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 applications in biophysics, particularly the measurement of time-resolved fluorescence spectra of proteins (with subpicosecond time resolution). Application of this technique to biophysical problems such as dynamics of tryptophan, peptides, proteins, and nucleic acids is reviewed.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Xu J,Knutson JRdoi
10.1016/S0076-6879(08)03408-3subject
Has Abstractpub_date
2008-01-01 00:00:00pages
159-83eissn
0076-6879issn
1557-7988pii
S0076-6879(08)03408-3journal_volume
450pub_type
杂志文章,评审abstract::Experimental screening for protein-ligand interactions is a central task in drug discovery. Nuclear magnetic resonance (NMR) spectroscopy enables the determination of binding affinities, as well as the measurement of structural and dynamic parameters governing the interaction. With traditional liquid-state NMR relying...
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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...
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abstract::Here we describe an optimized recombineering protocol for the creation of conditional alleles. Recombineering is a DNA engineering methodology based on homologous recombination in Escherichia coli. It presents a number of advantages over conventional engineering methods, including the ability to place target sites for...
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abstract::The Duffy blood group antigen is a serpentine protein with seven transmembrane domains that is not coupled to G-proteins or other known intracellular effectors. In addition to erythrocytes, it is also expressed in endothelial cells and neurons. In recent years the Duffy antigen has received much attention because of i...
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journal_title:Methods in enzymology
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abstract::Considering that HIV-1 accumulates and replicates actively within lymphoid tissues, any strategy that will decrease viral stores in these tissues might be beneficial to the infected host. Follicular dendritic cells (FDC), B lymphocytes, antigen-presenting cells like macrophages, and activated CD4(+) T cells are abunda...
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doi:10.1016/B978-0-12-391861-1.00008-3
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abstract::Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21-nt small interfering RNAs (siRNAs) during RNA interference and excises microRNAs (miRNAs) from precursor hairpins. PAZ and PIWI domain (PPD) proteins, also involved in RNAi and miRNA function, are the best-characterized proteins kno...
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abstract::Advanced glycation is one of the major pathophysiological posttranslational modifications. Under hyperglycemic conditions or oxidative stress, proteins and DNA are nonenzymatically modified by oxidative glycation and converted to advanced glycation endproducts (AGEs), which induce the loss of protein functions or apop...
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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...
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abstract::The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety o...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.09.028
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abstract::Endocytosis and autophagy are key vesicular pathways involved in degradation and recycling of cellular material. Both degradative pathways finally fuse with lysosome but are indeed interconnected at several levels. In particular, the fusion between endosomes and autophagosomes can generate intermediate vesicles named ...
journal_title:Methods in enzymology
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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...
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journal_title:Methods in enzymology
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abstract::The methods of computational chemistry and molecular modeling are becoming more and more accessible to biochemists with the advent of fast, inexpensive graphics workstations and well-tested computer programs. The state of the art in small molecules allows chemists to use these programs as "black boxes" and be confiden...
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doi:10.1016/0076-6879(94)43042-x
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abstract::This chapter presents methodologies for RNA extraction from soils coupled with competitive reverse transcription-polymerase chain reaction and capillary electrophoresis techniques. Combined, these approaches provide new capabilities to quantify gene expression in different environments and can aid our understanding of...
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journal_title:Methods in enzymology
pub_type: 杂志文章,评审
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abstract::RNA folds during transcription in the cell. Compared to most in vitro studies where the focus is generally on Mg(2+)-initiated refolding of fully synthesized transcripts, cotranscriptional RNA folding studies better replicate how RNA folds in a cellular environment. Unique aspects of cotranscriptional folding include ...
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)93007-3
更新日期:2005-01-01 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::ADP-ribosylation is a protein post-translational modification that is critically involved in a wide array of biological processes connected to cell stress responses. Enzymes known as poly-ADP-ribose polymerases (PARPs) catalyze the addition of the ADP-ribose units to amino acids with various side chain chemistries. In...
journal_title:Methods in enzymology
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更新日期:2019-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-405881-1.00005-7
更新日期:2013-01-01 00:00:00
abstract::In this chapter we have detailed a method that can be generalized to link virtually any DNA substrate to a chromatography matrix at its ends via an avidin-biotin linkage. We have used this technique to construct a left-handed Z-DNA column for the purpose of identification and purification of Z-DNA-binding proteins. Th...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(90)84290-w
更新日期:1990-01-01 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
pub_type: 杂志文章,评审
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)08002-5
更新日期:2006-01-01 00:00:00
abstract::Microtubule (MT)-based motor proteins transport many cellular factors to their functionally relevant locations within cells, and defects in transport are linked to human disease. Understanding the mechanism and regulation of this transport process in living cells is difficult because of the complex in vivo environment...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-397924-7.00013-3
更新日期:2014-01-01 00:00:00