Reconstitution of microtubule-dependent organelle transport.

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：:Currently, over a hundred high-resolution structures of serpins are available, exhibiting a wide range of conformations. However, our understanding of serpin dynamics and conformational change is still limited, mainly due to challenges of monitoring structural changes and characterizing transient conformations using e...

journal_title：Methods in enzymology

authors： Kass I,Reboul CF,Buckle AM

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：:Autophagy is an ancient cell survival pathway that is induced by metabolic stress and that helps prevent bioenergetic failure. This pathway has emerged as a promising new target in cancer treatment, where agents that inhibit autophagic degradation have efficacy in preventing cancer and in treating resistant disease wh...

journal_title：Methods in enzymology

authors： Dorsey FC,Steeves MA,Prater SM,Schröter T,Cleveland JL

更新日期：2009-01-01 00:00:00

abstract：:The microbial production of commodity, fine, and specialty chemicals is a driving force in biotechnology. An essential requirement is to introduce biosynthetic pathways to the target compound(s) into chassis organisms. First suitable enzymes must be selected and characterized, and then genetic pathways must be designe...

journal_title：Methods in enzymology

authors： Robinson CJ,Dunstan MS,Swainston N,Titchmarsh J,Takano E,Scrutton NS,Jervis AJ

更新日期：2018-01-01 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 combined use of rotating-frame relaxation methods, temperature-dependent measurements of line shapes and magnetization transfer experiments allows in favorable cases the examination in some detail of exchange processes that occur on the millisecond time scale. It is possible to determine not only the rate constant...

journal_title：Methods in enzymology

authors： Lane AN,Lefèvre JF

更新日期：1994-01-01 00:00:00

abstract：:Intramembrane-cleaving proteases (I-CLiPs) are a group of membrane-associated proteases with a unique feature: they are believed to cleave their substrate within the hydrophobic lipid bilayer, even though peptide bond hydrolysis requires a water molecule. Escherichia coli RseP, which belongs to the S2P zinc metallopro...

journal_title：Methods in enzymology

authors： Hizukuri Y,Akiyama K,Akiyama Y

更新日期：2017-01-01 00:00:00

abstract：:Ubiquitin (Ub)-mediated protein degradation is a key cellular defense mechanism that detects and eliminates defective proteins. A major intracellular site of protein quality control degradation is the endoplasmic reticulum (ER), hence the term ER-associated degradation, or endoplasmic reticulum-associated degradation ...

journal_title：Methods in enzymology

authors： Mashahreh B,Reiss Y,Wiener R,Ravid T

更新日期：2019-01-01 00:00:00

abstract：:RNA modifications, with over one hundred known so far, are commonly proposed to fine-tune the structure and function of RNA. While modifications in rRNA and tRNA are used to modulate RNA folding and decoding properties, little is known about the function of internal modifications in mRNA/lncRNA, which includes N(6)-me...

journal_title：Methods in enzymology

authors： Liu N,Pan T

更新日期：2015-01-01 00:00:00

abstract：:A procedure for an in vitro signaling assay is described for the MAPK and NFkappaB pathways. The method uses a membrane-cleared lysate that contains all the soluble components required for activating these signaling cascades. The pathways can be activated by variety of molecules, including kinases, G-proteins, and E3 ...

journal_title：Methods in enzymology

authors： Mukherjee S,Orth K

更新日期：2008-01-01 00:00:00

abstract：:The Arc (anoxic redox control) two-component system (TCS) is a complex signal transduction system that plays an important role in regulating energy metabolism at the level of transcription in bacteria. This system comprises the ArcB protein, a hybrid membrane-associated sensor kinase, and the ArcA protein, a typical r...

journal_title：Methods in enzymology

authors： Alvarez AF,Georgellis D

更新日期：2010-01-01 00:00:00

abstract：:Because polysaccharides have very complicated chemical structures constructed by a great diversity of monosaccharide residues and glycosidic linkages, enzymatic approaches have been identified as powerful tools to precisely synthesize polysaccharides as the reactions progress in highly controlled regio- and stereoarra...

journal_title：Methods in enzymology

authors： Kadokawa JI

更新日期：2019-01-01 00:00:00

abstract：:Advanced glycation is one of the major pathophysiological posttranslational modifications. Under hyperglycemic conditions or oxidative stress, proteins and DNA are nonenzymatically modified by oxidative glycation and converted to advanced glycation endproducts (AGEs), which induce the loss of protein functions or apop...

journal_title：Methods in enzymology

authors： Inagi R

更新日期：2011-01-01 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：: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：: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：:Classifications and characterizations of specific proteins, such as enzymes, not only allow us to understand biosynthetic and metabolic pathways but they also help to drive our understanding of protein structure and function. How those characterizations are evaluated, however, may change our interpretations and lead u...

journal_title：Methods in enzymology

authors： Bradshaw HB,Leishman E

更新日期：2017-01-01 00:00:00

abstract：:Riboswitches present a ubiquitous genetic regulatory mechanism for prokaryotes and have been found in HIV1, fungi, plants, and even H. sapiens. We present an overview of approaches to predict riboswitch aptamers and, more generally, RNA conformational switches. ...

journal_title：Methods in enzymology

authors： Clote P

更新日期：2015-01-01 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：:Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21-nt small interfering RNAs (siRNAs) during RNA interference and excises microRNAs (miRNAs) from precursor hairpins. PAZ and PIWI domain (PPD) proteins, also involved in RNAi and miRNA function, are the best-characterized proteins kno...

journal_title：Methods in enzymology

authors： Kolb FA,Zhang H,Jaronczyk K,Tahbaz N,Hobman TC,Filipowicz W

更新日期：2005-01-01 00:00:00

abstract：:Genetically encodable RNA devices that directly detect small molecules in the cellular environment are of increasing interest for a variety of applications including live cell imaging and synthetic biology. Riboswitches are naturally occurring sensors of intracellular metabolites, primarily found in the bacterial mRNA...

journal_title：Methods in enzymology

authors： Trausch JJ,Batey RT

更新日期：2015-01-01 00:00:00

abstract：:Anomalous small angle X-ray scattering (ASAXS) exploits contrast variation methods to highlight the scattering from one elemental component in a multielement sample, such as one ion species in an ion-DNA system. The ASAXS method has been applied to measure ions condensed around short nucleic acid duplexes. This chapte...

journal_title：Methods in enzymology

authors： Pabit SA,Finkelstein KD,Pollack L

更新日期：2009-01-01 00:00:00

abstract：:Cytoskeletal motors utilize the energy stored in ATP to generate linear motion along rigid filaments. Because their enzymatic cycles are tightly coupled to the production of force and forward movement, the optical-trapping technique is uniquely suited for studying their mechanochemical cycle. Here, we discuss the prac...

journal_title：Methods in enzymology

authors： Belyy V,Yildiz A

更新日期：2017-01-01 00:00:00

abstract：:Circadian rhythms generated by cell autonomous biological clocks allow for the appropriate temporal synchronization of physiology and behavior, optimizing the efficiency of biological systems. Circadian oscillators and functions have been uncovered in both central and peripheral tissues. This article describes methodo...

journal_title：Methods in enzymology

authors： Rudic RD,Curtis AM,Cheng Y,FitzGerald G

更新日期：2005-01-01 00:00:00

abstract：:In this chapter we discuss methods to study autophagic cell death. A large body of evidence demonstrates that autophagy is a cell survival mechanism in response to starvation. The role of autophagy in cell death, however, has long been controversial. Recently, molecular approaches have provided direct evidence that au...

journal_title：Methods in enzymology

authors： Lenardo MJ,McPhee CK,Yu L

更新日期：2009-01-01 00:00:00

abstract：:Ubiquitin-like protein (Ubl) ligation is common to diverse archaea and targets many cellular pathways, including those associated with sulfur mobilization, and also tags proteins as substrates for degradation by the proteasome. Here we highlight protocols to assay proteasome function and Ubl ligation in archaea. A cha...

journal_title：Methods in enzymology

authors： Fu X,Adams Z,Maupin-Furlow J

更新日期：2019-01-01 00:00:00

abstract：:Recent advances have demonstrated the feasibility and robustness of chemical synthesis for the production of homogeneously glycosylated protein forms (glycoforms). By taking advantage of the unmatchable flexibility and precision provided by chemical synthesis, the quantitative effects of glycosylation were obtained us...

journal_title：Methods in enzymology

authors： Li Y,Tran AH,Danishefsky SJ,Tan Z

更新日期：2019-01-01 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：:Autophagy is the major cellular process of degradation and is modulated by several signaling pathways. Phosphatidylinositol 3-kinase (PtdIns3K) class III (Vps34) and PtdIns3K class I regulate the autophagy pathway positively and negatively, respectively. Both classes of PtdIns3K participate in the synthesis of phospha...

journal_title：Methods in enzymology

authors： Yakhine-Diop SM,Martínez-Chacón G,González-Polo RA,Fuentes JM,Niso-Santano M

更新日期：2017-01-01 00:00:00