Biophysical approach to studies of cap-eIF4E interaction by synthetic cap analogs.

abstract：:Protein kinases transfer a phosphoryl group from ATP onto target proteins and play a critical role in signal transduction and other cellular processes. Here, we review the kinase kinetic and chemical mechanisms and their application in understanding kinase structure and function. Aberrant kinase activity has been impl...

journal_title：Methods in enzymology

authors： Wang Z,Cole PA

更新日期：2014-01-01 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：:Retinoic acid (RA), the biologically active metabolite of vitamin A, regulates a vast spectrum of biological processes, such as cell differentiation, proliferation, apoptosis, and morphogenesis. microRNAs (miRNAs) play a crucial role in regulating gene expression by binding to messenger RNA (mRNA) which leads to mRNA ...

journal_title：Methods in enzymology

authors： Wang L,Rohatgi AP,Wan YY

更新日期：2020-01-01 00:00:00

abstract：:With the rapid development of nanotechnology, inorganic magnetic nanoparticles, especially iron oxide nanoparticles (IOs), have emerged as great vehicles for biomedical diagnostic and therapeutic applications. In order to rationally design IO-based gene delivery nanovectors, surface modification is essential and deter...

journal_title：Methods in enzymology

authors： Liu G,Wang Z,Lee S,Ai H,Chen X

更新日期：2012-01-01 00:00:00

abstract：:Significant progress has been made in discovering and cloning a host of proteins, including a range of glycoproteins. The availability of their predicted amino acid sequences provides useful information, including potential N-linked glycosylation sites. However, only a limited number of protein structures have been so...

journal_title：Methods in enzymology

authors： Yen TY,Macher BA

更新日期：2006-01-01 00:00:00

abstract：:Intracellular protein degradation is one of the most precisely regulated processes in living cells. The main component of the degradation machinery is the 20S proteasome present in eukaryotes as well as in prokaryotes. We have developed successful purification protocols for the 20S proteasome in its native state using...

journal_title：Methods in enzymology

authors： Groll M,Huber R

更新日期：2005-01-01 00:00:00

abstract：:Glycoproteins are a major class of glycoconjugates displaying a variety of mutual interactions between glycan and protein moieties that ultimately affect molecular organization. Modulation of the pendant glycan structures is important in tuning the functions of glycoproteins. Here we discuss structural aspects and som...

journal_title：Methods in enzymology

authors： Barb AW,Borgert AJ,Liu M,Barany G,Live D

更新日期：2010-01-01 00:00:00

abstract：:Genome editing using the Cas9 endonuclease of Streptococcus pyogenes has demonstrated unprecedented efficacy and facility in a wide variety of biological systems. In zebrafish, specifically, studies have shown that Cas9 can be directed to user-defined genomic target sites via synthetic guide RNAs, enabling random or h...

journal_title：Methods in enzymology

authors： Gonzales AP,Yeh JR

更新日期：2014-01-01 00:00:00

abstract：:It is widely acknowledged that mitochondria are highly active structures that rapidly respond to cellular and environmental perturbations by changing their shape, number, and distribution. Mitochondrial remodeling is a key component of diverse biological processes, ranging from cell cycle progression to autophagy. In ...

journal_title：Methods in enzymology

authors： Marchi S,Bonora M,Patergnani S,Giorgi C,Pinton P

更新日期：2017-01-01 00:00:00

abstract：:Genetically encodable RNA devices that directly detect small molecules in the cellular environment are of increasing interest for a variety of applications including live cell imaging and synthetic biology. Riboswitches are naturally occurring sensors of intracellular metabolites, primarily found in the bacterial mRNA...

journal_title：Methods in enzymology

authors： Trausch JJ,Batey RT

更新日期：2015-01-01 00:00:00

abstract：:We have shown that Rab34/Rah participates in the promotion of macropinosome formation. Here we describe procedures for the analyses of intracellular localization and some functional properties of Rab34. Rab34 lacks a consensus sequence of the fourth motif for GTP/GDP binding and GTPase activities. Indeed, GTPase assay...

journal_title：Methods in enzymology

authors： Sun P,Endo T

更新日期：2005-01-01 00:00:00

abstract：:Complex I is the major entry point in the bacterial and mitochondrial respiratory chain. Structural knowledge of the enzyme is still limited because of its large size and complicated architecture. Only the structure of the hydrophilic domain of a bacterial Complex I has been solved to high resolution by X-ray crystall...

journal_title：Methods in enzymology

authors： Radermacher M

更新日期：2009-01-01 00:00:00

abstract：:Studies on DNA replication in S. pombe have provided powerful insights into the way in which the genome of this model eukaryote is replicated and how the replication process is controlled. These studies have been facilitated by the simplicity and range of methods available in this organism for physiological and geneti...

journal_title：Methods in enzymology

authors： MacNeill SA,Fantes PA

更新日期：1997-01-01 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：:Uncoupling protein 2 (UCP2) is a member of the uncoupling protein family. It is expressed in the inner mitochondrial membrane and plays a role in the control of free radical production, oxidative damage, insulin secretion, and fatty-acid peroxide exportation. Although UCP2 expression occurs in several tissues, some of...

journal_title：Methods in enzymology

authors： Velloso LA,Degasperi GR,Vercesi AE,Saad MA

更新日期：2009-01-01 00:00:00

abstract：:5-FOA is an extremely useful reagent for the selection of Ura- cells amid a population of Ura+ cells. The selection is effective in transformation and recombination studies where loss of URA3+ is desired. A new plasmid shuffling procedure based on the 5-FOAR selection permits the recovery of conditional lethal mutatio...

journal_title：Methods in enzymology

authors： Boeke JD,Trueheart J,Natsoulis G,Fink GR

更新日期：1987-01-01 00:00:00

abstract：:A procedure for an in vitro signaling assay is described for the MAPK and NFkappaB pathways. The method uses a membrane-cleared lysate that contains all the soluble components required for activating these signaling cascades. The pathways can be activated by variety of molecules, including kinases, G-proteins, and E3 ...

journal_title：Methods in enzymology

authors： Mukherjee S,Orth K

更新日期：2008-01-01 00:00:00

abstract：:Posttranslational modification of circadian clock proteins by phosphorylation is an essential regulatory process in the control of eukaryotic circadian clocks. In the Neurospora circadian clock, the key clock protein FREQUENCY (FRQ) is progressively phosphorylated. The phosphorylation of FRQ is regulated by both kinas...

journal_title：Methods in enzymology

authors： Liu Y

更新日期：2005-01-01 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 remarkable success of cancer immunotherapies, especially the checkpoint blocking antibodies, in a subset of patients has reinvigorated the study of tumor-immune crosstalk and its role in heterogeneity of response. High-throughput sequencing and imaging technologies can help recapitulate various aspects of the tumo...

journal_title：Methods in enzymology

authors： Bhinder B,Elemento O

更新日期：2020-01-01 00:00:00

abstract：:Pulsed EPR methods for the study of drug binding to heme-thiolate enzymes such as cytochrome P450 and nitric oxide synthase are discussed. HYSCORE and ENDOR methods to measure (1)H of axial ligands of the heme group are described with illustrations of water serving as the axial ligand in the drug-free enzyme and ligan...

journal_title：Methods in enzymology

authors： Cruce AA,Lockart M,Bowman MK

更新日期：2015-01-01 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：:Dynamin I is a large GTPase enzyme required in membrane constriction and fission during multiple forms of endocytosis. The first method described here is for the rapid purification of native dynamin from peripheral membrane extracts of sheep brain using ammonium sulfate precipitation and affinity purification on recom...

journal_title：Methods in enzymology

authors： Quan A,Robinson PJ

更新日期：2005-01-01 00:00:00

abstract：:Endosomes are isolated from rat liver using high-speed centrifugation through sucrose density gradients. They are distinguishable from Golgi elements, with which they coisolate, by their capacity to concentrate internalized protein ligands (viz., insulin and epidermal growth factor (EGF)) in receptor-bound intact form...

journal_title：Methods in enzymology

authors： Posner BI,Bergeron JJ

更新日期：2014-01-01 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：: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：: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：:Oligomerization is a frequently encountered physical characteristic of biological molecules that occurs for a wide number of transcription factors, ion channels, oxygen-carrying macromolecules such as hemocyanin and enzymes. On the other hand, unwanted protein oligomerization can lead to the formation of pathogenic st...

journal_title：Methods in enzymology

authors： Barranco-Medina S,Dietz KJ

更新日期：2009-01-01 00:00:00

abstract：:The identification and isolation of the soluble catalytic domains of adenylyl cyclase have provided investigators with useful reagents for the study of these enzymes. They have permitted detailed mechanistic investigation of the actions of forskolin, Gs alpha, and the inhibitory G protein, Gi alpha. They have served a...

journal_title：Methods in enzymology

authors： Hatley ME,Gilman AG,Sunahara RK

更新日期：2002-01-01 00:00:00

abstract：:Accurate protein structure determination by solution-state NMR is challenging for proteins greater than about 20kDa, for which extensive perdeuteration is generally required, providing experimental data that are incomplete (sparse) and ambiguous. However, the massive increase in evolutionary sequence information coupl...

journal_title：Methods in enzymology

authors： Huang YJ,Brock KP,Ishida Y,Swapna GVT,Inouye M,Marks DS,Sander C,Montelione GT

更新日期：2019-01-01 00:00:00