Videos
NMR approaches for intrinsically disordered proteins
During the 91st session of the Global NMR Discussion Meetings held on November 5th, 2024, via Zoom, Prof. Julie Forman-Kay from the University of Toronto & SickKids Research Institute, Canada, gave a talk on the topic "NMR approaches for intrinsically disordered proteins". The recording serves as a tutorial.
Abstract: NMR is a powerful tool for obtaining site-specific information about dynamic systems, including intrinsically disordered proteins and protein regions (IDPs/IDRs) which do not adopt unique, stable folded structures. While computational approaches are increasingly powerful for stable proteins and protein domains, there is a huge need for experimental information about IDPs, IDRs and the highly dynamic complexes that they often make with other disordered proteins, folded domains and other biomolecules. The lecture will highlight examples of NMR studies of IDPs and their dynamic complexes, including condensed state models of those found in biomolecular condensates.
Find out more about Prof. Julie Forman-Kay's research: https://biochemistry.utoronto.ca/person/julie-d-forman-kay/
Advances in the Computation of NMR Interactions in Materials
During the 81st session of the Global NMR Discussion Meetings held on February 27th, 2024 via Zoom, Dr. Sean T. Holmes from the Florida State University, United States, gave a talk on the topic "Advances in the computation of NMR interactions in materials". The recording serves as a tutorial.
Abstract: This lecture will discuss recent advances in the computation of NMR interactions in materials using density functional theory methods. These include methods for accounting for intermolecular interactions, the role of relativistic effects (especially for heavy atoms), and the choice of density functional approximation. Applications to elements from across the Periodic Table will be presented.
Explorations in NMR Relaxation
During the 72nd session of the Global NMR Discussion Meetings held on October 10th, 2023 via Zoom, Prof. Alexej Jerschow gave a talk on the topic "Explorations in NMR Relaxation by Experiments and MD/Ab Initio Computation". The recording serves as a tutorial.
Prof. Alexej Jerschow is a Professor of Chemistry at New York University, USA.
Website: https://wp.nyu.edu/jerschow/
Google scholar: https://scholar.google.com/citations?...
X (previously Twitter): https://twitter.com/ajerschow
NMR Crystallography: Integrative Foundations and Applications
During the 64th session of the Global NMR Discussion Meetings held on March 21st, 2023 via Zoom, Prof. Leonard Mueller gave a talk on the topic "NMR Crystallography: Integrative Foundations and Applications to Materials Chemistry and Structural Biology". The recording serves as a tutorial.
Abstract: NMR crystallography – the integrated application of solid-state NMR, X-ray diffraction, and first-principles computational chemistry – is rapidly developing as an atomic-resolution probe of structure and function across the molecular sciences. Here, I will discuss critical aspects in the integration of these three techniques, including the need for a priori determination of linear rescaling parameters and rigorous methods of statistical analysis. I will present two recent examples from my group's work that highlight these factors. The first is to photomechanical materials, connecting the molecular-level structural rearrangement to the experimentally-observed macroscopic response. The second is to integrative structural biology, revealing chemically-detailed structure and dynamics in the enzyme active site of tryptophan synthase, and how this has changed our understanding of its mechanism and inhibition.
Prof. Leonard Mueller is a Professor of Chemistry at the University of California Riverside, USA.
Website: https://sites.google.com/ucr.edu/muel...
Google scholar: https://scholar.google.com/citations?...
Using Deep Learning to Transform and Analyse NMR Data
During the 55th session of the Global NMR Discussion Meetings held on November 1st, 2022 via Zoom, Prof. Flemming Hansen from University College London, gave a talk on the topic "Using Deep Learning to Transform and Analyse NMR Data". The recording serves as a tutorial.
It will be shown how deep neural networks (DNNs) can be trained for reconstruction of sparsely sampled NMR spectra and for virtual homonuclear decoupling. Another area covered in the talk will be autonomous analysis of chemical exchange saturation transfer (CEST) data, where the trained DNN accurately predicts both the chemical shifts and the uncertainties associated with these.
Speaker's biography:
1997-2003: BSc+MSc, Chemistry + Physics, University of Copenhagen
2003-2005: PhD in Biophysical Chemistry (Prof. Jens Led) , University of Copenhagen
2005-2010: Postdoctoral fellow (Prof Lewis E. Kay), University of Toronto
2010-present: PI, University College London. Full Professor since 2017.
Follow Prof. Hansen's work here:
Twitter: https://twitter.com/dflemminghansen?l...
Google scholar: https://scholar.google.com/citations?...
Website: https://www.ucl.ac.uk/hansen-lab/flem...
From genome to NMR spectrum
During the 41st session of the Global NMR Discussion Meetings on Zoom held on 25th January 2022, Prof. Rachel W. Martin, University of California, Irvine, USA, gave a talk on the topic "From genome to NMR spectrum".
The slides in the talk can be downloaded here: https://drive.google.com/file/d/1OPde...
Abstract: As structural biologists, we spend much of our time preparing samples for biomolecular NMR and collecting and analyzing the data. These experimental efforts are very time- and resource-intensive, suggesting that we should pay closer attention to systematically choosing targets for investigation. The advent of inexpensive nucleic acid sequencing technology has led to the rapid proliferation of genome and transcriptome data. Thus, tens of thousands of unique and potentially valuable enzymes have been “discovered” in principle, but in reality are languishing uncharacterized in databases. Furthermore, in many enzyme discovery studies, researchers choose proteins for investigation based on factors such as expression level in the host organism, which may not reflect suitability for the desired chemical application. In this talk, I will discuss our recent efforts toward developing a workflow for efficient target selection using bioinformatics and in silico methodology. Finally, I will present molecular modeling and experimental results, including NMR spectra, for Droserasin 1, a novel antimicrobial peptide we discovered from the genome of the carnivorous plant Drosera capensis.
Prof. Martin's Biography:
2002: PhD, Yale University, USA (with Prof. Kurt W. Zilm)
2002-2005: Postdoc, University of California, Berkeley (with Prof. Alex Pines)
2005-present: Professor, Department of Chemistry and Biochemistry, University of California, Irvine
Follow Prof. Rachel W. Martin and her work on social media:
Twitter: @rachelwmartin
Website: https://probemonkey.com/
Free online resources (sequence level):
• GenBank (repository of annotated DNA sequences): https://www.ncbi.nlm.nih.gov/genbank/
• BLAST (find similar nucleic acid/protein sequences to a given sequence): https://blast.ncbi.nlm.nih.gov/Blast.cgi
• Expasy translate tool (translate nucleic acid to protein): https://web.expasy.org/translate/
• Clustal Omega (align multiple sequences, can use nucleic acid or protein): https://www.ebi.ac.uk/Tools/msa/clust...
• UniProt (find what has been published for your protein): https://www.uniprot.org/
• SignalP (predict signal sequences / targeting sequences) https://services.healthtech.dtu.dk/se...
• Scampi (predict whether your protein is a membrane protein, if yes, predict topology): https://scampi.cbr.su.se/pred/help/ Free online resources (structure level):
• Rosetta, iTasser, AlphaFold (predict protein structures from amino acid sequence) https://www.rosettacommons.org/software https://zhanggroup.org/I-TASSER/ https://alphafold.ebi.ac.uk/ https://colab.research.google.com/git...
• Modeller (Make homology models if you have the structure of a similar protein) https://salilab.org/modeller/
• Protein Data Bank (find solved structures of biological macromolecules) https://www.rcsb.org/ (North America) https://www.ebi.ac.uk/pdbe/node/1 (Europe)
What goes on inside the nucleus?
During the 39th session of the Global NMR Discussion Meetings held on November 23rd, 2021 via Zoom, Prof. Ilya Kuprov gave a talk on "What goes on inside the nucleus: origins of nuclear magnetogyric ratio and quadrupole moment". The recording serves as a tutorial.
Prof. Kuprov is a world renowned magnetic resonance spectroscopy and imaging specialist with a particular focus on large-scale computer simulation of magnetic processes in chemical and biological systems; this includes quantum optimal control and machine learning methods.
2005: DPhil, Chemistry, University of Oxford (with Prof. Peter Hore)
2005-2010: Fellow by Examination, Magdalen College, Oxford
2007-2009: Lecturer in Chemistry, University of Durham
2009-2011: EPSRC Early Career Fellow, University of Oxford
2011-present: Associate Professor of Chemical Physics at the University of Southampton
2018-present: Associate Editor, Science Advances.
Website: https://spindynamics.org
Google Scholar: https://scholar.google.com/citations?...
Practicalities of SPINACH - a tutorial lecture
In Session 33 of the Global NMR Discussion Meetings, Prof. Ilya Kuprov gave a second talk on performing nuclear magnetic resonance (NMR) simulations using the SPINACH program, with an emphasis on practical aspects.
Watch Part 1 here: https://youtu.be/3fnRgGCKnLU
Download related resources from Prof. Kuprov: https://www.dropbox.com/sh/55kn4enfve...
Website and SPINACH download: https://spindynamics.org
Google Scholar: https://scholar.google.com/citations?...
Prof. Kuprov is a world renowned magnetic resonance spectroscopy and imaging specialist with a particular focus on large-scale computer simulation of magnetic processes in chemical and biological systems; this includes quantum optimal control and machine learning methods.
Bio:
2005: DPhil, Chemistry, University of Oxford (with Prof. Peter Hore)
2005-2010: Fellow by Examination, Magdalen College, Oxford 2
007-2009: Lecturer in Chemistry, University of Durham
2009-2011: EPSRC Early Career Fellow, University of Oxford
2011-present: Associate Professor of Chemical Physics at the University of Southampton
2018-present: Associate Editor, Science Advances.
Large-scale liquid state NMR and MRI Simulations
In Session 32 of the Global NMR Discussion Meetings, Prof. Ilya Kuprov gave a talk on "Large-scale liquid state NMR and MRI Simulations" and the inner workings of the magnetic resonance simulation software SPINACH.
Prof. Kuprov is a world renowned magnetic resonance spectroscopy and imaging specialist with a particular focus on large-scale computer simulation of magnetic processes in chemical and biological systems; this includes quantum optimal control and machine learning methods.
Website and SPINACH download: https://spindynamics.org
Google Scholar: https://scholar.google.com/citations?...
Bio:
2005: DPhil, Chemistry, University of Oxford (with Prof. Peter Hore)
2005-2010: Fellow by Examination, Magdalen College, Oxford
2007-2009: Lecturer in Chemistry, University of Durham
2009-2011: EPSRC Early Career Fellow, University of Oxford
2011-present: Associate Professor of Chemical Physics at the University of Southampton
2018-present: Associate Editor, Science Advances.
Two-dimensional lineshape analysis of biomolecular interactions
In session 30 held on 22nd June 2021, Dr. Chris Waudby gave a talk on Two-dimensional lineshape analysis of biomolecular interactions, via Zoom. The video was recorded live during the presentation and serves as an educative lecture. For more information on TITAN 2D NMR lineshape analysis, see https://www.nmr-titan.com.
Bio: Dr. Chris Waudby
2000-2004: BA MSci, Natural Sciences (Chemistry), University of Cambridge, UK
2004-2009: PhD, Chemistry, Prof. Chris Dobson, University of Cambridge, UK
2010-present: Postdoc, Prof. John Christodoulou, University College London, UK
Follow Dr. Waubdy: Google scholar: https://scholar.google.com/citations?...
Website: https://www.ucl.ac.uk/biosciences/dep...
Twitter: https://twitter.com/chris_waudby
Abstract: NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes in 2D spectra. We will review the basic principles of chemical exchange in one-dimensional NMR, and then discuss a range of surprising and useful effects that can arise when these principles are applied to multi-dimensional experiments. We will touch on the optimal design of titration experiments and selection of pulse programs, and give a tutorial on data analysis using the TITAN software package.
References:
https://www.nature.com/articles/srep2...
Optimal control and its application in solid-state NMR
In session 26 held on 27th April 2021, Dr. Jan Blahut gave a talk on "Optimal control and its application in solid-state Nuclear Magnetic Resonance (NMR) spectroscopy", via Zoom. The video was recorded live during the presentation and serves as an educative lecture.
Optimal-NMR webpage: https://optimal-nmr.net
Bio:
Dr. Jan Blahut
2008-2013 M.S. in Organic Chemistry, Charles University in Prague
2013-2018 Ph.D. in Inorganic Chemistry, group of prof. P. Hermann, Charles University in Prague
2018-2020 Postdoctoral position in the group of prof. G. Pintacuda, High-filed NMR centre Lyon
2020-present: Postdoctoral position in the group of Dr. Zdenek Tosner, Charles University in Prague
Publons profile: https://publons.com/researcher/216308...
Abstract: Optimal control has its origins in economy and engineering as a mathematical tool to maximize profit or minimize disposed energy. Magnetic resonance is well suited for optimal-control application to design new pulse sequences with improved properties. We will focus on application in solid-state NMR, where the combination of sample spinning, powder averaging, dense network of involved interactions and RF field inhomogeneity render analytical approaches based on Average Hamiltonian Theory unfeasible. Despite the complexity of the problem, the practical application of optimal control based techniques is straightforward. It this tutorial we will also demonstrate how they can be implemented to your work-flow in a simple copy-paste manner, replacing traditional recoupling techniques.
Programming Basics and How to Write NMR Simulation Software
The 13th session of the Global NMR Discussion Meeting was held on 21st August 2020 via Zoom. Dr. Frédéric Perras gave a talk on some programming basics and writing NMR simulation software with static and magic angle spinning (MAS) chemical shift anisotropy (CSA) lineshapes as examples. The video was recorded live during the presentation and serves as an educative lecture.
The programs described in the video can be found and run online:
https://repl.it/@fperras/staticCSA
https://repl.it/@fperras/MASCSA
Dr. Frédéric Perras is an Associate Scientist at Ames Laboratory, Iowa, U.S.A.
Follow Dr. Perras on Twitter: @Fred_A_Perras
Website: https://www.ameslab.gov/directory/fre...
Google Scholar: https://scholar.google.ca/citations?u...
Numerical Simulations in Solid-State NMR (SIMPSON)
The 12th session of the Global NMR Discussion Meeting was held on 7th August 2020 via Zoom. Prof. Thomas Vosegaard gave a talk on Numerical Simulations in Solid-State NMR Spectroscopy with a particular emphasis on SIMPSON. The video was recorded live during the presentation and serves as an educative lecture.
Prof. Thomas Vosegaard is a Professor of Chemistry at the Aarhus University in Denmark.
Follow Prof. Thomas Vosegaard on Twitter: @TVosegaard
Website: https://pure.au.dk/portal/en/persons/...
Google scholar: https://scholar.google.co.uk/citation...
Useful links: SIMPSON website: https://inano.au.dk/about/research-ce...
Chapter with examples of SIMPSON: https://www.sciencedirect.com/science...
Online examples from the chapter: https://easynmr.pastis.dk/arns/
Link: https://youtu.be/47p-LRDhVuE
Line Shape Analysis and Tensor Interplay
The 9th session of the Global NMR Discussion Meeting was held on 3rd July 2020 via Zoom. Prof. David Bryce gave a talk on the following topic: Solid-State Nuclear Magnetic Resonance (SSNMR) Spectra Line Shape Analysis and Tensor Interplay. The video was recorded live during the presentation and serves as an educative lecture. Prof. David Bryce is the University of Ottawa Research Chair in Nuclear Magnetic Resonance and the Chair of the Department of Chemistry and Biomolecular Sciences. He is also the Editor-in-Chief of the journal Solid State Nuclear Magnetic Resonance.
Follow Prof. David Bryce on Twitter: @BryceNation
Website: https://mysite.science.uottawa.ca/dbr...
Google Scholar: https://scholar.google.ca/citations?u...