Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-ray Crystallography and Computational Analysis

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.

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Structure of the nitrosoguanidine complexes of nickel(II) and copper(II) by X-ray crystallography and computational analysis

Journal of Coordination Chemistry ◽

10.1080/0095897042000327950 ◽

2005 ◽

Vol 58 (3) ◽

pp. 279-294 ◽

Cited By ~ 3

Author(s):

R. Kent Murmann ◽

Rainer Glaser ◽

Charles L. Barnes

Keyword(s):

Computational Analysis ◽

X Ray ◽

X Ray Crystallography

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Multiple binding modes of a small molecule to human Keap1 revealed by X-ray crystallography and molecular dynamics simulation

FEBS Open Bio ◽

10.1016/j.fob.2015.06.011 ◽

2015 ◽

Vol 5 (1) ◽

pp. 557-570 ◽

Cited By ~ 22

Author(s):

Mikiya Satoh ◽

Hajime Saburi ◽

Tomoyuki Tanaka ◽

Yoshinori Matsuura ◽

Hisashi Naitow ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Small Molecule ◽

Dynamics Simulation ◽

Binding Modes ◽

X Ray ◽

X Ray Crystallography ◽

Multiple Binding

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Movements at the hemoglobin A-hemes and their role in ligand binding, analyzed by X-ray crystallography

Biopolymers ◽

10.1002/bip.21197 ◽

2009 ◽

Vol 91 (12) ◽

pp. 1056-1063 ◽

Cited By ~ 2

Author(s):

Eleanor Dodson ◽

Guy Dodson

Keyword(s):

Ligand Binding ◽

X Ray ◽

X Ray Crystallography ◽

Hemoglobin A

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Structural basis for the binding of SNAREs to the multisubunit tethering complex Dsl1

10.1101/2020.04.07.029496 ◽

2020 ◽

Author(s):

Sophie M. Travis ◽

Kevin DAmico ◽

I-Mei Yu ◽

Safraz Hamid ◽

Gabriel Ramirez-Arellano ◽

...

Keyword(s):

Membrane Trafficking ◽

Relative Orientation ◽

Snare Complex ◽

Structural Basis ◽

Binding Modes ◽

Range Interaction ◽

X Ray ◽

X Ray Crystallography ◽

Long Range Interaction ◽

Target Membrane

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.

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Cooperative Cobinding of Synthetic and Natural Ligands to the Nuclear Receptor PPARγ

10.1101/252817 ◽

2018 ◽

Cited By ~ 1

Author(s):

Jinsai Shang ◽

Richard Brust ◽

Sarah A. Mosure ◽

Jared Bass ◽

Paola Munoz-Tello ◽

...

Keyword(s):

Ligand Binding ◽

Peroxisome Proliferator ◽

Binding Modes ◽

Endogenous Ligand ◽

Peroxisome Proliferator Activated Receptor ◽

X Ray Crystallography ◽

Natural Ligands ◽

Synthetic Ligand ◽

Dynamics Simulations ◽

And Function

Crystal structures of peroxisome proliferator-activated receptor gamma (PPARγ) have revealed overlapping binding modes for synthetic and natural/endogenous ligands, indicating competition for the orthosteric pocket. Here we show that cobinding of a synthetic ligand to the orthosteric pocket can push natural and endogenous PPARγ ligands (fatty acids) out of the orthosteric pocket towards an alternate ligand-binding site near the functionally important omega (Ω) loop. X-ray crystallography, NMR spectroscopy, all-atom molecular dynamics simulations, and mutagenesis coupled to quantitative functional assays reveal that synthetic ligand and fatty acid cobinding can form a “ligand link” to the Ω loop and synergistically affect the structure and function of PPARγ. These findings contribute to a growing body of evidence indicating ligand binding to nuclear receptors can be more complex than the classical one-for-one orthosteric exchange of a natural or endogenous ligand with a synthetic ligand.

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X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

10.26434/chemrxiv.11444877 ◽

2019 ◽

Author(s):

Willem Jespers ◽

Grégory Verdon ◽

Jhonny Azuaje ◽

maria majellaro ◽

Henrik Keränen ◽

...

Keyword(s):

Free Energy ◽

Adenosine Receptor ◽

Free Energy Calculations ◽

Binding Modes ◽

A2a Adenosine Receptor ◽

Binding Model ◽

Energy Calculations ◽

X Ray ◽

X Ray Crystallography ◽

Pharmacological Data

<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>

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