scholarly journals Three thymine/adenine binding modes of the ruthenium complex Λ-[Ru(TAP)2(dppz)]2+ to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography

2019 ◽  
Vol 55 (62) ◽  
pp. 9116-9119 ◽  
Author(s):  
Kane McQuaid ◽  
James P. Hall ◽  
Lena Baumgaertner ◽  
David J. Cardin ◽  
Christine J. Cardin

Λ-[Ru(TAP)2(dppz)]2+ was crystallised with the G-quadruplex-forming heptamer d(TAGGGTT).

2019 ◽  
Vol 47 (12) ◽  
pp. 6059-6072 ◽  
Author(s):  
Ashok Nuthanakanti ◽  
Ishtiyaq Ahmed ◽  
Saddam Y Khatik ◽  
Kayarat Saikrishnan ◽  
Seergazhi G Srivatsan

Abstract Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves as a common probe to detect and correlate different GQ structures and ligand binding under equilibrium conditions and in 3D by fluorescence and X-ray crystallography techniques. The probe (SedU) is composed of a microenvironment-sensitive fluorophore and an excellent anomalous X-ray scatterer (Se), which is assembled by attaching a selenophene ring at 5-position of 2′-deoxyuridine. SedU incorporated into the loop region of human telomeric DNA repeat fluorescently distinguished subtle differences in GQ topologies and enabled quantify ligand binding to different topologies. Importantly, anomalous X-ray dispersion signal from Se could be used to determine the structure of GQs. As the probe is minimally perturbing, a direct comparison of fluorescence data and crystal structures provided structural insights on how the probe senses different GQ conformations without affecting the native fold. Taken together, our dual-app probe represents a new class of tool that opens up new experimental strategies to concurrently investigate nucleic acid structure and recognition in real time and 3D.


FEBS Open Bio ◽  
2015 ◽  
Vol 5 (1) ◽  
pp. 557-570 ◽  
Author(s):  
Mikiya Satoh ◽  
Hajime Saburi ◽  
Tomoyuki Tanaka ◽  
Yoshinori Matsuura ◽  
Hisashi Naitow ◽  
...  

2020 ◽  
Author(s):  
Sophie M. Travis ◽  
Kevin DAmico ◽  
I-Mei Yu ◽  
Safraz Hamid ◽  
Gabriel Ramirez-Arellano ◽  
...  

AbstractMultisubunit tethering complexes (MTCs) are large (250 to >750 kDa), conserved macromolecular machines that are essential for SNARE-mediated membrane fusion in all eukaryotes. MTCs are thought to function as organizers of membrane trafficking, mediating the initial, long-range interaction between a vesicle and its target membrane and promoting the formation of membrane-bridging SNARE complexes. Previously, we reported the structure of the Dsl1 complex, the simplest known MTC, which is essential for COPI-mediated transport from the Golgi to the endoplasmic reticulum (ER). This structure suggested how the Dsl1 complex might function to tether a vesicle to its target membrane by binding at one end to the COPI coat and at the other end to ER SNAREs. Here, we use x-ray crystallography to investigate these Dsl1-SNARE interactions in greater detail. The Dsl1 complex comprises three subunits that together form a two-legged structure with a central hinge. Our results show that distal regions of each leg bind N-terminal Habc domains of the ER SNAREs Sec20 (a Qb-SNARE) and Use1 (a Qc-SNARE). The observed binding modes appear to anchor the Dsl1 complex to the ER target membrane while simultaneously ensuring that both SNAREs are in open conformations with their SNARE motifs available for assembly. The proximity of the two SNARE motifs, and therefore their ability to enter the same SNARE complex, depends on the relative orientation of the two Dsl1 legs.


2019 ◽  
Author(s):  
Willem Jespers ◽  
Grégory Verdon ◽  
Jhonny Azuaje ◽  
maria majellaro ◽  
Henrik Keränen ◽  
...  

<div> <div> <div> <p>Nowadays, rigorous free energy calculations are routinely considered in pharmaceutical design strategies. One typical sce- nario is the lead-optimization based on well-defined protein-ligand binding modes, inferred by pharmacological data in com- putational models and ultimately revealed by structural data. In this work, we reveal the molecular determinants of antago- nist binding to the adenosine A2A adenosine receptor (AR), an emerging target in immuno-oncology, via a robust protocol that connects structural and pharmacological data through free energy perturbation (FEP) calculations. Eight A2AAR binding site mutations from biophysical mapping experiments were initially analyzed with FEP simulations of each side-chain mutation, performed on alternate binding modes previously proposed in the literature. The results strongly suggested that only one binding mode could explain this experimental data, which was used to subsequently design a series of 11 chromone deriva- tives. The experimental affinities of these new compounds were linked through a cycle of ligand-FEP calculations around selected ligand pairs, which allowed the identification of the optimal positioning of the different chemical substituents in the proposed binding model. Subsequent X-ray crystallography of the A2AAR with a low and high affinity chromone derivative confirmed the predicted binding orientation, and provided new insights in the role of the explored substituents in the chro- </p> </div> </div> <div> <div> <p>mone scaffold. </p> </div> </div> </div>


2019 ◽  
Vol 63 (4) ◽  
pp. 1528-1543 ◽  
Author(s):  
Mathieu Rappas ◽  
Ammar A. E. Ali ◽  
Kirstie A. Bennett ◽  
Jason D. Brown ◽  
Sarah J. Bucknell ◽  
...  

1995 ◽  
Vol 73 (3) ◽  
pp. 401-413 ◽  
Author(s):  
Pierre G. Potvin ◽  
Benjamin G. Fieldhouse

The reactions of amines and amino alcohols with diisopropyl or diethyl R,R- or S,S-tartrate and Ti(OiPr)4 were examined by 1H and 13C NMR to obtain and characterize nonfluxional complexes with the tartrate units in novel binding modes. The mildly acidic 8-hydroxyquinoline and N-phenyl-N-benzoylhydroxylamine selectively formed the products of a double OiPr substitution, Ti2(tartrate)2(ligand)2(OiPr)2, and the products of double tartrate substitution, Ti(ligand)2(OiPr)2, while 2,4-pentanedione formed only the latter Basic amino alkanols formed diastereomerically pure Ti2(tartrate)2(aminoalkoxide)(OiPr)3 species. N,N-Dimethyl-2-aminoethanol (Hdmae) also and uniquely formed monomeric Ti(tartrate)2(Hdmae)2 species that could be described as doubly zwitterionic. Secondary or tertiary amines formed triply C2-symmetric Ti3(tartrate)4(amine)2(OiPr)4 assemblies. Some minor components were believed to be μ-OiPr species. All mixed complexes except Ti(tartrate)2(Hdmae)2 contained chelating and bridging tartrate units, without coordination by ester carbonyls. A nonchelating, nonbridging tartrate unit was also present in the amino alcohol cases. Primary amines, aromatic amines, and hydrazines all failed to provide identifiable complexes. As well, N,N-dibenzylhydroxylamine failed to generate in solution the complex that had previously been characterized by X-ray crystallography. Amidst the rich chemistry of TiIV-tartrate systems, the evident selectivities in product formation were ascribed to macro-ring closures that are specifically directed by the electronic nature of the addend. Transient OiPr-bridged intermediates were also implicated. Keywords: mixed TiIV alkoxides, chiral TiIV alkoxides, enantiospecific complexation.


2011 ◽  
Vol 54 (15) ◽  
pp. 5454-5467 ◽  
Author(s):  
Stefano Mangani ◽  
Laura Cancian ◽  
Rosalida Leone ◽  
Cecilia Pozzi ◽  
Sandra Lazzari ◽  
...  

2018 ◽  
Vol 22 (09n10) ◽  
pp. 944-952 ◽  
Author(s):  
Fen Li ◽  
Yongjie Zhang ◽  
Lina Zhou ◽  
Xin Zhang ◽  
Zhijian Chen

Two boron-dipyrromethene dyes bearing a conjugated guanine unit (G-BODIPYs) 1 and 2 were synthesized and fully characterized. The self-assembly properties of these dyes were investigated by X-ray crystallography, [Formula: see text]H NMR and UV-vis spectroscopy. As revealed by X-ray crystal structure studies, G-BODIPY 1 self-assembled into ribbon-like structures due to the intermolecular hydrogen bonding and [Formula: see text]–[Formula: see text] stacking interaction. Concentration-dependent [Formula: see text]H NMR experiments confirmed the formation of hydrogen bonds of the guanine units in solution for both dye 1 and 2. In the presence of K[Formula: see text], the characteristic signals for the formation of cyclic G-quadruplex structures were observed in the [Formula: see text]H NMR study. Aggregation of G-BODIPY dyes was further monitored by UV-vis absorption spectroscopy by varying the solvent polarity and temperature. H-type aggregates of dye 1, which was characterized by a new hypsochromically shifted absorption band with [Formula: see text] 461 nm, was obtained. In the presence of K[Formula: see text], the enhancement of stability was observed for the H-aggregates of dye 1.


Sign in / Sign up

Export Citation Format

Share Document