Measuring the activity and structure of functional RNAs inside compartments formed by liquid-liquid phase separation.

abstract：:The steady technical advances of nuclear magnetic resonance (NMR) over the past decades enabled a significant increase in the molecular size of protein particles that can be subjected to a structural and functional characterization in solution. The larger molecular weight of such proteins is accompanied with an increa...

journal_title：Methods in enzymology

authors： Michel E,Allain FH

更新日期：2015-01-01 00:00:00

abstract：:Although the function of histone deacetylases (HDACs) have primarily been associated with influencing transcription through chromatin remodeling, the capacity of these enzymes to interface with a diverse array of biologic processes by modulating a growing list of nonhistone substrates has gained recent attention. Rece...

journal_title：Methods in enzymology

authors： Kahali S,Sarcar B,Chinnaiyan P

更新日期：2011-01-01 00:00:00

abstract：:Changes in chromatin structure emanating from DNA breaks are among the most initiating events in the damage response of the cell. In higher eukaryotes, poly(ADP-ribose) polymerase-1 (PARP-1) translates the occurrence of DNA breaks detected by its zinc-finger domain into a signal, poly ADP-ribose, synthesized and ampli...

journal_title：Methods in enzymology

authors： Dantzer F,Amé JC,Schreiber V,Nakamura J,Ménissier-de Murcia J,de Murcia G

更新日期：2006-01-01 00:00:00

abstract：:Benzylisoquinoline alkaloids (BIAs) constitute a diverse class of plant secondary metabolites that includes the opiate analgesics morphine and codeine. Collectively, BIAs exhibit a myriad of pharmacological activities, including antimicrobial, antitussive, antispasmodic, and anticancer properties. Despite 2500 known B...

journal_title：Methods in enzymology

authors： Pyne ME,Narcross L,Fossati E,Bourgeois L,Burton E,Gold ND,Martin VJ

更新日期：2016-01-01 00:00:00

abstract：:We describe the basic principles for imaging frozen-hydrated specimens in a transmission electron microscope and provide a step-by-step guide to a new user, from starting up and aligning the microscope, to loading a cryo-grid into the specimen holder and inserting the holder into the microscope, to setting up the low ...

journal_title：Methods in enzymology

authors： Sun J,Li H

更新日期：2010-01-01 00:00:00

abstract：:Nitration and oxidation of tyrosine, tryptophan, and methionine residues in proteins are potential markers of their interaction with peroxynitrite. This chapter describes the procedure for the detection of these nitro-oxidative modifications by tandem mass spectrometry. The peptide YGDLANWMIPGK, shown to contain a nit...

journal_title：Methods in enzymology

authors： Rebrin I,Bregere C,Gallaher TK,Sohal RS

更新日期：2008-01-01 00:00:00

abstract：:Protein splicing is an autocatalytic reaction in which an internal protein domain, the intein, excises itself out of a precursor protein and concomitantly links the two flanking sequences, the exteins, with a native peptide bond. In split inteins, the intein domain is divided into two parts that undergo fragment assoc...

journal_title：Methods in enzymology

authors： Ludwig C,Schwarzer D,Zettler J,Garbe D,Janning P,Czeslik C,Mootz HD

更新日期：2009-01-01 00:00:00

abstract：:The epitope tagging approach offers advantages of economy, universality, and precision over the use of antibodies raised directly against a protein of interest. The latter strategy promises a potentially greater diversity of reagents and obviates the need to modify the protein, but it may not yield sufficiently high-a...

journal_title：Methods in enzymology

authors： Kolodziej PA,Young RA

更新日期：1991-01-01 00:00:00

abstract：:There is a great need for practicing scientists to volunteer their time and expertise in the K-12th grade science classroom. We have found that bioluminescence is a fun and exciting way to teach basic science concepts and is an excellent tool for the volunteering scientist. We have had very positive reactions from bot...

journal_title：Methods in enzymology

authors： Hammer M,Andrade JD

更新日期：2000-01-01 00:00:00

abstract：:Peptide-based strategies represent transformative approaches to fabricate functional inorganic materials under sustainable conditions by modeling the methods exploited in biology. In general, peptides with inorganic affinity and specificity have been isolated from organisms and through biocombinatorial selection techn...

journal_title：Methods in enzymology

authors： Bedford NM,Munro CJ,Knecht MR

更新日期：2016-01-01 00:00:00

abstract：:In this chapter we have detailed a method that can be generalized to link virtually any DNA substrate to a chromatography matrix at its ends via an avidin-biotin linkage. We have used this technique to construct a left-handed Z-DNA column for the purpose of identification and purification of Z-DNA-binding proteins. Th...

journal_title：Methods in enzymology

authors： Fishel R,Anziano P,Rich A

更新日期：1990-01-01 00:00:00

abstract：:There is now considerable experimental evidence that aberrant activation of Rho family small GTPases promotes uncontrolled proliferation, invasion, and metastatic properties of human cancer cells. Therefore, there is considerable interest in the development of small molecule inhibitors of Rho GTPase function. However,...

journal_title：Methods in enzymology

authors： Onesto C,Shutes A,Picard V,Schweighoffer F,Der CJ

更新日期：2008-01-01 00:00:00

abstract：:The yeast Saccharomyces cerevisiae is an ideal model system for examining fundamental nitrogen oxide biochemistry. The utility of this model system lies in both the similarities and the differences between yeast and mammalian cells. The similarities between the two systems, with regards to many of the fundamental bioc...

journal_title：Methods in enzymology

authors： Shinyashiki M,Lopez BE,Rodriguez CE,Fukuto JM

更新日期：2005-01-01 00:00:00

abstract：:The nematode Caenorhabditis elegans has served as a fruitful setting for cell death research for over three decades. A conserved pathway of four genes, egl-1/BH3-only, ced-9/Bcl-2, ced-4/Apaf-1, and ced-3/caspase, coordinates most developmental cell deaths in C. elegans. However, other cell death forms, programmed and...

journal_title：Methods in enzymology

authors： Kinet MJ,Shaham S

更新日期：2014-01-01 00:00:00

abstract：:A direct transport route from early/recycling endosome (EE/RE) to the trans-Golgi network (TGN) is exploited by Shiga toxin (Mallard et al., 1998) and TGN38 (Ghosh et al., 1998). To facilitate the study of this pathway, both in vivo and in vitro transport assays using recombinant Shiga toxin B fragments (STxB) as prot...

journal_title：Methods in enzymology

authors： Tai G,Lu L,Johannes L,Hong W

更新日期：2005-01-01 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：: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：: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：:Protein (poly-)ubiquitination is a posttranslational modification that plays a key role in almost all cellular processes. It involves the installment of either single ubiquitin (Ub) moieties or one of eight different polyUb linkage types, each giving a distinct cellular outcome. Deubiquitinating enzymes (DUBs) reverse...

journal_title：Methods in enzymology

authors： Geurink PP,van der Heden van Noort GJ,Mulder MPC,Knaap RCM,Kikkert M,Ovaa H

更新日期：2019-01-01 00:00:00

abstract：:The innate immune system provides host defense against a variety of threats, including microbial infection and cellular damage. Pattern recognition receptors identify both pathogen and damage associated molecular motifs associated with these events. Nucleic acid is one such danger signal that is detected by a set of c...

journal_title：Methods in enzymology

authors： Antiochos B

更新日期：2019-01-01 00:00:00

abstract：:The fact that chemical exchange processes occur at rates that cover a broad range and produce readily detectable effects on the spectrum is one of the attractive features of high-resolution NMR. The description of these line shapes in the presence of spin-spin coupling requires the density matrix theory which is rathe...

journal_title：Methods in enzymology

authors： Rao BD

更新日期：1989-01-01 00:00:00

abstract：:In order to produce a full quantitative description of yeast metabolism, a number of kinetic parameters of enzymes that are important for energy metabolism must be determined experimentally. We aim to determine the prospective in vivo kinetic properties of a range of yeast-purified isoenzymes that are important in ene...

journal_title：Methods in enzymology

authors： Messiha HL,Malys N,Carroll KM

更新日期：2011-01-01 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：:We have described procedures for collecting, processing, and analyzing kinetic data obtained by photobleaching microscopy of GFP-tagged chromatin proteins in nuclei of cultured living cells. These procedures are useful for characterizing the in vivo binding of chromatin proteins to their natural template--unperturbed,...

journal_title：Methods in enzymology

authors： Phair RD,Gorski SA,Misteli T

更新日期：2004-01-01 00:00:00

abstract：:Undiluted cytoplasmic extract prepared from unfertilized Xenopus laevis eggs by low-speed centrifugation (CSF extracts) is useful for reconstitution of egg microtubule dynamics and meiosis-II spindle organization, but it suffers limitations for biochemical analysis due to abundant particulates. Here, we describe prepa...

journal_title：Methods in enzymology

authors： Groen AC,Ngyuen PA,Field CM,Ishihara K,Mitchison TJ

更新日期：2014-01-01 00:00:00

abstract：:Neuroblastoma (NB) is the most common extracranial solid tumor in childhood and the most frequently diagnosed neoplasm during infancy. Despite of aggressive treatment strategies, the 5-year survival rate for metastatic disease is still less than 60% and, consequently, novel therapeutic approaches are needed. For incre...

journal_title：Methods in enzymology

authors： Di Paolo D,Loi M,Pastorino F,Brignole C,Marimpietri D,Becherini P,Caffa I,Zorzoli A,Longhi R,Gagliani C,Tacchetti C,Corti A,Allen TM,Ponzoni M,Pagnan G

更新日期：2009-01-01 00:00:00

abstract：:Electrochemical microsensors for O2, pH, H2S, H2, and N2O are now available commercially, thus it has become a relatively simple task to analyze the microenvironment in stratified microbial communities for several chemical species. In addition, sensors are available for the physical parameters diffusivity and flow, an...

journal_title：Methods in enzymology

authors： Revsbech NP

更新日期：2005-01-01 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：:Although most eukaryotic mRNAs are degraded by exonucleases acting on either end of the molecule, a subset of mRNAs undergo endonuclease cleavage within the mRNA body. Endonuclease cleavage can be activated by cellular stress, extracellular signals, or by ribosome stalling, as might occur at a premature termination co...

journal_title：Methods in enzymology

authors： Otsuka Y,Schoenberg DR

更新日期：2008-01-01 00:00:00

abstract：:Endothelial cell adhesion and migration is fundamental to a number of physiologic processes, including vascular development and angiogenesis. It has been investigated in a variety of contexts, including tumorigenesis, wound healing, tissue engineering, and biomaterial design. The chemical and mechanical extracellular ...

journal_title：Methods in enzymology

authors： Reinhart-King CA

更新日期：2008-01-01 00:00:00