Yeast model systems for examining nitrogen oxide biochemistry/signaling.

abstract：:Retinoic acid (RA), the biologically active metabolite of vitamin A, regulates a vast spectrum of biological processes, such as cell differentiation, proliferation, apoptosis, and morphogenesis. microRNAs (miRNAs) play a crucial role in regulating gene expression by binding to messenger RNA (mRNA) which leads to mRNA ...

journal_title：Methods in enzymology

authors： Wang L,Rohatgi AP,Wan YY

更新日期：2020-01-01 00:00:00

abstract：:Ubiquitination is a prevalent protein modification catalyzed by E1, E2, and E3 enzymes that activate, conjugate, and ligate, respectively, the ubiquitin protein to substrate protein. In order to establish a mutualistic or parasitic relationship with their eukaryotic hosts, many microorganisms hijack different aspects ...

journal_title：Methods in enzymology

authors： Qiu J,Luo ZQ

更新日期：2019-01-01 00:00:00

abstract：:Monte Carlo simulations of neighbor exclusion models have been used to demonstrate the importance of collecting and fitting data over a wide range of saturation. Low saturation data are important for good estimates of the affinity K of a drug or protein for the lattice site. High saturation data are important for dist...

journal_title：Methods in enzymology

authors： Correia JJ,Chaires JB

更新日期：1994-01-01 00:00:00

abstract：:Complex RNA structures regulate many biological processes but are often too large for structure determination by nuclear magnetic resonance (NMR) methods. We determined the solution structure of domain II of the hepatitis C viral internal ribosome entry site (HCV IRES), a 25-kDa RNA, using a novel NMR approach. Conven...

journal_title：Methods in enzymology

authors： Lukavsky PJ,Puglisi JD

更新日期：2005-01-01 00:00:00

abstract：:Reliable modeling of RNA tertiary structures is key to both understanding these structures' roles in complex biological machines and to eventually facilitating their design for molecular computing and robotics. In recent years, a concerted effort to improve computational prediction of RNA structure through the RNA-Puz...

journal_title：Methods in enzymology

authors： Cheng CY,Chou FC,Das R

更新日期：2015-01-01 00:00:00

abstract：:In polarized epithelial cells, the tight junction has been ascribed several functions including the regulation of the paracellular permeability, an impediment to the diffusion of molecules between the apical and basolateral domains, a site of delivery of transport vesicles for basolateral proteins, and a scaffold for ...

journal_title：Methods in enzymology

authors： Luton F

更新日期：2005-01-01 00:00:00

abstract：:This chapter outlines methods that can be applied to determine the levels of lipids in cells and tissues. In particular, the methods focus upon the extraction and analysis of those lipids critical for monitoring signal transduction pathways. The methods address the analysis of the phosphoinositides, the lipid agonists...

journal_title：Methods in enzymology

authors： Wakelam MJ,Pettitt TR,Postle AD

更新日期：2007-01-01 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：:kappaB-Ras1 and kappaB-Ras2 are two small proteins that display similarity at the amino acid level to Ras-like small GTPases. Although little is known about the function of the kappaB-Ras proteins, they have been shown to interfere with activation of transcription factor NF-kappaB. They accomplish this by binding to I...

journal_title：Methods in enzymology

authors： Huxford T,Ghosh G

更新日期：2006-01-01 00:00:00

abstract：:Silica biomorphs and silica gardens are canonical examples of precipitation phenomena yielding self-assembled nanocrystalline composite materials with outstanding properties in terms of morphology and texture. Both types of structures form spontaneously in alkaline environments and rely on simple, and essentially simi...

journal_title：Methods in enzymology

authors： Kellermeier M,Glaab F,Melero-García E,García-Ruiz JM

更新日期：2013-01-01 00:00:00

abstract：:The target-of-rapamycin (TOR) pathway is a major regulator of cellular growth, division, and metabolism by coupling growth and nutrient cues to fundamental processes such as translation and transcription. In vertebrate models, disruptions affecting components of the TOR pathway result in cilia size abnormalities and c...

journal_title：Methods in enzymology

authors： Yuan S,Zhao L,Sun Z

更新日期：2013-01-01 00:00:00

abstract：:The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information archives and freely distributes high-throughput molecular abundance data, predominantly gene expression data generated by DNA microarray technology. The database has a flexible design that can handle diverse styles of bot...

journal_title：Methods in enzymology

authors： Barrett T,Edgar R

更新日期：2006-01-01 00:00:00

abstract：:Obtaining patient-specific information through the quantification of small molecules and proteins in bodily fluids is essential for personalized therapies. Point-of-care (POC) diagnostic devices hold the promise of delivering such benefit to a wide range of patients. However, there is a lack of enabling technology, as...

journal_title：Methods in enzymology

authors： Yu Q,Griss R,Schena A,Johnsson K

更新日期：2017-01-01 00:00:00

abstract：:Enzymology is approaching an era where many problems can benefit from computational studies. While ample challenges remain in quantitatively predicting behavior for many enzyme systems, the insights that often come from computations are an important asset for the enzymology community. Here we provide a primer for enzy...

journal_title：Methods in enzymology

authors： Roston D,Cui Q

更新日期：2016-01-01 00:00:00

abstract：:Primary mixed liver cells were isolated from rats that had been fed an amino acid (AA) diet in which natural protein was replaced with a defined mixture of pure AAs. Nitric oxide (NO) production from these cells in vitro was monitored using a nitric oxide (NO)-selective fluorescent probe, diaminofluorescein, followed ...

journal_title：Methods in enzymology

authors： Kotake Y,Kishida H,Nakae D,Floyd RA

更新日期：2005-01-01 00:00:00

abstract：:Polyacrylamide gel electrophoresis under native conditions (native PAGE) is a well-established and versatile method for probing nucleic acid conformation and nucleic acid-protein interactions. Native PAGE has been used to measure RNA folding equilibria and kinetics under a wide variety of conditions. Advantages of thi...

journal_title：Methods in enzymology

authors： Woodson SA,Koculi E

更新日期：2009-01-01 00:00:00

abstract：:A variety of recent advances in single-molecule methods are now making possible the routine measurement of the distinct catalytic trajectories of individual enzymes. Unlike their bulk counterparts, these measurements directly reveal the fluctuations inherent to enzymatic dynamics, and statistical measures of these flu...

journal_title：Methods in enzymology

authors： Moffitt JR,Chemla YR,Bustamante C

更新日期：2010-01-01 00:00:00

abstract：:Antimicrosomal antibodies in inflammatory liver diseases all seem to be directed against members of the cytochrome P450 family of proteins. These autoantigens seem to be genetically polymorphic, the autoantibodies are inhibitory, and the autoepitopes are generally conserved among species. Anti-P450 autoantibodies shar...

journal_title：Methods in enzymology

authors： Manns MP,Johnson EF

更新日期：1991-01-01 00:00:00

abstract：:Circadian clocks are present in most cells and are essential for maintenance of daily rhythms in physiology, mood, and cognition. Thus, not only neurons of the central circadian pacemaker but also many other peripheral tissues possess the same functional and self-sustained circadian clocks. Surprisingly, however, thei...

journal_title：Methods in enzymology

authors： Gaspar L,Brown SA

更新日期：2015-01-01 00:00:00

abstract：:Extracellular signals dictate the biological processes of neural stem cells (NSCs) both in vivo and in vitro. The intracellular response elicited by these signals is dependent on the context in which the signal is received, which in turn is decided by previous and concurrent signals impinging on the cell. A synthesis ...

journal_title：Methods in enzymology

authors： Rajan P,Snyder E

更新日期：2006-01-01 00:00:00

abstract：:It has become increasingly clear that large RNA molecules, especially long noncoding RNAs, function in almost all gene regulatory processes (Cech & Steitz, 2014). Many large RNAs appear to be structural scaffolds for assembly of important RNA/protein complexes. However, the structures of most large cellular RNA molecu...

journal_title：Methods in enzymology

authors： Lin Y,May GE,Joel McManus C

更新日期：2015-01-01 00:00:00

abstract：:Hypoxia and inflammation are coincidental events in an array of diseased tissues, including chronically inflamed sites (e.g., inflammatory bowel disease, rheumatoid arthritis), growing tumors, myocardial infarcts, atherosclerotic plaques, healing wounds, and sites of bacterial infection (Murdoch et al., 2005). An unde...

journal_title：Methods in enzymology

authors： Cummins EP,Comerford KM,Scholz C,Bruning U,Taylor CT

更新日期：2007-01-01 00:00:00

abstract：:G-protein-coupled receptors (GPCRs) form a superfamily of membrane proteins that play a crucial role in mediating physiological processes as well as pathogenesis of many critical diseases. They are one of the most successful drug targets, accounting for more than 30% of prescription drugs on the market today. Three-di...

journal_title：Methods in enzymology

authors： Vaidehi N,Pease JE,Horuk R

更新日期：2009-01-01 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：:Inositol phosphates (InsPs) are an important group of eukaryotic messengers and mediate a wide range of processes. To elucidate the biological functions of these molecules, robust techniques to characterize inositol phosphate metabolism at the cellular level are highly sought after. This chapter provides a detailed pr...

journal_title：Methods in enzymology

authors： Puschmann R,Harmel RK,Fiedler D

更新日期：2020-01-01 00:00:00

abstract：:When yeast are faced with irreparable DNA damage, they will first arrest in G2/M, via the DNA damage checkpoint pathway, but will subsequently adapt to that arrest and resume division. Here, we summarize assays that we have used to examine checkpoint adaptation. Specifically, we discuss the merits of inducing DNA dama...

journal_title：Methods in enzymology

authors： Toczyski DP

更新日期：2006-01-01 00:00:00

abstract：:Extracellular thiol/disulfide redox environments are highly regulated in healthy individuals and become oxidized in disease. This oxidation affects the function of cell surface receptors, ion channels, and structural proteins. Downstream signaling due to changes in extracellular redox potential can be studied using a ...

journal_title：Methods in enzymology

authors： Go YM,Jones DP

更新日期：2010-01-01 00:00:00

abstract：:Hybrid proteins or chimeras are generated by recombination of protein fragments. In the course of evolution, this mechanism has led to major diversification of protein folds and their functionalities. Similarly, protein engineers have taken advantage of this attractive strategy to build new proteins. Methods that use ...

journal_title：Methods in enzymology

authors： Rico JA,Höcker B

更新日期：2013-01-01 00:00:00

abstract：:Dimethylsulfoniopropionate (DMSP) demethylase is a tetrahydrofolate-dependent enzyme that initiates the DMSP demethylation pathway in marine bacteria. This enzyme is important for understanding of organic sulfur flux from the oceans because it directs the sulfur from DMSP away from dimethylsulfide. This enzyme has bee...

journal_title：Methods in enzymology

authors： Reisch CR

更新日期：2018-01-01 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