Peripheral clocks and the regulation of cardiovascular and metabolic function.

abstract：:The Escherichia coli fumarate and nitrate reductase (FNR) regulator protein is an important transcriptional regulator that controls the expression of a large regulon of more than 100 genes in response to changes in oxygen availability. FNR is active when it acquires a [4Fe-4S](2+) cluster under anaerobic conditions. T...

journal_title：Methods in enzymology

authors： Crack JC,Le Brun NE,Thomson AJ,Green J,Jervis AJ

更新日期：2008-01-01 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：:Given the increasing evidence of oxidative stress in AD brain and studies from different perspectives that appear to show a converging, central role for A beta in the pathogenesis and etiology of AD, insight into A beta-associated free radical oxidative stress will likely lead to a greater understanding of AD and, pot...

journal_title：Methods in enzymology

authors： Butterfield DA,Yatin SM,Varadarajan S,Koppal T

更新日期：1999-01-01 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：: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：:Optical imaging of reporter molecules such as firefly luciferase has become a popular method of tracking and visualizing cells in living animals. Many biological processes involve ubiquitin ligases, which target specific proteins for destruction under specific sets of conditions. Importantly, the motifs recognized by ...

journal_title：Methods in enzymology

authors： Zhang GJ,Kaelin WG Jr

更新日期：2005-01-01 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：:Ion channels open and close in response to diverse stimuli, and the molecular events underlying these processes are extensively modulated by ligands of both endogenous and exogenous origin. In the past decade, high-resolution structures of several channel types have been solved, providing unprecedented details of the ...

journal_title：Methods in enzymology

authors： Chakrapani S

更新日期：2015-01-01 00:00:00

abstract：:Use of fluorescence in biology and biochemistry for imaging and characterizing equilibrium and dynamic processes is growing exponentially. Much progress has been made in the last few years on the microscopic understanding of the underlying principles of what controls the wavelength and quenching of fluorescence in bio...

journal_title：Methods in enzymology

authors： Callis PR

更新日期：2011-01-01 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：:Given recent efforts to determine the sequence information on thousands of genes in the human genome, the current challenge is to identify the functions of these genes, including those encoding the regulator of G-protein signaling protein gene superfamily, and to establish their roles in particular signaling pathways ...

journal_title：Methods in enzymology

authors： Wang Q,Liu M,Kozasa T,Rothestein JD,Sternweis PC,Neubig RR

更新日期：2004-01-01 00:00:00

abstract：:Fragment-based drug discovery has emerged over the past 15 years as an effective lead discovery paradigm that is complementary to traditional high-throughput screening. The starting point for fragment-based drug discovery is the identification of low-molecular weight, typically low-affinity compounds that bind to a ta...

journal_title：Methods in enzymology

authors： Desjarlais RL

更新日期：2011-01-01 00:00:00

abstract：:This chapter outlined the methods used to study intra- and extracellular modifications of apolipoproteins. These and other related studies have shown that several of the apolipoproteins undergo a series of intra- and extracellular modifications as follows: All apolipoproteins studied contain an 18-26 long signal pepti...

journal_title：Methods in enzymology

authors： Zannis VI,Karathanasis SK,Forbes GM,Breslow JL

更新日期：1986-01-01 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：:Once the appropriate site has been selected for the attachment of GFP to the sarcomeric protein, it is quite remarkable that the large size of the GFP molecule does not appear to interfere with the localization of the fluorescent sarcomeric proteins into the sarcomeric regions of the myofibrils. A similar approach usi...

journal_title：Methods in enzymology

authors： Dabiri GA,Ayoob JC,Turnacioglu KK,Sanger JM,Sanger JW

更新日期：1999-01-01 00:00:00

abstract：:Proteins are fragile molecules that often require great care during purification to ensure that they remain intact and fully active. Nowadays, many proteins are also purified in small amounts under denaturing conditions by various gel electrophoretic techniques, such that inactive proteins are obtained. But even here,...

journal_title：Methods in enzymology

authors： Deutscher MP

更新日期：2009-01-01 00:00:00

abstract：:Apical caspases 8, 9, and 10 are only active as dimers. These dimers are unstable, and to characterize their activity they need to be maintained in vitro in a dimeric state. We provide updated methods for those looking to characterize various aspects of caspase function. We describe full methods for those looking to a...

journal_title：Methods in enzymology

authors： Mace PD,Riedl SJ,Salvesen GS

更新日期：2014-01-01 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：: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：:Formation of a Lys48-linked polyubiquitin chain is required for destruction of targeted proteins by the 26S proteasome, whereas formation of a Lys63-linked polyubiquitin chain is required for modulation of protein-protein interaction, enzyme activity, and intracellular localization. In addition, monoubiquitination pla...

journal_title：Methods in enzymology

authors： Fujimuro M,Yokosawa H

更新日期：2005-01-01 00:00:00

abstract：:Protein matrix cavities and extended tunnels can effectively channel substrates and products to and from active sites in enzymes. Substrate and product channeling can enhance catalytic efficiency by reducing the intramolecular diffusion times to and from reaction centers. Moreover, protected transfer between sites may...

journal_title：Methods in enzymology

authors： Pesce A,Milani M,Nardini M,Bolognesi M

更新日期：2008-01-01 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：:The study of hormone secretion by anterior pituitary cells is complicated by the presence of multiple cell types. For unambiguous interpretation of data it is necessary to identify the cells from which measurements are made. We have described a reliable experimental approach involving the identification of cultured ce...

journal_title：Methods in enzymology

authors： Croxton TL,Armstrong WM,Ben-Jonathan N

更新日期：1989-01-01 00:00:00

abstract：:For mRNAs encoding secretory and integral membrane proteins, translation initiation is thought to begin a process of mRNA localization where mRNA/ribosome/nascent chain complexes (RNCs) are trafficked from the cytosol compartment to the endoplasmic reticulum (ER). At the ER membrane, RNCs bind to a protein-conducting ...

journal_title：Methods in enzymology

authors： Stephens SB,Nicchitta CV

更新日期：2007-01-01 00:00:00

abstract：:RNA and DNA carry out diverse functions in biology including catalysis, splicing, gene regulation, and storage of genetic information. Interest has grown in understanding how nucleic acids perform such sophisticated functions given their limited molecular repertoire. RNA can fold into diverse shapes that often perturb...

journal_title：Methods in enzymology

authors： Thaplyal P,Bevilacqua PC

更新日期：2014-01-01 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：:The histamine H(1) receptor (H(1)R) is a key player in acute inflammatory responses. Antihistamines are widely used to relief the symptoms of allergic rhinitis by antagonizing histamine binding to the H(1)R, without possessing intrinsic activity in classical assays such as guinea pig ileum contraction assays or intrac...

journal_title：Methods in enzymology

authors： Nijmeijer S,Leurs R,Vischer HF

更新日期：2010-01-01 00:00:00

abstract：:Intrinsically disordered proteins (IDPs) sample structurally diverse ensembles. Characterizing the underlying distributions of conformations is a key step toward understanding the structural and functional properties of IDPs. One increasingly popular method for obtaining quantitative information on intramolecular dist...

journal_title：Methods in enzymology

authors： Holmstrom ED,Holla A,Zheng W,Nettels D,Best RB,Schuler B

更新日期：2018-01-01 00:00:00

abstract：:Here we describe an optimized recombineering protocol for the creation of conditional alleles. Recombineering is a DNA engineering methodology based on homologous recombination in Escherichia coli. It presents a number of advantages over conventional engineering methods, including the ability to place target sites for...

journal_title：Methods in enzymology

authors： Fu J,Teucher M,Anastassiadis K,Skarnes W,Stewart AF

更新日期：2010-01-01 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