Analysis of posttranslational regulations in the Neurospora circadian clock.

abstract：:We have developed a genetic system, termed IVET (in vivo expression technology), designed to identify bacterial genes that are induced when a pathogen infects its host. A subset of these induced genes should include those that encode virulence factors, products specifically required for the infection process. The syst...

journal_title：Methods in enzymology

authors： Slauch JM,Mahan MJ,Mekalanos JJ

更新日期：1994-01-01 00:00:00

abstract：:Guanine nucleotide dissociation inhibitor (GDI) is a central regulator of Rab GTPase family members. GDI recycles Rab proteins from the membrane and sequesters the inactive GDP-bound form of Rab in the cytosol for use in multiple rounds of transport. The balance between the membrane-bound form of Rab and the cytosolic...

journal_title：Methods in enzymology

authors： Chen CY,Sakisaka T,Balch WE

更新日期：2005-01-01 00:00:00

abstract：:Protein-protein interactions (PPIs) are universal to life and their study and understanding is critical to drug discovery and bioengineering efforts. Historically, X-ray crystallography, isothermal titration calorimetry and other biophysical methods have been used to study PPIs, but can be costly and are low throughpu...

journal_title：Methods in enzymology

authors： Charov K,Burkart MD

更新日期：2020-01-01 00:00:00

abstract：:Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computa...

journal_title：Methods in enzymology

authors： Gunner MR,Baker NA

更新日期：2016-01-01 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：: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：:Membrane-initiated steroid signaling (MISS) involves rapid second messenger based intracellular signaling without coupling to transcription or translation. MISS activates important cellular signaling cascades such as mitogen-activated protein kinase (MAPK) or adenylate cyclase pathways. Despite its vital role in signa...

journal_title：Methods in enzymology

authors： Jani MS,Veetil AT,Krishnan Y

更新日期：2020-01-01 00:00:00

abstract：:Small GTPases of the Ras and Rho families are among the most studied signaling proteins and represent promising therapeutic targets for human neoplastic disease. Despite the high level of interest in these proteins, direct analysis of most aspects of Ras protein biology in living cells has not been possible, because m...

journal_title：Methods in enzymology

authors： Westwick JK,Michnick SW

更新日期：2006-01-01 00:00:00

abstract：:Hsp70 chaperones and their obligatory J-protein cochaperones function together in many cellular processes. Via cycles of binding to short stretches of exposed amino acids on substrate proteins, Hsp70/J-protein chaperones not only facilitate protein folding but also drive intracellular protein transport, biogenesis of ...

journal_title：Methods in enzymology

authors： Dutkiewicz R,Nowak M,Craig EA,Marszalek J

更新日期：2017-01-01 00:00:00

abstract：:The Rcs phosphorelay, consisting of a hybrid sensor kinase, a phosphotransferase, and a response regulator, regulates a large number of bacterial functions. These include capsule production, the target originally defined for these regulators, a small regulatory RNA, and a growing list of additional genes, many of unkn...

journal_title：Methods in enzymology

authors： Majdalani N,Gottesman S

更新日期：2007-01-01 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：:Perhaps the most important contribution of FLN is that it provides an experimental approach to relate physical changes in the protein to predicted dynamical behavior. It is clear that the sample is inhomogeneously broadened in a continuous manner, consistent with the damped motion of proteins. At the same time configu...

journal_title：Methods in enzymology

authors： Vanderkooi JM,Angiolillo PJ,Laberge M

更新日期：1997-01-01 00:00:00

abstract：:Patient-derived xenografts are a useful tool in cancer immunology, as they allow researchers to study human cancers in vivo when starting with a relatively small amount of human tumor tissue. These models make it possible to study tumor cell-intrinsic changes that occur in response to external stimuli including cytoki...

journal_title：Methods in enzymology

authors： Cardenas JJ,Robles-Oteiza C,Politi K

更新日期：2020-01-01 00:00:00

abstract：:Nucleic acid aptamers find widespread use as targeting and sensing agents in nature and biotechnology. Their ability to bind an extensive range of molecular targets, including small molecules, proteins, and ions, with high affinity and specificity enables their use in diverse diagnostic, therapeutic, imaging, and gene...

journal_title：Methods in enzymology

authors： Chang AL,McKeague M,Smolke CD

更新日期：2014-01-01 00:00:00

abstract：:Neutron reflectometry (NR) is uniquely positioned in structural biology, because of its ability to characterize biomolecular interfacial architectures like lipid membranes and membrane-associated proteins nondestructively and in their native environment. Mimicking biological processes, samples can be manipulated and t...

journal_title：Methods in enzymology

authors： Heinrich F

更新日期：2016-01-01 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：:Glass microfluidic devices have been fabricated to monitor the secretion of glycerol or fatty acids from cultured murine 3T3-L1 adipocytes. In the current studies, adipocytes are perfused in a reversibly sealed cell chamber, and secreted products are analyzed by enzyme assay on either a single- or dual-chip device. Th...

journal_title：Methods in enzymology

authors： Dugan CE,Kennedy RT

更新日期：2014-01-01 00:00:00

abstract：:There are estimated to be >300,000 plant species, producing >200,000 metabolites. Many of these metabolites are restricted to specific plant lineages and are referred to as "specialized" metabolites. These serve varied functions in plants including defense against biotic and abiotic stresses, plant-plant and plant-mic...

journal_title：Methods in enzymology

authors： Fan P,Moghe GD,Last RL

更新日期：2016-01-01 00:00:00

abstract：:We have used a shortened construct form of the CYP26A1 gene promoter, in a promoter-less vector with either luciferase (known as E4) or a red fluorescent protein, RFP (known as E4.2) as the reporter gene and examined their responses to retinoids in transfected HepG2 and HEK293T cells. The promoter responded linearly t...

journal_title：Methods in enzymology

authors： Zolfaghari R,Mattie FJ,Wei CH,Chisholm DR,Whiting A,Ross AC

更新日期：2020-01-01 00:00:00

abstract：:Superoxide dismutases (SODs; EC 1.15.1.1) are a group of metalloenzymes which are essential to protect cells under aerobic conditions. In biological systems, it has been reported that SODs and other proteins are susceptible to be attacked by peroxynitrite (ONOO(-)) which can be originated from the reaction of nitric o...

journal_title：Methods in enzymology

authors： Larrainzar E,Urarte E,Auzmendi I,Ariz I,Arrese-Igor C,González EM,Moran JF

更新日期：2008-01-01 00:00:00

abstract：:A central goal of biology is to understand how transcription factors target and regulate specific genes and networks to control cell fate and function. An equally important goal of synthetic biology, chemical biology, and personalized medicine is to devise molecules that can regulate genes and networks in a programmab...

journal_title：Methods in enzymology

authors： Tietjen JR,Donato LJ,Bhimisaria D,Ansari AZ

更新日期：2011-01-01 00:00:00

abstract：:The existence of an accurate force field (FF) model that reproduces the free-energy landscape is a key prerequisite for the simulation of biomineralization. Here, the stages in the development of such a model are discussed including the quality of the water model, the thermodynamics of polymorphism, and the free energ...

journal_title：Methods in enzymology

authors： Raiteri P,Demichelis R,Gale JD

更新日期：2013-01-01 00:00:00

abstract：:Nitric oxide formation in ischemia-reperfusion injury can be identified and measured directly using EPR of nitroso-heme complexes comprising NO bound to either Mb or Hb-Fe2+. This article described the successful use of this method to detect and quantify the generation of NO formed independently of nitric oxide syntha...

journal_title：Methods in enzymology

authors： Lepore DA

更新日期：2002-01-01 00:00:00

abstract：:Single-molecule Förster resonance energy transfer (smFRET) is a versatile tool for studying biomolecules in a quantitative manner. Multiple conformations within and interactions between biomolecules can be detected and their kinetics can be determined. Thus, smFRET has become an essential tool in enzymology. Ordinary ...

journal_title：Methods in enzymology

authors： Götz M,Wortmann P,Schmid S,Hugel T

更新日期：2016-01-01 00:00:00

abstract：:The nitrogen (N) cycle is the only global biogeochemical cycle that is driven by biological functions involving the interaction of many microorganisms. The N cycle has evolved over geological time and its interaction with the oxygen cycle has had profound effects on the evolution and timing of Earth's atmosphere oxyge...

journal_title：Methods in enzymology

authors： Godfrey LV,Glass JB

更新日期：2011-01-01 00:00:00

abstract：:White adipose tissue (WAT) is a heterogeneous tissue composed of lipid-filled adipocytes and several nonadipocyte cell populations, including endothelial, blood, uncharacterized stromal, and adipocyte precursor cells. Although lipid-filled adipocytes account for the majority of WAT volume and mass, nonadipocyte cell p...

journal_title：Methods in enzymology

authors： Church CD,Berry R,Rodeheffer MS

更新日期：2014-01-01 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：:When yeast are faced with irreparable DNA damage, they will first arrest in G2/M, via the DNA damage checkpoint pathway, but will subsequently adapt to that arrest and resume division. Here, we summarize assays that we have used to examine checkpoint adaptation. Specifically, we discuss the merits of inducing DNA dama...

journal_title：Methods in enzymology

authors： Toczyski DP

更新日期：2006-01-01 00:00:00

abstract：:EPR long-range distance measurements on spin-labeled macromolecules have recently become a popular tool in structural biology. The method can be used to obtain coarse-grained structures of biomolecules, to track conformational changes and dynamics, to dock macromolecular complexes, or to localize spin centers within m...

journal_title：Methods in enzymology

authors： Hagelueken G,Abdullin D,Schiemann O

更新日期：2015-01-01 00:00:00

abstract：:The bromodomain (BrD) represents an evolutionarily conserved protein domain whose function mostly is to recognize acetylated lysine residues in histones and nuclear proteins in regulation of gene transcription in chromatin. The highly conserved BrD structure features an unusual left-handed, antiparallel four-helix bun...

journal_title：Methods in enzymology

authors： Ren C,Zeng L,Zhou MM

更新日期：2016-01-01 00:00:00