Assays for dissecting the in vitro enzymatic activity of yeast Ubc7.

abstract：:Plasminogen activator inhibitor-1 (PAI-1) is the main inhibitor of tissue-type plasminogen activator (t-PA) and urokinase-type plasminogen activator (u-PA) and therefore plays an important role in the plasminogen/plasmin system. PAI-1 is involved in a variety of cardiovascular diseases (mainly through inhibition of t-...

journal_title：Methods in enzymology

authors： Declerck PJ,Gils A,De Taeye B

更新日期：2011-01-01 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：:The qualitative detection, quantification, and structural characterization of analytes in biological systems are important requirements for objectives to be fulfilled in systems biology research. One analytical tool applied to a multitude of systems biology studies is mass spectrometry, particularly for the study of p...

journal_title：Methods in enzymology

authors： Dunn WB

更新日期：2011-01-01 00:00:00

abstract：:Coat protein complex II (COPII) vesicle-mediated protein export from the endoplasmic reticulum (ER) can be controlled by linear, independent motifs embedded within the cargo. ER export motifs directly interact with selective components of COPII vesicles and enhance cargo recruitment onto COPII vesicles. Moreover, ER e...

journal_title：Methods in enzymology

authors： Wu G

更新日期：2013-01-01 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：:Plots of free energy versus temperature are commonly called stability curves or Gibbs-Helmholtz curves, and they have proven to be extremely useful in protein folding and ligand-binding studies. Curvature in a Gibbs-Helmholtz or stability plot is indicative of a heat capacity change, and some of their primary uses in ...

journal_title：Methods in enzymology

authors： LiCata VJ,Liu CC

更新日期：2011-01-01 00:00:00

abstract：:Histone variants and posttranslational modifications (PTMs) are essential for epigenetic regulation of transcriptional expression. Single and/or combinatorial PTMs of histones play important roles in development and disease formation. Mass spectrometry (MS) has been a powerful tool to study histone variants and PTMs, ...

journal_title：Methods in enzymology

authors： Lin S,Garcia BA

更新日期：2012-01-01 00:00:00

abstract：:Since the onset of the genomic era more than 1000 bacterial genomes have been sequenced and several fold more are expected to be completed in the near future. These genome sequences supply a wealth of information that can be exploited by statistical methods to gain significant insights into cellular processes. In Volu...

journal_title：Methods in enzymology

authors： Lunt B,Szurmant H,Procaccini A,Hoch JA,Hwa T,Weigt M

更新日期：2010-01-01 00:00:00

abstract：:Although the use of monoclonal antibodies to characterize the Ia antigen system is still in its infancy, the usefulness of this approach is clearly apparent. Since xenogeneic immunization can be used to generate these antibodies, the chances are good that a greater variety of Ia types and determinants will be detected...

journal_title：Methods in enzymology

authors： Zweig SE,Shevach EM

更新日期：1983-01-01 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

abstract：:The unexpected discovery of graphene and especially the follow-up explosion of interest in its properties and applications marked the beginning of a new carbon era. Graphene-based nanostructured materials are highly useful because they show great promise in the field of biotechnology and biomedicine. Owing to their un...

journal_title：Methods in enzymology

authors： Khan M,Husain Q,Asmat S

更新日期：2018-01-01 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：:Live cell microscopy using fluorescent proteins and small fluorescent probes is a well-established and essential tool for cell biology; however, there is a considerable need for noninvasive techniques able to study tissue and cell dynamics without the need to introduce chemical or genetically encoded probes. Coherent ...

journal_title：Methods in enzymology

authors： Pope I,Langbein W,Borri P,Watson P

更新日期：2012-01-01 00:00:00

abstract：:Vitamin K-dependent carboxylation, an essential posttranslational modification catalyzed by gamma-glutamyl carboxylase, is required for the biological functions of proteins that control blood coagulation, vascular calcification, bone metabolism, and other important physiological processes. Concomitant with carboxylati...

journal_title：Methods in enzymology

authors： Tie JK,Stafford DW

更新日期：2017-01-01 00:00:00

abstract：:Reviewing the circumstances that have led to the first monoclonal antibody against the disease-associated form of PrP, we consider the availability of PrP knockout mice and recombinant PrP, as well as a reliable conformational screening protocol as being important prerequisites for a successful immunization approach. ...

journal_title：Methods in enzymology

authors： Korth C,Streit P,Oesch B

更新日期：1999-01-01 00:00:00

abstract：:Acidic organelles and vesicles, such as endosomes, lysosomes, autophagosomes, trans-Golgi network, and synaptic vesicles, are known to play important roles in a broad range of cellular events. To facilitate studying these multifunctional systems, we describe here an acid-brightening fluorescent protein (abFP), which f...

journal_title：Methods in enzymology

authors： Wang N,Wang L

更新日期：2020-01-01 00:00:00

abstract：:Mitochondrial RNAs in the myxomycete Physarum polycephalum differ from the templates from which they are transcribed in defined ways. Most transcripts contain nucleotides that are not present in their respective genes. These "extra" nucleotides are added during RNA synthesis by an unknown mechanism. Other differences ...

journal_title：Methods in enzymology

authors： Byrne EM,Visomirski-Robic L,Cheng YW,Rhee AC,Gott JM

更新日期：2007-01-01 00:00:00

abstract：:Ras proteins are small GTPases that exhibit high-affinity binding to GDP and GTP and hydrolyze bound GTP to GDP. The intrinsic GTPase activity of Ras proteins is accelerated by GTPase activating proteins (GAPs), which act to attenuate GTPase signaling by accelerating the conversion of bound GTP to bound GDP. Tumor-ass...

journal_title：Methods in enzymology

authors： Shutes A,Der CJ

更新日期：2006-01-01 00:00:00

abstract：:Powerful specialized software is essential for managing, quantifying, and ultimately deriving scientific insight from results of a microarray experiment. We have developed a suite of software applications, known as TM4, to support such gene expression studies. The suite consists of open-source tools for data managemen...

journal_title：Methods in enzymology

authors： Saeed AI,Bhagabati NK,Braisted JC,Liang W,Sharov V,Howe EA,Li J,Thiagarajan M,White JA,Quackenbush J

更新日期：2006-01-01 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：:Gene regulatory grids (GRGs) encompass the space of all the possible transcription factor (TF)-target gene interactions that regulate gene expression, with gene regulatory networks (GRNs) representing a temporal and spatial manifestation of a portion of the GRG, essential for the specification of gene expression. Thus...

journal_title：Methods in enzymology

authors： Yang F,Ouma WZ,Li W,Doseff AI,Grotewold E

更新日期：2016-01-01 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：:Genomes can be viewed in terms of their gene content and the order in which the genes appear along each chromosome. Evolutionary events that affect the gene order or content are "rare genomic events" (rarer than events that affect the composition of the nucleotide sequences) and have been advocated by systematists for...

journal_title：Methods in enzymology

authors： Moret BM,Warnow T

更新日期：2005-01-01 00:00:00

abstract：:The above methodology has been used to prepare a variety of PE-immunotoxins. These reagents are potent cytotoxic agents for cells in culture that bind the appropriate antibody and nontoxic when cells do not bind the antibody. PE-immunotoxins can be used to select for mutant cultured cells which lack the target of the ...

journal_title：Methods in enzymology

authors： FitzGerald DJ

更新日期：1987-01-01 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：:This chapter presents the application of capillary electrophoresis coupled to electrospray mass spectrometry (CE-ES-MS) for the analysis of complex bacterial lipopolysaccharides (LPS) from pathogenic strains of Haemophilus influenzae and Neisseria meningitidis. A discussion is included of the development of electropho...

journal_title：Methods in enzymology

authors： Li J,Martin A,Cox AD,Moxon ER,Richards JC,Thibault P

更新日期：2005-01-01 00:00:00

abstract：:Genome sequencing projects have provided the substrate for an unimaginable number of biological experiments. Further, genomic technologies such as microarrays and quantitative and exquisitely sensitive techniques such as real-time quantitative polymerase chain reaction have made it possible to reliably generate millio...

journal_title：Methods in enzymology

authors： Scheele C,Larsson O,Timmons JA

更新日期：2009-01-01 00:00:00

abstract：:Many DNA repair enzymes, including the human adenine glycosylase MUTYH, require iron-sulfur (Fe-S) cluster cofactors for DNA damage recognition and subsequent repair. MUTYH prokaryotic and eukaryotic homologs are a family of adenine (A) glycosylases that cleave A when mispaired with the oxidatively damaged guanine les...

journal_title：Methods in enzymology

authors： Majumdar C,Nuñez NN,Raetz AG,Khuu C,David SS

更新日期：2018-01-01 00:00:00

abstract：:The coat protein complex II (COPII) coat is responsible for direct capture of membrane cargo proteins and for the physical deformation of the endoplasmic reticulum (ER) membrane that drives the transport vesicle formation. The use of an in vitro reconstitution system comprising purified components is desirable for stu...

journal_title：Methods in enzymology

authors： Sato K,Nakano A

更新日期：2005-01-01 00:00:00

abstract：:Precisely imaging and tracking dynamic biological processes in live cells are crucial for both fundamental research in life sciences and biomedical applications. Nonfluorescent nanoparticles are emerging as important optical probes in live-cell imaging because of their excellent photostability, large optical cross sec...

journal_title：Methods in enzymology

authors： Wang G,Fang N

更新日期：2012-01-01 00:00:00