Abstract:
:Monte Carlo simulations of neighbor exclusion models have been used to demonstrate the importance of collecting and fitting data over a wide range of saturation. Low saturation data are important for good estimates of the affinity K of a drug or protein for the lattice site. High saturation data are important for distinguishing between negatively cooperative and noncooperative binding modes. Neglect of negative cooperativity (omega < 1) has in general little effect on the estimation of K. The error is mostly absorbed by increasing the value of n. This kind of behavior was previously observed with the fitting of nonideal, monomer-dimer, ultracentrifugation data where variations in B, the second virial coefficient, and K2, the dimerization equilibrium constant, are highly correlated, thus making their individual determination difficult. Within experimental error the distinction between a noncooperative model [Eq. (1)] and a negatively cooperative model [Eq. (3) or (4) with omega < 1] may require additional evidence to justify the choice of one model over another. For example, for homogeneous lattices of synthetic deoxyoligonucleotides, n may be constrained with some validity, thus allowing a more accurate and precise determination of K and omega. In fact, n may be established independently, for example, by nuclear magnetic resonance (NMR) methods. However, the assumption of an integral value of n for natural DNA samples may not be valid because of sequence heterogeneity. Unconstrained fitting of negatively cooperative data to Eq. (4) will thus be a very difficult problem (Table V). At an experimental error of only 2.3%, n and K can be reasonably determined but with a large error in omega. Data from the final 20% of saturation are essential in extracting omega. This may in part explain the absence of more reports of negatively cooperative behavior in the literature. This analysis is independent of the systematic error that may be induced by the transformation of data to the Scatchard plot, or the omission of drug self-association, or the occurrence of wall binding by ligand, or variable point density, or non-Gaussian noise, or the occurrence of another mode of binding distinct from the models of McGhee and von Hippel. Each of these will introduce additional error, possibly biased error, in the parameters estimated; however, this does not obviate our conclusion. Even under these ideal circumstances there are serious limitations that must be considered when fitting neighbor exclusion model data. The direct fitting of absorbance data [to Eq. (2) or functions that incorporate other parameters] will also be sensitive to these considerations.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Correia JJ,Chaires JBdoi
10.1016/s0076-6879(94)40065-2subject
Has Abstractpub_date
1994-01-01 00:00:00pages
593-614eissn
0076-6879issn
1557-7988pii
S0076-6879(94)40065-2journal_volume
240pub_type
杂志文章abstract::Antimicrosomal antibodies in inflammatory liver diseases all seem to be directed against members of the cytochrome P450 family of proteins. These autoantigens seem to be genetically polymorphic, the autoantibodies are inhibitory, and the autoepitopes are generally conserved among species. Anti-P450 autoantibodies shar...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(91)06092-h
更新日期:1991-01-01 00:00:00
abstract::The relative structural conservation of "internal glycans" in the cell walls of pathogens suggests that they might as target epitopes less prone to variation and hence with greater potential universality as vaccine targets. Examples of such glycans include the inner core sugars of lipopolysaccharides in Gram-negative ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2017.06.008
更新日期:2017-01-01 00:00:00
abstract::Mathematical computer-assisted simulations of episodic hormone, substrate, or metabolite release can be accomplished using explicit algebra and high-speed microprocessors. Such simulations are useful to describe the behavior of single or multiple pulse generators, as well as the expected output of these systems. Simul...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/s0076-6879(94)40056-3
更新日期:1994-01-01 00:00:00
abstract::We have developed an array-based whole-genome genotyping (WGG) assay (Infinium) using our BeadChip platform that effectively enables unlimited multiplexing and unconstrained single nucleotide polymorphism (SNP) selection. A single tube whole-genome amplification reaction is used to amplify the genome, and loci of inte...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(06)10017-8
更新日期:2006-01-01 00:00:00
abstract::A significant proportion of RNA decay in eukaryotes takes place in the nucleus. In addition to targeting nongenic RNAs such as products of processing and spurious transcription events, nuclear RNA decay also removes aberrant transcripts from regular genes. Moreover, a small list of genes utilizes nuclear RNA turnover ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)02410-5
更新日期:2008-01-01 00:00:00
abstract::Vertebrate odorant-binding proteins (OBPs) are small soluble proteins abundantly secreted in the olfactory mucus of many animal species, including humans. Vertebrate OBPs reversibly bind odorant molecules with micromolar range affinities. Although their physiological role is not clearly understood, OBPs are proposed t...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.05.002
更新日期:2020-01-01 00:00:00
abstract::Two-hybrid systems are one of the most popular, preferred, cost effective, and scalable in vivo genetic approaches for screening protein-protein interactions. A number of variants of yeast and bacterial two-hybrid systems exist, rendering them ideal for modern, flexible proteomics-driven studies. For mapping protein i...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.10.020
更新日期:2017-01-01 00:00:00
abstract::Complex RNA structures regulate many biological processes but are often too large for structure determination by nuclear magnetic resonance (NMR) methods. We determined the solution structure of domain II of the hepatitis C viral internal ribosome entry site (HCV IRES), a 25-kDa RNA, using a novel NMR approach. Conven...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)94016-0
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
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)04421-2
更新日期:2009-01-01 00:00:00
abstract::The hypoxia-inducible factor (HIF) is a heterodimeric basic helix-loop-helix (bHLH) transcription factor that controls the mammalian cellular transcriptional response to low oxygen tension by up-regulating genes including glycolytic enzymes and angiogenic factors, such as the vascular endothelial growth factor (VEGF)....
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(07)35005-2
更新日期:2007-01-01 00:00:00
abstract::Antibody unfolding and aggregation have been gaining increasing concern as the need for pharmaceutical antibodies with high quality has increased. Assays for continuous application of severe stress to antibodies, which are typically employed to evaluate tolerance to aggregation or to understand the mechanism of aggreg...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2019.02.021
更新日期:2019-01-01 00:00:00
abstract::Contemporary high-throughput sequencing methods, notably RNA-Seq, permit the systematic identification and characterization of transcripts whose levels change significantly in response to altered biological states. We have described methods for the application of this methodology to a definition of the transcripts reg...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.09.005
更新日期:2018-01-01 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
pub_type: 杂志文章
doi:10.1016/B978-0-12-385950-1.00004-3
更新日期:2011-01-01 00:00:00
abstract::β-arrestins (βarrs) are multifunctional proteins that interact with activated and phosphorylated G protein-coupled receptors (GPCRs) to regulate their signaling and trafficking. Understanding the intricate details of GPCR-βarr interaction continues to be a key research area in the field of GPCR biology. Bimane fluores...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2019.11.009
更新日期:2020-01-01 00:00:00
abstract::Iron-sulfur (Fe/S) proteins are involved in numerous key biological functions such as respiration, metabolic processes, protein translation, DNA synthesis, and DNA repair. The simplest types of Fe/S clusters include [2Fe-2S], [3Fe-4S], and [4Fe-4S] forms that sometimes are present in multiple copies. De novo assembly ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2017.11.034
更新日期:2018-01-01 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
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.08.028
更新日期:2016-01-01 00:00:00
abstract::White adipose tissue (WAT) is a heterogeneous tissue composed of lipid-filled adipocytes and several nonadipocyte cell populations, including endothelial, blood, uncharacterized stromal, and adipocyte precursor cells. Although lipid-filled adipocytes account for the majority of WAT volume and mass, nonadipocyte cell p...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-411619-1.00003-3
更新日期:2014-01-01 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
pub_type: 杂志文章
doi:10.1016/s0076-6879(00)15851-3
更新日期:2000-01-01 00:00:00
abstract::We have described procedures for collecting, processing, and analyzing kinetic data obtained by photobleaching microscopy of GFP-tagged chromatin proteins in nuclei of cultured living cells. These procedures are useful for characterizing the in vivo binding of chromatin proteins to their natural template--unperturbed,...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/s0076-6879(03)75025-3
更新日期:2004-01-01 00:00:00
abstract::Peptide-based strategies represent transformative approaches to fabricate functional inorganic materials under sustainable conditions by modeling the methods exploited in biology. In general, peptides with inorganic affinity and specificity have been isolated from organisms and through biocombinatorial selection techn...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.05.010
更新日期:2016-01-01 00:00:00
abstract::Death receptors are a subgroup of the tumor necrosis factor receptor superfamily (TNFRSF) and mediate activation of what is widely known as the "extrinsic" apoptosis pathway. TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) is one of the most recent death receptor ligands identified. The TRAIL receptor ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)01618-2
更新日期:2008-01-01 00:00:00
abstract::We have developed a genetic system, termed IVET (in vivo expression technology), designed to identify bacterial genes that are induced when a pathogen infects its host. A subset of these induced genes should include those that encode virulence factors, products specifically required for the infection process. The syst...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/0076-6879(94)35164-3
更新日期:1994-01-01 00:00:00
abstract::Membrane fission, which divides membrane surfaces into separate compartments, is essential to diverse cellular processes including membrane trafficking and cell division. Quantitative assays are needed to elucidate the physical mechanisms by which proteins drive membrane fission. Toward this goal, several experimental...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.08.014
更新日期:2018-01-01 00:00:00
abstract::Human embryonic stem cells (hESCs) are derived from preimplantation embryos. Approximately 60% of human embryos are blocked during in vitro development. Although statistics are inconclusive, experience demonstrates that hESCs are more effectively derived from high-quality embryos. In this way, optimal human embryo cul...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)20001-6
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
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(07)26004-5
更新日期:2007-01-01 00:00:00
abstract::The microbial production of commodity, fine, and specialty chemicals is a driving force in biotechnology. An essential requirement is to introduce biosynthetic pathways to the target compound(s) into chassis organisms. First suitable enzymes must be selected and characterized, and then genetic pathways must be designe...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.04.011
更新日期:2018-01-01 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
pub_type: 杂志文章
doi:10.1016/S0076-6879(07)38024-5
更新日期:2008-01-01 00:00:00
abstract::In the least-squares fitting of data, there is a unique answer to the question of how the data should be weighted: inversely as their variance. Any other weighting gives less than optimal efficiency and leads to unreliable estimates of the parameter uncertainties. In calibration, knowledge of the data variance permits...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)03810-X
更新日期:2009-01-01 00:00:00
abstract::The reverse dot-blot method is a simple and rapid diagnostic procedure that allows screening of sample for a variety of mutations/polymorphisms in a single hybridization reaction. Several methods of immobilizing the oligonucleotide probes are discussed. The reverse dot-blot method has several unique properties that ar...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(93)18029-c
更新日期:1993-01-01 00:00:00
abstract::Numerous aspects of the immune system operate on the basis of complex regulatory networks that are amenable to mathematical and computational modeling. Several modeling frameworks have recently been applied to simulating the immune system, including systems of ordinary differential equations, delay differential equati...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(09)67004-X
更新日期:2009-01-01 00:00:00