scholarly journals Use of High Pressure NMR Spectroscopy to Rapidly Identify Proteins with Internal Ligand-Binding Voids

2020 ◽  
Author(s):  
Donald Gagné ◽  
Roksana Azad ◽  
Uthama R. Edupuganti ◽  
Justin Williams ◽  
James M. Aramini ◽  
...  
Keyword(s):  
High Pressure ◽  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Ligand Binding ◽  
Small Molecule ◽  
A Priori ◽  
Solution Nmr ◽  
Internal Cavities ◽  
Small Molecule Ligands ◽  
Solution Nmr Spectroscopy

AbstractSmall molecule binding within internal cavities provides a way to control protein function and structure, as exhibited in numerous natural and artificial settings. Unfortunately, most ways to identify suitable cavities require high-resolution structures a priori and may miss potential cryptic sites. Here we address this limitation via high-pressure solution NMR spectroscopy, taking advantage of the distinctive nonlinear pressure-induced chemical shift changes observed in proteins containing internal cavities and voids. We developed a method to rapidly characterize such nonlinearity among backbone 1H and 15N amide signals without needing to have sequence-specific chemical shift assignments, taking advantage of routinely available 15N-labeled samples, instrumentation, and 2D 1H/15N HSQC experiments. From such data, we find a strong correlation in the site-to-site variability in such nonlinearity with the total void volume within proteins, providing insights useful for prioritizing domains for ligand binding and indicating mode-of-action among such protein/ligand systems. We suggest that this approach provides a rapid and useful way to rapidly assess otherwise hidden dynamic architectures of protein that reflect fundamental properties associated with ligand binding and control.Significance StatementMany proteins can be regulated by internally binding small molecule ligands, but it is often not clear a priori which proteins are controllable in such a way. Here we describe a rapid method to address this challenge, using solution NMR spectroscopy to monitor the response of proteins to the application of high pressure. While the locations of NMR signals from most proteins respond to high pressure with linear chemical shift changes, proteins containing internal cavities that can bind small molecule ligands respond with easily identified non-linear changes. We demonstrate this approach on several proteins and protein/ligand complexes, suggesting that it has general utility.

9Be nuclear magnetic resonance spectroscopy trends in discrete complexes: an update

2020 ◽  
Vol 75 (5) ◽  
pp. 459-472 ◽  
Author(s):  
Jenna K. Buchanan ◽  
Paul G. Plieger
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Nmr Spectroscopy ◽  
Magnetic Resonance ◽  
Chemical Shift ◽  
Chemical Shifts ◽  
Solution Nmr ◽  
Resonance Spectroscopy ◽  
Coordination Numbers ◽  
Solution Nmr Spectroscopy ◽  
Beryllium Complexes

Abstract9Be solution NMR spectroscopy is a useful tool for the characterisation of beryllium complexes. An updated comprehensive table of the 9Be NMR chemical shifts of beryllium complexes in solution is presented. The recent additions span a greater range of chemical shifts than those previously reported, and more overlap is observed between the chemical shift regions of four-coordinate complexes and those with lower coordination numbers. Four-coordinate beryllium species have smaller ω1/2 values than the two- and three-coordinate species due to their higher order symmetry. In contrast to previous studies, no clear relationship is observed between chemical shift and the size and number of chelate rings.

scholarly journals A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery

Molecules ◽  
2020 ◽  
Vol 25 (13) ◽  
pp. 2974
Author(s):  
Qingxin Li ◽  
CongBao Kang
Keyword(s):  
Drug Discovery ◽  
Nmr Spectroscopy ◽  
Ligand Binding ◽  
Conformational Changes ◽  
Solution Nmr ◽  
Binding Modes ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Solution Nmr Spectroscopy ◽  
Solution Nuclear Magnetic Resonance

Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to study structures and dynamics of biomolecules under physiological conditions. As there are numerous NMR-derived methods applicable to probe protein–ligand interactions, NMR has been widely utilized in drug discovery, especially in such steps as hit identification and lead optimization. NMR is frequently used to locate ligand-binding sites on a target protein and to determine ligand binding modes. NMR spectroscopy is also a unique tool in fragment-based drug design (FBDD), as it is able to investigate target-ligand interactions with diverse binding affinities. NMR spectroscopy is able to identify fragments that bind weakly to a target, making it valuable for identifying hits targeting undruggable sites. In this review, we summarize the roles of solution NMR spectroscopy in drug discovery. We describe some methods that are used in identifying fragments, understanding the mechanism of action for a ligand, and monitoring the conformational changes of a target induced by ligand binding. A number of studies have proven that 19F-NMR is very powerful in screening fragments and detecting protein conformational changes. In-cell NMR will also play important roles in drug discovery by elucidating protein-ligand interactions in living cells.

Intermolecular Interactions of Xe Atoms Confined in One-dimensional Nanochannels of Tris(o-phenylenedioxy)cyclotriphosphazene as Studied by High-pressure 129Xe NMR

2003 ◽  
Vol 58 (12) ◽  
pp. 727-734 ◽  
Author(s):  
Hirokazu Kobayashi ◽  
Takahiro Ueda ◽  
Keisuke Miyakubo ◽  
Taro Eguchi
Keyword(s):  
High Pressure ◽  
Nmr Spectroscopy ◽  
Chemical Shift ◽  
Pressure Dependence ◽  
Average Distance ◽  
Chemical Shift Tensor ◽  
Axially Symmetric ◽  
One Dimensional ◽  
129Xe Nmr ◽  
The One

The pressure dependence of the 129Xe chemical shift tensor confined in the Tris(o-phenylenedioxy) cyclotriphosphazene (TPP) nanochannel was investigated by high-pressure 129Xe NMR spectroscopy. The observed 129Xe spectrum in the one-dimensional TPP nanochannel (0.45 nm in diameter) exhibits a powder pattern broadened by an axially symmetric chemical shift tensor. As the pressure increases from 0.02 to 7.0 MPa, a deshielding of 90 ppm is observed for the perpendicularcomponent of the chemical shift tensor δ⊥, whereas a deshielding of about 30 ppm is observed for the parallel one, δ‖. This suggests that the components of the chemical shift tensor, δ‖ and δ⊥, are mainly dominated by the Xe-wall and Xe-Xe interaction, respectively. Furthermore, the effect of helium, which is present along with xenon gas, on the 129Xe chemical shift is examined in detail. The average distance between the Xe atoms in the nanochannel is estimated to be 0.54 nm. This was found by using δ⊥ at the saturated pressure of xenon, and comparing the increment of the chemicalshift value in δ⊥ to that of a β -phenol/Xe compound.

scholarly journals Ligands with poly-fluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities

2021 ◽  
Author(s):  
Sharif Anisuzzaman ◽  
Ivan M Geraskin ◽  
Muslum Ilgu ◽  
Lee Bendickson ◽  
George A Kraus ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Ligand Binding ◽  
Small Molecule ◽  
Binding Pocket ◽  
Structural Rearrangement ◽  
Structural Reorganization ◽  
Ligand Binding Pocket ◽  
Rna Remodeling ◽  
Small Molecule Ligands ◽  
Target Molecules

The interaction of nucleic acids with their molecular targets often involves structural reorganization that may traverse a complex folding landscape. With the more recent recognition that many RNAs, both coding and noncoding, may regulate cellular activities by interacting with target molecules, it becomes increasingly important to understand the means by which nucleic acids interact with their targets and how drugs might be developed that can influence critical folding transitions. We have extensively investigated the interaction of the Spinach2 and Broccoli aptamers with a library of small molecule ligands modified by various extensions from the imido nitrogen of DFHBI (3,5-difluoro-4-hydroxybenzylidene imidazolinone) that reach out from the Spinach2 ligand binding pocket. Studies of the interaction of these compounds with the aptamers revealed that poly-fluorophenyl-modified ligands initiate a slow change in aptamer affinity that takes an extended time (half-life of ~40 min) to achieve. The change in affinity appears to involve an initial disruption of the entrance to the ligand binding pocket followed by a gradual lockdown for which the most likely driving force is an interaction of the gateway adenine with a nearby 2'OH group. These results suggest that poly-fluorophenyl modifications might increase the ability of small molecule drugs to disrupt local structure and promote RNA remodeling.

Solution NMR Spectroscopy of Food Polysaccharides

2012 ◽  
Vol 52 (2) ◽  
pp. 81-114 ◽  
Author(s):  
H. N. Cheng ◽  
Thomas G. Neiss
Keyword(s):  
Nmr Spectroscopy ◽  
Solution Nmr ◽  
Solution Nmr Spectroscopy
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