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 from sequence data alone is an extremely important field of study in bioinformatics. This is especially so as genomic studies expand beyond model system organisms to encompass the full diversity of eukaryotes. Here we review some of the more commonly used programs for prediction of proteins that function in mitochondria, or mitochondrion-related organelles in diverse eukaryotic lineages and provide recommendations on how to apply these methods. Furthermore, we compare the predictive performance of these programs on a mixed set of mitochondrial and non-mitochondrial proteins. Although N-terminal targeting peptide prediction programs tend to have the highest accuracy, they cannot be effectively used for partial coding sequences derived from high-throughput expressed sequence tag surveys where data for the N-terminus of the encoded protein is often missing. Therefore methods that do not rely on the presence of an N-terminal targeting sequence alone are extremely useful, especially for expressed sequence tag data. The best strategy for classification of unknown proteins is to use multiple programs, incorporating a variety of prediction strategies, and closely examine the predictions with an understanding of how each of those programs will likely handle the data.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Gaston D,Tsaousis AD,Roger AJdoi
10.1016/S0076-6879(09)05002-2subject
Has Abstractpub_date
2009-01-01 00:00:00pages
21-47eissn
0076-6879issn
1557-7988pii
S0076-6879(09)05002-2journal_volume
457pub_type
杂志文章,评审abstract：:Superoxide dismutases (SODs; EC 1.15.1.1) are a group of metalloenzymes which are essential to protect cells under aerobic conditions. In biological systems, it has been reported that SODs and other proteins are susceptible to be attacked by peroxynitrite (ONOO(-)) which can be originated from the reaction of nitric o...
journal_title：Methods in enzymology
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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
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abstract：:Extracellular signals dictate the biological processes of neural stem cells (NSCs) both in vivo and in vitro. The intracellular response elicited by these signals is dependent on the context in which the signal is received, which in turn is decided by previous and concurrent signals impinging on the cell. A synthesis ...
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更新日期：2006-01-01 00:00:00
abstract：:Biochemical analysis of the components of the mRNA decay machinery is crucial to understand the mechanisms of mRNA decay. The Lsm1p-7p-Pat1p complex is a key activator of decapping in the 5' to 3'-mRNA decay pathway that is highly conserved in all eukaryotes. The first step in this pathway is poly(A) shortening that i...
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journal_title：Methods in enzymology
pub_type： 杂志文章,评审
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abstract：:Retinoic acid (RA), the biologically active metabolite of vitamin A, regulates a vast spectrum of biological processes, such as cell differentiation, proliferation, apoptosis, and morphogenesis. microRNAs (miRNAs) play a crucial role in regulating gene expression by binding to messenger RNA (mRNA) which leads to mRNA ...
journal_title：Methods in enzymology
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journal_title：Methods in enzymology
pub_type： 杂志文章
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更新日期：2018-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-381296-4.00003-8
更新日期：2010-01-01 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
pub_type： 杂志文章
doi：10.1016/S0076-6879(08)36007-8
更新日期：2008-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
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更新日期：2009-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(07)00409-0
更新日期：2008-01-01 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：:PYP-phytochrome (Ppr) is a unique photoreceptor that contains a blue light-absorbing photoactive yellow protein (PYP) domain, a red light-absorbing phytochrome domain, and a histidine kinase domain. This chapter describes overexpression of Ppr in a strain of Escherichia coli that allows covalent attachment of substoic...
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doi：10.1016/S0076-6879(06)22009-3
更新日期：2007-01-01 00:00:00
abstract：:Pathogen-host interactions are mediated in part by secreted microbial proteins capable of exploiting host cells for their survival. Several of these manipulations involve, but are not limited to, suppression of defense responses, alterations in host vesicular trafficking, and manipulation of gene expression. The deliv...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-397925-4.00007-9
更新日期：2014-01-01 00:00:00
abstract：:Neurofilament biology is important to understanding structural properties of axons, such as establishment of axonal diameter by radial growth. In order to study the function of neurofilaments, a series of genetically modified mice have been generated. Here, we describe a brief history of genetic modifications used to ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2015.07.027
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(09)67014-2
更新日期：2009-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)03069-7
更新日期：2005-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
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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,评审
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journal_title：Methods in enzymology
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更新日期：2011-01-01 00:00:00
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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
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更新日期：2020-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
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更新日期：2016-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(06)06026-5
更新日期：2006-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)95004-0
更新日期：2005-01-01 00:00:00
abstract：:The Escherichia coli fumarate and nitrate reductase (FNR) regulator protein is an important transcriptional regulator that controls the expression of a large regulon of more than 100 genes in response to changes in oxygen availability. FNR is active when it acquires a [4Fe-4S](2+) cluster under anaerobic conditions. T...
journal_title：Methods in enzymology
pub_type： 杂志文章,评审
doi：10.1016/S0076-6879(07)37011-0
更新日期：2008-01-01 00:00:00
abstract：:Enzymes in the α-d-phosphohexomutase (PHM) superfamily catalyze a multistep reaction, entailing two successive phosphoryl transfers. Key to this reaction is a conserved phosphoserine in the active site, which serves alternately as a phosphoryl donor and acceptor during the catalytic cycle. In addition to its role in t...
journal_title：Methods in enzymology
pub_type： 杂志文章
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更新日期：2018-01-01 00:00:00
abstract：:Nitrite and nitrate represent the final products of nitric oxide (NO) oxidation pathways, and their hematic concentrations are frequently assessed as an index of systemic NO production. However, their intake with food can influence their levels. Nitrite and nitrate could have a role by producing NO, because nitrite ca...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(07)00823-3
更新日期：2008-01-01 00:00:00
abstract：:Antibodies will be immobilized on a cyanogen bromide-activated Sepharose for subsequent use in pull-down assays or immunoaffinity purification. ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-420119-4.00003-3
更新日期：2014-01-01 00:00:00
abstract：:Modular calcium-dependent carbohydrate-recognition domains (CRDs) of mammalian glycan-binding receptors (C-type lectins), engineered to have novel glycan-binding selectivity, have been developed as tools for the study of glycans on cell surfaces. Structure-based specificity swapping between domains can be complemented...
journal_title：Methods in enzymology
pub_type： 杂志文章,评审
doi：10.1016/S0076-6879(10)80009-6
更新日期：2010-01-01 00:00:00
