Computational chemistry and molecular modeling of electron-transfer proteins.

abstract：:Several genetically encoded fluorescent biosensors for Ras family GTPases have been developed that permit spatiotemporal analysis of the activation of these signaling molecules in living cells. We describe here the use of the simplest of these probes, the Ras binding domain (RBD) of selected effectors fused with green...

journal_title：Methods in enzymology

authors： Bivona TG,Quatela S,Philips MR

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：:Linkers play essential roles in the engineering of fusion proteins, and have been extensively demonstrated to affect protein properties such as expression level, solubility, and biological functions. For linker design and optimization, one of the key factors is the flexibility or rigidity of linkers, which describes t...

journal_title：Methods in enzymology

authors： Huang Z,Zhang C,Xing XH

更新日期：2021-01-01 00:00:00

abstract：:Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved mechanism of specific degradation of transcripts with a premature stop codon. NMD eliminates aberrant mRNAs arising from mutations, alternative splicing, and other events in cells. In addition, many normal transcripts undergo NMD. Recent studies demonst...

journal_title：Methods in enzymology

authors： Gurskaya NG,Pereverzev AP,Staroverov DB,Markina NM,Lukyanov KA

更新日期：2016-01-01 00:00:00

abstract：:A variety of recent advances in single-molecule methods are now making possible the routine measurement of the distinct catalytic trajectories of individual enzymes. Unlike their bulk counterparts, these measurements directly reveal the fluctuations inherent to enzymatic dynamics, and statistical measures of these flu...

journal_title：Methods in enzymology

authors： Moffitt JR,Chemla YR,Bustamante C

更新日期：2010-01-01 00:00:00

abstract：:Using the expression strategies described here, we have demonstrated a model system whereby the sequential signaling events involved in cell proliferation and subsequent transformation regulated by G alpha 12 can be investigated. The model system presented here can also be used to study the temporal interrelationships...

journal_title：Methods in enzymology

authors： Dermott JM,Dhanasekaran N

更新日期：2002-01-01 00:00:00

abstract：:The mapping and characterization of the vasculature using proteomics offers the opportunity to better understand the steps and molecular mechanisms involved in vascular development, and angiogenesis in particular. Proteomics has many key advantages over genomics, especially in directly determining protein expression. ...

journal_title：Methods in enzymology

authors： Griffin NM,Schnitzer JE

更新日期：2008-01-01 00:00:00

abstract：:Nitric oxide (NO) is a ubiquitous gas with potent biological effects, including vasodilation, neuronal signaling, and antimicrobial activity. NO is a free radical and can readily react with other molecules, in particular, iron centers and oxygen. At physiological concentrations in aqueous solutions, even in the presen...

journal_title：Methods in enzymology

authors： Laver JR,Stevanin TM,Read RC

更新日期：2008-01-01 00:00:00

abstract：:Extracellular thiol/disulfide redox environments are highly regulated in healthy individuals and become oxidized in disease. This oxidation affects the function of cell surface receptors, ion channels, and structural proteins. Downstream signaling due to changes in extracellular redox potential can be studied using a ...

journal_title：Methods in enzymology

authors： Go YM,Jones DP

更新日期：2010-01-01 00:00:00

abstract：:Essentially the same steps are required to solve the crystal structure of a serpin as for any other protein: produce and purify protein, grow crystals, collect diffraction data, find estimates of the phase angles, and then refine and validate the structure. For the phasing step, experimental phasing methods involving ...

journal_title：Methods in enzymology

authors： Read RJ,Zhou A,Stein PE

更新日期：2011-01-01 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：:Respiration is widely used for evaluation of the metabolic capabilities or physiological state of the microbial culture. This chapter describes novel approaches for characterization of respiration at a single cell level: (1) flow cytometry-based redox sensing (FCRS) of actively metabolizing microbes; (2) respiration r...

journal_title：Methods in enzymology

authors： Konopka MC,McQuaide S,Ojala DS,Kalyuzhnaya MG,Lidstrom ME

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：:Embryonic stem (ES) cells are cells derived from the inner cell mass of a blastocyst stage embryo. These self-renewing multipotent cells are able to differentiate to the three embryonic germ layers, the endoderm, ectoderm, and mesoderm, and are thus able to produce virtually all cell types. The ES cell capacity to gen...

journal_title：Methods in enzymology

authors： Goldberg-Cohen I,Beck G,Ziskind A,Itskovitz-Eldor J

更新日期：2006-01-01 00:00:00

abstract：:Undiluted cytoplasmic extract prepared from unfertilized Xenopus laevis eggs by low-speed centrifugation (CSF extracts) is useful for reconstitution of egg microtubule dynamics and meiosis-II spindle organization, but it suffers limitations for biochemical analysis due to abundant particulates. Here, we describe prepa...

journal_title：Methods in enzymology

authors： Groen AC,Ngyuen PA,Field CM,Ishihara K,Mitchison TJ

更新日期：2014-01-01 00:00:00

abstract：:Heterodimeric complexes between individual members of the R7 subfamily of regulators of G-protein signaling proteins and the Gbeta5 isoform of the heterotrimeric G-protein beta subunit family are strongly expressed in the cell nucleus in neurons and brain, as well as in the cytoplasm and plasma membrane. Native and re...

journal_title：Methods in enzymology

authors： Simonds WF,Woodard GE,Zhang JH

更新日期：2004-01-01 00:00:00

abstract：:Concomitant with the rapid development in biomedical knowledge, including the methods of molecular biology and proteomics, and the manufacture of ever more precise optical instruments, powerful lasers, and sophisticated microcomputing hardware and software, laser microdissection systems have emerged which are now ente...

journal_title：Methods in enzymology

authors： Willenberg HS,Walters R,Bornstein SR

更新日期：2002-01-01 00:00:00

abstract：:Biotinylated molecules are extensively employed in bioanalytics and biotechnology. The currently available assays for quantification of biotin groups suffer from low sensitivity, low accuracy, or provide highly variable responses for different biotin derivatives. We developed a competitive binding assay in which avidi...

journal_title：Methods in enzymology

authors： Oberbichler E,Wiesauer M,Schlögl E,Stangl J,Faschinger F,Knör G,Gruber HJ,Hytönen VP

更新日期：2020-01-01 00:00:00

abstract：:The binding of the chemokine [C-X-C motif] ligand 12 (CXCL12 or stromal cell-derived factor 1alpha [SDF-1alpha]) constitutively produced by bone marrow stromal cells and osteoblasts, to the CXC receptor (CXCR) 4, a transmembrane chemokine receptor expressed on hematopoietic stem and progenitor cells (HSPCs), has emerg...

journal_title：Methods in enzymology

authors： Rettig MP,Ramirez P,Nervi B,DiPersio JF

更新日期：2009-01-01 00:00:00

abstract：:Chromatin plays a vital role in regulating cellular processes that occur on the DNA. Modulation of chromatin structure is conducted through interactions with binding factors that direct critical actions such as posttranslational modifications, nucleosome remodeling, and incorporation of histone variants. Specific fact...

journal_title：Methods in enzymology

authors： Winkler DD,Luger K,Hieb AR

更新日期：2012-01-01 00:00:00

abstract：:Two lymphoid cell-specific proteins, called RAG-1 and RAG-2, initiate the process of antigen receptor gene rearrangement, termed V(D)J recombination, by assembling a protein-DNA complex with two recombination signal sequences (RSSs), each of which adjoins a different receptor gene segment, and then introducing a DNA d...

journal_title：Methods in enzymology

authors： Bergeron S,Anderson DK,Swanson PC

更新日期：2006-01-01 00:00:00

abstract：:Classifications and characterizations of specific proteins, such as enzymes, not only allow us to understand biosynthetic and metabolic pathways but they also help to drive our understanding of protein structure and function. How those characterizations are evaluated, however, may change our interpretations and lead u...

journal_title：Methods in enzymology

authors： Bradshaw HB,Leishman E

更新日期：2017-01-01 00:00:00

abstract：:Scanning fluorescence correlation spectroscopy (sFCS) is the generic term for a group of fluorescence correlation techniques where the measurement volume is moved across the sample in a defined way. The introduction of scanning is motivated by its ability to alleviate or remove several distinct problems often encounte...

journal_title：Methods in enzymology

authors： Petrásek Z,Ries J,Schwille P

更新日期：2010-01-01 00:00:00

abstract：:In vivo genome manipulation through site-directed mutagenesis and chromosome rearrangements has been hindered by the difficulty in achieving high frequencies of targeting and the intensive labor required to create altered genomes that do not contain any heterologous sequence. Here we describe our approach, referred to...

journal_title：Methods in enzymology

authors： Storici F,Resnick MA

更新日期：2006-01-01 00:00:00

abstract：:Integrins are large modular cell-surface receptors that regulate almost every aspect of cellular function through bidirectional signals transmitted across the lipid bilayer. Regulation of integrin activity is accomplished by complex and still incompletely understood biochemical pathways that modify integrin ligand bin...

journal_title：Methods in enzymology

authors： Xiong JP,Goodman SL,Arnaout MA

更新日期：2007-01-01 00:00:00

abstract：:Hybrid proteins or chimeras are generated by recombination of protein fragments. In the course of evolution, this mechanism has led to major diversification of protein folds and their functionalities. Similarly, protein engineers have taken advantage of this attractive strategy to build new proteins. Methods that use ...

journal_title：Methods in enzymology

authors： Rico JA,Höcker B

更新日期：2013-01-01 00:00:00

abstract：:Over the past 19 years, we have developed a novel myxoma virus-derived anti-inflammatory serine protease inhibitor, termed a serpin, as a new class of immunomodulatory therapeutic. This review will describe the initial identification of viral serpins with anti-inflammatory potential, beginning with preclinical analysi...

journal_title：Methods in enzymology

authors： Chen H,Zheng D,Davids J,Bartee MY,Dai E,Liu L,Petrov L,Macaulay C,Thoburn R,Sobel E,Moyer R,McFadden G,Lucas A

更新日期：2011-01-01 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：:ADP-ribosylation factor domain protein 1 (ARD1) is a multifunctional protein that belongs to the family of 20-kDa ARF proteins. The ARD1 gene encodes a 64-kDa protein with a structure comprising an 18-kDa ADP-ribosylation factor (ARF) domain at the C-terminus (amino acids 403-574), and a 46-kDa N-terminal domain (amin...

journal_title：Methods in enzymology

authors： Vichi A,Moss J,Vaughan M

更新日期：2005-01-01 00:00:00

abstract：:Glycosylation is a complex form of protein modification occurring in the secretory pathway. The addition of N- and O-glycans affects intracellular processes like the folding and trafficking of most glycoproteins. To better understand the impact of glycosylation in protein folding and maturation, parameters like glycos...

journal_title：Methods in enzymology

authors： Hülsmeier AJ,Welti M,Hennet T

更新日期：2011-01-01 00:00:00