Videos
Integrative Structural Biology: Challenges and Opportunities for MR
During the 93rd session of the Global NMR Discussion Meetings held on December 3rd, 2024, via Zoom, Prof. Tatyana Polenova from the University of Delaware, USA, gave a talk on the topic "Integrative Structural Biology of Protein Assemblies: Challenges and Opportunities for Magnetic Resonance". The recording serves as a tutorial.
Abstract: I will present recent developments in MAS NMR techniques for atomic-resolution structural analysis of large biological assemblies. Drawing on studies of diverse systems from our lab, including the kinesin motor domain with polymerized microtubules, cofilin bound to filamentous actin, and HIV-1 protein assemblies interacting with small-molecule maturation inhibitors, I will illustrate how with MAS NMR, structural and dynamic details, as well as drug interactions were uncovered, that are inaccessible using other approaches. Additionally, I will discuss the benefits of combining MAS NMR with medium-resolution cryo-EM and MD simulations to enhance structural understanding, and address the current challenges and future directions for magnetic resonance in integrative structural biology.
Find out more about Prof. Tatyana Polenova's research: https://www.udel.edu/faculty-staff/experts/tatyana-polenova/
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/
High-Dimensional Spectroscopy to Tackle Complexity in Bio-NMR
During the 75th session of the Global NMR Discussion Meetings held on November 21st, 2023 via Zoom, Prof. Jan Stanek from the University of Warsaw in Poland, gave a talk on the topic "High-dimensional spectroscopy and other tools to tackle complexity in biological solid-state NMR". The recording serves as a tutorial.
Abstract:
Fast (sup. 60 kHz) magic-angle spinning provides high sensitivity and narrowed 1H linewidths. However, spectral analysis of large proteins are often severely hampered by peak overlap and/or ambiguity, depending on system size and sample quality. In this tutorial lecture, I will discuss several experimental techniques to address this, namely high-dimensional (4D, 5D) spectroscopy with non-uniform sampling, projection spectroscopy and time-shared acquisition. Additionally, I will explore selected tools for automation of resonance assignment and present early data on protein dynamics measurement as pseudo-4D series.
Website: http://nmr.cent3.uw.edu.pl/stanek
Dihedral Angle Measurements by Solid-State NMR
During the 70th session of the Global NMR Discussion Meetings held on August 29th, 2023 via Zoom, Prof. Patrick van der Wel gave a talk on the topic "Dihedral angle measurements by solid-state NMR". The recording serves as a tutorial.
Prof. Patrick van der Wel is an Associate Professor at the University of Groningen, Netherlands.
Abstract: Dihedral angle measurements represent an important complement to distance-based structural data in solid-state NMR studies of (bio)molecular structure. In this tutorial I will discuss the role of angular restraints in ssNMR structure analysis, historical and recent case studies, and the underlying principles of representative approaches.
Website: https://vanderwellab.org/
Google scholar: https://scholar.google.com/citations?...
Twitter: https://twitter.com/p_vanderwel
Measuring Dynamics Using Anisotropic Interactions in MAS-NMR
During the 68th session of the Global NMR Discussion Meetings held on May 30th, 2023 via Zoom, Dr. Kaustubh Mote gave a talk on the topic "Measuring dynamics using anisotropic interactions in MAS-NMR". The recording serves as a tutorial.
Abstract: Solid-state MAS NMR gives direct access to anisotropic interactions such as CSA, dipole-dipole and quadrupolar couplings. The precise measurement of these interactions, in addition to providing structural features, also gives access to dynamics via their partial averaging due to molecular motion. This tutorial will explore various techniques that are available to extract details of molecular motion via the measurement of these anisotropic interactions, with a particular focus on the measurement of dipole-dipole couplings.
Dr. Kaustubh Mote is a Reader at Tata Institute of Fundamental Research (TIFR) Hyderabad, India.
Website: https://www.tifrh.res.in/~kaustubh/
Google scholar: https://scholar.google.com/citations?...
Twitter: https://twitter.com/kaustubhmote_?lan...
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?...
EPR-NMR for Protein Modeling
During the 57th session of the Global NMR Discussion Meetings held on November 29th, 2022 via Zoom, Prof. Gunnar Jeschke from ETH Zurich, gave a talk on the topic "Integrating EPR distance distribution restraints with NMR data in protein models". The recording serves as a tutorial.
Abstract:
This zoominar will start with a short explanation of in silico spin labelling, which is useful for planning paramagnetic relaxation enhancement (PRE) NMR experiments as well as DEER EPR experiments for measuring distance distributions. I will continue with a primer on converting DEER data into distance distributions. The zoominar concludes with an example of using distance distributions in modelling a weakly structured low-complexity domain of an RNA-binding protein.
Speaker's biography:
1993-1996 PhD at ETH Zurich, Switzerland, with A. Schweiger
1998-2006 Group Leader, Max Planck Institute for Polymer Science in Mainz, Germany, with H. W. Spiess
2006-2008 Professor at the University of Konstanz, Germany
2008- Professor at ETH Zurich
Follow Prof. Jeschke's work here:
Website: https://epr.ethz.ch/
Emerging frontiers in solution NMR of large protein systems
During the 54th session of the Global NMR Discussion Meetings held on October 18th, 2022 via Zoom, Prof. Haribabu Arthanari from Harvard Medical School, gave a talk on the topic "Emerging frontiers to address large protein systems by solution NMR". The recording serves as a tutorial.
Speaker's biography:
1994-1996: MSc Chemistry - IIT Madras, India
1996-2003: PhD - Wesleyan University, USA
2003-2010: Research Associate - Harvard Medical School, USA
2010-2016: Lecturer - Harvard Medical School, USA
2016-present: Professor - Harvard Medical School, USA
Follow Prof. Arthanari's work here:
Google scholar: https://scholar.google.com/citations?...
Website: https://artlab.dana-farber.org/
1H Detection, MAS & High Fields for Membrane Proteins
During the 49th session of the Global NMR Discussion Meetings held on June 14, 2022 via Zoom, Dr. Loren Andreas from Max Planck Institute for Multidisciplinary Sciences gave a talk on the topic "Proton Detection, Magic-Angle Spinning and High Magnetic Fields for Membrane Protein Structural ". The recording serves as a tutorial.
Abstract:
I will present several topics, starting with the practical aspects of setting up proton-detection measurements with 1.3 mm and 0.7 mm rotors capable of 60 and greater than 100 kHz spinning. From there, I will highlight some of our recent results including detection of bound water, hydrogen bonding interaction, as well as new developments in pulse sequences aimed at global structure determination. I may also briefly mention some DNP results.
Speaker's Biography:
2016-Present: Professor, Group Leader, MPI Göttingen, Germany
2014-2016: Postdoc ENS, Lyon, France
2014: Ph.D. MIT, Boston, USA
Website: https://www.mpinat.mpg.de/andreas
Google scholar: https://scholar.google.com/citations?...
Structure and Dynamics of Viruses by MAS NMR
During the 48th session of the Global NMR Discussion Meetings held on May 17, 2022 via Zoom, Gal Porat-Dahlerbruch from the University of Delaware gave a talk on the topic "Structure and Dynamics of Viruses by MAS NMR". The recording serves as a tutorial.
Abstract:
Magic angle spinning (MAS) NMR has been widely used to characterize the structure and dynamics of viruses at all levels of organization. In this talk, I will cover the basics of MAS NMR spectroscopy with specific emphasis on experiments designed to study viruses, discuss the advantages and complementarity of MAS NMR with respect to other structural biology techniques, and present examples of unique insights gained into HIV-1, Influenza A, Hepatitis B, and other viruses.
Read their recent review here:
Gal Porat-Dahlerbruch, Amir Goldbourt, Tatyana Polenova (2021) Virus Structures and Dynamics by Magic-Angle-Spinning NMR. Annual Review in Virology. 8(1):219-237. DOI: 10.1146/annurev-virology-011921-064653.
Speaker's biography:
2015-2018: BS Chemistry, Tel Aviv University, Israel
2018-2019: Graduate Research Assistant, Tel Aviv University, Israel (Prof. Amir Goldbourt)
2019-Present: Ph.D. Candidate, University of Delaware, USA (Prof. Tatyana Polenova)
Twitter: @MagicAngleGal
Polenova laboratory website: https://sites.udel.edu/polenova-group/
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)
Time-resolved solid-state NMR: Overview, Application in Biophysics
During the 38th session of the Global NMR Discussion Meetings on Zoom, Dr. Blake Wilson, National Institute of Health (NIH) Bethesda, gave a tutorial on "Time-resolved solid-state nuclear magnetic resonance (NMR) spectroscopy: an overview, with applications to biophysical systems".
Bio of Dr. Blake Wilson:
2013: B.S. Physics, Massachusetts Institute of Technology (Prob. Bob Griffin)
2013 - 2019: PhD, University of California, Santa Barbara (Prof. Mark Sherwin and Prof. Songi Han)
2019 - Present: Postdoctoral fellow, NIH Bethesda (Dr. Rob Tycko)
Follow Dr. Wilson and his work:
Twitter: https://twitter.com/blkwiln
Google scholar: https://scholar.google.com/citations?...
Abstract: I will give an overview of time-resolved solid-state NMR techniques, and how they can be used to study structural conversion processes in biophysical systems. A variety of methods, including rapid pH jumps, rapid temperature jumps, and rapid mixing of different species, can be used to initiate biophysical processes, which can subsequently be probed with millisecond time resolution by sudden freezing followed by interrogation with solid-state NMR. I will discuss how dynamic nuclear polarization (DNP) has been shown to dramatically improve the sensitivity of time-resolved NMR techniques, with the aim of capturing structural information from sparsely populated intermediate states.
NMR Studies of DNA Structure and Dynamics
During the 35th session of the Global NMR Discussion Meetings on Zoom, Dr. Bharathwaj Sathyamoorthy, IISER Bhopal, India, gave a talk on the Nuclear Magnetic Resonance (NMR) studies of DNA structure and dynamics.
Abstract: Characterizing conformational preferences of biomolecules is essential to understand their function. NMR spectroscopy has been instrumental in unravelling the conformational polymorphism of DNA and sequence-specific signatures, both of which are critical for their function. This talk shall describe the journey over the past five decades towards our current understanding of DNA structure and dynamics obtained from solution-state NMR spectroscopy.
Dr. Sathyamoorthy's Biography:
2005: B.Sc. (Chemistry), University of Madras, India
2007: M.Sc. (Chemistry), Indian Institute of Technology Madras, India
2013: Ph.D. (Chemistry), State University of New York at Buffalo, USA (Prof. Thomas Szyperski)
2013-2015: Postdoctoral Research Fellow, University of Michigan/Duke University, USA (Prof. Hashim M. Al-Hashimi)
2016 – present: Assistant Professor, IISER Bhopal, India
Follow Dr. Sathyamoorthy and his work on social media:
Twitter: @bwajtweeting
Website: https://bionmr.wordpress.com
Google Scholar: https://scholar.google.com/citations?...
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...
Methyl Sidechain Probes for Solution NMR of Large Proteins
In session 25 held on 13th April 2021, Dr. Andrew McShan gave a talk on "Utility of Methyl Sidechain Probes for Solution Nuclear Magnetic Resonance (NMR) spectroscopy of large proteins", via Zoom. The video was recorded live during the presentation and serves as an educative lecture.
Follow Dr. McShan's work on Google scholar: https://scholar.google.com/citations?...
Biography: Andrew received a B.S. in Biochemistry and Ph.D. in Molecular, Cellular & Developmental Biology from the University of Kansas with Roberto De Guzman. During their Ph.D., they used methyl-based solution-state NMR to characterize the structure and function of bacterial type III secretion systems. In 2016, they moved to the University of California, Santa Cruz and joined the lab of Nik Sgourakis where methyl NMR was used to elucidate mechanistic aspects of large molecular machines of the adaptive immune system. Currently, Andrew is a postdoctoral fellow at the Children’s Hospital of Philadelphia where they continue to harness the power of methyl NMR to discern the structure and function of proteins complexes of the innate immune system.
Abstract: In recent years, the use of site-specific methyl probes has pushed the molecular weight limit of solution-state NMR to beyond 1 MDa. In this tutorial, we will discuss practical aspects of methyl NMR. The first section will summarize approaches for methyl resonance assignment, including recent advances in automated assignment using methyl-methyl nuclear Overhauser effect measurements. The second section will describe methyl-based NMR methods to uncover biomolecular structure, function and dynamics. Throughout the discussion, a range of large molecular machines where methyl probes have been exploited will be highlighted, including a handful of important immunological protein complexes.
Chemical biology tools for the NMR structural biologist
Session 23 held virtually via zoom on 2nd March 2021 featured Prof. Galia Debelouchina, Assistant Professor at University of California San Diego (UCSD), U.S.A. Prof. Debelouchina gave a talk on "Chemical biology tools for the Nuclear Magnetic Resonance (NMR) structural biologist ". The video was recorded live during the presentation and serves as an educative lecture.
Follow Prof. Debelouchina's work:
Website: http://debelouchinalab.ucsd.edu
Google scholar: https://scholar.google.com/citations?...
Twitter: @GaliaLab
Education 2011 Ph.D., Physical Chemistry, Massachusetts Institute of Technology 2005 B.A., Chemistry, Mathematics, Colby College Appointments 2017 - present Assistant Professor, UCSD 2012 - 2017 Postdoctoral Associate, Chemical Biology, Princeton University
Abstract: Many of the challenging biological problems that NMR spectroscopists study involve large and complex proteins that are also often post-translationally modified. In this tutorial, I will cover NMR friendly approaches to install post-translational modifications efficiently, to segmentally label proteins, and to install various spectroscopic probes in a selective manner. I will cover tools such as inteins and sortase, unnatural amino acid incorporation, native and expressed protein ligation, and bio-orthogonal chemical approaches for protein labeling. I will discuss the advantages and challenges of these tools and present applications from my own lab and the recent literature.
Nanoparticle-assisted NMR relaxation in protein dynamics & metabolomics
The 18th session of the Global NMR Discussion Meeting was held on 10th November 2020 via Zoom. Dr. Mouzhe Xie gave a talk on nanoparticle-assisted nuclear magnetic resonance (NMR) relaxation in protein dynamics and metabolomics. The video was recorded live during the presentation and serves as an educative lecture.
Bio: Mouzhe Xie studied chemical biology at Xiamen University (China) from 2009-2013. He received his Ph.D. degree from The Ohio State University (USA) in 2018, where he developed and applied solution NMR spectroscopy to study protein dynamics and metabolomics. He then spent 5 months at EPFL (Switzerland) as a visiting scientist. Currently, he is conducting postdoctoral research on nanoscale NMR and quantum sensing at the University of Chicago (USA).
Personal website: https://sites.google.com/view/xiemouzhe
Google scholar: https://scholar.google.com/citations?...
LinkedIn: https://www.linkedin.com/in/mouzhe-xi...
Abstract: In nanoparticle-assisted solution NMR, synthetic nanoparticles are added to NMR samples, which reduce the reorientational motion of molecules or protein regions in a selective or differential way. This leads to interesting spectral observations that contain critical information about the physicochemical properties, structures, dynamics, and functions of biomolecules. In this tutorial, I will introduce the basics of NMR relaxation theories, followed by some technical details including pulse selection and data processing. The discussion will be buttressed by recent studies on some important topics, such as supra-τc (slow) internal motions of globular proteins, cooperative binding of intrinsically disordered proteins to inorganic surfaces, and accurate metabolite identification in the context of NMR-based metabolomics."
Protein Structure Determination Using Paramagnetic NMR
The 17th session of the Global NMR Discussion Meeting was held on 27th October 2020 via Zoom. Dr. Alireza Bahramzadeh gave a talk on the use of paramagnetic nuclear magnetic resonance (NMR) spectroscopy for protein structure determination. The video was recorded live during the presentation and serves as an educative lecture.
Abstract: The long-range nature of the paramagnetic effects arising from unpaired electrons of metal ions renders them a powerful NMR spectroscopic tool for the study of the structure and dynamics of biological macromolecules. In this tutorial, we will discuss protein structure determination using paramagnetic NMR. The first part will cover different types of paramagnetic metal ions and their paramagnetic effects in NMR, mainly focusing on using techniques which better immobilize metal ions onto the proteins and do not impact the protein structure; the second part will consider Pseudocontact Shifts (PCSs) for determining the 3D structure of proteins.
Biography: Alireza received a bachelor of Chemical Engineering and a master of Polymer engineering from the University of Tehran, Iran. During his master’s project, he worked on developing new nanomembranes for heavy metal ions removal in water. In 2015, he moved to Australia and joined the research group of Professor Gottfried Otting to undertake a Ph.D. During his Ph.D., he worked on developing new ways of studying protein structure using paramagnetic NMR spectroscopy.
Follow Alireza on Twitter: @alireza_bahramz
Google scholar page: https://scholar.google.com/citations?...
Research Gate: https://www.researchgate.net/profile/...