scholarly journals RNA stabilization by a poly(A) tail 3ʹ-end binding pocket and other modes of poly(A)-RNA interaction

Science ◽  
2021 ◽  
pp. eabe6523
Author(s):  
Seyed-Fakhreddin Torabi ◽  
Anand T. Vaidya ◽  
Kazimierz T. Tycowski ◽  
Suzanne J. DeGregorio ◽  
Jimin Wang ◽  
...  
Keyword(s):  
Binding Pocket ◽  
Minor Groove ◽  
Major Groove ◽  
Cis Acting ◽  
Wide Range ◽  
Triple Helices ◽  
Rna Triplex ◽  
Rna Stabilization ◽  
Rna Interaction ◽  
Modes Of Interaction

Poly(A) tail addition to the 3ʹ end of a wide range of RNAs is a highly conserved modification that plays a central role in cellular RNA function. Elements for nuclear expression (ENEs) are cis-acting RNA elements that stabilize poly(A) tails by sequestering them in RNA triplex structures. A 2.89-Å resolution crystal structure of a double ENE from a rice hAT transposon mRNA complexed with poly(A)28 reveals multiple modes of interaction with poly(A), including major-groove triple helices, extended minor-groove interactions with RNA double helices, a quintuple-base motif that transitions poly(A) from minor-groove associations to major-groove triple helices, and a poly(A) 3ʹ-end binding pocket. Our findings both expand the repertoire of motifs involved in long-range RNA interactions and provide insights into how polyadenylation can protect an RNA’s extreme 3ʹ end.

scholarly journals Modes of Interaction in Naturally Occurring Medical Encounters With General Practitioners: The “One in a Million” Study

2021 ◽  
pp. 104973232199379
Author(s):  
Olaug S. Lian ◽  
Sarah Nettleton ◽  
Åge Wifstad ◽  
Christopher Dowrick
Keyword(s):  
General Practitioners ◽  
Narrative Analysis ◽  
Mode Competition ◽  
General Applicability ◽  
Naturally Occurring ◽  
Wide Range ◽  
The One ◽  
Narrative Mode ◽  
Modes Of Interaction

In this article, we qualitatively explore the manner and style in which medical encounters between patients and general practitioners (GPs) are mutually conducted, as exhibited in situ in 10 consultations sourced from the One in a Million: Primary Care Consultations Archive in England. Our main objectives are to identify interactional modes, to develop a classification of these modes, and to uncover how modes emerge and shift both within and between consultations. Deploying an interactional perspective and a thematic and narrative analysis of consultation transcripts, we identified five distinctive interactional modes: question and answer (Q&A) mode, lecture mode, probabilistic mode, competition mode, and narrative mode. Most modes are GP-led. Mode shifts within consultations generally map on to the chronology of the medical encounter. Patient-led narrative modes are initiated by patients themselves, which demonstrates agency. Our classification of modes derives from complete naturally occurring consultations, covering a wide range of symptoms, and may have general applicability.

Targeted chemical nucleases have a wide range of untapped applications in biological fields, including gene therapy

2021 ◽  
Author(s):  
Moataz Dowaidar
Keyword(s):  
Metal Complex ◽  
Dna Cleavage ◽  
Therapeutic Potential ◽  
Chemical Reactivity ◽  
Major Groove ◽  
Sequence Recognition ◽  
Wide Range ◽  
Chemical Nucleases

A feasible alternative to state-of-the-art enzymatic nucleases was created by regulating the cleavage activity of metal complexes using (covalent or non-covalent) homing agents. Targeted AMNs, unlike enzymatic nucleases, break DNA by an oxidative mechanism and can therefore permanently knock off genes. Compared to larger enzymatic nucleases, the modest size of the metal complex may aid cellular transfection. Furthermore, the painstaking construction of the sequence-specific probe permits a metal complex to be directed to dsDNA's minor or major groove. To direct the chemical reactivity of several small-molecule compounds to dsDNA's minor groove, covalently bonded polyamide samples were used. PNA and DNA were also used to construct antisense and antigen hybrids, with Watson–Crick or Hoogsteen base pairing with major groove nucleobases giving sequence recognition. Click chemistry created chimeric AMN-TFOs with desirable focused effects and negligible off-target cleavage. Clip-Phen-modified TFOs, 230 polypyridyl-modified TFOs, 232 and intercalating phenanthrene-modified TFOs are three contemporary instances of copper AMN–TFOs. All three systems have distinct advantages in maintaining the desired 2:1 phenthroline/copper ratio for DNA cleavage (clip-Phen TFOs), caging the copper center and facilitating efficient ROS-mediated strand scission (polypyridyl-modified TFO) and improving triplex stability (polypyridyl-modified TFO) (phenanthrene-TFOs). Cerium (IV)/EDTA complexes, recently shown to bind and hydrolytically cleave ssDNA/dsDNA junctions and used in conjunction with PNA to successfully introduce genome changes in vitro and in vivo, are another important class of targeted chemical nucleases. The chemical reactivity and wide flexibility of metal complex design, combined with their coupling to sequence specific samples for directed applications, show that these compounds have a wide range of untapped applications in biological fields such as chemotherapy, protein engineering, DNA footprinting, and gene editing. Parallel advancements in cell and tissue targeting will be essential to maximise their therapeutic potential, either by using specific ligands or creating new targeting modalities.

scholarly journals Application of Cu(I)-catalyzed azide–alkyne cycloaddition for the design and synthesis of sequence specific probes targeting double-stranded DNA

2016 ◽  
Vol 12 ◽  
pp. 1348-1360 ◽  
Author(s):  
Svetlana V Vasilyeva ◽  
Vyacheslav V Filichev ◽  
Alexandre S Boutorine
Keyword(s):  
Minor Groove ◽  
Binding Parameters ◽  
Design And Synthesis ◽  
Minor Groove Binders ◽  
Double Stranded Dna ◽  
Triple Helices ◽  
Gel Shift ◽  
Groove Binders

Efficient protocols based on Cu(I)-catalyzed azide–alkyne cycloaddition were developed for the synthesis of conjugates of pyrrole–imidazole polyamide minor groove binders (MGB) with fluorophores and with triplex-forming oligonucleotides (TFOs). Diverse bifunctional linkers were synthesized and used for the insertion of terminal azides or alkynes into TFOs and MGBs. The formation of stable triple helices by TFO-MGB conjugates was evaluated by gel-shift experiments. The presence of MGB in these conjugates did not affect the binding parameters (affinity and triplex stability) of the parent TFOs.

Cadmium Inhibits BPDE Alkylation of DNA in the Major Groove but Not in the Minor Groove

1998 ◽  
Vol 244 (1) ◽  
pp. 198-203 ◽  
Author(s):  
Arungundrum S. Prakash ◽  
Koyyalamudi S. Rao ◽  
Charles T. Dameron
Keyword(s):  
Minor Groove ◽  
Major Groove

scholarly journals Structural basis for amino acid exchange by a human heteromeric amino acid transporter

2020 ◽  
Vol 117 (35) ◽  
pp. 21281-21287 ◽  
Author(s):  
Di Wu ◽  
Tamara N. Grund ◽  
Sonja Welsch ◽  
Deryck J. Mills ◽  
Max Michel ◽  
...  
Keyword(s):  
Amino Acid ◽  
Heavy Chain ◽  
Light Chain ◽  
Basic Amino Acid ◽  
Binding Pocket ◽  
Structural Basis ◽  
Amino Acid Transporters ◽  
Wide Range ◽  
Functional Complex ◽  
Protein Components

Heteromeric amino acid transporters (HATs) comprise a group of membrane proteins that belong to the solute carrier (SLC) superfamily. They are formed by two different protein components: a light chain subunit from an SLC7 family member and a heavy chain subunit from the SLC3 family. The light chain constitutes the transport subunit whereas the heavy chain mediates trafficking to the plasma membrane and maturation of the functional complex. Mutation, malfunction, and dysregulation of HATs are associated with a wide range of pathologies or represent the direct cause of inherited and acquired disorders. Here we report the cryogenic electron microscopy structure of the neutral and basic amino acid transport complex (b[0,+]AT1-rBAT) which reveals a heterotetrameric protein assembly composed of two heavy and light chain subunits, respectively. The previously uncharacterized interaction between two HAT units is mediated via dimerization of the heavy chain subunits and does not include participation of the light chain subunits. The b(0,+)AT1 transporter adopts a LeuT fold and is captured in an inward-facing conformation. We identify an amino-acid–binding pocket that is formed by transmembrane helices 1, 6, and 10 and conserved among SLC7 transporters.

Major groove or minor groove?

Nature ◽  
1986 ◽  
Vol 319 (6050) ◽  
pp. 183-184 ◽  
Author(s):  
WANG JIA-HUAI
Keyword(s):  
Minor Groove ◽  
Major Groove

Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study

2015 ◽  
Vol 93 (3) ◽  
pp. 348-361 ◽  
Author(s):  
C. Izanloo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Double Helix ◽  
Melting Process ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Transition Curve ◽  
Water Molecules ◽  
Major Groove ◽  
Dna Duplex

A molecular dynamics simulation was performed on a B-DNA duplex (CGCGAATTGCGC) at different temperatures. The DNA was immerged in a saltwater medium with 1 mol/L NaCl concentration. The arrangements of water molecules and cations around the different atoms of DNA on the melting pathway were investigated. Almost for all atoms of the DNA by double helix → single-stranded transition, the water molecules released from the DNA duplex and cations were close to single-stranded DNA, but this behavior was not clearly seen at melting temperatures. Therefore, release of water molecules and cations approaching the DNA by the increase of temperature does not have any effect on the sharpness of the transition curve. Most of the water molecules and cations were found to be around the negatively charged phosphate oxygen atoms. The number of water molecules released from the first shell hydration upon melting in the minor groove was higher than in the major groove, and intrusion of cations into the minor groove after melting was higher than into the major groove. The hydrations of imino protons were different from each other and were dependent on DNA bases.

Allosteric Inhibition of Zinc-Finger Binding in the Major Groove of DNA by Minor-Groove Binding Ligands†

Biochemistry ◽  
2004 ◽  
Vol 43 (13) ◽  
pp. 3880-3890 ◽  
Author(s):  
Doan H. Nguyen-Hackley ◽  
Elizabeth Ramm ◽  
Christina M. Taylor ◽  
J. Keith Joung ◽  
Peter B. Dervan ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Minor Groove ◽  
Minor Groove Binding ◽  
Major Groove ◽  
Groove Binding ◽  
Allosteric Inhibition

Structures of the PKC-ι kinase domain in its ATP-bound and apo forms reveal defined structures of residues 533–551 in the C-terminal tail and their roles in ATP binding

2010 ◽  
Vol 66 (5) ◽  
pp. 577-583 ◽  
Author(s):  
Tetsuo Takimura ◽  
Kenji Kamata ◽  
Kazuhiro Fukasawa ◽  
Hirokazu Ohsawa ◽  
Hideya Komatani ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Binding Pocket ◽  
Kinase Domain ◽  
Van Der Waals Interactions ◽  
Side Chain ◽  
Phosphoryl Transfer ◽  
Atp Binding ◽  
Cellular Functions ◽  
Substrate Complex ◽  
Wide Range

Protein kinase C (PKC) plays an essential role in a wide range of cellular functions. Although crystal structures of the PKC-θ, PKC-ι and PKC-βII kinase domains have previously been determined in complexes with small-molecule inhibitors, no structure of a PKC–substrate complex has been determined. In the previously determined PKC-ι complex, residues 533–551 in the C-terminal tail were disordered. In the present study, crystal structures of the PKC-ι kinase domain in its ATP-bound and apo forms were determined at 2.1 and 2.0 Å resolution, respectively. In the ATP complex, the electron density of all of the C-terminal tail residues was well defined. In the structure, the side chain of Phe543 protrudes into the ATP-binding pocket to make van der Waals interactions with the adenine moiety of ATP; this is also observed in other AGC kinase structures such as binary and ternary substrate complexes of PKA and AKT. In addition to this interaction, the newly defined residues around the turn motif make multiple hydrogen bonds to glycine-rich-loop residues. These interactions reduce the flexibility of the glycine-rich loop, which is organized for ATP binding, and the resulting structure promotes an ATP conformation that is suitable for the subsequent phosphoryl transfer. In the case of the apo form, the structure and interaction mode of the C-terminal tail of PKC-ι are essentially identical to those of the ATP complex. These results indicate that the protein structure is pre-organized before substrate binding to PKC-ι, which is different from the case of the prototypical AGC-branch kinase PKA.

scholarly journals The Ribosomal S10 Protein Is a General Target for Decreased Tigecycline Susceptibility

2015 ◽  
Vol 59 (9) ◽  
pp. 5561-5566 ◽  
Author(s):  
Kathryn Beabout ◽  
Troy G. Hammerstrom ◽  
Anisha Maria Perez ◽  
Bárbara Freitas Magalhães ◽  
Amy G. Prater ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Experimental Evolution ◽  
Binding Pocket ◽  
Gram Positive ◽  
Content Type ◽  
E Coli ◽  
Species Cluster ◽  
Wide Range ◽  
Translational Inhibitor

ABSTRACTTigecycline is a translational inhibitor with efficacy against a wide range of pathogens. Using experimental evolution, we adaptedAcinetobacter baumannii,Enterococcus faecium,Escherichia coli, andStaphylococcus aureusto growth in elevated tigecycline concentrations. At the end of adaptation, 35 out of 47 replicate populations had clones with a mutation inrpsJ, the gene that encodes the ribosomal S10 protein. To validate the role of mutations inrpsJin conferring tigecycline resistance, we showed that mutation ofrpsJalone inEnterococcus faecaliswas sufficient to increase the tigecycline MIC to the clinical breakpoint of 0.5 μg/ml. Importantly, we also report the first identification ofrpsJmutations associated with decreased tigecycline susceptibility inA. baumannii,E. coli, andS. aureus. The identified S10 mutations across both Gram-positive and -negative species cluster in the vertex of an extended loop that is located near the tigecycline-binding pocket within the 16S rRNA. These data indicate that S10 is a general target of tigecycline adaptation and a relevant marker for detecting reduced susceptibility in both Gram-positive and -negative pathogens.

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