NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology

Quinn, Caitlin M.; Wang, Mingzhang; Polenova, Tatyana

doi:10.1007/978-1-4939-7386-6_1

Cited by 27 publications

(17 citation statements)

References 201 publications

(221 reference statements)

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“…Should isotope-enriched VLM samples become available, other SSNMR spectral markers might include the 17 O parameters [ 31 ] or 1 H amid – 15 N amid and 1 H α – 13 C α dipolar couplings [ 32 ]. In addition, investigations of the chemical shift anisotropies could be performed [ 33 , 34 , 35 ] which would likely require measurements at very high (>20 T) magnetic fields [ 36 , 37 , 38 ].…”

Section: Discussionmentioning

confidence: 99%

Polymorphic Forms of Valinomycin Investigated by NMR Crystallography

Czernek

Brus

2020

IJMS

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A dodecadepsipeptide valinomycin (VLM) has been most recently reported to be a potential anti-coronavirus drug that could be efficiently produced on a large scale. It is thus of importance to study solid-phase forms of VLM in order to be able to ensure its polymorphic purity in drug formulations. The previously available solid-state NMR (SSNMR) data are combined with the plane-wave DFT computations in the NMR crystallography framework. Structural/spectroscopical predictions (the PBE functional/GIPAW method) are obtained to characterize four polymorphs of VLM. Interactions which confer a conformational stability to VLM molecules in these crystalline forms are described in detail. The way how various structural factors affect the values of SSNMR parameters is thoroughly analyzed, and several SSNMR markers of the respective VLM polymorphs are identified. The markers are connected to hydrogen bonding effects upon the corresponding (13C/15N/1H) isotropic chemical shifts of (CO, Namid, Hamid, Hα) VLM backbone nuclei. These results are expected to be crucial for polymorph control of VLM and in probing its interactions in dosage forms.

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Section: Discussionmentioning

confidence: 99%

Polymorphic Forms of Valinomycin Investigated by NMR Crystallography

Czernek

Brus

2020

IJMS

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“…In addition, we believe that, properly modified, these approaches can be applied to study the dynamics and interactions of other eukaryotic membrane proteins as well. We anticipate that further technological developments, including those in sample preparation [e.g., additional labeling strategies (Robson, Takeuchi, Boeszoermenyi, Coote, Dubey, Hyberts et al, 2018), ways to improve sample stability or concentration via improved membrane-mimetics such as smaller, more "NMR-friendly" nanodiscs (Chien, Helfinger, Bostock, Solt, Tan, & Nietlispach, 2017;Hagn, Etzkorn, Raschle, & Wagner, 2013)], NMR data acquisition [e.g., ultrahigh field NMR systems (Quinn, Wang, & Polenova, 2018), improved 13 C/ 15 N direct detection methods (Takeuchi, Heffron, Sun, Frueh, & Wagner, 2010)], and analysis [e.g., improved methods for chemical shift assignment through PRE or NOESY experiments (Lescanne, Skinner, Blok, Timmer, Cerofolini, Fragai et al, 2017)], will only further improve such prospects in the future. A) and B) General schematics of WT and optimized MFα signal sequences prior to start of WT GPCR gene of interest.…”

Section: Discussionmentioning

confidence: 99%

Isotopic Labeling of Eukaryotic Membrane Proteins for NMR Studies of Interactions and Dynamics

Dikiy

Clark

Gardner

et al. 2019

Biological NMR Part A

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Membrane proteins, and especially G-protein coupled receptors (GPCRs), are increasingly important targets of structural biology studies due to their involvement in many biomedicallycritical pathways in humans. These proteins are often highly dynamic and thus benefit from studies by NMR spectroscopy in parallel with complementary crystallographic and cryo-EM analyses. However, such studies are often complicated by a range of practical concerns, including challenges in preparing suitably isotopically-labeled membrane protein samples, large sizes of protein/detergent or protein/lipid complexes, and limitations on sample concentrations and stabilities. Here we describe our approach to addressing these challenges via the use of simple eukaryotic expression systems and modified NMR experiments, using the human adenosine A 2A receptor as an example. Protocols are provided for the preparation of U-2 H ( 13 C, 1 H-Ile δ1) labeled membrane proteins from overexpression in the methylotrophic yeast Pichia pastoris, as well as techniques for studying the fast psec-nsec sidechain dynamics of the methyl groups of such samples. We believe that, with the proper optimization, these protocols should be generalizable to other GPCRs and human membrane proteins.

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“…On the one hand, new ssNMR instrumentation developments have significantly enhanced the effective sensitivity and productivity of biomolecular ssNMR. This is due, in part, to increased access to high-field NMR instruments that increase resolution and sensitivity (reviewed in [ 17 ]). Other critical improvements affect the ssNMR probes that feature the coil used for the detection and application of radio frequency (RF) pulses, and the ‘stator' assembly that enables MAS sample rotation.…”

Section: Expanding Horizons In Biomolecular Ssnmrmentioning

confidence: 99%

“…ssNMR also revealed the structures of various membrane-associated proteins [ 59 ], including those of the M2 channel of influenza A and sensory rhodopsin ( Figure 1B ) [ 60 – 64 ]. However, recent ssNMR structures go well beyond these traditional types of protein samples with an expanding repertoire of biologically functional protein assemblies, such as viral capsid proteins, motor proteins, α-helical protein assemblies ( Figure 1C,D ) and functional amyloids [ 17 , 65 , 66 ].…”

Section: Recent Protein and Peptide Structures Obtained By Ssnmrmentioning

confidence: 99%

New applications of solid-state NMR in structural biology

Wel

2018

Emerging Topics in Life Sciences

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Various recent developments in solid-state nuclear magnetic resonance (ssNMR) spectroscopy have enabled an array of new insights regarding the structure, dynamics, and interactions of biomolecules. In the ever more integrated world of structural biology, ssNMR studies provide structural and dynamic information that is complementary to the data accessible by other means. ssNMR enables the study of samples lacking a crystalline lattice, featuring static as well as dynamic disorder, and does so independent of higher-order symmetry. The present study surveys recent applications of biomolecular ssNMR and examines how this technique is increasingly integrated with other structural biology techniques, such as (cryo) electron microscopy, solution-state NMR, and X-ray crystallography. Traditional ssNMR targets include lipid bilayer membranes and membrane proteins in a lipid bilayer environment. Another classic application has been in the area of protein misfolding and aggregation disorders, where ssNMR has provided essential structural data on oligomers and amyloid fibril aggregates. More recently, the application of ssNMR has expanded to a growing array of biological assemblies, ranging from non-amyloid protein aggregates, protein–protein complexes, viral capsids, and many others. Across these areas, multidimensional magic angle spinning (MAS) ssNMR has, in the last decade, revealed three-dimensional structures, including many that had been inaccessible by other structural biology techniques. Equally important insights in structural and molecular biology derive from the ability of MAS ssNMR to probe information beyond comprehensive protein structures, such as dynamics, solvent exposure, protein–protein interfaces, and substrate–enzyme interactions.

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NMR of Macromolecular Assemblies and Machines at 1 GHz and Beyond: New Transformative Opportunities for Molecular Structural Biology

Cited by 27 publications

References 201 publications

Polymorphic Forms of Valinomycin Investigated by NMR Crystallography

Polymorphic Forms of Valinomycin Investigated by NMR Crystallography

Isotopic Labeling of Eukaryotic Membrane Proteins for NMR Studies of Interactions and Dynamics

New applications of solid-state NMR in structural biology

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