Biological NMR
Understanding antimicrobial activity in live cells
Ángela Serrano Sánchez – @Angelasrno99
We have optimised a new, simple methodology to assess membrane permeability of drugs making use of the paramagnetic relaxation enhancement (PRE) effect in lipid vesicles that is applicable to any type of cell membrane. Using this assay, we have been able to find important differences in the permeability of new families of antimicrobial compounds, providing unique information for the further development of this family of compounds. In addition, we have now expanded this assay to live cells making use of a NMR-coupled bioreactor. Using this set up, we are to monitor both the drug permeation into live cells, as well as changes in the bacterial metabolism as a result of the antimicrobial agent added.
Structural characterization by NMR spectroscopy of a DnaX mini-intein derived from Spirulina platensis
Soumendu Boral – @BoralSoumendu
Inteins perform protein splicing reaction. We solved solution NMR structure (PDB code: 7CFV) of a 136-residue DnaX mini-intein. The NMR structural ensemble has backbone and heavy atom RMSD of 0.27 and 0.52 Å, respectively. NMR-based HX and 15N-relaxation experiments showed the presence of a very stable core and conserved motions.
Triggered functional dynamics of AsLOV2 by time-resolved electron paramagnetic resonance at high magnetic fields
Brad D. Price – @braddprice
An in-depth functional understanding of proteins requires a technique for tracking their movement in real time. We present high-field, (tr)EPR ‘filming’ of room-temperature protein motion as progress toward real-time distance tracking in lifelike environments.
NMRTools.jl: a simple, open source interface for NMR data in Julia
Chris Waudby – @chris_waudby
Julia is a modern language optimised for scientific computation. To facilitate the use of Julia by the NMR community, here we introduce NMRTools.jl, an open source package providing an interface to import and visualise NMR data. Interested users are welcomed to contribute to the development of this ongoing project.
A New solid-state NMR Homonuclear Correlation Method and its Application for Detecting Nucleotides and Their Hydrogen Bonds in Intact Viral RNA
Orr Simon Lusky – @ItIsLusk
We present a new solid state NMR method we developed for studying biological macromolecules called ‘Pulse induced resonance with angular dependent total enhancement’ (PIRATE). We demonstrate a new resonance condition, and the application on finding hydrogen bond patterns in intact viral RNA harvested directly from the MS2 bacteriophage.
Structural properties of the SARS-CoV-2 Envelope viroporin
Joao Medeiros Silva – @JMSism
The Envelope Protein of SARS-CoV-2 forms a viroporin that induces inflammation and acute respiratory symptoms associated with COVID-19. Using ssNMR, we describe the structure and gating mechanisms governing this viroporin. 19F-NMR experiments revealed an aromatic network regulating the channel, which adopts an open-configuration at acidic pH and presence of calcium.
Dynamics and interactions in the 410 kDa RNA exosome
Jobst Liebau – @Jobst_Liebau
Solution-state NMR of large protein complexes is difficult yet of huge interest. We demonstrate how it can be done on an asymmetric 410 kDa decamer, using methyl- and 19F-labeling. We validate structures and measure dynamics and transient RNA substrate interactions, thus expanding solution-state NMR into the realm of cryo-EM structures.
Uncovering global dynamics and an allosteric response in a synthetase cyclization domain
Kenneth Marincin – @KennyMarincin
Nonribosomal peptide synthetase (NRPS) cyclization (Cy) domains are central to the biosynthesis of many medicinal and virulent compounds. Using solution NMR and mutagenesis, we showed that global dynamics convey an allosteric response to a partner domain which may be key to communication and substrate recognition in Cy domains.
Structural Analysis of Human Prion Protein using NMR Methodologies Under Cell Mimicking Conditions
Manoj Madheswaran – @Mano_Sampath
Using Nuclear Magnetic Resonance (NMR) spectroscopy to investigate conformational equilibria of human prion protein in cell mimicking conditions, using ficoll, an inert crowding agent. Using CD and NMR methodologies, we carried out an atom by atom analysis of human prion thermal unfolding in the presence of ficoll.
DNP-enhanced solid-state NMR spectroscopy of chromatin polymers
Nesreen Elathram – @NesreenElathram
Chromatin is a complex biological polymer that packages DNA and regulates access to the genetic information in eukaryotic cells. Chromatin structural biology is hampered by the size, the heterogeneity and the presence of both dynamic and rigid components in the polymer. Here, we use DNP to enhance the ssNMR sensitivity of chromatin and investigate the effect of cryogenic temperatures on chromatin structure and spectral resolution.
Does Duplex Impact Quadruplex: Characterization using NMR and MD Simulations
Rajesh Kumar Reddy Sannapureddi – @RR_Sannapureddi
So far G-quadruplexes (G4) were studied individually, structural characteristics of G4s in presence of duplex is not well characterized. G4’s with duplex on 5'/3' are designed to mimic genome. Here, we present atomistic characterization G4 and impact of 5’/3’ duplex and linker length using NMR and molecular dynamic (MD) simulations.
Vitamin status assessments by NMR
Sofia Mariasina – @SMariasina
We try to assess vitamin status by 1H NMR using blood and urine samples of healthy volunteers who takes vitamins D, C, B1, B6, B9, or B12 as a supplementation to their diet. Some biomarkers of a person's vitamin status were found, which can be used for personalized vitamin therapy.
The RNA-binding preferences of the SARS-CoV-2 Nucleocapsid NTD
Sophie Marianne Korn – @Sophie__Korn
How the SARS-CoV-2 nucleocapsid protein (N) recognizes specific RNA motifs remains unanswered. We use NMR to analyze the interactions of N’s N-terminal RNA-binding domain with RNA elements in the viral genomic RNA. The domain uses defined sensory residues to read intrinsic signatures of preferred RNA elements from available motifs.
NMR-based metabolomic profiling of the differential concentration of phytomedicinal compounds in pericarp, skin and seeds of Momordica charantia (bitter melon)
Sumit Mishra – @sumitamu
Momordica charantia is a medicinal plant which is widely used to treat several diseases. We have identified the phytosterols in the pericarp, skin and seeds parts of M. charantia fruit via NMR spectroscopy. Multivariate statistical analysis showed a clustering of the metabolic profiles of seeds and pericarp, and their clear separation from the metabolic profile of the skin.
Mapping Molecular interactions of G quadruplex structure
Deepraj Negi – @ThevoiceDeepraj
G-quadruplexes (G4s) are known to be present in critical regions of the genome and their presence thus implicates them in several crucial biological processes. G4 is modulated by multiple factors, importantly by the primary nucleotides and the nature and concentration of the cation present. By altering the ions, loop length, and changing guanosine to inosine, the goal of this project is to determine the molecular interactions of the G-quad.
Conformational equilibria of the Mg2+-channel CorA
Tobias Schubeis – @TSchubeis
The CorA channel is the major Mg2+-influx pathway in prokaryotes. The mechanistic details of the channel gating and the transport of the metal ions are still not entirely understood. Here we investigate the dynamics of CorA in DMPC lipid bilayers with 1H-detected solid-state NMR at 100 kHz MAS.
Graphite based composites for Photocatalytic Water Splitting
Mummidivarapu Varkrishna – @VarkrishnaM
The concept of photocatalytic water splitting is revolutionary however the applications aren't so feasible to scale up. This research area has largely been dominated by the inorganic materials.However, organic ones are included every now and then. But the extent is less. The exploration and preparation of composites more based on the organic substances whereas the inorganic ones can be always supporting is a huge ocean of possibilities. And NMR is quite a powerful technique to explore it!
Protein Methyl-Side Chain Dynamics via Nanoparticle-Assisted NMR Spin Relaxation
Xinyao Xiang – @xxiang2022
The nanoparticle-assisted NMR spin relaxation (NASR) method measures the enhancement in transverse spin relaxation in the presence of slowly tumbling nanoparticles. It uncovers protein internal motions on the previously unobservable nanosecond to microsecond regime. We recently extended our NASR method to methyl-side chains using 2H or 13C spin relaxation.