Abstract:
:For screening a pool of potential substrates that load carrier domains found in nonribosomal peptide synthetases, large molecule mass spectrometry is shown to be a new, unbiased assay. Combining the high resolving power of Fourier transform mass spectrometry with the ability of adenylation domains to select their own substrates, the mass change that takes place upon formation of a covalent intermediate thus identifies the substrate. This assay has an advantage over traditional radiochemical assays in that many substrates, the substrate pool, can be screened simultaneously. Using proteins on the nikkomycin, clorobiocin, coumermycin A1, yersiniabactin, pyochelin, and enterobactin biosynthetic pathways as proof of principle, preferred substrates are readily identified from substrate pools. Furthermore, this assay can be used to provide insight into the timing of tailoring events of biosynthetic pathways as demonstrated using the bromination reaction found on the jamaicamide biosynthetic pathway. Finally, this assay can provide insight into the role and function of orphan gene clusters for which the encoded natural product is unknown. This is demonstrated by identifying the substrates for two NRPS modules from the pksN and pksJ genes that are found on an orphan NRPS/PKS hybrid cluster from Bacillus subtilis. This new assay format is especially timely for activity screening in an era when new types of thiotemplate assembly lines that defy classification are being discovered at an accelerating rate.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Dorrestein PC,Blackhall J,Straight PD,Fischbach MA,Garneau-Tsodikova S,Edwards DJ,McLaughlin S,Lin M,Gerwick WH,Kolter R,Walsh CT,Kelleher NLdoi
10.1021/bi052333ksubject
Has Abstractpub_date
2006-02-14 00:00:00pages
1537-46issue
6eissn
0006-2960issn
1520-4995journal_volume
45pub_type
杂志文章相关文献
BIOCHEMISTRY文献大全abstract::Indolotryptoline natural products represent a small family of structurally unique chromopyrrolic acid-derived antiproliferative agents. Like many prospective anticancer agents before them, the exploration of their potential clinical utility has been hindered by the limited information known about their mechanism of ac...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi501078j
更新日期:2014-11-18 00:00:00
abstract::The Fpg protein from Escherichia coli is a multifunctional protein that excises damaged purine bases from DNA to generate aldehydic abasic sites and then catalyzes the successive cleavage of the phosphodiester bonds first on the 3'-side and then on the 5'-side of the abasic site to generate 5'- and 3'-phosphate ends, ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi9522662
更新日期:1996-01-16 00:00:00
abstract::The fluorescent nucleotide analogue of ADP, 1,N6-ethenoadenosine diphosphate (epsilon ADP), has been used to probe the active site of myosin subfragment 1 (SF1). The Mg complex of ADP was shown to be trapped stoichiometrically at the active site by a variety of thiol cross-linking agents having sulfur to sulfur spanni...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00312a029
更新日期:1984-08-14 00:00:00
abstract::A mass transport theory of the gel chromatographic procedure of Hummel and Dreyer for measuring the binding of small ligand molecules to macromolecules has been formulated for ligand-mediated macromolecular association. It is concluded that the Hummel-Dreyer procedure is the method of choice for quantitating ligand bi...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00666a011
更新日期:1976-10-19 00:00:00
abstract::Peptides have important biomedical applications, but poor correlation between in vitro and in vivo activities can limit their development for clinical use. The ability to generate peptides and monitor their expression with new mass spectrometric methods and biological activities in vivo would be an advantage for the d...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.0c00600
更新日期:2020-09-15 00:00:00
abstract::cis peptide bonds in proteins are often rate-limiting steps in protein folding or conformational change and are frequently stabilized by metal ions. In the collagen-binding domain of Clostridium histolyticum collagenase, the binding of calcium ions triggers the formation of a cis peptide bond. We present free energy s...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi1007047
更新日期:2010-06-29 00:00:00
abstract::Human alpha-lactalbumin (alpha-LA), a 123-residue calcium-binding protein, has been studied using (15)N NMR relaxation methods in order to characterize backbone dynamics of the native state at the level of individual residues. Relaxation data were collected at three magnetic field strengths and analyzed using the mode...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi900023m
更新日期:2009-05-19 00:00:00
abstract::The inhibition mechanism of serpins requires a change in structure to entrap the target proteinase as a stable acyl-enzyme complex. Although it has generally been assumed that reactive center loop insertion and associated conformational change proceeds in a concerted manner, this has not been demonstrated directly. Th...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi025967p
更新日期:2002-10-08 00:00:00
abstract::Two terminally blocked peptides, acetylAETAAAKFLRQHMamide and acetylAETSSSRYLRQHMamide, were obtained by solid-phase synthesis, purified by reversed-phase chromatography, and characterized by fast atom bombardment mass spectrometry. Both peptides were soluble in aqueous solutions and remained monomeric over the concen...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00427a048
更新日期:1989-01-10 00:00:00
abstract::The disulfide bond location of a homodimeric peptide, prothoracicotropic hormone (PTTH) of the silkworm, Bombyx mori, was determined by a combination of partial reduction and sequence analysis of peptide fragments generated through a partial reduction of PTTH followed by alkylation and enzyme digestion. The partial re...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00185a031
更新日期:1994-05-17 00:00:00
abstract::Voltage-dependent anion channel 1 (VDAC1) situated in the outer mitochondrial membrane regulates the transfer of various metabolites and is a key player in mitochondria-mediated apoptosis. Although many small chemicals that modulate the functions of VDAC1 have been reported to date, most, if not all, of them cannot be...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b01209
更新日期:2019-02-26 00:00:00
abstract::OleD is shown to play a key reductive role in the generation of alkenes (olefins) from acyl thioesters in Stenotrophomonas maltophilia. The gene coding for OleD clusters with three other genes, oleABC, and all appear to be transcribed in the same direction as an operon in various olefin producing bacteria. In this stu...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi201096w
更新日期:2011-11-08 00:00:00
abstract::Disruption of the cell membrane by the β-amyloid (Aβ) peptides has been considered as a main mechanism of Alzheimer's disease. The peptide-to-lipid molar ratio (P:L) varies over a broad range biologically. We report here that two of the previously observed Aβ evolution pathways, fibrillation and induction of vesicle f...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.5b00321
更新日期:2015-06-09 00:00:00
abstract::Computer graphics and energy minimization techniques were used to construct a model of DNA containing cis-thymine glycol, an oxidation product of thymine formed in DNA by ionizing radiation. The model simulated an experimental DNA substrate used to study the effects of this lesion on DNA synthesis in vitro. The result...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00391a028
更新日期:1987-08-25 00:00:00
abstract::The membrane-active, cationic, β-hairpin peptide, arenicin, isolated from marine polychaeta Arenicola marina exhibits a broad spectrum of antimicrobial activity. The peptide in aqueous solution adopts the significantly twisted β-hairpin conformation without pronounced amphipathicity. To assess the mechanism of arenici...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi200746t
更新日期:2011-07-19 00:00:00
abstract::A human genomic DNA library was screened for the gene coding for the gamma chain of fibrinogen by using a human cDNA for the gamma chain as a hybridization probe. The gene was identified in three overlapping recombinant lambda bacteriophage, and its sequence, including the immediate 5' and 3' flanking regions, was det...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi00329a041
更新日期:1985-04-09 00:00:00
abstract::Studies reveal that it is possible to design a palladium(II)-containing porphyrin to bind exclusively by intercalation to double-stranded DNA while simultaneously enhancing the ability to sensitize the formation of singlet oxygen. The comparisons revolve around the cations [5,10,15,20-tetra(N-methylpyridinium-4-yl)por...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi401610t
更新日期:2014-02-04 00:00:00
abstract::Glucocorticoid (GC) hormones induce apoptosis in T-cell and pre-B-cell acute lymphoblastic leukemia (ALL) cells. Steroid-mediated apoptosis requires a threshold level of the glucocorticoid receptor (GR) protein, and increasing the intracellular GR levels in ALL cells would augment their hormone sensitivity. A protein ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi1007723
更新日期:2010-10-19 00:00:00
abstract::The carboxymethylation of RNase T1 at the gamma-carboxyl group of Glu58 leads to a complete loss of the enzymatic activity while it retains substrate-binding ability. Accompanying the carboxymethylation, RNase T1 undergoes a remarkable thermal stabilization of 9 degrees C in the melting temperature (Tm). In order to c...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi960493d
更新日期:1996-06-25 00:00:00
abstract::The dynamic cytoskeletal network of microtubules and actin filaments can be disassembled by drugs. Cytoskeletal drugs work by perturbing the monomer-polymer equilibrium, thus changing the size and number of macromolecular crowders inside cells. Changes in both crowding and nonspecific surface interactions ("sticking")...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.0c00299
更新日期:2020-07-21 00:00:00
abstract::In iron-deficient conditions, Pseudomonas aeruginosa secretes a major fluorescent siderophore named pyoverdin (Pvd), which after chelating iron(III) is transported back into the cell via its outer membrane receptor FpvA. FpvA is a TonB-dependent transport protein and has the ability to bind Pvd in its apo- or iron-loa...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi049768c
更新日期:2004-06-22 00:00:00
abstract::Tau fibrillization is a potential therapeutic target for Alzheimer's and other neurodegenerative diseases. Small molecules capable of both inhibiting aggregation and promoting filament disaggregation have been discovered, but knowledge of their mechanism of action and potential for testing in biological models is frag...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi050387o
更新日期:2005-08-02 00:00:00
abstract::The Autographa californica multinucleocapsid nuclear polyhedrosis virus genome contains nine homologous region (hr1, hr1a, hr2, hr2a, hr3, hr4a, hr4b, hr4c, and hr5) sequences that are thought to be involved in viral replication and activation of transcription. Our results show that the 750 bp hr1 sequence is capable ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi049953q
更新日期:2004-06-29 00:00:00
abstract::Low molecular weight protein tyrosine phosphatases (LMW-PTPs) are small enzymes that are ubiquitous in many organisms. They are important in biological processes such as cell proliferation, adhesion, migration, and invasiveness. LMW-PTP is expressed in mammalian cells as two isoforms (IF1 and IF2) originating through ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi0620858
更新日期:2007-05-29 00:00:00
abstract::Calmodulin (CaM) is composed of two EF-hand domains tethered by a flexible linker. Upon Ca2+-binding, a fragment of CaM encompassing EF-hands 2 and 3 (CaM2/3; residues 46-113) folds into a structure remarkably similar to the N- and C-domains of CaM. In this study, we demonstrate that Ca2+-ligated CaM2/3 can also bind ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi700265j
更新日期:2007-07-24 00:00:00
abstract::Cardiac troponin T (cTnT) is a myofibrillar protein essential for calcium-dependent contraction. This property has led to functional studies of developmentally expressed cTnT isoforms and mutants identified in patients with hypertrophic cardiomyopathy. The release of cTnT into the serum following myocardial infarction...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi7012596
更新日期:2008-02-19 00:00:00
abstract::Formation of protein-protein assemblies is essential in maintaining cell structure and function. Conservation of structural motifs and binding sites is the result of evolutionary pressure for solutions compatible with both molecular economy and regulation. PDZ domains are a typical example: A conserved fold governs sp...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi061869i
更新日期:2007-01-30 00:00:00
abstract::Z-Ala-Ala-Phe-glyoxal (where Z is benzyloxycarbonyl) has been shown to be a competitive inhibitor of pepsin with a Ki = 89 +/- 24 nM at pH 2.0 and 25 degrees C. Both the ketone carbon (R13COCHO) and the aldehyde carbon (RCO13CHO) of the glyoxal group of Z-Ala-Ala-Phe-glyoxal have been 13C-enriched. Using 13C NMR, it h...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi701000k
更新日期:2007-10-02 00:00:00
abstract::The field of chemical site-selective modification of proteins has progressed extensively in recent decades to enable protein functionalization for imaging, drug delivery, and functional studies. In this Perspective, we provide detailed insight into an alternative use of site-selective protein chemistry to probe the ro...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/acs.biochem.8b00639
更新日期:2018-10-30 00:00:00
abstract::Linker histones bind to the nucleosomes and linker DNA of chromatin fibers, causing changes in linker DNA structure and stabilization of higher order folded and oligomeric chromatin structures. Linker histones affect chromatin structure acting primarily through their approximately 100-residue C-terminal domain (CTD). ...
journal_title:Biochemistry
pub_type: 杂志文章
doi:10.1021/bi801636y
更新日期:2009-01-13 00:00:00