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The global protein crystallization and crystallography market is estimated to grow from USD 1.1 billion in 2020 to USD 1.7 billion by 2025, at a CAGR of 8.9% - Salamanca Press
Jul 06, 2020 - 10:57 PM - by nmrlearner
nmrlearner's Avatar The global protein crystallization and crystallography market is estimated to grow from USD 1.1 billion in 2020 to USD 1.7 billion by 2025, at a CAGR of 8.9% - Salamanca Press

The global protein crystallization and crystallography market is estimated to grow from USD 1.1 billion in 2020 to USD 1.7 billion by 2025, at a CAGR of 8.9% Salamanca Press Read here
0 Replies | 1 Views
[NMR paper] NMR pseudocontact shifts in a symmetric protein homotrimer.
Jul 06, 2020 - 10:08 AM - by nmrlearner
nmrlearner's Avatar NMR pseudocontact shifts in a symmetric protein homotrimer.

Related Articles NMR pseudocontact shifts in a symmetric protein homotrimer.

J Biomol NMR. 2020 Jul 03;:

Authors: Müntener T, Böhm R, Atz K, Häussinger D, Hiller S

Abstract
NMR pseudocontact shifts are a valuable tool for structural and functional studies of proteins. Protein multimers mediate key functional roles in biology, but methods for their study by pseudocontact shifts are so far not available. Paramagnetic tags attached to identical subunits in multimeric proteins cause a combined pseudocontact shift that cannot be described by the standard single-point model. Here, we report pseudocontact shifts generated simultaneously by three paramagnetic Tm-M7PyThiazole-DOTA tags to the trimeric molecular chaperone Skp and provide an approach for the analysis of this and related symmetric systems. The pseudocontact shifts were described by a "three-point" model, in which positions and parameters of the three paramagnetic tags were fitted. A good correlation between experimental data and predicted values was found, validating the approach. The study establishes that pseudocontact shifts can readily be applied to multimeric proteins, offering new perspectives for studies of large protein complexes by paramagnetic NMR spectroscopy.


PMID: 32621004 [PubMed - as supplied by publisher]



... [Read More]
0 Replies | 12 Views
[NMR paper] Protein-ligand structure determination with the NMR molecular replacement tool, NMR2.
Jul 06, 2020 - 10:08 AM - by nmrlearner
nmrlearner's Avatar Protein-ligand structure determination with the NMR molecular replacement tool, NMR2.

Related Articles Protein-ligand structure determination with the NMR molecular replacement tool, NMR2.

J Biomol NMR. 2020 Jul 03;:

Authors: Orts J, Riek R

Abstract
We recently reported on a new method called NMR Molecular Replacement that efficiently derives the structure of a protein-ligand complex at the interaction site. The method was successfully applied to high and low affinity complexes covering ligands from peptides to small molecules. The algorithm used in the NMR Molecular Replacement program has until now not been*described in detail. Here, we present a complete description of the NMR Molecular Replacement implementation as well as several new features that further reduce the time required for structure elucidation.


PMID: 32621003 [PubMed - as supplied by publisher]



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0 Replies | 7 Views
[NMR paper] Human urine 1H NMR metabolomics reveals alterations of the protein and carbohydrate metabolism when comparing habitual Average Danish diet vs. healthy New Nordic diet.
Jul 04, 2020 - 9:21 PM - by nmrlearner
nmrlearner's Avatar Human urine 1H NMR metabolomics reveals alterations of the protein and carbohydrate metabolism when comparing habitual Average Danish diet vs. healthy New Nordic diet.

Related Articles Human urine 1H NMR metabolomics reveals alterations of the protein and carbohydrate metabolism when comparing habitual Average Danish diet vs. healthy New Nordic diet.

Nutrition. 2020 May 22;79-80:110867

Authors: Trimigno A, Khakimov B, Savorani F, Poulsen SK, Astrup A, Dragsted LO, Engelsen SB

Abstract
OBJECTIVES: The aim of this study was to investigate the alteration of the human urine metabolome by means of diet and to compare the metabolic effects of the nutritionally healthy New Nordic Diet (NND) with an Average Danish Diet (ADD). The NND was designed a decade ago by scientists and chefs, based on local and sustainable foods, including fish, shellfish, vegetables, roots, fruit, and berries. The NND has been proven to lower blood pressure, reduce glycemia, and lead to weight loss.
METHODS: The human urine metabolome was measured by untargeted proton nuclear magnetic resonance spectroscopy in samples from 142 centrally obese Danes (20-66 years old), randomized to consume the ADD or the NND. The resulting metabolomics data was processed and analyzed using advanced multivariate data analysis methods to reveal effects related to the design factors, including diet, season, sex, and changes in... [Read More]
0 Replies | 24 Views
[NMR paper] Quantification of fractional and absolute functionalization of gelatin hydrogels by optimized ninhydrin assay and 1H NMR.
Jul 04, 2020 - 9:21 PM - by nmrlearner
nmrlearner's Avatar Quantification of fractional and absolute functionalization of gelatin hydrogels by optimized ninhydrin assay and 1H NMR.

Related Articles Quantification of fractional and absolute functionalization of gelatin hydrogels by optimized ninhydrin assay and 1H NMR.

Anal Bioanal Chem. 2020 Jul 03;:

Authors: Zatorski JM, Montalbine AN, Ortiz-Cárdenas JE, Pompano RR

Abstract
3D cell culture in protein-based hydrogels often begins with chemical functionalization of proteins with cross-linking agents such as methacryloyl or norbornene. An important and variable characteristic of these materials is the degree of functionalization (DoF), which controls the reactivity of the protein for cross-linking and therefore impacts the mechanical properties and stability of the hydrogel. Although 1H NMR has emerged as the most accurate technique for quantifying absolute DoF of chemically modified proteins, colorimetric techniques still dominate in actual use and may be more useful for quantifying fractional or percent DoF. In this work, we sought to develop an optimized colorimetric assay for DoF of common gelatin-based biomaterials and validate it versus NMR; along the way, we developed a set of best practices for both methods and considerations for their most appropriate use. First, the amine-reactive ninhydrin assay was optimized in terms of solvent properties, temperature, ninhydrin concentration, and range... [Read More]
0 Replies | 10 Views
[NMR paper] Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis.
Jul 04, 2020 - 9:21 PM - by nmrlearner
nmrlearner's Avatar Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis.

Related Articles Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis.

PeerJ. 2020;8:e9408

Authors: Wu S, Nguyen TTTN, Moroz OV, Turkenburg JP, Nielsen JE, Wilson KS, Rand KD, Teilum K

Abstract
Background: Several examples have emerged of enzymes where slow conformational changes are of key importance for function and where low populated conformations in the resting enzyme resemble the conformations of intermediate states in the catalytic process. Previous work on the subtilisin protease, Savinase, from Bacillus lentus by NMR spectroscopy suggested that this enzyme undergoes slow conformational dynamics around the substrate binding site. However, the functional importance of such dynamics is unknown.
Methods: Here we have probed the conformational heterogeneity in Savinase by following the temperature dependent chemical shift changes. In addition, we have measured changes in the local stability of the enzyme when the inhibitor phenylmethylsulfonyl fluoride is bound using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finally, we have used X-ray crystallography to compare electron densities collected at cryogenic and ambient temperatures and searched for possible low populated alternative conformations in the crystals.
Results: The... [Read More]
0 Replies | 13 Views
[NMR paper] NMR spectroscopy in the conformational analysis of peptides: an overview.
Jul 04, 2020 - 3:45 AM - by nmrlearner
nmrlearner's Avatar NMR spectroscopy in the conformational analysis of peptides: an overview.

Related Articles NMR spectroscopy in the conformational analysis of peptides: an overview.

Curr Med Chem. 2020 Jul 02;:

Authors: Vincenzi M, Mercurio FA, Leone M

Abstract
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... [Read More]
0 Replies | 15 Views
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