An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.

abstract：:Autophagy is a major intracellular catabolic pathway induced in response to amino acid starvation. Recent findings implicate it in diverse physiological/pathophysiological events, such as protein and organelle turnover, development, aging, pathogen infection, cell death, and neurodegeneration. However, experimental me...

journal_title：Methods in enzymology

authors： Shvets E,Elazar Z

更新日期：2009-01-01 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：: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：:The Omega class of cytosolic glutathione transferases was initially recognized by bioinformatic analysis of human sequence databases, and orthologous sequences were subsequently discovered in mouse, rat, pig, Caenorhabditis elegans, Schistosoma mansoni, and Drosophila melanogaster. In humans and mice, two GSTO genes h...

journal_title：Methods in enzymology

authors： Whitbread AK,Masoumi A,Tetlow N,Schmuck E,Coggan M,Board PG

更新日期：2005-01-01 00:00:00

abstract：:All cells in nature are covered with a dense and complex array of glycans. The total glycan repertoire expressed on cells, "the cellular glycome," varies at every level of biological organization, and in response to intrinsic and extrinsic stimuli. The cellular glycome is often referred to as the "cell face," which re...

journal_title：Methods in enzymology

authors： Tateno H,Kuno A,Itakura Y,Hirabayashi J

更新日期：2010-01-01 00:00:00

abstract：:Enzyme immobilization is a widespread empiric technology to achieve more stable, active and reusable enzymes. The empiricism can be reduced by the application of rational design procedures employing bioinformatic tools, engineered-proteins and detailed analyses of existent data. In this chapter, we describe relevant a...

journal_title：Methods in enzymology

authors： Sastre DE,Reis EA,Marques Netto CGC

更新日期：2020-01-01 00:00:00

abstract：:Cell migration plays a key role both in physiological conditions, such as tissue repair or embryonic development, and in pathological processes, including tumor metastasis. Understanding the mechanisms that allow cancer cells to invade tissues during metastasis requires studying their ability to migrate. While spectac...

journal_title：Methods in enzymology

authors： Vinot S,Anguille C,de Toledo M,Gadea G,Roux P

更新日期：2008-01-01 00:00:00

abstract：:In principle, the long emission lifetimes of lanthanide chelates should enable their ultrasensitive detection in biological systems by time-resolved optical microscopy. However, most lanthanide-imaging systems cannot achieve sensitivities that exceed those of conventional fluorescence microscopes, since they are limit...

journal_title：Methods in enzymology

authors： Ciepla P,Cho U,Chen JK

更新日期：2020-01-01 00:00:00

abstract：:Two-component signal transduction systems, composed of histidine kinases and response regulators, enable bacteria to sense, respond, and adapt to changes in their internal and external conditions. The importance of these signaling systems is reflected in their widespread distribution and prevalence in the bacterial ki...

journal_title：Methods in enzymology

authors： Laub MT,Biondi EG,Skerker JM

更新日期：2007-01-01 00:00:00

abstract：:A neuron is able to seamlessly respond to a number of signals, in a timely and specific manner. This process, of integrating multiple inputs, relays on the orchestration of intracellular events by signaling networks. The inherent complexity of signaling networks has made computational modeling a useful approach to und...

journal_title：Methods in enzymology

authors： Wenderski WC,Neves SR

更新日期：2012-01-01 00:00:00

abstract：:Drosophila melanogaster is a useful organism for determining protein function and modeling human disease. Drosophila offers a rapid generation time and an abundance of genomic resources and genetic tools. Conservation in protein structure, signaling pathways, and developmental processes make studies performed in Droso...

journal_title：Methods in enzymology

authors： Bohnekamp J,Cryderman DE,Thiemann DA,Magin TM,Wallrath LL

更新日期：2016-01-01 00:00:00

abstract：:Recurrent aliphatic hydrophobic amino acids which occur in the sequence of a protein or a peptide at positions which form an axial, hydrophobic strip when the sequence is coiled as an alpha helix might stabilize coiling against hydrophobic surfaces. That effect can lead to helix formation against hydrophobic cores of ...

journal_title：Methods in enzymology

authors： Reyes VE,Lew RA,Lu S,Humphreys RE

更新日期：1991-01-01 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：:ClpB belongs to the Hsp100 family of ring-forming heat-shock proteins involved in degradation of unfolded/misfolded proteins and in reactivation of protein aggregates. ClpB monomers reversibly associate to form the hexameric molecular chaperone that, together with the DnaK system, has the ability to disaggregate stres...

journal_title：Methods in enzymology

authors： Alfonso C,del Castillo U,Martín I,Muga A,Rivas G

更新日期：2015-01-01 00:00:00

abstract：:Amyloid aggregates are associated with a number of mammalian neurodegenerative diseases. Infectious aggregates of the mammalian prion protein PrP(sc) are hallmarks of transmissible spongiform encephalopathies in humans and cattle (Griffith, 1967; Legname et al., 2004; Prusiner, 1982; Silveira et al., 2004). Likewise, ...

journal_title：Methods in enzymology

authors： Bagriantsev SN,Kushnirov VV,Liebman SW

更新日期：2006-01-01 00:00:00

abstract：:The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information archives and freely distributes high-throughput molecular abundance data, predominantly gene expression data generated by DNA microarray technology. The database has a flexible design that can handle diverse styles of bot...

journal_title：Methods in enzymology

authors： Barrett T,Edgar R

更新日期：2006-01-01 00:00:00

abstract：:Integrin adhesion receptors mediate cell-cell and cell-substratum adhesion and provide a continuous link for the bidirectional transmission of mechanical force and biochemical signals across the plasma membrane. Integrin-dependent cellular activities such as adhesion, migration, proliferation, and survival rely upon t...

journal_title：Methods in enzymology

authors： Lad Y,Harburger DS,Calderwood DA

更新日期：2007-01-01 00:00:00

abstract：:Phosphoinositide-3-kinase (PI3K) signaling has been implicated in a panoply of cellular responses including survival, proliferation, protein synthesis, migration, and vesicular trafficking. In addition, alterations in the enzymatic activity of PI3Ks have been involved in the pathogenesis of multiple diseases, ranging ...

journal_title：Methods in enzymology

authors： Ciraolo E,Gulluni F,Hirsch E

更新日期：2014-01-01 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：: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：: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：: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：:Obtaining patient-specific information through the quantification of small molecules and proteins in bodily fluids is essential for personalized therapies. Point-of-care (POC) diagnostic devices hold the promise of delivering such benefit to a wide range of patients. However, there is a lack of enabling technology, as...

journal_title：Methods in enzymology

authors： Yu Q,Griss R,Schena A,Johnsson K

更新日期：2017-01-01 00:00:00

abstract：:Metagenomics has become an important tool for the characterization of microorganisms, as it is independent of their enrichment or cultivation in the laboratory. Its application has led to the discovery of metabolisms from widespread, yet uncharacterized organisms such as the ammonia-oxidizing archaea. Different approa...

journal_title：Methods in enzymology

authors： Reigstad LJ,Bartossek R,Schleper C

更新日期：2011-01-01 00:00:00

abstract：:The current treatment of neurological and psychiatric diseases is far beyond being satisfactory. In addition to highly complex disease mechanisms, the blood-brain barrier (BBB) also remains as a challenge by limiting the delivery of the majority of currently available therapeutics to the central nervous system. Severa...

journal_title：Methods in enzymology

authors： Yemişci M,Gürsoy-Özdemir Y,Caban S,Bodur E,Capan Y,Dalkara T

更新日期：2012-01-01 00:00:00

abstract：:Differential scanning calorimetry (DSC) detects protein thermal unfolding by directly measuring the heat absorbed. Simple DSC experiments that require relatively small amounts of pure material can provide a wealth of information related to structure, especially with respect to domain architecture, without the need for...

journal_title：Methods in enzymology

authors： Yang Z,Brouillette CG

更新日期：2016-01-01 00:00:00

abstract：:Inositol phosphates (InsPs) are an important group of eukaryotic messengers and mediate a wide range of processes. To elucidate the biological functions of these molecules, robust techniques to characterize inositol phosphate metabolism at the cellular level are highly sought after. This chapter provides a detailed pr...

journal_title：Methods in enzymology

authors： Puschmann R,Harmel RK,Fiedler D

更新日期：2020-01-01 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：:Carbohydrate microarrays are becoming a standard tool for glycobiologists to screen large numbers of sugars and elucidate the role of carbohydrates in biological systems. This article describes detailed methods to prepare and use microarrays containing synthetic oligosaccharides as well as a summary of the biological ...

journal_title：Methods in enzymology

authors： de Paz JL,Horlacher T,Seeberger PH

更新日期：2006-01-01 00:00:00