abstract：:RNA folds during transcription in the cell. Compared to most in vitro studies where the focus is generally on Mg(2+)-initiated refolding of fully synthesized transcripts, cotranscriptional RNA folding studies better replicate how RNA folds in a cellular environment. Unique aspects of cotranscriptional folding include ...

journal_title：Methods in enzymology

authors： Wong TN,Pan T

更新日期：2009-01-01 00:00:00

abstract：:Protein splicing is an autocatalytic reaction in which an internal protein domain, the intein, excises itself out of a precursor protein and concomitantly links the two flanking sequences, the exteins, with a native peptide bond. In split inteins, the intein domain is divided into two parts that undergo fragment assoc...

journal_title：Methods in enzymology

authors： Ludwig C,Schwarzer D,Zettler J,Garbe D,Janning P,Czeslik C,Mootz HD

更新日期：2009-01-01 00:00:00

abstract：:Nonribosomal peptides are natural products typically of bacterial and fungal origin. These highly complex molecules display a broad spectrum of biological activities, and have been exploited for the development of immunosuppressant, antibiotic, anticancer, and other therapeutic agents. The nonribosomal peptides are as...

journal_title：Methods in enzymology

authors： Wilkinson B,Micklefield J

更新日期：2009-01-01 00:00:00

abstract：:This chapter outlines the approaches and techniques that can be used to analyze the regulation of antibiotic production in streptomycetes. It describes how to isolate antibiotic nonproducing and overproducing mutants by UV, nitrosoguanidine (NTG), transposon, and insertion mutagenesis, and then how to use those mutant...

journal_title：Methods in enzymology

authors： Bibb M,Hesketh A

更新日期：2009-01-01 00:00:00

abstract：:Liposomes show great promise as intravenous drug delivery vehicles, but it is often difficult to combine stability in the circulation with rapid, targeted release at the site of interest. Targeting to specific tissues requires developing highly specific ligands with strong affinities to receptors overexpressed on dise...

journal_title：Methods in enzymology

authors： Wu G,Mikhailovsky A,Khant HA,Zasadzinski JA

更新日期：2009-01-01 00:00:00

abstract：:Enveloped virus particles select their lipid-protein components and egress by budding from the host cell membranes. The matrix protein of many enveloped viruses has been proposed as a crucial element for viral budding; however, molecular mechanisms behind membrane remodeling by the matrix protein are yet to be unravel...

journal_title：Methods in enzymology

authors： Shnyrova AV,Zimmerberg J

更新日期：2009-01-01 00:00:00

abstract：:The elucidation of structure-affinity relationships in EF-hand proteins requires a reliable assay of divalent ion affinity. In principle, isothermal titration calorimetry (ITC) should be capable of furnishing estimates for Ca2+- and Mg2+-binding constants in these systems. And because the method yields the binding ent...

journal_title：Methods in enzymology

authors： Henzl MT

更新日期：2009-01-01 00:00:00

abstract：:The Duffy blood group antigen is a serpentine protein with seven transmembrane domains that is not coupled to G-proteins or other known intracellular effectors. In addition to erythrocytes, it is also expressed in endothelial cells and neurons. In recent years the Duffy antigen has received much attention because of i...

journal_title：Methods in enzymology

authors： Rot A,Horuk R

更新日期：2009-01-01 00:00:00

abstract：:Paraquat (PQ) is a prototypical redox cycling agent commonly used experimentally to generate reactive oxygen species and oxidative stress. Recently, PQ has also come under investigation as a potential environmental neurotoxin associated with increased risk for neurodegenerative disease developing after chronic exposur...

journal_title：Methods in enzymology

authors： Drechsel DA,Patel M

更新日期：2009-01-01 00:00:00

abstract：:The enzymes involved in mitochondrial oxidative phosphorylation (OXPHOS) are coassembled into higher ordered supercomplexes within the mitochondrial inner membrane. The cytochrome bc(1)-cytochrome c oxidase (COX) supercomplex is formed by the coassociation of the two electron transport chain complexes, the cytochrome ...

journal_title：Methods in enzymology

authors： Stuart RA

更新日期：2009-01-01 00:00:00

abstract：:Complex I is the major entry point in the bacterial and mitochondrial respiratory chain. Structural knowledge of the enzyme is still limited because of its large size and complicated architecture. Only the structure of the hydrophilic domain of a bacterial Complex I has been solved to high resolution by X-ray crystall...

journal_title：Methods in enzymology

authors： Radermacher M

更新日期：2009-01-01 00:00:00

abstract：:Accurate diagnosis of attentional disorders such as attention-deficit hyperactivity disorder (ADHD) is imperative because there are multiple negative psychosocial sequelae related to undiagnosed and untreated ADHD. Early and accurate detection can lead to effective intervention and prevention of negative sequelae. Unf...

journal_title：Methods in enzymology

authors： Robeva R,Penberthy JK

更新日期：2009-01-01 00:00:00

abstract：:Numerous aspects of the immune system operate on the basis of complex regulatory networks that are amenable to mathematical and computational modeling. Several modeling frameworks have recently been applied to simulating the immune system, including systems of ordinary differential equations, delay differential equati...

journal_title：Methods in enzymology

authors： Kim PS,Levy D,Lee PP

更新日期：2009-01-01 00:00:00

abstract：:Oligomerization is a frequently encountered physical characteristic of biological molecules that occurs for a wide number of transcription factors, ion channels, oxygen-carrying macromolecules such as hemocyanin and enzymes. On the other hand, unwanted protein oligomerization can lead to the formation of pathogenic st...

journal_title：Methods in enzymology

authors： Barranco-Medina S,Dietz KJ

更新日期：2009-01-01 00:00:00

abstract：:Over the last 50 years cytochrome c has been used as a model system for studying electron transfer and protein folding processes. Recently, convincing evidence has been provided that this protein is also involved in other biological processes such as the apoptosis and α-synuclein aggregation. Numerous lines of evidenc...

journal_title：Methods in enzymology

authors： Schweitzer-Stenner R,Hagarman A,Verbaro D,Soffer JB

更新日期：2009-01-01 00:00:00

abstract：:Chaperone-mediated autophagy (CMA) is a selective type of autophagy responsible for the lysosomal degradation of soluble cytosolic proteins. In contrast to other forms of autophagy where cargo is sequestered and delivered to lysosomes through membrane fusion/excision, CMA substrates reach the lysosomal lumen after dir...

journal_title：Methods in enzymology

authors： Kaushik S,Cuervo AM

更新日期：2009-01-01 00:00:00

abstract：:Autophagy is a major intracellular catabolic pathway induced in response to amino acid starvation. Recent findings implicate it in diverse physiological/pathophysiological events, such as protein and organelle turnover, development, aging, pathogen infection, cell death, and neurodegeneration. However, experimental me...

journal_title：Methods in enzymology

authors： Shvets E,Elazar Z

更新日期：2009-01-01 00:00:00

abstract：:A fundamental function of the vasculature is to deliver oxygen to tissues and organs. The cells that make up the vasculature also require oxygen, and are acted upon by oxygen in direct and indirect ways that can have significant effects on acute and chronic vascular function and morphology. The role that oxygen, or it...

journal_title：Methods in enzymology

authors： Huang Y,Giordano FJ

更新日期：2008-01-01 00:00:00

abstract：:Adenoviral vectors expressing vascular permeability factor/vascular endothelial growth factor (VPF/VEGF, VEGF-A(164)) offer a powerful method for elucidating the mechanisms of pathological angiogenesis and lymphangiogenesis and for evaluating the effectiveness of pro- and anti-angiogenesis therapies. When injected int...

journal_title：Methods in enzymology

authors： Nagy JA,Shih SC,Wong WH,Dvorak AM,Dvorak HF

更新日期：2008-01-01 00:00:00

abstract：:Cell migration plays a key role both in physiological conditions, such as tissue repair or embryonic development, and in pathological processes, including tumor metastasis. Understanding the mechanisms that allow cancer cells to invade tissues during metastasis requires studying their ability to migrate. While spectac...

journal_title：Methods in enzymology

authors： Vinot S,Anguille C,de Toledo M,Gadea G,Roux P

更新日期：2008-01-01 00:00:00

abstract：:Mutations in regulators and effectors of the Rho GTPases underlie various forms of mental retardation (MR). Among them, oligophrenin-1 (OPHN1), which encodes a Rho-GTPase activating protein, was one of the first Rho-linked MR genes identified. Upon characterization of OPHN1 in hippocampal brain slices, we obtained evi...

journal_title：Methods in enzymology

authors： Kasri NN,Govek EE,Van Aelst L

更新日期：2008-01-01 00:00:00

abstract：:There is now considerable experimental evidence that aberrant activation of Rho family small GTPases promotes uncontrolled proliferation, invasion, and metastatic properties of human cancer cells. Therefore, there is considerable interest in the development of small molecule inhibitors of Rho GTPase function. However,...

journal_title：Methods in enzymology

authors： Onesto C,Shutes A,Picard V,Schweighoffer F,Der CJ

更新日期：2008-01-01 00:00:00

abstract：:A significant proportion of RNA decay in eukaryotes takes place in the nucleus. In addition to targeting nongenic RNAs such as products of processing and spurious transcription events, nuclear RNA decay also removes aberrant transcripts from regular genes. Moreover, a small list of genes utilizes nuclear RNA turnover ...

journal_title：Methods in enzymology

authors： Schmid M,Rougemaille M,Libri D,Jensen TH

更新日期：2008-01-01 00:00:00

abstract：:The mapping and characterization of the vasculature using proteomics offers the opportunity to better understand the steps and molecular mechanisms involved in vascular development, and angiogenesis in particular. Proteomics has many key advantages over genomics, especially in directly determining protein expression. ...

journal_title：Methods in enzymology

authors： Griffin NM,Schnitzer JE

更新日期：2008-01-01 00:00:00

abstract：:Scanning transmission electron microscopy (STEM) of unstained, freeze-dried biological macromolecules in the dark-field mode provides an image based on the number of electrons elastically scattered by the constituent atoms of the macromolecule. The image of each isolated particle provides information about the project...

journal_title：Methods in enzymology

authors： Wall JS,Simon MN,Lin BY,Vinogradov SN

更新日期：2008-01-01 00:00:00

abstract：:Protein matrix cavities and extended tunnels can effectively channel substrates and products to and from active sites in enzymes. Substrate and product channeling can enhance catalytic efficiency by reducing the intramolecular diffusion times to and from reaction centers. Moreover, protected transfer between sites may...

journal_title：Methods in enzymology

authors： Pesce A,Milani M,Nardini M,Bolognesi M

更新日期：2008-01-01 00:00:00

abstract：:Nitric oxide (NO) is a ubiquitous gas with potent biological effects, including vasodilation, neuronal signaling, and antimicrobial activity. NO is a free radical and can readily react with other molecules, in particular, iron centers and oxygen. At physiological concentrations in aqueous solutions, even in the presen...

journal_title：Methods in enzymology

authors： Laver JR,Stevanin TM,Read RC

更新日期：2008-01-01 00:00:00

abstract：:Nitrite and nitrate represent the final products of nitric oxide (NO) oxidation pathways, and their hematic concentrations are frequently assessed as an index of systemic NO production. However, their intake with food can influence their levels. Nitrite and nitrate could have a role by producing NO, because nitrite ca...

journal_title：Methods in enzymology

authors： Giustarini D,Rossi R,Milzani A,Dalle-Donne I

更新日期：2008-01-01 00:00:00

abstract：:Of all arginine catabolic enzymes, the arginases and nitric oxide (NO) synthases are the ones that are of greatest interest to many investigators. Mammalian arginases catalyze the hydrolysis of arginine to ornithine and urea and are composed of two distinct isozymes: arginase I, located within the cytosol, and arginas...

journal_title：Methods in enzymology

authors： Kepka-Lenhart D,Ash DE,Morris SM

更新日期：2008-01-01 00:00:00

abstract：:Protein oxidation is implicated in atherogenesis and other inflammatory conditions. Measuring levels of chlorinated and nitrated proteins in biological matrices serves as a quantitative index of oxidative stress in vivo. One potential mechanism for oxidative stress involves myeloperoxidase, a heme protein expressed by...

journal_title：Methods in enzymology

authors： Shao B,Heinecke JW

更新日期：2008-01-01 00:00:00

abstract：:Nitration and oxidation of tyrosine, tryptophan, and methionine residues in proteins are potential markers of their interaction with peroxynitrite. This chapter describes the procedure for the detection of these nitro-oxidative modifications by tandem mass spectrometry. The peptide YGDLANWMIPGK, shown to contain a nit...

journal_title：Methods in enzymology

authors： Rebrin I,Bregere C,Gallaher TK,Sohal RS

更新日期：2008-01-01 00:00:00

abstract：:Cells belonging to the monocyte/macrophage lineage are in general highly resistant to peroxynitrite. Resistance is not dependent on the scavenging of peroxynitrite itself, or of other secondary reactive species, but is rather associated with the prompt activation of a survival signaling leading to the prevention of to...

journal_title：Methods in enzymology

authors： Cantoni O,Tommasini I,Cerioni L

更新日期：2008-01-01 00:00:00

abstract：:This chapter reviews basic concepts of nonlinear fluorescence upconversion, a technique whose temporal resolution is essentially limited only by the pulse width of the ultrafast laser. Design aspects for upconversion spectrophotofluorometers are discussed, and a recently developed system is described. We discuss appli...

journal_title：Methods in enzymology

authors： Xu J,Knutson JR

更新日期：2008-01-01 00:00:00

abstract：:Death receptors are a subgroup of the tumor necrosis factor receptor superfamily (TNFRSF) and mediate activation of what is widely known as the "extrinsic" apoptosis pathway. TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) is one of the most recent death receptor ligands identified. The TRAIL receptor ...

journal_title：Methods in enzymology

authors： Harper N,MacFarlane M

更新日期：2008-01-01 00:00:00

abstract：:Protein kinase C (PKC), a family of serine/threonine kinases, plays an important role in apoptosis. Several members of the PKC family act as substrates for caspases. In addition, PKCs can also regulate caspase activation and cell death by apoptosis. The cleavage of PKCs separates the regulatory domain from the catalyt...

journal_title：Methods in enzymology

authors： Basu A,Persaud SD,Sivaprasad U

更新日期：2008-01-01 00:00:00

abstract：:In cultured tobacco (BY-2) cells, autophagy seems to be induced under nutrient-starvation conditions, whereas in root cells from Arabidopsis and barley, it occurs constitutively though is activated under nutrient starvation conditions. In both cases, protease inhibitors such as E-64, E-64c, antipain, and leupeptin blo...

journal_title：Methods in enzymology

authors： Moriyasu Y,Inoue Y

更新日期：2008-01-01 00:00:00

abstract：:Cryptococcus neoformans is a yeastlike fungus that causes a lethal meningoencephalitis in a broad spectrum of immunocompromised patients and has become the most common cause of meningitis due to AIDS-related infections in Africa. Key to the development of new agents to control and prevent this infection is the identif...

journal_title：Methods in enzymology

authors： Hu G,Gibbons J,Williamson PR

更新日期：2008-01-01 00:00:00

abstract：:Aging that involves contact with dying yeast cells is one of the differential processes between sparkling and still wine production. The release of the products of autolysis during this aging step is fundamental for the quality of sparkling wines made by the traditional method. These cells undergo an autolysis process...

journal_title：Methods in enzymology

authors： Cebollero E,Rejas MT,González R

更新日期：2008-01-01 00:00:00

abstract：:In the yeast Saccharomyces cerevisiae, autophagy contributes to the sustaining of cell viability under starvation conditions, possibly through the supply of amino acids that is generated as a result of the degradation of cytosolic materials. Therefore, cellular viability is one of the best indexes for monitoring the c...

journal_title：Methods in enzymology

authors： Noda T

更新日期：2008-01-01 00:00:00

abstract：:Superoxide dismutases (SODs; EC 1.15.1.1) are a group of metalloenzymes which are essential to protect cells under aerobic conditions. In biological systems, it has been reported that SODs and other proteins are susceptible to be attacked by peroxynitrite (ONOO(-)) which can be originated from the reaction of nitric o...

journal_title：Methods in enzymology

authors： Larrainzar E,Urarte E,Auzmendi I,Ariz I,Arrese-Igor C,González EM,Moran JF

更新日期：2008-01-01 00:00:00