Analysis of cell migration and its regulation by Rho GTPases and p53 in a three-dimensional environment.

abstract：:Malaria represents an emerging disease because of increasing parasite resistance against available drugs and because of increasing geographical distribution of the causative agent, Plasmodium falciparum. The complete genome of Plasmodium was sequenced recently, revealing that the parasite harbors only one glutathione ...

journal_title：Methods in enzymology

authors： Deponte M,Becker K

更新日期：2005-01-01 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：:Nonsense-mediated mRNA decay (NMD) is activated by exon-junction complexes (EJCs) that are located downstream of the termination codon of the substrate mRNAs. This situation can be imitated by tethering components of the EJC to the 3' untranslated region (3' UTR) of a reporter mRNA. Here we describe the detailed use o...

journal_title：Methods in enzymology

authors： Gehring NH,Hentze MW,Kulozik AE

更新日期：2008-01-01 00:00:00

abstract：:To elucidate the molecular mechanisms of vertebrate color vision, it is essential to establish associations between amino acid substitutions and the directions of lambda max shifts of visual pigments. In this way, we can identify critical amino acid changes that may be responsible for lambda max shifts of visual pigme...

journal_title：Methods in enzymology

authors： Yokoyama S

更新日期：2000-01-01 00:00:00

abstract：:The JNKs (c-Jun N-terminal protein kinases) play important roles in a variety of physiological and pathological functions including induction of apoptosis. A major pathway by which JNKs are activated in response to apoptotic stimuli includes the GTP*Rac1-binding scaffold protein POSH (plenty of SH3s). POSH acts as a s...

journal_title：Methods in enzymology

authors： Xu Z,Greene LA

更新日期：2006-01-01 00:00:00

abstract：:Membrane proteins (MPs) are insoluble in aqueous media as a result of incompatibility between the hydrophilic property of the solvent molecules and the hydrophobic nature of MP surfaces, normally associated with lipid membranes. Amphipathic compounds are necessary for extraction of these macromolecules from the native...

journal_title：Methods in enzymology

authors： Sadaf A,Cho KH,Byrne B,Chae PS

更新日期：2015-01-01 00:00:00

abstract：:Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is benefic...

journal_title：Methods in enzymology

authors： Imhof P

更新日期：2016-01-01 00:00:00

abstract：:High-content screening (HCS), a combination of fluorescence microscopic imaging and automated image analysis, has become a frequently applied tool to study test compound effects in cellular disease-modeling systems. This chapter describes the measurement of G protein-coupled receptor (GPCR) internalization in the HCS ...

journal_title：Methods in enzymology

authors： Haasen D,Schnapp A,Valler MJ,Heilker R

更新日期：2006-01-01 00:00:00

abstract：:Rac binds tightly to lipid membranes through a lipid modification. The influence of the lipid membrane environment on the multiple interactions of Rac has not been well documented. In this chapter, we detail a method to prepare geranyl-geranylated Rac bound to liposomes of defined composition. With this method, one ca...

journal_title：Methods in enzymology

authors： Mesmin B,Antonny B

更新日期：2006-01-01 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：:Paraquat (PQ) is a prototypical redox cycling agent commonly used experimentally to generate reactive oxygen species and oxidative stress. Recently, PQ has also come under investigation as a potential environmental neurotoxin associated with increased risk for neurodegenerative disease developing after chronic exposur...

journal_title：Methods in enzymology

authors： Drechsel DA,Patel M

更新日期：2009-01-01 00:00:00

abstract：:Model building studies may be used to supplement structurally low resolution experimental data with detailed three-dimensional hypothetical atomic models. Because of the strong relation between structure and function in biological molecules such models may give a consistent, integral view of a wealth of experimental d...

journal_title：Methods in enzymology

authors： von Kitzing E

更新日期：1992-01-01 00:00:00

abstract：:The Ras-regulatory network is a loosely defined composition of numerous Ras family members and effector pathways that couple to critical cell-regulatory processes. Investigators are increasingly turning to RNAi-mediated inhibition of gene expression as an effective tool to help generate authentic portraits of Ras prot...

journal_title：Methods in enzymology

authors： Whitehurst AW,White MA

更新日期：2006-01-01 00:00:00

abstract：:Peptides are multidentate chiral ligands capable of coordinating different metal ions. Nowadays, they can be obtained with high yield and purity, thanks to the advances on peptide/protein chemistry as well as in equipment (peptide synthesizers). Based on the identity and length of their amino acid sequences, peptides ...

journal_title：Methods in enzymology

authors： Lima LM,Iranzo O

更新日期：2016-01-01 00:00:00

abstract：:Microscopy is a simple, direct technique for examining the morphology of cells and their organelles. Embedding cells in agarose and then in paraffin as 'cell blocks' allows for them to be processed in the same manner that tissue specimens are processed for histology. This method is advantageous because numerous sectio...

journal_title：Methods in enzymology

authors： Koh CM

更新日期：2013-01-01 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：:Genetic modifier screens offer a powerful, indeed a uniquely powerful tool for the analysis and identification of elements capable of modulating specific cellular functions in development. Here, we describe the methodology that allowed us to explore the genetic circuitry that affects a Notch mutant phenotype caused by...

journal_title：Methods in enzymology

authors： Hori K,Sen A,Artavanis-Tsakonas S

更新日期：2014-01-01 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：: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：:Enveloped virus particles select their lipid-protein components and egress by budding from the host cell membranes. The matrix protein of many enveloped viruses has been proposed as a crucial element for viral budding; however, molecular mechanisms behind membrane remodeling by the matrix protein are yet to be unravel...

journal_title：Methods in enzymology

authors： Shnyrova AV,Zimmerberg J

更新日期：2009-01-01 00:00:00

abstract：:Isotopic enrichment of biomacromolecules is a widely used technique that enables the investigation of the structural and dynamic properties to provide information not accessible with natural abundance isotopic composition. This study reports an approach for deuterium incorporation into bacterial cellulose. A media for...

journal_title：Methods in enzymology

authors： O'Neill H,Shah R,Evans BR,He J,Pingali SV,Chundawat SP,Jones AD,Langan P,Davison BH,Urban V

更新日期：2015-01-01 00:00:00

abstract：:Reliable detection of keratins in tissues is important for investigating their physiological role and for using keratin expression as a biomarker in medical diagnostics. A particular challenge for the detection of keratins by immunofluorescence microscopy or immunohistochemistry relates to the fact that keratin interm...

journal_title：Methods in enzymology

authors： Stumptner C,Gogg-Kamerer M,Viertler C,Denk H,Zatloukal K

更新日期：2016-01-01 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 method presented here is intended as a compromise between finding a good overall alignment and the time taken to do so. Many multiple alignment algorithms spend an excessively large amount of effort trying to find the best global alignment. This time is often ill spent because the results of the standard dynamic p...

journal_title：Methods in enzymology

authors： Taylor WR

更新日期：1990-01-01 00:00:00

abstract：:Protein kinase C (PKC), a family of serine/threonine kinases, plays an important role in apoptosis. Several members of the PKC family act as substrates for caspases. In addition, PKCs can also regulate caspase activation and cell death by apoptosis. The cleavage of PKCs separates the regulatory domain from the catalyt...

journal_title：Methods in enzymology

authors： Basu A,Persaud SD,Sivaprasad U

更新日期：2008-01-01 00:00:00

abstract：:The elucidation of structure-affinity relationships in EF-hand proteins requires a reliable assay of divalent ion affinity. In principle, isothermal titration calorimetry (ITC) should be capable of furnishing estimates for Ca2+- and Mg2+-binding constants in these systems. And because the method yields the binding ent...

journal_title：Methods in enzymology

authors： Henzl MT

更新日期：2009-01-01 00:00:00

abstract：:Cholestatic syndromes are inborn or acquired disorders of bile formation. In recent years, several inherited cholestatic syndromes were characterized at the molecular level: progressive familial intrahepatic cholestasis (PFIC) and benign recurrent intrahepatic cholestasis (BRIC). Both PFIC and BRIC were divided phenot...

journal_title：Methods in enzymology

authors： Kubitz R,Keitel V,Häussinger D

更新日期：2005-01-01 00:00:00

abstract：:In human, rat, and mice, a UGT1 complex locus provides for developmental-, inducer-, and cell-specific synthesis of a family of chemical-detoxifying isozymes, UDP-glucuronosyltransferases, which prevent toxicities, mutagenesis, and/or carcinogenesis. Between 10 and 14 first exons with individual promoter elements are ...

journal_title：Methods in enzymology

authors： Owens IS,Basu NK,Banerjee R

更新日期：2005-01-01 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：: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