Biochemical pathway modeling tools for drug target detection in cancer and other complex diseases.

abstract：:Actinomycete bacteria of the genus Streptomyces are major producers of bioactive compounds for the biotechnology industry. They are the source of most clinically used antibiotics, as well as of several widely used drugs against common diseases, including cancer . Genome sequencing has revealed that the potential of St...

journal_title：Methods in enzymology

authors： Medema MH,Breitling R,Takano E

更新日期：2011-01-01 00:00:00

abstract：:Significant progress has been made in discovering and cloning a host of proteins, including a range of glycoproteins. The availability of their predicted amino acid sequences provides useful information, including potential N-linked glycosylation sites. However, only a limited number of protein structures have been so...

journal_title：Methods in enzymology

authors： Yen TY,Macher BA

更新日期：2006-01-01 00:00:00

abstract：:Membrane-initiated steroid signaling (MISS) involves rapid second messenger based intracellular signaling without coupling to transcription or translation. MISS activates important cellular signaling cascades such as mitogen-activated protein kinase (MAPK) or adenylate cyclase pathways. Despite its vital role in signa...

journal_title：Methods in enzymology

authors： Jani MS,Veetil AT,Krishnan Y

更新日期：2020-01-01 00:00:00

abstract：:Two-dimensional polyacrylomide gel electrophoresis remains a popular and powerful tool for identifying proteins that are differentially expressed across treatment conditions. Due to the overwhelming number of proteins and the tremendous variation shown in gel images, the differential analysis of 2D gel images is chall...

journal_title：Methods in enzymology

authors： Li F,Seillier-Moiseiwitsch F

更新日期：2011-01-01 00:00:00

abstract：:DNA repair complexes play crucial roles in maintaining genome integrity, which is essential for the survival of an organism. The understanding of their modes of action is often obscure due to limited structural knowledge. Structural characterizations of these complexes are often challenging due to a poor protein produ...

journal_title：Methods in enzymology

authors： Sawicka M,Aramayo R,Ayala R,Glyde R,Zhang X

更新日期：2017-01-01 00:00:00

abstract：:Phospholipase A(2)s (PLA(2)s) are a superfamily of enzymes involved in production of a wide variety of lipid mediators, including arachidonic acid, lysophospholipids, platelet activation factor, and eicosanoids. Fluorescence-based, real-time cellular activity assays for PLA(2)s have been developed as a tool for studyi...

journal_title：Methods in enzymology

authors： Manna D,Cho W

更新日期：2007-01-01 00:00:00

abstract：:The qualitative detection, quantification, and structural characterization of analytes in biological systems are important requirements for objectives to be fulfilled in systems biology research. One analytical tool applied to a multitude of systems biology studies is mass spectrometry, particularly for the study of p...

journal_title：Methods in enzymology

authors： Dunn WB

更新日期：2011-01-01 00:00:00

abstract：:Research on circadian biology over the past decade has paid increasing attention to the photoreceptor mechanisms that align the molecular clock to the 24-h light/dark cycle, and some of the results to emerge are surprising. For example, the rods and cones within the mammalian eye are not required for entrainment. A po...

journal_title：Methods in enzymology

authors： Peirson SN,Thompson S,Hankins MW,Foster RG

更新日期：2005-01-01 00:00:00

abstract：:Sedimentation velocity experiments measure the transport of molecules in solution under centrifugal force. Here, we describe a method for monitoring the sedimentation of very large biological molecular assemblies using the interference optical systems of the analytical ultracentrifuge. The mass, partial-specific volum...

journal_title：Methods in enzymology

authors： Rogge RA,Hansen JC

更新日期：2015-01-01 00:00:00

abstract：:Small GTPases of the Ras and Rho families are among the most studied signaling proteins and represent promising therapeutic targets for human neoplastic disease. Despite the high level of interest in these proteins, direct analysis of most aspects of Ras protein biology in living cells has not been possible, because m...

journal_title：Methods in enzymology

authors： Westwick JK,Michnick SW

更新日期：2006-01-01 00:00:00

abstract：:IF-liposomes are formed by a unique process that involves fusing small liposomes into interdigitated lipid sheets, using either ethanol or hydrostatic pressure. The interdigitation-fusion method requires liposome formulations with lipids that form the L beta I phase. Preparing ethanol-induced IF-liposomes is simple an...

journal_title：Methods in enzymology

authors： Ahl PL,Perkins WR

更新日期：2003-01-01 00:00:00

abstract：:Current methodologies available to quantify changes in mitochondrial turnover are limited to pulse-chase assays or specific assays that quantify mitophagy. Accordingly, new tools that can assess mitochondrial turnover are needed for the study of cellular, subcellular, and spatial parameters of mitochondrial turnover a...

journal_title：Methods in enzymology

authors： Trudeau KM,Gottlieb RA,Shirihai OS

更新日期：2014-01-01 00:00:00

abstract：:Complex synthetic schemes catalyzed by multienzyme systems immobilized on solid materials are gaining momentum in chemical biomanufacturing. These systems harness the high chemo-, regio-, and stereoselectivity of the enzymes and the recyclability of the heterogeneous catalysts. Moreover, when the enzymes become part o...

journal_title：Methods in enzymology

authors： López-Gallego F

更新日期：2019-01-01 00:00:00

abstract：:The Microsealed Drug Delivery (MDD) system was developed to achieve several objectives: to maximize the bioavailability of a therapeutic agent in a target tissue; to minimize the adverse side effects of a therapeutic agent or its metabolites; to optimize the onset, rate, and duration of drug delivery; to maintain the...

journal_title：Methods in enzymology

authors： Chien YW

更新日期：1985-01-01 00:00:00

abstract：:In human, rat, and mice, a UGT1 complex locus provides for developmental-, inducer-, and cell-specific synthesis of a family of chemical-detoxifying isozymes, UDP-glucuronosyltransferases, which prevent toxicities, mutagenesis, and/or carcinogenesis. Between 10 and 14 first exons with individual promoter elements are ...

journal_title：Methods in enzymology

authors： Owens IS,Basu NK,Banerjee R

更新日期：2005-01-01 00:00:00

abstract：:Embryonic stem (ES) cells are cells derived from the inner cell mass of a blastocyst stage embryo. These self-renewing multipotent cells are able to differentiate to the three embryonic germ layers, the endoderm, ectoderm, and mesoderm, and are thus able to produce virtually all cell types. The ES cell capacity to gen...

journal_title：Methods in enzymology

authors： Goldberg-Cohen I,Beck G,Ziskind A,Itskovitz-Eldor J

更新日期：2006-01-01 00:00:00

abstract：:The breakthrough discovery that double-stranded RNA of 21 nucleotides in length (referred to as short or small interfering RNA; siRNA) can trigger sequence-specific gene silencing in mammalian cells has led to the development of a powerful new approach to study gene function (Dillon et al., 2005; Dykxhoorn et al., 200...

journal_title：Methods in enzymology

authors： Janas J,Skowronski J,Van Aelst L

更新日期：2006-01-01 00:00:00

abstract：:Intracellular protein degradation is one of the most precisely regulated processes in living cells. The main component of the degradation machinery is the 20S proteasome present in eukaryotes as well as in prokaryotes. We have developed successful purification protocols for the 20S proteasome in its native state using...

journal_title：Methods in enzymology

authors： Groll M,Huber R

更新日期：2005-01-01 00:00:00

abstract：:Phosphoinositide-3-kinase (PI3K) signaling has been implicated in a panoply of cellular responses including survival, proliferation, protein synthesis, migration, and vesicular trafficking. In addition, alterations in the enzymatic activity of PI3Ks have been involved in the pathogenesis of multiple diseases, ranging ...

journal_title：Methods in enzymology

authors： Ciraolo E,Gulluni F,Hirsch E

更新日期：2014-01-01 00:00:00

abstract：:In mice with lupus nephritis qualitative changes in anti-DNA antibodies occur, such as IgG switch and increased cationic charge, to render these antibodies pathogenic. Pathogenic anti-DNA idiotypes can be encoded by genes of a normal mouse strain such as SWR, where they remain dormant. When the normal mice are crossed...

journal_title：Methods in enzymology

authors： Datta SK

更新日期：1988-01-01 00:00:00

abstract：:Atomic force microscopy (AFM) enables direct visualization of single-protein molecules in liquids at submolecular resolution. High-speed AFM further makes it possible to visualize dynamic biomolecular processes at subsecond resolution. However, dynamic imaging of biomolecular processes imposes various requirements on ...

journal_title：Methods in enzymology

authors： Yamamoto D,Uchihashi T,Kodera N,Yamashita H,Nishikori S,Ogura T,Shibata M,Ando T

更新日期：2010-01-01 00:00:00

abstract：:Integrins are large modular cell-surface receptors that regulate almost every aspect of cellular function through bidirectional signals transmitted across the lipid bilayer. Regulation of integrin activity is accomplished by complex and still incompletely understood biochemical pathways that modify integrin ligand bin...

journal_title：Methods in enzymology

authors： Xiong JP,Goodman SL,Arnaout MA

更新日期：2007-01-01 00:00:00

abstract：:Essentially the same steps are required to solve the crystal structure of a serpin as for any other protein: produce and purify protein, grow crystals, collect diffraction data, find estimates of the phase angles, and then refine and validate the structure. For the phasing step, experimental phasing methods involving ...

journal_title：Methods in enzymology

authors： Read RJ,Zhou A,Stein PE

更新日期：2011-01-01 00:00:00

abstract：:Covalent modification of proteins with ubiquitin plays an important role in a wide array of cellular processes (Hershko and Ciechanover, 1998; Pickart, 2004). For this reason an increasing number of investigators in diverse research fields are confronted with the question whether their favorite proteins are ubiquitina...

journal_title：Methods in enzymology

authors： Kaiser P,Tagwerker C

更新日期：2005-01-01 00:00:00

abstract：:The long-pulse spallation source of the European Spallation Source-a facility under construction in Lund, Sweden-is well suited for macromolecular crystallography experiments. We review briefly the particular properties of the long-pulse source and the associated high-brilliance moderators from the point of view of in...

journal_title：Methods in enzymology

authors： Markó M,Nagy G,Aprigliano G,Oksanen E

更新日期：2020-01-01 00:00:00

abstract：:The RNA-guided, sequence-specific endonuclease Cas9 has been widely adopted as genome engineering tool due to its efficiency and ease of use. Derived from the microbial CRISPR (clustered regularly interspaced short palindromic repeat) type II adaptive immune system, Cas9 has now been successfully engineered for genome...

journal_title：Methods in enzymology

authors： Trevino AE,Zhang F

更新日期：2014-01-01 00:00:00

abstract：:The genome integrity of living organisms is constantly threatened by endogenous cellular metabolic processes and environmental agents. To quantify these low, physiologically relevant levels of DNA damage, a single-cell gel electrophoresis (comet) combined with strand-specific fluorescence in situ hybridization (FISH)-...

journal_title：Methods in enzymology

authors： Mondal M,Guo J

更新日期：2017-01-01 00:00:00

abstract：:Life cell imaging is a tool for cell biology that has provided invaluable insights into many dynamic processes such as cell division, morphogenesis, or endo- and exocytosis. While observing cells by time-lapse imaging is a standard procedure in many systems, this technique was until recently not available for blood st...

journal_title：Methods in enzymology

authors： Grüring C,Spielmann T

更新日期：2012-01-01 00:00:00

abstract：:Stable isotope tracers are widely used to quantify metabolic rates, and yet a limited number of studies have considered the impact of analytical error on estimates of flux. For example, when estimating the contribution of de novo lipogenesis, one typically measures a minimum of four isotope ratios, i.e., the precursor...

journal_title：Methods in enzymology

authors： Previs SF,Herath K,Castro-Perez J,Mahsut A,Zhou H,McLaren DG,Shah V,Rohm RJ,Stout SJ,Zhong W,Wang SP,Johns DG,Hubbard BK,Cleary MA,Roddy TP

更新日期：2015-01-01 00:00:00

abstract：:Nucleotide excision repair is a multicomponent, multistep enzymatic system that removes a wide spectrum of DNA damage by dual incisions in the damaged strand on both sides of the lesion. The basic steps are damage recognition, dual incisions, resynthesis to replace the excised DNA, and ligation. Each step has been stu...

journal_title：Methods in enzymology

authors： Reardon JT,Sancar A

更新日期：2006-01-01 00:00:00