Type I polyketide synthases that require discrete acyltransferases.

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

authors： Raiteri P,Demichelis R,Gale JD

更新日期：2013-01-01 00:00:00

abstract：:Peptides are multidentate chiral ligands capable of coordinating different metal ions. Nowadays, they can be obtained with high yield and purity, thanks to the advances on peptide/protein chemistry as well as in equipment (peptide synthesizers). Based on the identity and length of their amino acid sequences, peptides ...

journal_title：Methods in enzymology

authors： Lima LM,Iranzo O

更新日期：2016-01-01 00:00:00

abstract：:This study designed, synthesized, and characterized a number of new heterobifunctional photocleavable cross-linking reagents that may be used to photomodulate the activity of proteins or to prepare caged fluorescent dyes. Biomolecules or fluorophores caged via a thiol group with the BNBASE reagent can be covalently li...

journal_title：Methods in enzymology

authors： Marriott G,Ottl J

更新日期：1998-01-01 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

authors： Barrett T,Edgar R

更新日期：2006-01-01 00:00:00

abstract：:Sedimentation velocity experiments measure the transport of molecules in solution under centrifugal force. Here, we describe a method for monitoring the sedimentation of very large biological molecular assemblies using the interference optical systems of the analytical ultracentrifuge. The mass, partial-specific volum...

journal_title：Methods in enzymology

authors： Rogge RA,Hansen JC

更新日期：2015-01-01 00:00:00

abstract：:The programmed death 1 (PD-1) and cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) are negative regulators of T-cell immune function. Removal of these "brakes" in T cells results in increased activation of the immune system and controlling and eradicating tumor. The development of immune checkpoint inhibitors (ICI...

journal_title：Methods in enzymology

authors： Nomura N,Nomura Y,Sato Y,Iwata S

更新日期：2019-01-01 00:00:00

abstract：:Membrane-bound pyrophosphatases couple the hydrolysis of inorganic pyrophosphate to the pumping of ions (sodium or protons) across a membrane in order to generate an electrochemical gradient. This class of membrane protein is widely conserved across plants, fungi, archaea, and bacteria, but absent in multicellular ani...

journal_title：Methods in enzymology

authors： Harborne SPD,Strauss J,Turku A,Watson MA,Tuma R,Harris SA,Goldman A

更新日期：2018-01-01 00:00:00

abstract：:ADP-ribosylation factor domain protein 1 (ARD1) is a multifunctional protein that belongs to the family of 20-kDa ARF proteins. The ARD1 gene encodes a 64-kDa protein with a structure comprising an 18-kDa ADP-ribosylation factor (ARF) domain at the C-terminus (amino acids 403-574), and a 46-kDa N-terminal domain (amin...

journal_title：Methods in enzymology

authors： Vichi A,Moss J,Vaughan M

更新日期：2005-01-01 00:00:00

abstract：:Mathematical computer-assisted simulations of episodic hormone, substrate, or metabolite release can be accomplished using explicit algebra and high-speed microprocessors. Such simulations are useful to describe the behavior of single or multiple pulse generators, as well as the expected output of these systems. Simul...

journal_title：Methods in enzymology

authors： Veldhuis JD,Johnson ML

更新日期：1994-01-01 00:00:00

abstract：:The above methodology has been used to prepare a variety of PE-immunotoxins. These reagents are potent cytotoxic agents for cells in culture that bind the appropriate antibody and nontoxic when cells do not bind the antibody. PE-immunotoxins can be used to select for mutant cultured cells which lack the target of the ...

journal_title：Methods in enzymology

authors： FitzGerald DJ

更新日期：1987-01-01 00:00:00

abstract：:Cellular signaling and regulatory cascades often rely on post-translational modification of proteins, particularly phosphorylation, to quickly and effectively relay signals from a variety of inputs. Numerous kinases, the effectors of phosphorylation, and kinase networks have been implicated in human diseases. Until re...

journal_title：Methods in enzymology

authors： Mohler K,Rinehart J

更新日期：2019-01-01 00:00:00

abstract：:ClpB belongs to the Hsp100 family of ring-forming heat-shock proteins involved in degradation of unfolded/misfolded proteins and in reactivation of protein aggregates. ClpB monomers reversibly associate to form the hexameric molecular chaperone that, together with the DnaK system, has the ability to disaggregate stres...

journal_title：Methods in enzymology

authors： Alfonso C,del Castillo U,Martín I,Muga A,Rivas G

更新日期：2015-01-01 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

authors： Negron C,Keating AE

更新日期：2013-01-01 00:00:00

abstract：:Epitope tagging has provided a useful experimental strategy with widespread applicability. The ample variety of epitope tag systems that have been put to use to date provide a collection of attributes relevant to virtually any experimental system. As a consequence, epitope tagging will continue to be a valuable tool f...

journal_title：Methods in enzymology

authors： Fritze CE,Anderson TR

更新日期：2000-01-01 00:00:00

abstract：:Mutations in regulators and effectors of the Rho GTPases underlie various forms of mental retardation (MR). Among them, oligophrenin-1 (OPHN1), which encodes a Rho-GTPase activating protein, was one of the first Rho-linked MR genes identified. Upon characterization of OPHN1 in hippocampal brain slices, we obtained evi...

journal_title：Methods in enzymology

authors： Kasri NN,Govek EE,Van Aelst L

更新日期：2008-01-01 00:00:00

abstract：:The Rcs phosphorelay, consisting of a hybrid sensor kinase, a phosphotransferase, and a response regulator, regulates a large number of bacterial functions. These include capsule production, the target originally defined for these regulators, a small regulatory RNA, and a growing list of additional genes, many of unkn...

journal_title：Methods in enzymology

authors： Majdalani N,Gottesman S

更新日期：2007-01-01 00:00:00

abstract：:Chloroplast genomes of land plants and algae contain generally between 100 and 150 genes. These genes are involved in plastid gene expression and photosynthesis and in various other tasks. The function of some chloroplast genes is still unknown and some of them appear to be essential for growth and survival. Repressib...

journal_title：Methods in enzymology

authors： Ramundo S,Rochaix JD

更新日期：2015-01-01 00:00:00

abstract：:When yeast are faced with irreparable DNA damage, they will first arrest in G2/M, via the DNA damage checkpoint pathway, but will subsequently adapt to that arrest and resume division. Here, we summarize assays that we have used to examine checkpoint adaptation. Specifically, we discuss the merits of inducing DNA dama...

journal_title：Methods in enzymology

authors： Toczyski DP

更新日期：2006-01-01 00:00:00

abstract：:This chapter provides the methodologies employed to study the polymorphism of human apoE. These and other related studies have advanced our understanding of the structure and function of this protein as follows: The complex array of human apoE observed by two-dimensional gel electrophoresis results from genetic variat...

journal_title：Methods in enzymology

authors： Zannis VI

更新日期：1986-01-01 00:00:00

abstract：:This chapter described the preparation and fractionation of libraries of M13 phage displaying proteins as fusions to the major coat protein. High titer (10(13) pfu/ml) phage libraries can readily be generated using a single vector and the level of display surpasses that of gene III fusion phage. Since the synthetic VI...

journal_title：Methods in enzymology

authors： Roberts BL,Markland W,Ladner RC

更新日期：1996-01-01 00:00:00

abstract：:Recent studies using sulfotransferase-deficient mice have revealed various physiological functions of sulfated glycans. Studies using gene-targeted mice deficient in both N-acetylglucosamine-6-O-sulfotransferase (GlcNAc6ST)-1 and GlcNAc6ST-2 showed that these sulfotransferases play critical roles in lymphocyte homing....

journal_title：Methods in enzymology

authors： Kawashima H

更新日期：2010-01-01 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

authors： Kavran JM,Leahy DJ

更新日期：2014-01-01 00:00:00

abstract：:Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA[uracil-54,C5]-MTases). In eukaryotes and many bacteria, the methyl donor for this reaction is generally S-adenosyl-L-methionine (S-AdoMet). However, in other bacteria, like ...

journal_title：Methods in enzymology

authors： Urbonavicius J,Brochier-Armanet C,Skouloubris S,Myllykallio H,Grosjean H

更新日期：2007-01-01 00:00:00

abstract：:With the rapid development of nanotechnology, inorganic magnetic nanoparticles, especially iron oxide nanoparticles (IOs), have emerged as great vehicles for biomedical diagnostic and therapeutic applications. In order to rationally design IO-based gene delivery nanovectors, surface modification is essential and deter...

journal_title：Methods in enzymology

authors： Liu G,Wang Z,Lee S,Ai H,Chen X

更新日期：2012-01-01 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

authors： Huang YJ,Brock KP,Ishida Y,Swapna GVT,Inouye M,Marks DS,Sander C,Montelione GT

更新日期：2019-01-01 00:00:00

abstract：:The aim of this chapter is to discuss the basic principles and reasoning behind elementary flux mode analysis (EFM analysis)--an important tool for the analysis of metabolic networks. We begin with a short introduction into metabolic pathway analysis and subsequently outline in detail fundamentals of EFM analysis by w...

journal_title：Methods in enzymology

authors： Schäuble S,Schuster S,Kaleta C

更新日期：2011-01-01 00:00:00

abstract：:Flavoenzymes comprise a large class of proteins that carry out a diverse range of important redox chemistry. Although X-ray crystal structures of many flavoenzymes have been determined, there are still unresolved questions regarding the actual oxidation state of the flavin cofactors in these structures due to photored...

journal_title：Methods in enzymology

authors： Kerber T,Vrielink A

更新日期：2020-01-01 00:00:00

abstract：:Protein kinases transfer a phosphoryl group from ATP onto target proteins and play a critical role in signal transduction and other cellular processes. Here, we review the kinase kinetic and chemical mechanisms and their application in understanding kinase structure and function. Aberrant kinase activity has been impl...

journal_title：Methods in enzymology

authors： Wang Z,Cole PA

更新日期：2014-01-01 00:00:00

abstract：:The circadian clock exists to synchronize inner physiology with the external world, allowing life to anticipate and adapt to the continual changes that occur in an organism's environment. The clock architecture is highly conserved, present in almost all major branches of life. Within eukaryotes, the filamentous fungus...

journal_title：Methods in enzymology

authors： Hurley J,Loros JJ,Dunlap JC

更新日期：2015-01-01 00:00:00

abstract：:In order to produce a full quantitative description of yeast metabolism, a number of kinetic parameters of enzymes that are important for energy metabolism must be determined experimentally. We aim to determine the prospective in vivo kinetic properties of a range of yeast-purified isoenzymes that are important in ene...

journal_title：Methods in enzymology

authors： Messiha HL,Malys N,Carroll KM

更新日期：2011-01-01 00:00:00