Quantum chemical studies of C-H activation reactions by high-valent nonheme iron centers.

Abstract:

:Activation of unactivated C-H bonds is an important process in nature and organic synthesis. Nature employs a wide range of metalloproteins to efficiently catalyze such reactions. Quantum chemistry can be used to explore the reactivity of such systems. Atomic level insight into the catalytic mechanisms can be gained through the calculation of reaction energies, barriers, isotope effects, and-where available-spectroscopic properties. This approach is illustrated for the case of the H-atom abstraction reaction performed by the quintet iron(IV)-oxo intermediate in the nonheme iron enzyme taurine-alpha-ketoglutarate dioxygenase (TauD). The careful analysis of the electronic structure of the reactant, transition state, and product indicates that the reaction involves a preparatory step in which an iron(III)-oxyl species is produced that is the active species in the actual C-H bond activation process.

journal_name

Curr Opin Chem Biol

authors

Ye S,Neese F

doi

10.1016/j.cbpa.2009.02.007

subject

Has Abstract

pub_date

2009-02-01 00:00:00

pages

89-98

issue

1

eissn

1367-5931

issn

1879-0402

pii

S1367-5931(09)00011-8

journal_volume

13

pub_type

杂志文章
  • Combinatorial engineering of microbes for optimizing cellular phenotype.

    abstract::Although random mutagenesis and screening and evolutionary engineering have long been the gold standards for strain improvement in industry, the development of more sophisticated recombinant DNA tools has led to the introduction of alternate methods for engineering strain diversity. Here, we summarize several combinat...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2008.01.017

    authors: Santos CN,Stephanopoulos G

    更新日期:2008-04-01 00:00:00

  • Structural dynamics of the ribosome.

    abstract::Protein synthesis is inherently a dynamic process, requiring both small-scale and large-scale movements of tRNA and mRNA. It has long been suspected that these movements might be coupled to conformational changes in the ribosome, and in its RNA moieties in particular. Recently, the nature of ribosome structural dynami...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2008.08.037

    authors: Korostelev A,Ermolenko DN,Noller HF

    更新日期:2008-12-01 00:00:00

  • Making drugs on proteins: site-directed ligand discovery for fragment-based lead assembly.

    abstract::Rapid progress in genomics and proteomics has provided a wealth of new targets for the pharmaceutical industry, even as many older targets still remain challenging for small-molecule drug discovery. Fragment-based lead discovery, in which leads are built progressively by expanding or combining small fragments, is a ra...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2004.06.010

    authors: Erlanson DA,Hansen SK

    更新日期:2004-08-01 00:00:00

  • Activity-based sensing fluorescent probes for iron in biological systems.

    abstract::Iron is an essential nutrient for life, and its capacity to cycle between different oxidation states is required for processes spanning oxygen transport and respiration to nucleotide synthesis and epigenetic regulation. However, this same redox ability also makes iron, if not regulated properly, a potentially dangerou...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2017.12.010

    authors: Aron AT,Reeves AG,Chang CJ

    更新日期:2018-04-01 00:00:00

  • Acylating drugs: redesigning natural covalent inhibitors.

    abstract::Structural modification of naturally occurring beta-lactams and beta-lactones is a highly effective strategy for generating drugs for treating bacterial infections, cancer, obesity, and hyperlipidemia. These drugs acylate catalytic amino acids (serine, threonine, or cysteine) in enzyme targets such as penicillin-bindi...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2010.03.035

    authors: Kluge AF,Petter RC

    更新日期:2010-06-01 00:00:00

  • Building better bioorthogonal reactions.

    abstract::Over the past two decades, there has been intense interest in designing and implementing selective (bioorthogonal) reactions for biomolecule tracking. Here we review the most widely used bioorthogonal chemistries in live cells and animals, drawing particular attention to the unique functional groups underlying these t...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2014.07.002

    authors: Shih HW,Kamber DN,Prescher JA

    更新日期:2014-08-01 00:00:00

  • Unlocked potential of dynamic elements in protein structures: channels and loops.

    abstract::Enzymes are nature's powerful catalytic proteins to perform reactions with often outstanding activity, selectivity and specificity. Moreover, the access to non-natural functions of biocatalysts can be facilitated by enzyme engineering. While rational approaches are often focused on an enzyme's active site, from random...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2018.09.010

    authors: Kreß N,Halder JM,Rapp LR,Hauer B

    更新日期:2018-12-01 00:00:00

  • Metal-mediated DNA assembly with ligand-based nucleosides.

    abstract::Nucleic acids such as DNA are increasingly being applied in nanotechnology, as a result of their capability to self-assemble reversibly. The formal replacement of canonical base pairs by metal-mediated ones enables a site-specific introduction of metal-based functionality into these biomolecules, leading to the format...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2017.01.019

    authors: Mandal S,Müller J

    更新日期:2017-04-01 00:00:00

  • Tools for visualizing cell-cell 'interactomes'.

    abstract::Cellular communication drives diverse aspects of organismal biology ranging from immune function to memory formation. The mechanisms by which cells transact information in vivo, though, are not completely understood. This is due, in part, to a lack of tools for observing collections of cells in their native habitats. ...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2014.11.006

    authors: Porterfield WB,Prescher JA

    更新日期:2015-02-01 00:00:00

  • Functional protein microarrays: ripe for discovery.

    abstract::The manufacture and use of protein microarrays with correctly folded and functional content presents significant challenges. Despite this, the feasibility and utility of such undertakings are now clear, and exciting progress has recently been demonstrated in the areas of content generation, printing strategies and pro...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2003.12.005

    authors: Predki PF

    更新日期:2004-02-01 00:00:00

  • Computational design strategies for combinatorial libraries.

    abstract::Medicinal chemistry principles are being increasingly applied to the design of smaller, high purity, information-rich libraries. Recent computational advances in statistical methodology, the design of libraries to reduce ADMET problems, targeting protein families and revisiting natural products as sources of inspirati...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/s1367-5931(03)00057-7

    authors: Rose S,Stevens A

    更新日期:2003-06-01 00:00:00

  • Modern methods to produce natural-product libraries.

    abstract::Natural sources offer a wealth of chemically diverse compounds that have been evolutionary preselected to modulate biochemical pathways. Several industrial and academic groups are accessing this source using advanced technology platforms. Methods have been reported to generate large and diverse natural-product librari...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/s1367-5931(02)00338-1

    authors: Abel U,Koch C,Speitling M,Hansske FG

    更新日期:2002-08-01 00:00:00

  • Chemical and biophysical methods to explore dynamic mechanisms of chromatin silencing.

    abstract::Chromatin, the nucleoprotein complex organizing the genome, is central in regulating gene expression and genome organization. Chromatin conformational dynamics, controlled by histone post-translational modifications (PTM) and effector proteins, play a key role in this regulatory function. Recent developments in chemic...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2019.01.022

    authors: Boichenko I,Fierz B

    更新日期:2019-08-01 00:00:00

  • Nucleic acid crystallography: current progress.

    abstract::Fifty years after the publication of the DNA double helix model by Watson and Crick, new nucleic acid structures keep emerging at an ever-increasing rate. The past three years have brought a flurry of new oligonucleotide structures, including those of a Hoogsteen-paired DNA duplex, Holliday junctions, DNA-drug complex...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2004.09.004

    authors: Egli M

    更新日期:2004-12-01 00:00:00

  • Stereo-electronic control of reaction selectivity in short-chain dehydrogenases: Decarboxylation, epimerization, and dehydration.

    abstract::Sugar nucleotide-modifying enzymes of the short-chain dehydrogenase/reductase type use transient oxidation-reduction by a tightly bound nicotinamide cofactor as a common strategy of catalysis to promote a diverse set of reactions, including decarboxylation, single- or double-site epimerization, and dehydration. Althou...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2020.09.010

    authors: Borg AJE,Beerens K,Pfeiffer M,Desmet T,Nidetzky B

    更新日期:2020-11-06 00:00:00

  • Proteins, air and water: reporter genes for ultrasound and magnetic resonance imaging.

    abstract::A long-standing goal of molecular imaging is to visualize cellular function within the context of living animals, necessitating the development of reporter genes compatible with deeply penetrant imaging modalities such as ultrasound and magnetic resonance imaging (MRI). Until recently, no reporter genes for ultrasound...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2018.02.011

    authors: Lu GJ,Farhadi A,Mukherjee A,Shapiro MG

    更新日期:2018-08-01 00:00:00

  • Peptide modification and cyclization via transition-metal catalysis.

    abstract::Transition-metal catalysis has unlocked new paradigms for the late-stage modification and cyclization of peptides by harnessing the innate reactivity of proteinogenic amino acids. The field is rapidly evolving, with recent advances encompassing three fundamental areas-heteroatom couplings, decarboxylative cross-coupli...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2018.03.019

    authors: Malins LR

    更新日期:2018-10-01 00:00:00

  • Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy.

    abstract::Due to the existence of numerous isomers, the in-depth analysis of glycans represents a major challenge. Currently, the majority of glycans are analysed using mass spectrometry (MS)-based techniques, which can provide information on regioisomers but usually fail to differentiate stereoisomers. A promising approach to ...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2017.10.021

    authors: Manz C,Pagel K

    更新日期:2018-02-01 00:00:00

  • The discovery of catalytically active peptides through combinatorial chemistry.

    abstract::In recent years, ogliopeptides have enjoyed ever increasing interest in two areas: first, approaches to biomimetic enzyme-like activity; and second, as metal-free catalysts for enantioselective transformations of synthetic interest. The discovery and optimization of peptides for these purposes has often used the metho...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/s1367-5931(03)00065-6

    authors: Berkessel A

    更新日期:2003-06-01 00:00:00

  • Ligand specificity, privileged substructures and protein druggability from fragment-based screening.

    abstract::Fragment-based screening has now become an established method for the generation of lead molecules against therapeutic targets. Fragment molecules are simple, low molecular-weight compounds with few chemical functionalities. These characteristics lead to high hit rates for fragment screening as compared to the more cl...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2011.02.020

    authors: Barelier S,Krimm I

    更新日期:2011-08-01 00:00:00

  • Genome-wide RNAi.

    abstract::In many species, double-stranded RNA can specifically and effectively silence genes. This newly discovered biological phenomenon, called RNA interference (RNAi), has practical implications for functional genomics. As shown by two recent reports, RNAi provides a rapid method to test the function of genes in the nematod...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/s1367-5931(00)00173-3

    authors: Barstead R

    更新日期:2001-02-01 00:00:00

  • Microbial transformations in phosphonate biosynthesis and catabolism, and their importance in nutrient cycling.

    abstract::Phosphorus cycling in the biosphere has traditionally been thought to involve almost exclusively transformations of the element in its pentavalent oxidation state. Recent evidence, however, suggests that a significant fraction of environmental phosphorus may exist in a more reduced form. Most abundant of these reduced...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2016.01.010

    authors: Chin JP,McGrath JW,Quinn JP

    更新日期:2016-04-01 00:00:00

  • Domains, motifs and clusters in the protein universe.

    abstract::The rapid growth of bio-sequence information has resulted in an increasing demand for reliable methods that group proteins. A few databases with curated alignments of protein families have demonstrated that expert-driven repositories can keep up with the data deluge in the genome era. These original resources implicit...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/s1367-5931(02)00003-0

    authors: Liu J,Rost B

    更新日期:2003-02-01 00:00:00

  • Chemical biology on PINs and NeeDLes.

    abstract::Systematic studies of the organization of biochemical networks that make up the living cell can be defined by studying the organization and dynamics of protein interaction networks (PINs). Here, we describe recent conceptual and experimental advances that can achieve this aim and how chemical perturbations of interact...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2004.12.009

    authors: Campbell-Valois FX,Michnick S

    更新日期:2005-02-01 00:00:00

  • Function of genetically encoded pyrrolysine in corrinoid-dependent methylamine methyltransferases.

    abstract::Methanogenesis from trimethylamine, dimethylamine or monomethylamine is initiated by a series of corrinoid-dependent methyltransferases. The non-homologous genes encoding the full-length methyltransferases each possess an in-frame UAG (amber) codon that does not terminate translation. The amber codon is decoded by a d...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2004.08.012

    authors: Krzycki JA

    更新日期:2004-10-01 00:00:00

  • Synthetic biology for natural product drug production and engineering.

    abstract::Natural products continue to provide privileged scaffolds for drug discovery. However, challenges in supply and structure diversification can limit development. Here, we discuss recent (2017-2020) examples of synthetic biology approaches used to address challenges in supply and contribute to structure diversification ...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2020.09.006

    authors: Romanowski S,Eustáquio AS

    更新日期:2020-10-01 00:00:00

  • Boundaries for an RNA world.

    abstract::Before large, specific peptides could be made, in an RNA world our ancestors may have used an RNA-like molecule for both catalysis and information storage. Taken together, RNA activities suggest RNA could have performed most of the essential informational functions of an ancient organism (i.e. those functions most sim...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/S1367-5931(99)80041-6

    authors: Yarus M

    更新日期:1999-06-01 00:00:00

  • Pattern-based sensing with simple metal-dye complexes.

    abstract::Different strategies for the creation of optical sensors with metal-dye complexes are discussed. The focus is on sensors, which are used in conjunction with pattern recognition protocols. It is shown that remarkably powerful sensors can be obtained by combining commercially available dyes with simple transition metal ...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2010.07.005

    authors: Severin K

    更新日期:2010-12-01 00:00:00

  • Fatty acid desaturation: variations on an oxidative theme.

    abstract::Significant progress in our understanding of the mechanism of fatty acid desaturation has been achieved. The site of initial oxidation has been determined for several membrane-bound desaturases and a common cryptoregiochemical theme has been revealed. The results of several studies, including a detailed analysis of a ...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/s1367-5931(02)00365-4

    authors: Behrouzian B,Buist PH

    更新日期:2002-10-01 00:00:00

  • Sense and sensitivity in bioprocessing-detecting cellular metabolites with biosensors.

    abstract::Biosensors use biological elements to detect or quantify an analyte of interest. In bioprocessing, biosensors are employed to monitor key metabolites. There are two main types: fully biological systems or biological recognition coupled with physical/chemical detection. New developments in chemical biosensors include m...

    journal_title:Current opinion in chemical biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.cbpa.2017.05.014

    authors: Dekker L,Polizzi KM

    更新日期:2017-10-01 00:00:00