Identification of binding sites for both dsRBMs of PKR on kinase-activating and kinase-inhibiting RNA ligands

Biochemistry
Richard J SpanggordPeter A Beal

Abstract

The RNA-dependent protein kinase (PKR) is an interferon-induced, RNA-activated enzyme that phosphorylates and inhibits the function of the translation initiation factor eIF-2. PKR has a double-stranded RNA-binding domain (dsRBD) composed of two copies of the dsRNA binding motif (dsRBM). PKR's dsRBD is involved in the regulation of the enzyme as dsRNAs of cellular and viral origins bind to the dsRBD, leading to either activation or inhibition of PKR's kinase activity. In this study, we site-specifically modified each of the dsRBMs of PKR's dsRBD with the hydroxyl radical generator EDTA small middle dotFe and performed cleavage studies on kinase-activating and kinase-inhibiting RNAs. These experiments led to the identification of binding sites for the individual dsRBMs on various RNA ligands including a viral activating RNA (TAR from HIV-1), a viral inhibiting RNA (VA(I) RNA from adenovirus), an aptamer RNA that activates PKR, and a small synthetic inhibiting RNA. These results indicate that some RNAs interact only with one dsRBM, while others can bind both dsRBMs of PKR. In addition, EDTA small middle dotFe modification coupled with site-directed mutagenesis was used to assess the extent of cooperativity in the binding of the tw...Continue Reading

Citations

Oct 16, 2012·Biochemistry·Bushra HusainJames L Cole
Sep 1, 2009·Journal of Interferon & Cytokine Research : the Official Journal of the International Society for Interferon and Cytokine Research·Cyril X GeorgeCharles E Samuel
May 5, 2006·Molecular Biology of the Cell·Ming XuRonald B Emeson
Aug 30, 2005·Nucleic Acids Research·Samuel Dugré-BrissonLuc DesGroseillers
Feb 6, 2008·Nucleic Acids Research·Veronica K Coventry, Graeme L Conn
May 7, 2004·European Journal of Biochemistry·Androulla EliaMichael J Clemens
Sep 9, 2004·Microbiology and Molecular Biology Reviews : MMBR·Qiaoqiao Wang, Gordon G Carmichael
Feb 5, 2015·Biophysical Journal·Katherine Launer-FeltyJames L Cole
Jun 28, 2015·Virus Research·Virginia K Vachon, Graeme L Conn
Nov 8, 2011·Fish & Shellfish Immunology·Carmelo S del CastilloTakashi Aoki
Jan 13, 2005·Chembiochem : a European Journal of Chemical Biology·Peter A Beal
Aug 20, 2003·Biopolymers·Coby B CarlsonPeter A Beal
Mar 5, 2004·Chembiochem : a European Journal of Chemical Biology·Sujiet PuthenveetilPeter A Beal
Feb 5, 2011·Reviews in Medical Virology·Guerline ClerziusAnne Gatignol
Oct 10, 2013·Reviews in Medical Virology·Waqar Ahmed, Gulfaraz Khan
Jun 10, 2010·Macromolecular Bioscience·James L Cole
Apr 4, 2006·Journal of Molecular Biology·Sean A McKennaJoseph D Puglisi
Mar 7, 2006·Journal of Molecular Biology·Insil KimJoseph D Puglisi
Jan 8, 2014·Journal of Molecular Biology·Katherine Launer-Felty, James L Cole
Sep 24, 2004·Chemistry & Biology·Olen M StephensPeter A Beal
May 19, 2009·Journal of Molecular Biology·Laurie A HeinickePhilip C Bevilacqua
Oct 22, 2015·Biochemistry·Bushra HusainJames L Cole
Apr 8, 2006·American Journal of Respiratory Cell and Molecular Biology·Steven R BarthelMats W Johansson
Oct 23, 2003·The Journal of Biological Chemistry·Carole GwizdekCatherine Dargemont
May 23, 2020·Developmental and Comparative Immunology·Jingguang WeiQiwei Qin
Jun 1, 2021·ACS Omega·Stephen HeslerJames L Cole
May 18, 2006·Virus Research·Jeffrey O LanglandBertram L Jacobs
Mar 17, 2020·Biochemistry·Cassie M Zerbe, James L Cole

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.