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, as it not only can identify novel PTMs but also can provide quantitative measurement of a spectrum of histone variants and PTMs in the same sample. In this chapter, we employ a combination of chemical derivation and high-resolution MS to identify and quantify multiple histone variants and PTMs. Histones are acid extracted and modified with propionyl groups and subsequently produces suitable sizes of fragments for MS analysis by trypsin digestion. The newly generated N-termini of histone peptides can be differentially marked by stable isotope labeling in a second reaction of propionylation, which enables direct comparison between two different samples in the following MS analysis.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Lin S,Garcia BAdoi
10.1016/B978-0-12-391940-3.00001-9subject
Has Abstractpub_date
2012-01-01 00:00:00pages
3-28eissn
0076-6879issn
1557-7988pii
B978-0-12-391940-3.00001-9journal_volume
512pub_type
杂志文章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
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abstract::Polarized epithelial cells are characterized by distinct plasma membrane domains and asymmetrical distribution of cell surface proteins and lipids. In vertebrates, tight junctions act as a fence between the apical and basolateral domains. Although many of the key components of the polarity machinery have been identifi...
journal_title:Methods in enzymology
pub_type: 杂志文章
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journal_title:Methods in enzymology
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abstract::In eukaryotes, determination of the subcellular location of a novel protein encoded in genomic or transcriptomic data provides useful clues as to its possible function. However, experimental localization studies are expensive and time-consuming. As a result, accurate in silico prediction of subcellular localization fr...
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,评审
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journal_title:Methods in enzymology
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abstract::Circadian clocks are present in most cells and are essential for maintenance of daily rhythms in physiology, mood, and cognition. Thus, not only neurons of the central circadian pacemaker but also many other peripheral tissues possess the same functional and self-sustained circadian clocks. Surprisingly, however, thei...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/bs.mie.2014.10.023
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abstract::Complex I is the major entry point in the bacterial and mitochondrial respiratory chain. Structural knowledge of the enzyme is still limited because of its large size and complicated architecture. Only the structure of the hydrophilic domain of a bacterial Complex I has been solved to high resolution by X-ray crystall...
journal_title:Methods in enzymology
pub_type: 杂志文章
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-391858-1.00009-5
更新日期:2012-01-01 00:00:00
abstract::Nitric oxide formation in ischemia-reperfusion injury can be identified and measured directly using EPR of nitroso-heme complexes comprising NO bound to either Mb or Hb-Fe2+. This article described the successful use of this method to detect and quantify the generation of NO formed independently of nitric oxide syntha...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/s0076-6879(02)59182-5
更新日期:2002-01-01 00:00:00
abstract::Small GTPases of the Ras and Rho families are among the most studied signaling proteins and represent promising therapeutic targets for human neoplastic disease. Despite the high level of interest in these proteins, direct analysis of most aspects of Ras protein biology in living cells has not been possible, because m...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)07032-1
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abstract::Organ-specific delivery of biofunctional agents is thought to enhance their activity and to reduce their side effects. Liposomes have been used as drug carriers in cancer chemotherapy, since they accumulate passively in tumor tissues due to an enhanced permeability and retention (EPR) effect. In addition, modification...
journal_title:Methods in enzymology
pub_type: 杂志文章
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abstract::Cells belonging to the monocyte/macrophage lineage are in general highly resistant to peroxynitrite. Resistance is not dependent on the scavenging of peroxynitrite itself, or of other secondary reactive species, but is rather associated with the prompt activation of a survival signaling leading to the prevention of to...
journal_title:Methods in enzymology
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doi:10.1016/S0076-6879(08)01205-6
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.09.069
更新日期:2017-01-01 00:00:00
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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,评审
doi:10.1016/S0076-6879(07)37001-8
更新日期:2008-01-01 00:00:00
abstract::Electrochemical microsensors for O2, pH, H2S, H2, and N2O are now available commercially, thus it has become a relatively simple task to analyze the microenvironment in stratified microbial communities for several chemical species. In addition, sensors are available for the physical parameters diffusivity and flow, an...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)97009-2
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abstract::Dimethylsulfoniopropionate (DMSP) demethylase is a tetrahydrofolate-dependent enzyme that initiates the DMSP demethylation pathway in marine bacteria. This enzyme is important for understanding of organic sulfur flux from the oceans because it directs the sulfur from DMSP away from dimethylsulfide. This enzyme has bee...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.03.001
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abstract::Scanning transmission electron microscopy (STEM) of unstained, freeze-dried biological macromolecules in the dark-field mode provides an image based on the number of electrons elastically scattered by the constituent atoms of the macromolecule. The image of each isolated particle provides information about the project...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)36027-3
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(10)76014-6
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)08022-0
更新日期:2006-01-01 00:00:00
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...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.08.016
更新日期:2019-01-01 00:00:00
abstract::Two factors, climate change brought on by rising atmospheric CO2 levels and the accelerating shift toward renewable energy sources, have together worked to heighten interest in understanding how biological catalysts so effectively bring about the reduction of CO2 to formate, with potential applications for both biorem...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.10.013
更新日期:2018-01-01 00:00:00
abstract::The steady technical advances of nuclear magnetic resonance (NMR) over the past decades enabled a significant increase in the molecular size of protein particles that can be subjected to a structural and functional characterization in solution. The larger molecular weight of such proteins is accompanied with an increa...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.05.028
更新日期:2015-01-01 00:00:00
abstract::Proteins are fragile molecules that often require great care during purification to ensure that they remain intact and fully active. Nowadays, many proteins are also purified in small amounts under denaturing conditions by various gel electrophoretic techniques, such that inactive proteins are obtained. But even here,...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(09)63010-X
更新日期:2009-01-01 00:00:00
abstract::The three major considerations in reducing metal-gel binding are (1) the type of gel to be used, (2) the ionic strength of the eluent, and (3) alkaline reduction of the gel. Each of these parameters should be considered in advance of an experiment. A method is offered for determining the optimal gel type, gel treatmen...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(88)58044-8
更新日期:1988-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)06046-0
更新日期:2006-01-01 00:00:00
abstract::Fluorescence-based imaging regimes require exposure of living samples under study to high intensities of focused incident illumination. An often underestimated, overlooked, or simply ignored fact in the design of any experimental imaging protocol is that exposure of the specimen to these excitation light sources must ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-391856-7.00039-1
更新日期:2012-01-01 00:00:00
abstract::PRA2 was found to interact with the ER-localized protein VAMP-associated protein of 33 kDa or VAP-33 by a yeast two-hybrid screen. We describe here the purification of PRA2 and VAP-33 as well as an in vitro pull-down procedure to verify the interaction. PRA2 was found to form a large sodium dodecyl sulfate (SDS)-insol...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)03069-7
更新日期:2005-01-01 00:00:00