A novel approach for sequential assignment of proton, carbon-13, and nitrogen-15 spectra of larger proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin

Biochemistry ◽  
1990 ◽  
Vol 29 (19) ◽  
pp. 4659-4667 ◽  
Author(s):  
Mitsuhiko Ikura ◽  
Lewis E. Kay ◽  
Ad Bax
Keyword(s):  
Nmr Spectroscopy ◽  
Three Dimensional ◽  
Sequential Assignment ◽  
Triple Resonance ◽  
Novel Approach

NMR spectroscopy: a multifaceted approach to macromolecular structure

2000 ◽  
Vol 33 (1) ◽  
pp. 29-65 ◽  
Author(s):  
Ann E. Ferentz ◽  
Gerhard Wagner
Keyword(s):  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Solution Structure ◽  
Residual Dipolar Couplings ◽  
Complete Solution ◽  
Protein Structures ◽  
Sequential Assignment ◽  
Resonance Spectroscopy ◽  
Triple Resonance ◽  
Membrane Bound

1. Introduction 292. Landmarks in NMR of macromolecules 322.1 Protein structures and methods development 322.1.1 Sequential assignment method 322.1.2 Triple-resonance experiments 342.1.3 Structures of large proteins 362.2 Protein–nucleic acid complexes 372.3 RNA structures 382.4 Membrane-bound systems 393. NMR spectroscopy today 403.1 State-of-the-art structure determination 413.2 New methods 443.2.1 Residual dipolar couplings 443.2.2 Direct detection of hydrogen bonds 443.2.3 Spin labeling 453.2.4 Segmental labeling 463.3 Protein complexes 473.4 Mobility studies 503.5 Determination of time-dependent structures 523.6 Drug discovery 534. The future of NMR 544.1 The ease of structure determination 544.2 The ease of making recombinant protein 554.3 Post-translationally modified proteins 554.4 Approaches to large and/or membrane-bound proteins 564.5 NMR in structural genomics 564.6 Synergy of NMR and crystallography in protein structure determination 565. Conclusion 576. Acknowledgements 577. References 57Since the publication of the first complete solution structure of a protein in 1985 (Williamson et al. 1985), tremendous technological advances have brought nuclear magnetic resonance spectroscopy to the forefront of structural biology. Innovations in magnet design, electronics, pulse sequences, data analysis, and computational methods have combined to make NMR an extremely powerful technique for studying biological macromolecules at atomic resolution (Clore & Gronenborn, 1998). Most recently, new labeling and pulse techniques have been developed that push the fundamental line-width limit for resolution in NMR spectroscopy, making it possible to obtain high-field spectra with better resolution than ever before (Dötsch & Wagner, 1998). These methods are facilitating the study of systems of ever-increasing complexity and molecular weight.

Improved resolution in three-dimensional constant-time triple resonance NMR spectroscopy of proteins

1992 ◽  
Vol 2 (1) ◽  
pp. 103-108 ◽  
Author(s):  
Arthur G. Palmer ◽  
Wayne J. Fairbrother ◽  
John Cavanagh ◽  
Peter E. Wright ◽  
Mark Rance
Keyword(s):  
Nmr Spectroscopy ◽  
Three Dimensional ◽  
Constant Time ◽  
Triple Resonance ◽  
Triple Resonance Nmr ◽  
Triple Resonance Nmr Spectroscopy

Assignment of the side-chain proton and carbon-13 resonances of interleukin-1.beta. using double- and triple-resonance heteronuclear three-dimensional NMR spectroscopy

Biochemistry ◽  
1990 ◽  
Vol 29 (35) ◽  
pp. 8172-8184 ◽  
Author(s):  
G. Marius Clore ◽  
Ad Bax ◽  
Paul C. Driscoll ◽  
Paul T. Wingfield ◽  
Angela M. Gronenborn
Keyword(s):  
Nmr Spectroscopy ◽  
Interleukin 1 ◽  
Three Dimensional ◽  
Side Chain ◽  
Triple Resonance ◽  
Interleukin 1 Beta

Assignment of the aliphatic proton and carbon-13 resonances of the Bacillus subtilis glucose permease IIA domain using double- and triple-resonance heteronuclear three-dimensional NMR spectroscopy

Biochemistry ◽  
1992 ◽  
Vol 31 (18) ◽  
pp. 4413-4425 ◽  
Author(s):  
Wayne J. Fairbrother ◽  
Arthur G. Palmer ◽  
Mark Rance ◽  
Jonathan Reizer ◽  
Milton H. Saier ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Nmr Spectroscopy ◽  
Three Dimensional ◽  
Triple Resonance

NMR spectroscopy in the conformational analysis of peptides: an overview

2020 ◽  
Vol 27 ◽  
Author(s):  
Marian Vincenzi ◽  
Flavia Anna Mercurio ◽  
Marilisa Leone
Keyword(s):  
Nmr Spectroscopy ◽  
Protein Interactions ◽  
3D Structure ◽  
Theoretical Background ◽  
Triple Resonance ◽  
Protein Protein Interactions ◽  
Nmr Studies ◽  
Conformational Preferences ◽  
Dynamic Perspective ◽  
Nmr Methods

Background: NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. Objective: This review provides a toolkit to investigate peptide conformational properties by NMR. Methods: Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through Pubmed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. Results: The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. Conclusion: NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.

scholarly journals Elastic transformation of histological slices allows precise co-registration with microCT data sets for a refined virtual histology approach

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonas Albers ◽  
Angelika Svetlove ◽  
Justus Alves ◽  
Alexander Kraupner ◽  
Francesca di Lillo ◽  
...  
Keyword(s):  
Three Dimensional ◽  
High Specificity ◽  
Histopathological Analysis ◽  
Specific Information ◽  
Data Sets ◽  
Virtual Histology ◽  
Novel Approach ◽  
Cell Tissue ◽  
Immuno Histochemistry ◽  
3D Information

AbstractAlthough X-ray based 3D virtual histology is an emerging tool for the analysis of biological tissue, it falls short in terms of specificity when compared to conventional histology. Thus, the aim was to establish a novel approach that combines 3D information provided by microCT with high specificity that only (immuno-)histochemistry can offer. For this purpose, we developed a software frontend, which utilises an elastic transformation technique to accurately co-register various histological and immunohistochemical stainings with free propagation phase contrast synchrotron radiation microCT. We demonstrate that the precision of the overlay of both imaging modalities is significantly improved by performing our elastic registration workflow, as evidenced by calculation of the displacement index. To illustrate the need for an elastic co-registration approach we examined specimens from a mouse model of breast cancer with injected metal-based nanoparticles. Using the elastic transformation pipeline, we were able to co-localise the nanoparticles to specifically stained cells or tissue structures into their three-dimensional anatomical context. Additionally, we performed a semi-automated tissue structure and cell classification. This workflow provides new insights on histopathological analysis by combining CT specific three-dimensional information with cell/tissue specific information provided by classical histology.

scholarly journals Artificial Tumor Microenvironments in Neuroblastoma

Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1629
Author(s):  
Colin H. Quinn ◽  
Andee M. Beierle ◽  
Elizabeth A. Beierle
Keyword(s):  
Extracellular Matrix ◽  
Three Dimensional ◽  
Therapeutic Interventions ◽  
3D Bioprinting ◽  
Culture Studies ◽  
In Vivo Models ◽  
Novel Treatments ◽  
Tumor Microenvironments ◽  
Novel Approach

In the quest to advance neuroblastoma therapeutics, there is a need to have a deeper understanding of the tumor microenvironment (TME). From extracellular matrix proteins to tumor associated macrophages, the TME is a robust and diverse network functioning in symbiosis with the solid tumor. Herein, we review the major components of the TME including the extracellular matrix, cytokines, immune cells, and vasculature that support a more aggressive neuroblastoma phenotype and encumber current therapeutic interventions. Contemporary treatments for neuroblastoma are the result of traditional two-dimensional culture studies and in vivo models that have been translated to clinical trials. These pre-clinical studies are costly, time consuming, and neglect the study of cofounding factors such as the contributions of the TME. Three-dimensional (3D) bioprinting has become a novel approach to studying adult cancers and is just now incorporating portions of the TME and advancing to study pediatric solid. We review the methods of 3D bioprinting, how researchers have included TME pieces into the prints, and highlight present studies using neuroblastoma. Ultimately, incorporating the elements of the TME that affect neuroblastoma responses to therapy will improve the development of innovative and novel treatments. The use of 3D bioprinting to achieve this aim will prove useful in developing optimal therapies for children with neuroblastoma.

scholarly journals Integrated impedance sensing of liquid sample plug flow enables automated high throughput NMR spectroscopy

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Omar Nassar ◽  
Mazin Jouda ◽  
Michael Rapp ◽  
Dario Mager ◽  
Jan G. Korvink ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
High Throughput ◽  
Plug Flow ◽  
Microfluidic System ◽  
High Resolution Spectroscopy ◽  
Dead Volume ◽  
Absolute Difference ◽  
Immiscible Fluid ◽  
Flow Sensors ◽  
Novel Approach

AbstractA novel approach for automated high throughput NMR spectroscopy with improved mass-sensitivity is accomplished by integrating microfluidic technologies and micro-NMR resonators. A flow system is utilized to transport a sample of interest from outside the NMR magnet through the NMR detector, circumventing the relatively vast dead volume in the supplying tube by loading a series of individual sample plugs separated by an immiscible fluid. This dual-phase flow demands a real-time robust sensing system to track the sample position and velocities and synchronize the NMR acquisition. In this contribution, we describe an NMR probe head that possesses a microfluidic system featuring: (i) a micro saddle coil for NMR spectroscopy and (ii) a pair of interdigitated capacitive sensors flanking the NMR detector for continuous position and velocity monitoring of the plugs with respect to the NMR detector. The system was successfully tested for automating flow-based measurement in a 500 MHz NMR system, enabling high resolution spectroscopy and NMR sensitivity of 2.18 nmol s1/2 with the flow sensors in operation. The flow sensors featured sensitivity to an absolute difference of 0.2 in relative permittivity, enabling distinction between most common solvents. It was demonstrated that a fully automated NMR measurement of nine individual 120 μL samples could be done within 3.6 min or effectively 15.3 s per sample.

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