzymes found only in type I polyketide polyether gene clusters that are responsible for the epoxidation and cyclization of polyene biosynthetic intermediates are described. The macrotetrolide biosynthetic gene cluster, which is an ACP‐less type II polyketide synthase that functions noniteratively is reviewed.
Post‐Translational Modifications to Regulate Protein Function
Authors: Lin Hening , Du Jintang , Jiang Hong
Published: February 2008

Protein post‐translational modifications (PTM) are very important to regulate protein function and to control numerous important biological processes. Here a brief review of commonly found enzyme‐catalyzed PTM is given. These PTM include modifications that occur on protein side chains and those that involve protein backbones. The introduction of different PTM is followed by a summary of the molecular basis for the regulation of protein function by PTM. The focus is then given to a few major PTM that play important roles in eukaryotes, such as phosphorylation, methylation, acetylation, glycosylation, ubiquitylation, and proteolysis. For each modification, a description will be given about the residues modified, the enzymatic reaction mechanisms, the major known biological functions, and its relevance to human diseases. At the end, we discuss challenges in identifying new pathways regulated by known PTM and discovering new PTM.
Protease Inhibitors: Mechanisms
Authors: Farady Christopher J. , Craik Charles S.
Published: February 2008

Relatively few design principles underlie the mechanisms of inhibition of a myriad range of protease inhibitors. Protease inhibitors tend to be competitive and to compete with substrate binding, either through direct competition or deformation of the protease active site. Although protein inhibitors can gain potency through the burial of a large surface area and specificity through contacts with specific exosites, small‐molecule inhibitors primarily gain potency through interactions with the catalytic machinery of the enzyme and specificity through interactions with the substrate binding sites. Incorporation of these design principles into chemical probes and drugs have improved greatly our ability to create potent and specific protease inhibitors.
Amyloid Formation
Authors: Abedini Andisheh , Raleigh Daniel P
Published: February 2008

Amyloids are β‐sheet rich fibrillar protein structures that result from the self‐assembly of polypeptides and proteins. A wide range of proteins are known to form amyloid fibrilsin vivoand an even larger number do soin vitro. More than 20 different human diseases involve amyloid formation, and the amyloid fibril or intermediates populated during its assembly are cytotoxic. All amyloid fibrils share common structural features despite exhibiting considerable variation in primary sequence. These features include a crossed β‐sheet organization in which the individual β‐strands are arranged perpendicular to the fiber axis such that the hydrogen bonds are oriented parallel to the fibril axis, resistance to proteolysis, and the ability to bind to certain dyes. Normally, the aggregation of proteins into amyloid is a pathological event; however, evidence indicates that naturally occurring amyloids may also play a beneficial biological rolein vivo.
RNA
Interference: Mechanisms and Proteins Involved
Authors: Wang Wang‐Xia , Nelson Peter T. , Tang Guiliang
Published: February 2008

RNA interference (RNAi) and microRNA (miRNA) pathways participate in posttranscriptional gene expression regulation. RNAi and miRNA biochemistry involve short (∼22 nucleotide) regulatory RNAs: small interfering RNA (siRNA) and miRNA. Both siRNAs and miRNAs guide RNA–protein complexes to “target” complementary messenger RNAs (mRNAs) for cleavage or translational repression. Many proteins involved in these pathways have been elucidated. The biochemical mechanisms of miRNA/siRNA processing have been dissected in detail in plants and in animals using biochemical and genetic approaches. Here we review the current literature on RNAi and miRNA mechanisms with a special focus on the protein components.
Pre‐mRNASplicing
Authors: Karijolich John , Yi‐Tao Yu
Published: February 2008

Pre‐mRNA splicing is an RNA processing reaction by which introns are removed from an mRNA precursor and exons are precisely joined together to form a functional mature mRNA. Splicing involves two successivetrans‐esterification reactions that occur in the spliceosome, which is a multicomponent complex composed of a large number of protein factors and five small nuclear RNAs (snRNAs), each functioning as an RNA–protein complex (ribonucleoprotein or snRNP). A significant body of evidence indicates that both spliceosome assembly and catalytic core formation are orchestrated by an intricate network of RNA–RNA interactions. Most eukaryotic introns invariably start with the dinucleotide GT (GU in RNA) and end with the dinucleotide AG. Splicing of these introns occurs in the major spliceosome containing five abundant snRNPs (U1, U2, U4, U5, and U6). In high eukaryotes, a rare class of introns also exists, beginning with the dinucleotide AT (AU in RNA) and ending with the dinucleotide AC. Removal of this class of introns requires the participation of a different set of snRNPs, namely U11, U12, U5, U4atac, and U6atac. Recent advances in pre‐mRNA splicing have provided strong evidence for an RNA enzyme catalyzing the twotrans‐esterification reactions in the spliceosome.
RNAStability: Chemistry, Measurement and Modulation
Authors: McDowall Kenneth J.
Published: February 2008

Molecules composed of RNA perform many roles that are vital for the life and reproduction of all cellular organisms and viruses, one of which is the role of messengers that carry from genes the information required for the production of protein. A typical feature of messenger RNA (mRNA) is its relative instability, which ensures that the production of any particular protein soon comes to an end when it is no longer required and synthesis of the message is downregulated. Moreover, while a transcript is being produced, its rate of decay is as important as its rate of synthesis in determining its cellular concentration and thus, to a large extent, its level of function. The turnover of mRNA, and indeed all other types of RNA, is mediated by multiple ribonucleases. The activity of these enzymes in cells can be inhibited rapidly by chemical treatments; thus, for many experimental systems their presence does not pose a significant barrier to the study of gene regulation at the RNA level. However, the development of RNA‐based therapeutics such as small interfering RNAs and aptamers has required the introduction of modifications to prevent their degradation by ribonucleases within the cells and body fluids of humans. This article describes the properties of RNA that make it susceptible to ribonucleases and the techniques used to determine the stability of RNA molecules. It also provides examples of how RNA stability in livings cells is being modulated for biotechnology and clinical applications, and it reviews the strategies that are being adopted to increase thein vivostability of RNAs with therapeutic potential.
Symbiosis, Chemical Biology of
Authors: Flachshaar Daniel , Piel Jörn
Published: February 2008

The term “symbiosis” was defined by Anton de Bary in his monograph “Die Erscheinung der Symbios” as “the living together of unlike organisms” (1). His studies were based on the formation of lichens, which are the result of an association between a fungus and an alga or cyanobacterium. The definition was coined in the end of the nineteenth century but is regarded by most symbiosis researchers as largely valid today. Accordingly, any specific association between two or more species can be classified as symbiosis. It should be noted that many scientists use symbiosis in a more restricted way to denote a mutually beneficial relationship. This article will give an overview of various biologic manifestations of symbiosis and discuss selected examples, where primary or secondary metabolites play a crucial role in the association. If the partners in a symbiosis differ in size, the larger member is termed “host” and the smaller member is termed “symbiont” or “symbiote.” The more common term “symbiont” will be used here. One general way to distinguish between various forms of symbiosis is to identify the location of the attachment of the symbiont to the host. Symbionts that live on the host surface, including internal surfaces like the digestive tube, participate in ectosymbiosis (Greek: ɛκτoς = outside). If a symbiont is localized within the tissues of the host, the association is termed “endosymbiosis” (Greek: ɛνδoν = within). Endosymbionts can be found either in the extracellular space or intracellularly.