Crystallization and X-ray structure determination of an RNA-dependent hexameric helicase.

abstract：:An overview of resolution enhancement of conventional, field-swept, continuous-wave electron paramagnetic resonance spectra using Fourier transform-based deconvolution methods is presented. Basic steps that are involved in resolution enhancement of calculated spectra using an implementation based on complex discrete F...

journal_title：Methods in enzymology

authors： Reed GH,Poyner RR

更新日期：2015-01-01 00:00:00

abstract：:A neuron is able to seamlessly respond to a number of signals, in a timely and specific manner. This process, of integrating multiple inputs, relays on the orchestration of intracellular events by signaling networks. The inherent complexity of signaling networks has made computational modeling a useful approach to und...

journal_title：Methods in enzymology

authors： Wenderski WC,Neves SR

更新日期：2012-01-01 00:00:00

abstract：:Recurrent aliphatic hydrophobic amino acids which occur in the sequence of a protein or a peptide at positions which form an axial, hydrophobic strip when the sequence is coiled as an alpha helix might stabilize coiling against hydrophobic surfaces. That effect can lead to helix formation against hydrophobic cores of ...

journal_title：Methods in enzymology

authors： Reyes VE,Lew RA,Lu S,Humphreys RE

更新日期：1991-01-01 00:00:00

abstract：:Precise investigation and manipulation of gene function often require modulation in a controlled and dynamic manner. In this chapter, we describe the methods to apply HIT systems for drug inducible transcriptional activation or simultaneous activation and genome editing in human cells. Together with those for editing,...

journal_title：Methods in enzymology

authors： Zhao C,Wei S,Wang Y

更新日期：2019-01-01 00:00:00

abstract：:Considering that HIV-1 accumulates and replicates actively within lymphoid tissues, any strategy that will decrease viral stores in these tissues might be beneficial to the infected host. Follicular dendritic cells (FDC), B lymphocytes, antigen-presenting cells like macrophages, and activated CD4(+) T cells are abunda...

journal_title：Methods in enzymology

authors： Désormeaux A,Bergeron MG

更新日期：2005-01-01 00:00:00

abstract：:The functional properties of proteins are decided not only by their relatively rigid overall structures, but even more importantly, by their dynamic properties. In a protein, some regions of structure exhibit highly correlated or anti-correlated motions with others, some are highly dynamic but uncorrelated, while othe...

journal_title：Methods in enzymology

authors： Yu H,Dalby PA

更新日期：2020-01-01 00:00:00

abstract：:In eukaryotes, determination of the subcellular location of a novel protein encoded in genomic or transcriptomic data provides useful clues as to its possible function. However, experimental localization studies are expensive and time-consuming. As a result, accurate in silico prediction of subcellular localization fr...

journal_title：Methods in enzymology

authors： Gaston D,Tsaousis AD,Roger AJ

更新日期：2009-01-01 00:00:00

abstract：:Iron-sulfur (Fe/S) proteins are involved in numerous key biological functions such as respiration, metabolic processes, protein translation, DNA synthesis, and DNA repair. The simplest types of Fe/S clusters include [2Fe-2S], [3Fe-4S], and [4Fe-4S] forms that sometimes are present in multiple copies. De novo assembly ...

journal_title：Methods in enzymology

authors： Freibert SA,Weiler BD,Bill E,Pierik AJ,Mühlenhoff U,Lill R

更新日期：2018-01-01 00:00:00

abstract：:Expressed protein ligation (EPL) combines two methods to ligate a synthetic peptide to a recombinant protein. Native chemical ligation (NCL) is a process in which two synthesized peptides are ligated by reaction of a C-terminal thioester on one peptide with an N-terminal cysteine residue of another protein. The chemis...

journal_title：Methods in enzymology

authors： Mitchell SF,Lorsch JR

更新日期：2014-01-01 00:00:00

abstract：:Rarely is any solution simply solute and water. In vivo, solutes, such as proteins and nucleic acids, swim in a sea of water, salts, ions, small molecules, and lipids, not to mention other macromolecules. In vitro, virtually all solutions contain a mixture of aqueous solvents, or "cosolvents" [i.e., solvent(s) in addi...

journal_title：Methods in enzymology

authors： Beck DA,Bennion BJ,Alonso DO,Daggett V

更新日期：2007-01-01 00:00:00

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：:The neutral arachidonic acid derivatives N-arachidonoyl ethanolamine (anandamide or AEA), and 2-arachidonoylglycerol (2-AG) have been identified as endogenous ligands for the cannabinoid receptors. Additionally, these compounds have been identified as substrates of the second isoform of the cyclooxygenase enzyme (COX-...

journal_title：Methods in enzymology

authors： Kingsley PJ,Marnett LJ

更新日期：2007-01-01 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：:In this article, we have described methods used to purify Rnt1p and study its biochemical properties. Rnt1p can be easily purified from bacteria as N-terminal His6-tagged protein and its activity may be monitored in vitro. Rnt1p cleaves the RNA by binding to a cleavage site followed by hydrolysis and product release. ...

journal_title：Methods in enzymology

authors： Lamontagne B,Elela SA

更新日期：2001-01-01 00:00:00

abstract：:Amyloid aggregates are associated with a number of mammalian neurodegenerative diseases. Infectious aggregates of the mammalian prion protein PrP(sc) are hallmarks of transmissible spongiform encephalopathies in humans and cattle (Griffith, 1967; Legname et al., 2004; Prusiner, 1982; Silveira et al., 2004). Likewise, ...

journal_title：Methods in enzymology

authors： Bagriantsev SN,Kushnirov VV,Liebman 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：:Transfer RNA is extensively modified by the actions of a variety of enzymes. The radical S-adenosyl-l-methionine enzyme TYW1 modifies tRNAPhe forming the characteristic tricyclic ring via the condensation of carbons 2 and 3 of pyruvate. This chapter details methods that are required for studies of TYW1. ...

journal_title：Methods in enzymology

authors： Young AP,Bandarian V

更新日期：2018-01-01 00:00:00

abstract：:A synthetic ligand regulable system for gene transfer and expression has been developed in our laboratory based on mechanistic studies of steriod hormone receptor and transcriptional regulation. This gene switch system possesses most of the important features that are required for application of the system in biologic...

journal_title：Methods in enzymology

authors： Ye X,Schillinger K,Burcin MM,Tsai SY,O'Malley BW

更新日期：2002-01-01 00:00:00

abstract：:The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety o...

journal_title：Methods in enzymology

authors： Palmer AG 3rd,Koss H

更新日期：2019-01-01 00:00:00

abstract：:Synthetic hydrogen sulfide (H2S) donors are useful research tools as well as potential therapeutic agents. In this chapter, we report the detailed protocols for the synthesis and evaluation of a series of phosphorodithioate-based H2S donors. Fluorescence assays were used to determine H2S release from the donors in bot...

journal_title：Methods in enzymology

authors： Park CM,Xian M

更新日期：2015-01-01 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：:In budding yeast and higher eukaryotic genomes, there are, respectively, 50 and up to 400 or more distinct genes that encode for ubiquitin-ligases, and approximately 15-90 genes that encode for ubiquitin isopeptidases (TM and RJD, Semple et al., 2003). This puts ubiquitylation on par with phosphorylation as the most c...

journal_title：Methods in enzymology

authors： Mayor T,Deshaies RJ

更新日期：2005-01-01 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：:Recent advances in functional genomics have enabled genome-wide genetic studies in mammalian cells. These include the establishment of high-throughput transfection and viral propagation methodologies, the production of large-scale cDNA and siRNA libraries, and the development of sensitive assay detection processes and...

journal_title：Methods in enzymology

authors： Rines DR,Tu B,Miraglia L,Welch GL,Zhang J,Hull MV,Orth AP,Chanda SK

更新日期：2006-01-01 00:00:00

abstract：:By far the highest resolution of all separation techniques for intact proteins in a single analytical run continues to be by the combination of isoelectric focusing (IEF) and SDS-PAGE, originally introduced by O'Farrell [(1975). J. Biol. Chem.250, 4007-4021]. This analytical platform has seen a number of significant a...

journal_title：Methods in enzymology

authors： Friedman DB,Hoving S,Westermeier R

更新日期：2009-01-01 00:00:00

abstract：:Intracellular calcium (Ca2+) is involved in the regulation of a variety of biological functions in cancer cells, including growth inhibition, tumor invasiveness, and drug resistance. To gain insight into the possible role played by Ca2+ in the development of drug resistance in breast cancer, we performed a comparative...

journal_title：Methods in enzymology

authors： DeBernardi MA,Brooker G

更新日期：2006-01-01 00:00:00

abstract：:The human cannabinoid receptor, CB1, has been difficult to purify in a functional form, hampering structural and biophysical studies. Here, we present our approaches for obtaining pure, detergent solubilized, functional CB1. We also discuss our site-directed fluorescence labeling (SDFL) methods for identifying differe...

journal_title：Methods in enzymology

authors： Fay JF,Farrens DL

更新日期：2017-01-01 00:00:00

abstract：:Enzyme immobilization is a widespread empiric technology to achieve more stable, active and reusable enzymes. The empiricism can be reduced by the application of rational design procedures employing bioinformatic tools, engineered-proteins and detailed analyses of existent data. In this chapter, we describe relevant a...

journal_title：Methods in enzymology

authors： Sastre DE,Reis EA,Marques Netto CGC

更新日期：2020-01-01 00:00:00

abstract：:The characterization of microbial adhesins is greatly facilitated by the use of synthetic peptides. Synthetic peptides can be used to identify specific antigenic epitopes, to delineate receptor-binding domain of adhesins, and to facilitate the characterization of the adhesin, and they allow for a direct examination of...

journal_title：Methods in enzymology

authors： Lee KK,Wong WY,Sheth HB,Hodges RS,Paranchych W,Irvin RT

更新日期：1995-01-01 00:00:00

abstract：:In this chapter, we describe the currently most advanced methods applied for the quantitative assessment of ROS homeostasis inside the mitochondrion. These techniques are of particular interest in the field of oxidative stress. After discussing the importance of quantifying mitochondrial ROS homeostasis, three major a...

journal_title：Methods in enzymology

authors： Tretter L,Ambrus A

更新日期：2014-01-01 00:00:00