UP CIISB Kick-Off Meeting, Monday, December 2, 2019
UP CIISB Kick-Off Meeting will gather the CIISB Core Facility Heads, Executive Committee members, and administration staff of CEITEC and BIOCEV to discuss the starting OP VVV investment project UP CIISB.
Petr Sedmera Prize 2020 - Call for Nominations Announced
The Petr Sedmera Prize is awarded for best published work in the field of nuclear magnetic resonance and is dedicated to the memory of a leading expert who has been instrumental in the development of NMR in Czechoslovakia and the Czech Republic.
What’s ahead of us - A growing number of research agencies is assigning money randomly
Using lottery as a fairer and more open system in awarding grants? Read an interesting Nature’s article about a new trend.
Update of roadmap of Large Research Infrastructures of the Czech Republic
A new update of Roadmap of Large Research Infrastructures of the Czech Republic is now available.
Save the date - NMR Valtice
35th Central European NMR Meeting will take place in Valtice in April 19-22 2020.
ARIA Workshop and User Group meeting
Instruct-ERIC is hosting an ARIA workshop and User Group meeting on 25th February in Amsterdam.
CIISB UP project approved for financing during 2020-2022
The project CIISB UP submitted to the OP VVV Call 02-18-046 Research Infrastructures II has been positively evaluated and will receive funding to reinvest into the existing equipment and to purchase new instrumentation in the amount 22 mil. EUR.
Magnetic Resonance - An Interactive Open Access Publication of the Groupement AMPERE
The AMPERE Society has decided to launch a new publication called “Magnetic Resonance, An Interactive Open Access Publication of the Groupement AMPERE” for articles on Nuclear and Electron Magnetic Resonance and Imaging.
Reader's Corner Archive
Principles for Integrative Structural Biology Studies
Guru of integrative structural biology computation Andrej Sali and Michale P. Rout summarize in the recent Cell Primer Principles for Integrative Structural Biology Studies.
PEGylated surfaces for the study of DNA–protein interactions by atomic force microscopy
DNA–protein interactions are vital to cellular function, with key roles in the regulation of gene expression and genome maintenance. Atomic force microscopy (AFM) offers the ability to visualize DNA–protein interactions at nanometer resolution in near-physiological buffers, but it requires that the DNA be adhered to the surface of a solid substrate. This presents a problem when working in biologically relevant protein concentrations, where proteins may be present in large excess in solution; much of the biophysically relevant information can therefore be occluded by non-specific protein binding to the underlying substrate. Here we explore the use of PLLx-b-PEGy block copolymers to achieve selective adsorption of DNA on a mica surface for AFM studies. Through varying both the number of lysine and ethylene glycol residues in the block copolymers, Bart Hoogenboom, Alice Pyne et al. show selective adsorption of DNA on mica that is functionalized with a PLL10-b-PEG113/PLL1000–2000 mixture as viewed by AFM imaging in a solution containing high concentrations of streptavidin. They demonstrate – through the use of biotinylated DNA and streptavidin – that this selective adsorption extends to DNA–protein complexes and that DNA-bound streptavidin can be unambiguously distinguished in spite of an excess of unbound streptavidin in solution. Finally, they apply this to the nuclear enzyme PARP1, resolving the binding of individual PARP1 molecules to DNA by in-liquid AFM.
More than Proton Detection—New Avenues for NMR Spectroscopy of RNA
This minireview written by Harald Schwalbe, Boris Fürtig and coworkers reports on the development of NMR methods that utilize detection on low-g nuclei (heteronuclei like 13C or 15N with lower gyromagnetic ratio than 1H) to obtain unique structural and dynamic information for large RNA molecules in solution. Experiments involve through-bond correlations of nucleobases and the phosphodiester backbone of RNA for chemical shift assignment and make information on hydrogen bonding uniquely accessible. Previously unobservable NMR resonances of amino groups in RNA nucleobases are now detected in experiments involving conformational exchange-resistant double-quantum 1H coherences, detected by 13C NMR spectroscopy. Furthermore, 13C and 15N chemical shifts provide valuable information on conformations. All the covered aspects point to the advantages of low-g nuclei detection experiments in RNA.
Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging
Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein’s location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, Florian Schur reviews current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA.
Chemical cross-linking with mass spectrometry: a tool for systems structural biology
Biological processes supporting life are orchestrated by a highly dynamic array of protein structures and interactions comprising the interactome. Defining the interactome, visualizing how structures and interactions change and function to support life is essential to improved understanding of fundamental molecular processes, but represents a challenge unmet by any single analytical technique. Chemical cross-linking with mass spectrometry provides identification of proximal amino acid residues within proteins and protein complexes, yielding low resolution structural information. This approach has predominantly been employed to provide structural insight on isolated protein complexes, and has been particularly useful for molecules that are recalcitrant to conventional structural biology studies. In this review, Juan D. Chavez and James E. Bruce discuss recent developments in cross-linking and mass spectrometry technologies that are providing large-scale or systems-level interactome data with successful applications to isolated organelles, cell lysates, virus particles, intact bacterial and mammalian cultured cells and tissue samples.
In‐Cell EPR: Progress towards Structural Studies Inside Cells
Exploring the structure and dynamics of biomolecules in the context of their intracellular environment has become the ultimate challenge for structural biology. As the cellular environment is barely reproducible in vitro, investigation of biomolecules directly inside cells has attracted a growing interest. Among magnetic resonance approaches, site‐directed spin labeling (SDSL) coupled to electron paramagnetic resonance (EPR) spectroscopy provides competitive and advantageous features to capture protein structure and dynamics inside cells. To date, several in‐cell EPR approaches have been successfully applied to both bacterial and eukaryotic cells. In this minireview, the major advances of in‐cell EPR spectroscopy are summarized, as well as the challenges this approach still poses.
A standardized citation metrics author database annotated for scientific field
Citation metrics are widely used and misused. John P. A. Ioannidis et. al. created a publicly available data-base of 100,000 top scientists that provides standardized information on citations, h-index, co-authorship-adjusted hm-index, citations to papers in different authorship positions, and a composite indicator. Separate data are shown for career-long and single-year impact. Metrics with and without self-citations and ratio of citations to citing papers are given. Scientists are classified into 22 scientific fields and 176 subfields. Field- and subfield-specific percentiles are also provided for all scientists who have published at least five papers. Career-long data are updated to end of 2017 and to end of 2018 for comparison.
How structure informs and transforms chemogenetics
Chemogenetic technologies such as Designer Receptors Exclusively Activated by Designer Drugs (DREADDs) are widely used to remotely control neuronal and non-neuronal signaling. DREADDs exist for most of the canonical G protein-coupled receptor signaling pathways, and provide a synthetic biology platform useful for elucidating the role of neuronal signaling for brain function. Here, Bryan L. Roth presents a focused review that shows how recent insights obtained from GPCR structural studies inform our understanding of these chemogenetic tools from a structural perspective.