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 binding, clustering, trafficking, and signaling functions. The dynamic tertiary and quaternary changes required to channel some of these activities have hampered, until recently, the crystal structure determination of these heterodimeric receptors. In this chapter, we review the methods used to purify and characterize these proteins biophysically and functionally, and to derive their three-dimensional structures.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Xiong JP,Goodman SL,Arnaout MAdoi
10.1016/S0076-6879(07)26014-8subject
Has Abstractpub_date
2007-01-01 00:00:00pages
307-36eissn
0076-6879issn
1557-7988pii
S0076-6879(07)26014-8journal_volume
426pub_type
杂志文章,评审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
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.10.015
更新日期:2017-01-01 00:00:00
abstract::The monitoring of trace amounts of nitric oxide (NO) is of great interest for biomedical applications. High-resolution infrared spectroscopy, like laser magnetic resonance spectroscopy (LMRS), is a versatile technique for the quantitative and isotope-selective analysis of low concentrations of NO. The ability to disti...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)96005-9
更新日期:2005-01-01 00:00:00
abstract::In vitro assembly of eukaryotic translation initiation complexes requires purification of ribosomal subunits, eukaryotic initiation factors, and initiator tRNA from natural sources and therefore yields only limited material for functional and structural studies. In this chapter, we describe a robust, affinity chromato...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(07)29005-6
更新日期:2007-01-01 00:00:00
abstract::This chapter reviews basic concepts of nonlinear fluorescence upconversion, a technique whose temporal resolution is essentially limited only by the pulse width of the ultrafast laser. Design aspects for upconversion spectrophotofluorometers are discussed, and a recently developed system is described. We discuss appli...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(08)03408-3
更新日期:2008-01-01 00:00:00
abstract::Autophagy is the major cellular process of degradation and is modulated by several signaling pathways. Phosphatidylinositol 3-kinase (PtdIns3K) class III (Vps34) and PtdIns3K class I regulate the autophagy pathway positively and negatively, respectively. Both classes of PtdIns3K participate in the synthesis of phospha...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.09.060
更新日期:2017-01-01 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
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.11.004
更新日期:2019-01-01 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
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
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(06)12003-0
更新日期:2006-01-01 00:00:00
abstract::Sulfate-reducing prokaryotes (SRPs) exploit sulfate as an electron acceptor for anaerobic respiration and exclusively catalyze this essential step of the world's sulfur cycle. Because SRPs are found in many prokaryotic phyla and are often closely related to non-SRPs, 16S rRNA gene-based analyses are inadequate to iden...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)97029-8
更新日期:2005-01-01 00:00:00
abstract::This protocol describes Coomassie brilliant blue staining, one of the most common methods of detecting proteins in polyacrylamide gels (PAGE). ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-420119-4.00013-6
更新日期:2014-01-01 00:00:00
abstract::Signal transduction by vascular endothelial growth factors (VEGFs) through their cognate VEGF receptor tyrosine kinases follows the consensus scheme for receptor tyrosine kinases. Thus, binding of ligand induces receptor dimerization and activation of the tyrosine kinase through transphosphorylation between receptor m...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)02013-2
更新日期:2008-01-01 00:00:00
abstract::Hydrogen sulfide is an endogenous gaseous mediator that plays important roles in many physiological processes in microbes, plants, and animals. This chapter focuses on the important roles of hydrogen sulfide in protecting tissues against injury, promoting the repair of damage, and downregulating the inflammatory respo...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2014.11.034
更新日期:2015-01-01 00:00:00
abstract::Gene therapy vectors based on murine retroviruses have now been in clinical trials for over 20 years. During that time, a variety of novel vector pseudotypes were developed in an effort to improve gene transfer. Lentiviral vectors are now in clinical trials and a similar evolution of vector technology is anticipated. ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-386509-0.00005-3
更新日期:2012-01-01 00:00:00
abstract::Fragment-based drug discovery has emerged over the past 15 years as an effective lead discovery paradigm that is complementary to traditional high-throughput screening. The starting point for fragment-based drug discovery is the identification of low-molecular weight, typically low-affinity compounds that bind to a ta...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-381274-2.00006-6
更新日期:2011-01-01 00:00:00
abstract::To maintain cellular homeostasis, the levels of transmembrane receptors found on the plasma membrane must be tightly regulated. Endocytosis of activated receptors and the eventual degradation of these transmembrane proteins in the lysosome serve a vital role in maintaining the plasma membrane receptor levels as well a...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)03049-1
更新日期:2005-01-01 00:00:00
abstract::Guanine nucleotide dissociation inhibitor (GDI) is a central regulator of Rab GTPase family members. GDI recycles Rab proteins from the membrane and sequesters the inactive GDP-bound form of Rab in the cytosol for use in multiple rounds of transport. The balance between the membrane-bound form of Rab and the cytosolic...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)03029-6
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
pub_type: 杂志文章
doi:10.1016/S0076-6879(09)69019-4
更新日期:2009-01-01 00:00:00
abstract::Recent advances have demonstrated the feasibility and robustness of chemical synthesis for the production of homogeneously glycosylated protein forms (glycoforms). By taking advantage of the unmatchable flexibility and precision provided by chemical synthesis, the quantitative effects of glycosylation were obtained us...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2019.02.030
更新日期:2019-01-01 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
pub_type: 杂志文章
doi:10.1016/bs.mie.2019.10.028
更新日期:2020-01-01 00:00:00
abstract::This protocol describes a general protein-to-protein cross-linking procedure using the water-soluble amine-reactive homobifunctional BS(3) (bis[sulfosuccinimidyl] suberate); however, the protocol can be easily adapted using other cross-linkers of similar properties. BS(3) is composed of two sulfo-NHS ester groups and ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-420120-0.00006-2
更新日期:2014-01-01 00:00:00
abstract::Hsp70 chaperones and their obligatory J-protein cochaperones function together in many cellular processes. Via cycles of binding to short stretches of exposed amino acids on substrate proteins, Hsp70/J-protein chaperones not only facilitate protein folding but also drive intracellular protein transport, biogenesis of ...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/bs.mie.2017.07.004
更新日期:2017-01-01 00:00:00
abstract::Inducible expression systems represent the founding technology for the emergence of synthetic biology in mammalian cells. The core molecules in these systems are bacterial regulator proteins that bind to or dissociate from a cognate DNA operator sequence in response to an exogenous stimulus like a small-molecule induc...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-385075-1.00011-1
更新日期:2011-01-01 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
pub_type: 杂志文章,评审
doi:10.1016/0076-6879(92)11024-d
更新日期:1992-01-01 00:00:00
abstract::Structure-based protein design is a powerful technique with great potential. Challenges in two areas limit performance: structure scoring and sequence-structure searching. Many of the functions used to describe the relationship between protein sequence and energy are computationally expensive to evaluate, and the spac...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-394292-0.00008-4
更新日期:2013-01-01 00:00:00
abstract::Among posttranslational modifications of proteins entailed with signal transduction, the redox transition is today brought to the focus as a major biochemical event accounting for the signaling functions of reactive oxygen species. Thermodynamic and kinetic criteria highlight hydroperoxides and protein disulfides as s...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(10)73011-1
更新日期:2010-01-01 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
pub_type: 杂志文章
doi:10.1016/S0076-6879(10)78008-3
更新日期:2010-01-01 00:00:00
abstract::Microbes are now well recognized as major drivers of the biogeochemical cycling that fuels the Earth, and their viruses (phages) are known to be abundant and important in microbial mortality, horizontal gene transfer, and modulating microbial metabolic output. Investigation of environmental phages has been frustrated ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-407863-5.00008-3
更新日期:2013-01-01 00:00:00
abstract::Mitochondrial uncoupling protein-2 (UCP2) regulates glucose-stimulated insulin secretion (GSIS) by pancreatic beta cells-the physiological role of the beta cell UCP2 remains a subject of debate. Experimental studies informing this debate benefit from reliable measurements of UCP2 protein level and activity. In this ch...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-405881-1.00015-X
更新日期:2013-01-01 00:00:00
abstract::Acetyl CoA:arylamine N-acetyltransferase (NAT; E.C. 2.3.1.5) enzymes play a key role in the metabolic activation of aromatic amine and nitroaromatic mutagens to electrophilic reactive intermediates. We have developed a system in which the activation of mutagens by recombinant human NAT2, expressed in Escherichia coli,...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)00011-X
更新日期:2005-01-01 00:00:00
abstract::Human embryonic stem cells hold great promise in furthering our treatment of disease and increasing our understanding of early development. This chapter describes protocols for the derivation and maintenance of human embryonic stem cells. In addition, it summarizes briefly several alternative methods for the culture o...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)18005-2
更新日期:2006-01-01 00:00:00