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 pigments. In this process, we may consider only highly conserved residues, simply because the evolutionary conservation often implies functional importance. Using such an "evolutionary model" as a convenient tool in designing mutagenesis experiments, we can test specific hypotheses on the molecular mechanisms that are responsible for color vision in vertebrates. Virtually any vertebrate opsin cDNA can be expressed in COS cells, reconstituted with 11-cis-retinal, and the lambda max values of the regenerated pigments can be measured rather easily. By constructing mutant pigments with desired amino acid changes and conducting the in vitro assay and comparing their lambda max values with those of corresponding wild-type pigments, we can elucidate the molecular mechanisms of lambda max shifts--and color vision--of vertebrates rigorously.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Yokoyama Sdoi
10.1016/s0076-6879(00)15851-3subject
Has Abstractpub_date
2000-01-01 00:00:00pages
312-25eissn
0076-6879issn
1557-7988journal_volume
315pub_type
杂志文章abstract：:Crystallographic studies on flavodiiron proteins (FDPs) have revealed that the common sequence core ( approximately 400 residues) that defines this protein family comprises two structural domains. The N-terminal domain (of approximately 250 residues) displays a metallo-beta-lactamase-like-fold, being indeed structural...
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：: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 characterization of microbial adhesins is greatly facilitated by the use of synthetic peptides. Synthetic peptides can be used to identify specific antigenic epitopes, to delineate receptor-binding domain of adhesins, and to facilitate the characterization of the adhesin, and they allow for a direct examination of...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/s0076-6879(95)53013-4
更新日期：1995-01-01 00:00:00
abstract：:Plasminogen activator inhibitor-1 (PAI-1) is the main inhibitor of tissue-type plasminogen activator (t-PA) and urokinase-type plasminogen activator (u-PA) and therefore plays an important role in the plasminogen/plasmin system. PAI-1 is involved in a variety of cardiovascular diseases (mainly through inhibition of t-...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-386471-0.00005-5
更新日期：2011-01-01 00:00:00
abstract：:In this chapter we have discussed the methodology used to identify and characterize three intermediates in protein transport from the ER that represent stages of transport vesicle budding, targeting, and fusion. The intermediates are obtained using a variety of transport inhibitors: low-temperature incubations, additi...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/0076-6879(92)19028-5
更新日期：1992-01-01 00:00:00
abstract：:This protocol describes the expression and analysis of membrane proteins produced in yeast, as illustrated with Yarrowia lipolytica and Pichia pastoris. Step by step, we explain how to generate a yeast strain expressing the membrane protein of interest, how to prepare a membrane protein sample from yeast, and how to a...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2014.12.010
更新日期：2015-01-01 00:00:00
abstract：:In vivo genome manipulation through site-directed mutagenesis and chromosome rearrangements has been hindered by the difficulty in achieving high frequencies of targeting and the intensive labor required to create altered genomes that do not contain any heterologous sequence. Here we describe our approach, referred to...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)09019-1
更新日期：2006-01-01 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：:The specificity of CRISPR-Cas systems for nucleic acid targets is determined by a combination of binding and cleavage. Understanding the mechanisms by which Cas proteins specifically select their targets is critical for the development of CRISPR-Cas systems for biotechnology applications. Moreover, the specificity of ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2018.10.019
更新日期：2019-01-01 00:00:00
abstract：:The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modelin...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2015.07.007
更新日期：2015-01-01 00:00:00
abstract：:Undiluted cytoplasmic extract prepared from unfertilized Xenopus laevis eggs by low-speed centrifugation (CSF extracts) is useful for reconstitution of egg microtubule dynamics and meiosis-II spindle organization, but it suffers limitations for biochemical analysis due to abundant particulates. Here, we describe prepa...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-397924-7.00023-6
更新日期：2014-01-01 00:00:00
abstract：:Slp4-a/granuphilin-a is a member of the synaptotagmin-like protein (Slp) family and consists of an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains. Slp4-a is specifically localized on secretory granules in some endocrine and exocrine cells through its SHD, and it attenuates Ca(2+)-dependent dense...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)03039-9
更新日期：2005-01-01 00:00:00
abstract：:Immunogenic cell death (ICD), induced by certain anticancer chemotherapeutics, leads to the emission of danger associated molecular patterns (DAMP) by cancer cells, which facilitates the attraction, activation and maturation of dendritic cells (DC) as well as the subsequent priming of effector T cells. In this context...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2019.07.021
更新日期：2020-01-01 00:00:00
abstract：:Lysosomes are specialized organelles for protein recycling and as such are involved in the terminal steps of autophagy. However, it has become evident that lysosomes also play an important role in the progression of apoptosis. This latter function seems to be dependent on lysosomal proteases, which need to be released...
journal_title：Methods in enzymology
pub_type： 杂志文章,评审
doi：10.1016/S0076-6879(08)01409-2
更新日期：2008-01-01 00:00:00
abstract：:Pulsed electron double resonance technique, also known as double electron-electron resonance, jointly with site-directed spin labeling (SDSL) have been used extensively for studying structures and structural change. During the last decades, significant enhancements have been made by optimization of the experimental pr...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2015.05.027
更新日期：2015-01-01 00:00:00
abstract：:Histone acetylation is a dynamic epigenetic modification that functions in the regulation of DNA-templated reactions, such as transcription. This lysine modification is reversibly controlled by histone (lysine) acetyltransferases and deacetylases. Here, we present methods employing isotopic labeling and mass spectrome...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2016.01.007
更新日期：2016-01-01 00:00:00
abstract：:The existence of an accurate force field (FF) model that reproduces the free-energy landscape is a key prerequisite for the simulation of biomineralization. Here, the stages in the development of such a model are discussed including the quality of the water model, the thermodynamics of polymorphism, and the free energ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-416617-2.00001-1
更新日期：2013-01-01 00:00:00
abstract：:Natural products continue to demonstrate their utility both as therapeutics and as molecular probes for the discovery and mechanistic deconvolution of various cellular processes. However, this utility is dampened by the inherent difficulties involved in isolating and characterizing new bioactive natural products, in o...
journal_title：Methods in enzymology
pub_type： 杂志文章,评审
doi：10.1016/S0076-6879(07)31014-8
更新日期：2007-01-01 00:00:00
abstract：:Since its major launch into academia in the mid-1990s, spotted DNA microarray technology has expanded and matured into an important mainstream tool for genomic-scale gene expression studies across many species with many applications. Based on the principles of enzymatic nucleic acid labeling and DNA hybridization, the...
journal_title：Methods in enzymology
pub_type： 杂志文章,评审
doi：10.1016/S0076-6879(06)10007-5
更新日期：2006-01-01 00:00:00
abstract：:Quantitative real-time polymerase chain reaction (qRT-PCR) is a flexible and scalable method for analyzing transcript abundance that can be used at a single gene or high-throughput (>100 genes) level. Information obtained from this technique can be used as an indicator of potential regulation of glycosylation at the t...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(10)79004-2
更新日期：2010-01-01 00:00:00
abstract：:Microscopy is a simple, direct technique for examining the morphology of cells and their organelles. Embedding cells in agarose and then in paraffin as 'cell blocks' allows for them to be processed in the same manner that tissue specimens are processed for histology. This method is advantageous because numerous sectio...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-420067-8.00018-0
更新日期：2013-01-01 00:00:00
abstract：:G-protein-coupled receptors (GPCRs) represent a major class of receptors through which a number of signals ranging from photons to large glycoprotein hormones are recognized. Human genome encodes about 800 GPCRs, yet very little structural information is available on this class of receptors. Structural studies provide...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-391861-1.00008-3
更新日期：2013-01-01 00:00:00
abstract：:Silica biomorphs and silica gardens are canonical examples of precipitation phenomena yielding self-assembled nanocrystalline composite materials with outstanding properties in terms of morphology and texture. Both types of structures form spontaneously in alkaline environments and rely on simple, and essentially simi...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-416617-2.00011-4
更新日期：2013-01-01 00:00:00
abstract：:Liquid-liquid phase separation (LLPS) has been known to drive formation of biomolecular compartments, which can encapsulate RNA and proteins among other cosolutes. Such compartments, which lack a lipid membrane, have been implicated in origins of life scenarios as they can easily uptake and concentrate biomolecules, s...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2020.06.010
更新日期：2021-01-01 00:00:00
abstract：:The combined use of rotating-frame relaxation methods, temperature-dependent measurements of line shapes and magnetization transfer experiments allows in favorable cases the examination in some detail of exchange processes that occur on the millisecond time scale. It is possible to determine not only the rate constant...
journal_title：Methods in enzymology
pub_type： 杂志文章,评审
doi：10.1016/s0076-6879(94)39023-1
更新日期：1994-01-01 00:00:00
abstract：:Yeast cells in an isogenic population do not all display the same phenotypes. To study such variation within a population of cells, we need to perform measurements on each individual cell instead of measurements that average out the behavior of a cell over the entire population. Here, we provide the basic concepts and...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(10)70017-3
更新日期：2010-01-01 00:00:00
abstract：:The recalcitrance of the cell wall to enzymatic hydrolysis represents one of the greatest challenges for using biomass to replace the petroleum as a feedstock for fuels and chemicals. Cell walls are complex in architecture and composition, posing a biochemical challenge for the development of efficient enzymes to rele...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-415931-0.00003-3
更新日期：2012-01-01 00:00:00
abstract：:A fundamental function of the vasculature is to deliver oxygen to tissues and organs. The cells that make up the vasculature also require oxygen, and are acted upon by oxygen in direct and indirect ways that can have significant effects on acute and chronic vascular function and morphology. The role that oxygen, or it...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(08)02813-9
更新日期：2008-01-01 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：: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
更新日期：2019-01-01 00:00:00
