Engineering Short Preorganized Peptide Sequences for Metal Ion Coordination: Copper(II) a Case Study.

abstract：:Quantitative real-time polymerase chain reaction (qRT-PCR) is a flexible and scalable method for analyzing transcript abundance that can be used at a single gene or high-throughput (>100 genes) level. Information obtained from this technique can be used as an indicator of potential regulation of glycosylation at the t...

journal_title：Methods in enzymology

authors： Nairn AV,dela Rosa M,Moremen KW

更新日期：2010-01-01 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

abstract：:Delivery of drugs and molecules to eukaryote animal and plant cells can be enhanced when mediated by mesoporous silica nanoparticle (MSN) materials. This chapter describes, in detail, the synthesis of several different MSN materials used for the transport of various hydrophilic and hydrophobic drug molecules, neurotra...

journal_title：Methods in enzymology

authors： Fang IJ,Trewyn BG

更新日期：2012-01-01 00:00:00

abstract：:To maintain cellular homeostasis, the levels of transmembrane receptors found on the plasma membrane must be tightly regulated. Endocytosis of activated receptors and the eventual degradation of these transmembrane proteins in the lysosome serve a vital role in maintaining the plasma membrane receptor levels as well a...

journal_title：Methods in enzymology

authors： Davies BA,Carney DS,Horazdovsky BF

更新日期：2005-01-01 00:00:00

abstract：:The monitoring of trace amounts of nitric oxide (NO) is of great interest for biomedical applications. High-resolution infrared spectroscopy, like laser magnetic resonance spectroscopy (LMRS), is a versatile technique for the quantitative and isotope-selective analysis of low concentrations of NO. The ability to disti...

journal_title：Methods in enzymology

authors： Gäbler R,Lehmann J

更新日期：2005-01-01 00:00:00

abstract：:Malaria represents an emerging disease because of increasing parasite resistance against available drugs and because of increasing geographical distribution of the causative agent, Plasmodium falciparum. The complete genome of Plasmodium was sequenced recently, revealing that the parasite harbors only one glutathione ...

journal_title：Methods in enzymology

authors： Deponte M,Becker K

更新日期：2005-01-01 00:00:00

abstract：:Aliphatic carbon-halogen (C-X) bonds are prevalent in modern pharmaceuticals and bioactive natural products. Three distinct chemical strategies are known in Nature to generate these structural motifs. The first is via the nucleophilic substitution at a prefunctionalized electrophilic carbon center with a halide anion ...

journal_title：Methods in enzymology

authors： Liu X

更新日期：2018-01-01 00:00:00

abstract：:Astrocytes are the most abundant cell type in the brain and are a crucial part of solving its mysteries. Originally assumed to be passive supporting cells, astrocyte's functions are now recognized to include active modulation and information processing at the neural synapse. The full extent of the astrocyte contributi...

journal_title：Methods in enzymology

authors： Preston AN,Cervasio DA,Laughlin ST

更新日期：2019-01-01 00:00:00

abstract：:Approximately one-third of all newly translated polypeptides interact with the endoplasmic reticulum (ER), an event that is essential to target these nascent proteins to distinct compartments within the cell or to the extracellular milieu. Thus, the ER houses molecular chaperones that augment the folding of this diver...

journal_title：Methods in enzymology

authors： Brodsky JL

更新日期：2010-01-01 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：:The history of free radical biochemistry is briefly reviewed in respect to major trend shifts from the focus on radiation damage toward enzymology of radical production and removal and ultimately the role of radicals, hydroperoxides, and related fast reacting compounds in metabolic regulation. Selected aspects of the ...

journal_title：Methods in enzymology

authors： Flohé L

更新日期：2010-01-01 00:00:00

abstract：:In this chapter we have discussed the methodology used to identify and characterize three intermediates in protein transport from the ER that represent stages of transport vesicle budding, targeting, and fusion. The intermediates are obtained using a variety of transport inhibitors: low-temperature incubations, additi...

journal_title：Methods in enzymology

authors： Rexach MF,Schekman RW

更新日期：1992-01-01 00:00:00

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：:RNA-binding proteins (RBPs) coordinate post-transcriptional control of gene expression, often through sequence-specific recognition of primary transcripts or mature messenger RNAs. Hundreds of RBPs are encoded in the human genome, most with undefined or incompletely defined biological roles. Understanding the function...

journal_title：Methods in enzymology

authors： Lambert NJ,Robertson AD,Burge CB

更新日期：2015-01-01 00:00:00

abstract：:Protein kinases transfer a phosphoryl group from ATP onto target proteins and play a critical role in signal transduction and other cellular processes. Here, we review the kinase kinetic and chemical mechanisms and their application in understanding kinase structure and function. Aberrant kinase activity has been impl...

journal_title：Methods in enzymology

authors： Wang Z,Cole PA

更新日期：2014-01-01 00:00:00

abstract：:The circadian clock exists to synchronize inner physiology with the external world, allowing life to anticipate and adapt to the continual changes that occur in an organism's environment. The clock architecture is highly conserved, present in almost all major branches of life. Within eukaryotes, the filamentous fungus...

journal_title：Methods in enzymology

authors： Hurley J,Loros JJ,Dunlap JC

更新日期：2015-01-01 00:00:00

abstract：:This chapter discusses experimental methods and protocols for the purification and preliminary characterization of DNA polymerases that are specialized for the replicative bypass (translesion DNA synthesis) of base or other types of DNA damage that typically arrest high-fidelity DNA synthesis, with particular emphasis...

journal_title：Methods in enzymology

authors： Fischhaber PL,McDaniel LD,Friedberg EC

更新日期：2006-01-01 00:00:00

abstract：:Transporters are crucial in a number of cellular functions, including nutrient uptake, cell signaling, and toxin removal. As such, transporters are important drug targets and their malfunction is related to several disease states. Treating transporter-related diseases and developing pharmaceuticals targeting transport...

journal_title：Methods in enzymology

authors： Mulligan C,Mindell JA

更新日期：2017-01-01 00:00:00

abstract：:PYP-phytochrome (Ppr) is a unique photoreceptor that contains a blue light-absorbing photoactive yellow protein (PYP) domain, a red light-absorbing phytochrome domain, and a histidine kinase domain. This chapter describes overexpression of Ppr in a strain of Escherichia coli that allows covalent attachment of substoic...

journal_title：Methods in enzymology

authors： Chung YH,Masuda S,Bauer CE

更新日期：2007-01-01 00:00:00

abstract：:Human embryonic stem cells (hESCs) are derived from preimplantation embryos. Approximately 60% of human embryos are blocked during in vitro development. Although statistics are inconclusive, experience demonstrates that hESCs are more effectively derived from high-quality embryos. In this way, optimal human embryo cul...

journal_title：Methods in enzymology

authors： Mercader A,Valbuena D,Simón C

更新日期：2006-01-01 00:00:00

abstract：:PRA2 was found to interact with the ER-localized protein VAMP-associated protein of 33 kDa or VAP-33 by a yeast two-hybrid screen. We describe here the purification of PRA2 and VAP-33 as well as an in vitro pull-down procedure to verify the interaction. PRA2 was found to form a large sodium dodecyl sulfate (SDS)-insol...

journal_title：Methods in enzymology

authors： Gougeon PY,Ngsee JK

更新日期：2005-01-01 00:00:00

abstract：:Posttranslational modification of circadian clock proteins by phosphorylation is an essential regulatory process in the control of eukaryotic circadian clocks. In the Neurospora circadian clock, the key clock protein FREQUENCY (FRQ) is progressively phosphorylated. The phosphorylation of FRQ is regulated by both kinas...

journal_title：Methods in enzymology

authors： Liu Y

更新日期：2005-01-01 00:00:00

abstract：:Recent work demonstrates that RNA interference (RNAi) can coordinate protein expression. Inhibitory RNAs are expressed naturally in cells as microRNAs (miRNAs) or introduced into cells as small interfering RNAs (siRNAs). Both types of small RNAs can be used at the bench to silence mRNA expression. For many researchers...

journal_title：Methods in enzymology

authors： Davidson BL,Harper SQ

更新日期：2005-01-01 00:00:00

abstract：:The properties of a collection of transposon Tn5 derivatives that generate reporter gene fusions and internal protein tags are summarized. Procedures utilizing several of the transposons for generating genes activated by Cre-loxP recombination and for creating large sequence-defined mutant libraries are described in d...

journal_title：Methods in enzymology

authors： Gallagher L,Turner C,Ramage E,Manoil C

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：:Determination of the three-dimensional structures of the globins led to the problem of determining how the ligands bound to the heme. In many of these structures there was no clear path from the solvent to the ligand-binding site. Even in those structures that appeared to have one or more tunnels from the exterior to ...

journal_title：Methods in enzymology

authors： Golden SD,Olsen KW

更新日期：2008-01-01 00:00:00

abstract：:Neurons are probably the most highly polarized cell type and typically develop a single axon and several dendrites. The establishment of a polarized morphology and the functional specialization of axonal and dendritic compartments are essential steps in the differentiation of neurons. Primary cultures of dissociated h...

journal_title：Methods in enzymology

authors： Schwamborn JC,Li Y,Püschel AW

更新日期：2006-01-01 00:00:00

abstract：:Regulator of G-protein signaling (RGS) domains bind directly to GTP-bound Galpha subunits and accelerate their intrinsic GTPase activity by up to several thousandfold. The selectivity of RGS proteins for individual Galpha subunits has been illustrated. Thus, the expression of RGS proteins can be used to inhibit signal...

journal_title：Methods in enzymology

authors： Hains MD,Siderovski DP,Harden TK

更新日期：2004-01-01 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：:Unfolded protein response (UPR) is a major reaction to intrinsic stress of eukaryotic organisms and is also related to environmental stress reactions. Among yeasts, stress regulation has mainly been investigated in Saccharomyces cerevisiae, while other species with biotechnological or medical interest are less well un...

journal_title：Methods in enzymology

authors： Dragosits M,Mattanovich D,Gasser B

更新日期：2011-01-01 00:00:00