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Journal of Biomolecular NMR

Malene V Christensen, Kenneth T Kongstad, Teis Esben Sondergaard, Dan Staerk, Hanne M Nielsen, Henrik Franzyk, Reinhard Wimmer
Current methods for assessment of cellular uptake of cell-penetrating peptides (CPPs) often rely on detection of fluorophore-labeled CPPs. However, introduction of the fluorescent probe often confers changed physicochemical properties, so that the fluorophore-CPP conjugate may exhibit cytotoxic effects and membrane damage not exerted by the native CPP. In the present study, introduction of fluorine probes was investigated as an alternative to fluorophore labeling of a CPP, since this only confers minor changes to its overall physicochemical properties...
March 18, 2019: Journal of Biomolecular NMR
Ryan W Russell, Matthew P Fritz, Jodi Kraus, Caitlin M Quinn, Tatyana Polenova, Angela M Gronenborn
We present a systematic investigation into the attainable accuracy and precision of protein structures determined by heteronuclear magic angle spinning solid-state NMR for a set of four proteins of varied size and secondary structure content. Structures were calculated using synthetically generated random sets of C-C distances up to 7 Å at different degrees of completeness. For single-domain proteins, 9-15 restraints per residue are sufficient to derive an accurate model structure, while maximum accuracy and precision are reached with over 15 restraints per residue...
March 7, 2019: Journal of Biomolecular NMR
Arthur G Palmer
No abstract text is available yet for this article.
March 1, 2019: Journal of Biomolecular NMR
Gerhard Wagner
No abstract text is available yet for this article.
March 1, 2019: Journal of Biomolecular NMR
Robert J Mallis, Kristine N Brazin, Jonathan S Duke-Cohan, Wonmuk Hwang, Jia-Huai Wang, Gerhard Wagner, Haribabu Arthanari, Matthew J Lang, Ellis L Reinherz
Early studies of T cell structural biology using X-ray crystallography, surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) focused on a picture of the αβT cell receptor (αβTCR) component domains and their cognate ligands (peptides bound to MHC molecules, i.e. pMHCs) as static interaction partners. Moving forward requires integrating this corpus of data with dynamic technologies such as NMR, molecular dynamics (MD) simulations and real-time single molecule (SM) studies exemplified by optical tweezers (OT)...
February 27, 2019: Journal of Biomolecular NMR
T Gopinath, Songlin Wang, John Lee, Hideki Aihara, Gianluigi Veglia
Magic angle spinning (MAS) solid-state NMR (ssNMR) spectroscopy is a major technique for the characterization of the structural dynamics of biopolymers at atomic resolution. However, the intrinsic low sensitivity of this technique poses significant limitations to its routine application in structural biology. Here we achieve substantial savings in experimental time using a new subclass of Polarization Optimized Experiments (POEs) that concatenate TEDOR and SPECIFIC-CP transfers into a single pulse sequence...
February 25, 2019: Journal of Biomolecular NMR
Lewis E Kay
With the development of sophisticated pulsed field gradient- and phase cycling-approaches for suppressing certain coherence transfer pathways and selecting for others it is sometimes easy to forget that the process is not flawless. In some cases artifacts can emerge because unwanted transfers are immune to the phase cycle or the application of gradients. We consider here a simple 1 H,13 C HMQC pulse scheme and show that imperfections in the single 1 H 180° refocusing pulse can give rise to small artifacts in methyl spectra that cannot be eliminated through extensive phase cycling or the use of gradients, but that are easily removed when the pulse is of the composite variety...
February 23, 2019: Journal of Biomolecular NMR
Jonas Fredriksson, Wolfgang Bermel, Martin Billeter
A flexible and scalable approach for protein NMR is introduced that builds on rapid data collection via projection spectroscopy and analysis of the spectral input data via joint decomposition. Input data may originate from various types of spectra, depending on the ultimate goal: these may result from experiments based on triple-resonance pulse sequences, or on TOCSY or NOESY sequences, or mixtures thereof. Flexible refers to the free choice of spectra for the joint decompositions depending on the purpose: assignments, structure, dynamics, interactions...
February 15, 2019: Journal of Biomolecular NMR
Kumar Tekwani Movellan, Eszter E Najbauer, Supriya Pratihar, Michele Salvi, Karin Giller, Stefan Becker, Loren B Andreas
We describe a new labeling method that allows for full protonation at the backbone Hα position, maintaining protein side chains with a high level of deuteration. We refer to the method as alpha proton exchange by transamination (α-PET) since it relies on transaminase activity demonstrated here using Escherichia coli expression. We show that α-PET labeling is particularly useful in improving structural characterization of solid proteins by introduction of an additional proton reporter, while eliminating many strong dipolar couplings...
February 14, 2019: Journal of Biomolecular NMR
David Schweida, Pierre Barraud, Christof Regl, Fionna E Loughlin, Christian G Huber, Chiara Cabrele, Mario Schubert
N-terminal gluconoylation is a moderately widespread modification in recombinant proteins expressed in Escherichia coli, in particular in proteins bearing an N-terminal histidine-tag. This post-translational modification has been investigated mainly by mass spectrometry. Although its NMR signals must have been observed earlier in spectra of 13 C/15 N labeled proteins, their chemical shifts were not yet reported. Here we present the complete 1 H and 13 C chemical shift assignment of the N-terminal gluconoyl post-translational modification, based on a selection of His-tagged protein constructs (CCL2, hnRNP A1 and Lin28) starting with Met-Gly-...
February 8, 2019: Journal of Biomolecular NMR
Rachel A Munro, Jeffrey de Vlugt, Meaghan E Ward, So Young Kim, Keon Ah Lee, Kwang-Hwan Jung, Vladimir Ladizhansky, Leonid S Brown
The isomerization of a covalently bound retinal is an integral part of both microbial and animal rhodopsin function. As such, detailed structure and conformational changes in the retinal binding pocket are of significant interest and are studied in various NMR, FTIR, and Raman spectroscopy experiments, which commonly require isotopic labeling of retinal. Unfortunately, the de novo organic synthesis of an isotopically-labeled retinal is complex and often cost-prohibitive, especially for large scale expression required for solid-state NMR...
February 4, 2019: Journal of Biomolecular NMR
Susanne Penzel, Andres Oss, Mai-Liis Org, Ago Samoson, Anja Böckmann, Matthias Ernst, Beat H Meier
We report linewidth and proton T1 , T1ρ and T2 ' relaxation data of the model protein ubiquitin acquired at MAS frequencies up to 126 kHz. We find a predominantly linear improvement in linewidths and coherence decay times of protons with increasing spinning frequency in the range from 93 to 126 kHz. We further attempt to gain insight into the different contributions to the linewidth at fast MAS using site-specific analysis of proton relaxation parameters and present bulk relaxation times as a function of the MAS frequency...
January 24, 2019: Journal of Biomolecular NMR
Ved Prakash Tiwari, Subhendu Pandit, Pramodh Vallurupalli
Protein molecules sample different conformations in solution and characterizing these conformations is crucial to understanding protein function. 15 N CEST experiments are now routinely used to study slow conformational exchange of protein molecules between a 'visible' major state and 'invisible' minor states. These experiments have also been adapted to measure the solvent exchange rates of amide protons by exploiting the one bond deuterium isotope effect on the amide 15 N chemical shifts. However at moderately high temperatures (~ 50 °C) that are sometimes required to populate protein minor conformers to levels (~ 1%) that can be detected by CEST experiments solvent H/D exchange can lead to 'dips' in low B1 15 N CEST profiles that can be wrongly assigned to the conformational exchange process being characterized...
January 19, 2019: Journal of Biomolecular NMR
Stephan B Azatian, Navneet Kaur, Michael P Latham
We describe a general and simple modification to the standard M9 minimal medium recipe that leads to an approximate twofold increase in the yield of heterologously expressed proteins in Escherichia coli BL21(DE3) bacteria. We monitored the growth of bacteria transformed with plasmids for three different test proteins in five minimal media with different concentrations of buffering salts and/or initial media pH. After purification of the over-expressed proteins, we found a clear correlation between the protein yield and change in media pH over time, where the minimal media that were the most buffered and therefore most resistant to change in pH produced the most protein...
January 7, 2019: Journal of Biomolecular NMR
Daniel Lane, Thomas E Skinner, Naum I Gershenzon, Wolfgang Bermel, Ronald Soong, Rudraksha Dutta Majumdar, Yalda Liaghati Mobarhan, Sebastian Schmidt, Hermann Heumann, Martine Monette, Myrna J Simpson, André J Simpson
In vivo Nuclear Magnetic Resonance (NMR) spectroscopy has great potential to interpret the biochemical response of organisms to their environment, thus making it an essential tool in understanding toxic mechanisms. However, magnetic susceptibility distortions lead to 1D NMR spectra of living organisms with lines that are too broad to identify and quantify metabolites, necessitating the use of 2D 1 H-13 C Heteronuclear Single Quantum Coherence (HSQC) as a primary tool. While quantitative 2D HSQC is well established, to our knowledge it has yet to be applied in vivo...
January 2, 2019: Journal of Biomolecular NMR
Eldon L Ulrich, Kumaran Baskaran, Hesam Dashti, Yannis E Ioannidis, Miron Livny, Pedro R Romero, Dimitri Maziuk, Jonathan R Wedell, Hongyang Yao, Hamid R Eghbalnia, Jeffrey C Hoch, John L Markley
The growth of the biological nuclear magnetic resonance (NMR) field and the development of new experimental technology have mandated the revision and enlargement of the NMR-STAR ontology used to represent experiments, spectral and derived data, and supporting metadata. We present here a brief description of the NMR-STAR ontology and software tools for manipulating NMR-STAR data files, editing the files, extracting selected data, and creating data visualizations. Detailed information on these is accessible from the links provided...
December 22, 2018: Journal of Biomolecular NMR
Thomas Wiegand, Andreas Hunkeler, Alexander Däpp, Joeri Verasdonck, Riccardo Cadalbert, Luc Bousset, Ronald Melki, Anja Böckmann, Beat H Meier
Magic-angle spinning (MAS) is mandatory in solid-state NMR experiments to achieve resolved spectra. In rare cases, instabilities in the rotation or damage of either the rotor or the rotor cap can lead to a so called "rotor crash" involving a disintegration of the sample container and possibly the release of an aerosol or of dust. We present a modified design of a 3.2 mm probe with a confining chamber which in case of a rotor crash prevents the release of aerosols and possibly hazardous materials...
December 10, 2018: Journal of Biomolecular NMR
Carolina Lixa, Amanda Mujo, Mariana T Q de Magalhães, Fabio C L Almeida, Luis Mauricio T R Lima, Anderson S Pinheiro
Human antigen R (HuR) functions as a major post-transcriptional regulator of gene expression through its RNA-binding activity. HuR is composed by three RNA recognition motifs, namely RRM1, RRM2, and RRM3. The two N-terminal RRM domains are disposed in tandem and contribute mostly to HuR interaction with adenine and uracil-rich elements (ARE) in mRNA. Here, we used a combination of NMR and electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) to characterize the structure, dynamics, RNA recognition, and dimerization of HuR RRM1...
December 8, 2018: Journal of Biomolecular NMR
Luke W Arbogast, Frank Delaglio, Joel R Tolman, John P Marino
While the use of 1 H-13 C methyl correlated NMR spectroscopy at natural isotopic abundance has been demonstrated as feasible on protein therapeutics as large as monoclonal antibodies, spectral interference from aliphatic excipients remains a significant obstacle to its widespread application. These signals can cause large baseline artifacts, obscure protein resonances, and cause dynamic range suppression of weak peaks in non-uniform sampling applications, thus hampering both traditional peak-based spectral analyses as well as emerging chemometric methods of analysis...
November 27, 2018: Journal of Biomolecular NMR
Nina Eleni Christou, Bernhard Brutscher
Aromatic amino-acid side chains are essential components for the structure and function of proteins. We present herein a set of NMR experiments for time-efficient resonance assignment of histidine and tyrosine side chains in uniformly 13 C/15 N-labeled proteins. The use of band-selective 13 C pulses allows to deal with linear chains of coupled spins, thus avoiding signal loss that occurs in branched spin systems during coherence transfer. Furthermore, our pulse schemes make use of longitudinal 1 H relaxation enhancement, Ernst-angle excitation, and simultaneous detection of 1 H and 13 C steady-state polarization to achieve significant signal enhancements...
November 21, 2018: Journal of Biomolecular NMR
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